Add CI for Hercules #2131
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WalterKolczynski-NOAA
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Jan 13, 2024
global-workflow: 02Jan24, 9d901db
UFS: 21Dec23, 991d652
UPP: 07Nov23, 78f369b
Squashed commit of the following:
commit 4e4e50803d95566e1c7967cf4cfa575391d77f25
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
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 <Judy.K.Henderson@noaa.gov>
Date: Thu Jan 11 23:34:36 2024 +0000
Add namelist parameter, nord_tr, for GSL suites
commit c4a41de7ebcda2f80ce69ac94bd2b3a6f5d04ed5
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
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 <Judy.K.Henderson@noaa.gov>
Date: Tue Jan 9 02:26:22 2024 +0000
Add experiment setup script for p8_ugwpv1
commit c5a3697d22fdbb02bb80ddffee2629dddc10c702
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
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 <Judy.K.Henderson@noaa.gov>
Date: Tue Jan 9 02:13:42 2024 +0000
Updated GSL-specific files under ufs_utils.fd_gsl
commit 1b153fc95b93a16eb40b791be7322100fde4a3d4
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date: Tue Jan 2 10:30:33 2024 -0700
Stop Gempak pgrb2 spec from modifying $DATA (#2147)
This PR addresses issue #1224. The following is accomplished:
- Instances where `DATA` is modified, corrections are made to use a locally defined variable such that `DATA` is no longer modified at run-time;
- Shell linter exceptions are addressed accordingly;
- The respective GEMPAK tasks is added to the Rocoto mesh.
Resolves #1224
commit 31ad23527802f7d07171132cc620f7135c4d8cba
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date: Tue Jan 2 10:27:30 2024 -0700
Reorganize NPOESS scripts (#2166)
This PR addresses issue #1226. The following is accomplished:
- Using the GEMPAK j-job script `JGFS_ATMOS_GEMPAK_PGRB2_SPEC`, the structure
of `JGFS_ATMOS_PGRB2_SPEC_NPOESS` is updated;
- Environment variables specific to the script `exgfs_atmos_grib2_special_npoess.sh`
are moved accordingly; this specifically applies to the environment variable `FHOUR`,
`SHOUR`, `FHINC`, `SLEEP_TIME`, and `SLEEP_INT`;
- The `SLEEP_TIME` and `SLEEP_INT` parameters can now be defined at the top-level
(if necessary);
- Restart file checks are move to `exgfs_atmos_grib2_special_npoess.sh`; however,
this may not be necessary (see `TODO` note within draft PR.
Resolves #1226
commit 22bd82fa93b49e5ce98eb3f69123956dd5018049
Author: Kate Friedman <kate.friedman@noaa.gov>
Date: Tue Jan 2 11:55:03 2024 -0500
Orog fix file reorg and fix directory variable standardization (#2181)
This PR makes updates to use the newly reorganized `orog/20231027`
fix file version and standardizes the fix file directory variables.
Changes:
1. Update UFS_UTILS hash to ce385ce
2. Update fix file version file to use new orog timestamp: `orog_ver=20231027`
3. Add ".mx$(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 <40322596+ADCollard@users.noreply.github.com>
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 <jessica.meixner@noaa.gov>
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 <69919478+DavidHuber-NOAA@users.noreply.github.com>
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 <bbakernoaa@users.noreply.github.com>
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 <aerorahul@users.noreply.github.com>
commit e55a05980709288d902ad1bd894164bfa5a18a65
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
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 <terrence.mcguinness@cox.net>
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 <58948505+AndrewEichmann-NOAA@users.noreply.github.com>
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 <69919478+DavidHuber-NOAA@users.noreply.github.com>
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 <kate.friedman@noaa.gov>
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 <kate.friedman@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <terrence.mcguinness@cox.net>
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 <aerorahul@users.noreply.github.com>
Date: Thu Dec 14 16:05:33 2023 -0500
Correct fbwind (#2161)
commit f3f3e05e6325e6c2e8ddab186f1ed2f985fec49a
Author: Kate Friedman <kate.friedman@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <69919478+DavidHuber-NOAA@users.noreply.github.com>
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 <kate.friedman@noaa.gov>
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 <cory.r.martin@noaa.gov>
Date: Thu Dec 7 15:12:05 2023 -0500
Update GDAS hash to most recent stable versions (#2138)
commit 93da9f105502e24f1a1a621f05ea49e1fdfe0102
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date: Thu Dec 7 10:41:05 2023 -0700
Corrected typo in a gempak job gempakncdcupapgif . (#2137)
commit 3483f550db1ae35a680de49f7485ce5a11902dd9
Author: Cory Martin <cory.r.martin@noaa.gov>
Date: Thu Dec 7 12:34:56 2023 -0500
Add support for FGAT and IAU for aerosol DA (#1940)
commit e2664c011bf5fb03a9b1b37878cad423a1fde6f9
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
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 <Walter.Kolczynski@noaa.gov>
commit a29f751aed05312da3d80d396159bb5a906d6ce4
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date: Wed Dec 6 13:45:56 2023 -0700
Adds GEMPAK and related jobs to rocoto task mesh (#2127)
commit 1fc8b5bf55581de18e786611c65bc3f84bb0c082
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
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 <kate.friedman@noaa.gov>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <kate.friedman@noaa.gov>
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 <terrence.mcguinness@cox.net>
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 <69919478+DavidHuber-NOAA@users.noreply.github.com>
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 <jiande.wang@noaa.gov>
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 <58948505+AndrewEichmann-NOAA@users.noreply.github.com>
Date: Wed Nov 29 15:17:36 2023 -0500
Added variables to config.prepoceanobs (#2101)
commit c2d78a61a224678fb804eed19f39d1f07408ae5f
Author: Kate Friedman <kate.friedman@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <kate.friedman@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <kate.friedman@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <kate.friedman@noaa.gov>
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 <kate.friedman@noaa.gov>
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 <jessica.meixner@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <48260754+WenMeng-NOAA@users.noreply.github.com>
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 <Walter.Kolczynski@noaa.gov>
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 <aerorahul@users.noreply.github.com>
Date: Wed Nov 15 16:44:03 2023 -0500
Fix missing _PREV in ocean restart file location (#2070)
commit 255616d37505c785bdddd5d3e39e8399110b626e
Author: mdtoyNOAA <73618848+mdtoyNOAA@users.noreply.github.com>
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 <guillaume.vernieres@noaa.gov>
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 <guoqing.ge@noaa.gov>
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 <kate.friedman@noaa.gov>
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 <kate.friedman@noaa.gov>
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 <aerorahul@users.noreply.github.com>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <kate.friedman@noaa.gov>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <Walter.Kolczynski@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <jiande.wang@noaa.gov>
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 <bbakernoaa@users.noreply.github.com>
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 <69919478+DavidHuber-NOAA@users.noreply.github.com>
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 <terrence.mcguinness@cox.net>
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 <guillaume.vernieres@noaa.gov>
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 <jiande.wang@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <58948505+AndrewEichmann-NOAA@users.noreply.github.com>
Date: Thu Nov 2 16:09:59 2023 -0400
changed optional script name vars for ocean analysis (#2025)
commit 93bc918cdabee771c182c6f33cc54a20b5bb86c6
Author: Kate Friedman <kate.friedman@noaa.gov>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <58948505+AndrewEichmann-NOAA@users.noreply.github.com>
Date: Wed Nov 1 14:19:55 2023 -0400
Updates to prep ocean obs task (#1870)
commit 77be0ec6a3117b9f7e71a19c69ac64c09b521ecd
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <69919478+DavidHuber-NOAA@users.noreply.github.com>
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 <Walter.Kolczynski@noaa.gov>
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 <terrence.mcguinness@cox.net>
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 <terrence.mcguinness@cox.net>
Date: Tue Oct 31 13:57:02 2023 +0000
Allow CI case to exclude running on certain platforms (#2001)
commit 7cc137116f1619bf1e5a12eaacb98d17da97c223
Author: Jeff Whitaker <jswhit@fastmail.fm>
Date: Tue Oct 31 07:54:24 2023 -0600
Add initial C96/1 deg coupled model support (#1991)
commit 7086ddc4bece6fb2a8c1c2e6090800d4293e410e
Author: AndrewEichmann-NOAA <58948505+AndrewEichmann-NOAA@users.noreply.github.com>
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 <guillaume.vernieres@noaa.gov>
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 <108816337+AnilKumar-NOAA@users.noreply.github.com>
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 <26926959+RussTreadon-NOAA@users.noreply.github.com>
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 <69919478+DavidHuber-NOAA@users.noreply.github.com>
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 <jessica.meixner@noaa.gov>
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 <aerorahul@users.noreply.github.com>
Date: Wed Oct 25 16:15:28 2023 -0400
Fix incorrect usage of CFP on WCOSS2 (#1977)
commit 0b5cf9b67a8146d9d4815ea6545f7f2524120d83
Author: Kate Friedman <kate.friedman@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <terrence.mcguinness@cox.net>
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 <terry.mcguinness@noaa.gov>
commit c58deae0cf078d1ee093529064d74f60482aa3f4
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <henry.winterbottom.wxdev@gmail.com>
commit 1b00224e18842cd873eb1779be08f96687e49e1f
Author: Kate Friedman <kate.friedman@noaa.gov>
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 <26926959+RussTreadon-NOAA@users.noreply.github.com>
Date: Tue Oct 24 13:32:52 2023 -0400
Refactor UFSDA ATM var and ens layout (#1945)
commit 8940adddfe9d21189740e71487603fb2acee2336
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Tue Oct 24 11:02:29 2023 -0400
Optimize the checkout script (#1956)
* Multithread the checkout script #1953
commit 4b5cd0bc435fc158258ca38c3d5f44add6b60469
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
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 <Walter.Kolczynski@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <aerorahul@users.noreply.github.com>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <terrence.mcguinness@cox.net>
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 <terry.mcguinness@noaa.gov>
commit ea4dfa5800b5cb529478cc64d329f567393fa37d
Author: Guillaume Vernieres <guillaume.vernieres@noaa.gov>
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 <terrence.mcguinness@cox.net>
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 <terrence.mcguinness@cox.net>
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 <terrence.mcguinness@cox.net>
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 <aerorahul@users.noreply.github.com>
Date: Wed Oct 4 09:42:12 2023 -0400
Fix typo in cice history filename
commit d50938bc4f6705b722338bbea03f925614f953ed
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
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 <aerorahul@users.noreply.github.com>
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 <kate.friedman@noaa.gov>
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 <26926959+RussTreadon-NOAA@users.noreply.github.com>
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 <aerorahul@users.noreply.github.com>
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 <terrence.mcguinness@cox.net>
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 <Walter.Kolczynski@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <aerorahul@users.noreply.github.com>
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 <kate.friedman@noaa.gov>
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 <71304161+andytangborn@users.noreply.github.com>
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 <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Tue …
jkhender
added a commit
to jkhender/global-workflow
that referenced
this issue
Jan 29, 2024
Squashed commit of the following:
commit 3c0c126a376af31866a93aef4cdd0b4145150c58
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
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 <Judy.K.Henderson@noaa.gov>
Date: Tue Jan 16 16:46:25 2024 +0000
Update link script for ufs_utils.fd
commit 5b21b31900955013b4e8106d3ae906b9da93b361
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Tue Jan 16 16:45:25 2024 +0000
Add GSL archive scripts for initial conditions
commit abb88baf9dd536a3b2ea1e24eaa99cbfe85af799
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
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 <Judy.K.Henderson@noaa.gov>
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 <Judy.K.Henderson@noaa.gov>
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 <Judy.K.Henderson@noaa.gov>
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 <Judy.K.Henderson@noaa.gov>
Date: Thu Jan 11 23:34:36 2024 +0000
Add namelist parameter, nord_tr, for GSL suites
commit c4a41de7ebcda2f80ce69ac94bd2b3a6f5d04ed5
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
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 <Judy.K.Henderson@noaa.gov>
Date: Tue Jan 9 02:26:22 2024 +0000
Add experiment setup script for p8_ugwpv1
commit c5a3697d22fdbb02bb80ddffee2629dddc10c702
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
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 <Judy.K.Henderson@noaa.gov>
Date: Tue Jan 9 02:13:42 2024 +0000
Updated GSL-specific files under ufs_utils.fd_gsl
commit 1b153fc95b93a16eb40b791be7322100fde4a3d4
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date: Tue Jan 2 10:30:33 2024 -0700
Stop Gempak pgrb2 spec from modifying $DATA (#2147)
This PR addresses issue #1224. The following is accomplished:
- Instances where `DATA` is modified, corrections are made to use a locally defined variable such that `DATA` is no longer modified at run-time;
- Shell linter exceptions are addressed accordingly;
- The respective GEMPAK tasks is added to the Rocoto mesh.
Resolves #1224
commit 31ad23527802f7d07171132cc620f7135c4d8cba
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date: Tue Jan 2 10:27:30 2024 -0700
Reorganize NPOESS scripts (#2166)
This PR addresses issue #1226. The following is accomplished:
- Using the GEMPAK j-job script `JGFS_ATMOS_GEMPAK_PGRB2_SPEC`, the structure
of `JGFS_ATMOS_PGRB2_SPEC_NPOESS` is updated;
- Environment variables specific to the script `exgfs_atmos_grib2_special_npoess.sh`
are moved accordingly; this specifically applies to the environment variable `FHOUR`,
`SHOUR`, `FHINC`, `SLEEP_TIME`, and `SLEEP_INT`;
- The `SLEEP_TIME` and `SLEEP_INT` parameters can now be defined at the top-level
(if necessary);
- Restart file checks are move to `exgfs_atmos_grib2_special_npoess.sh`; however,
this may not be necessary (see `TODO` note within draft PR.
Resolves #1226
commit 22bd82fa93b49e5ce98eb3f69123956dd5018049
Author: Kate Friedman <kate.friedman@noaa.gov>
Date: Tue Jan 2 11:55:03 2024 -0500
Orog fix file reorg and fix directory variable standardization (#2181)
This PR makes updates to use the newly reorganized `orog/20231027`
fix file version and standardizes the fix file directory variables.
Changes:
1. Update UFS_UTILS hash to ce385ce
2. Update fix file version file to use new orog timestamp: `orog_ver=20231027`
3. Add ".mx$(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 <40322596+ADCollard@users.noreply.github.com>
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 <jessica.meixner@noaa.gov>
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 <69919478+DavidHuber-NOAA@users.noreply.github.com>
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 <bbakernoaa@users.noreply.github.com>
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 <aerorahul@users.noreply.github.com>
commit e55a05980709288d902ad1bd894164bfa5a18a65
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
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 <terrence.mcguinness@cox.net>
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 <58948505+AndrewEichmann-NOAA@users.noreply.github.com>
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 <69919478+DavidHuber-NOAA@users.noreply.github.com>
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 <kate.friedman@noaa.gov>
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 <kate.friedman@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <terrence.mcguinness@cox.net>
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 <aerorahul@users.noreply.github.com>
Date: Thu Dec 14 16:05:33 2023 -0500
Correct fbwind (#2161)
commit f3f3e05e6325e6c2e8ddab186f1ed2f985fec49a
Author: Kate Friedman <kate.friedman@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <69919478+DavidHuber-NOAA@users.noreply.github.com>
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 <kate.friedman@noaa.gov>
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 <cory.r.martin@noaa.gov>
Date: Thu Dec 7 15:12:05 2023 -0500
Update GDAS hash to most recent stable versions (#2138)
commit 93da9f105502e24f1a1a621f05ea49e1fdfe0102
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date: Thu Dec 7 10:41:05 2023 -0700
Corrected typo in a gempak job gempakncdcupapgif . (#2137)
commit 3483f550db1ae35a680de49f7485ce5a11902dd9
Author: Cory Martin <cory.r.martin@noaa.gov>
Date: Thu Dec 7 12:34:56 2023 -0500
Add support for FGAT and IAU for aerosol DA (#1940)
commit e2664c011bf5fb03a9b1b37878cad423a1fde6f9
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
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 <Walter.Kolczynski@noaa.gov>
commit a29f751aed05312da3d80d396159bb5a906d6ce4
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date: Wed Dec 6 13:45:56 2023 -0700
Adds GEMPAK and related jobs to rocoto task mesh (#2127)
commit 1fc8b5bf55581de18e786611c65bc3f84bb0c082
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
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 <kate.friedman@noaa.gov>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <kate.friedman@noaa.gov>
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 <terrence.mcguinness@cox.net>
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 <69919478+DavidHuber-NOAA@users.noreply.github.com>
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 <jiande.wang@noaa.gov>
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 <58948505+AndrewEichmann-NOAA@users.noreply.github.com>
Date: Wed Nov 29 15:17:36 2023 -0500
Added variables to config.prepoceanobs (#2101)
commit c2d78a61a224678fb804eed19f39d1f07408ae5f
Author: Kate Friedman <kate.friedman@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <kate.friedman@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <kate.friedman@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <kate.friedman@noaa.gov>
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 <kate.friedman@noaa.gov>
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 <jessica.meixner@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <48260754+WenMeng-NOAA@users.noreply.github.com>
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 <Walter.Kolczynski@noaa.gov>
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 <aerorahul@users.noreply.github.com>
Date: Wed Nov 15 16:44:03 2023 -0500
Fix missing _PREV in ocean restart file location (#2070)
commit 255616d37505c785bdddd5d3e39e8399110b626e
Author: mdtoyNOAA <73618848+mdtoyNOAA@users.noreply.github.com>
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 <guillaume.vernieres@noaa.gov>
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 <guoqing.ge@noaa.gov>
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 <kate.friedman@noaa.gov>
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 <kate.friedman@noaa.gov>
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 <aerorahul@users.noreply.github.com>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <kate.friedman@noaa.gov>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <Walter.Kolczynski@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <jiande.wang@noaa.gov>
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 <bbakernoaa@users.noreply.github.com>
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 <69919478+DavidHuber-NOAA@users.noreply.github.com>
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 <terrence.mcguinness@cox.net>
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 <guillaume.vernieres@noaa.gov>
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 <jiande.wang@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <58948505+AndrewEichmann-NOAA@users.noreply.github.com>
Date: Thu Nov 2 16:09:59 2023 -0400
changed optional script name vars for ocean analysis (#2025)
commit 93bc918cdabee771c182c6f33cc54a20b5bb86c6
Author: Kate Friedman <kate.friedman@noaa.gov>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <58948505+AndrewEichmann-NOAA@users.noreply.github.com>
Date: Wed Nov 1 14:19:55 2023 -0400
Updates to prep ocean obs task (#1870)
commit 77be0ec6a3117b9f7e71a19c69ac64c09b521ecd
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <69919478+DavidHuber-NOAA@users.noreply.github.com>
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 <Walter.Kolczynski@noaa.gov>
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 <terrence.mcguinness@cox.net>
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 <terrence.mcguinness@cox.net>
Date: Tue Oct 31 13:57:02 2023 +0000
Allow CI case to exclude running on certain platforms (#2001)
commit 7cc137116f1619bf1e5a12eaacb98d17da97c223
Author: Jeff Whitaker <jswhit@fastmail.fm>
Date: Tue Oct 31 07:54:24 2023 -0600
Add initial C96/1 deg coupled model support (#1991)
commit 7086ddc4bece6fb2a8c1c2e6090800d4293e410e
Author: AndrewEichmann-NOAA <58948505+AndrewEichmann-NOAA@users.noreply.github.com>
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 <guillaume.vernieres@noaa.gov>
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 <108816337+AnilKumar-NOAA@users.noreply.github.com>
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 <26926959+RussTreadon-NOAA@users.noreply.github.com>
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 <69919478+DavidHuber-NOAA@users.noreply.github.com>
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 <jessica.meixner@noaa.gov>
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 <aerorahul@users.noreply.github.com>
Date: Wed Oct 25 16:15:28 2023 -0400
Fix incorrect usage of CFP on WCOSS2 (#1977)
commit 0b5cf9b67a8146d9d4815ea6545f7f2524120d83
Author: Kate Friedman <kate.friedman@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <terrence.mcguinness@cox.net>
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 <terry.mcguinness@noaa.gov>
commit c58deae0cf078d1ee093529064d74f60482aa3f4
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <henry.winterbottom.wxdev@gmail.com>
commit 1b00224e18842cd873eb1779be08f96687e49e1f
Author: Kate Friedman <kate.friedman@noaa.gov>
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 <26926959+RussTreadon-NOAA@users.noreply.github.com>
Date: Tue Oct 24 13:32:52 2023 -0400
Refactor UFSDA ATM var and ens layout (#1945)
commit 8940adddfe9d21189740e71487603fb2acee2336
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Tue Oct 24 11:02:29 2023 -0400
Optimize the checkout script (#1956)
* Multithread the checkout script #1953
commit 4b5cd0bc435fc158258ca38c3d5f44add6b60469
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
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 <Walter.Kolczynski@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <aerorahul@users.noreply.github.com>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <terrence.mcguinness@cox.net>
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 <terry.mcguinness@noaa.gov>
commit ea4dfa5800b5cb529478cc64d329f567393fa37d
Author: Guillaume Vernieres <guillaume.vernieres@noaa.gov>
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 <terrence.mcguinness@cox.net>
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 <terrence.mcguinness@cox.net>
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 <terrence.mcguinness@cox.net>
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 <aerorahul@users.noreply.github.com>
Date: Wed Oct 4 09:42:12 2023 -0400
Fix typo in cice history filename
commit d50938bc4f6705b722338bbea03f925614f953ed
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
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 <aerorahul@users.noreply.github.com>
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 <kate.friedman@noaa.gov>
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 <26926959+RussTreadon-NOAA@users.noreply.github.com>
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 <aerorahul@users.noreply.github.com>
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 <terrence.mcguinness@cox.net>
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 <Walter.Kolczynski@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <aerorahul@users.noreply.github.com>
Date: Thu Sep 28 16:21:52 2023 -0400
Fix a few bugs reported by devs (#1893)
This PR fixes a …
jkhender
added a commit
to jkhender/global-workflow
that referenced
this issue
Jan 29, 2024
- based on gsl_ufs_dev from Judy's fork
global-workflow: 02Jan24, 9d901db [dev_02jan24_9d901db]
UFS: 21Dec23, 991d652
UPP: 07Nov23, 78f369b
- uses submodules instead of checkout.sh
- gfsatmprod tasks replace gfspost tasks
Squashed commit of the following:
commit 2e95cb5ed49ca24fb8e48bad0e2948e6abff7202
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Mon Jan 29 18:02:12 2024 +0000
Create links to GSL files
scripts/exglobal_archive.sh
ush/hpssarch_gen.sh
workflow/hosts/jet.yaml
workflow/rocoto/workflow_xml.py
Update paths in experiment setup scripts
Fix spelling typo in config.fcst
commit 4a0501cef14ac4437c09bcb70f65073f8f705bad
Merge: 783ef7406 73e518e2f
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Mon Jan 29 17:18:40 2024 +0000
Merge branch 'update_rt' of github.com:jkhender/global-workflow into update_rt
commit 783ef74063b28eaa88de208ec966c4238f3217c0
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Sat Jan 27 02:29:00 2024 +0000
Create GSL and EMC versions of python scripts under workflow/rocoto
commit 4b0ecb25802afb63346076d882eed67f2ee1518c
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Sat Jan 27 02:09:56 2024 +0000
Update archive scripts for GSL
commit 5224148e1c782a79d68d207d5dc410b70142e2e9
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Sat Jan 27 01:50:57 2024 +0000
Update tracker files for GSL
commit 6a4be178fbf921d39c54a89a35b5d77b131a8581
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Sat Jan 27 00:49:41 2024 +0000
Update atmos_products configuration file for GSL
- set downset to 1 so pgrb2b files are not created
- set FLXGF to "NO" so interpolated sflux.1p00 files are not created
commit 4949edaa4e974654f40e1caa04e31901a2b5b1c6
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Sat Jan 27 00:42:57 2024 +0000
Create separate config.ufs files for different C768 configurations for GSL (default is 12x12)
- 12x12 layout, 2 threads, 1 write group/40 write tasks (56 nodes)
- 16x16 layout, 2 threads, 2 write group/40 write tasks (101 nodes)
commit 74be3bed051e30498508b74df8d1ad164d2a11a1
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Sat Jan 27 00:00:36 2024 +0000
Update workflow directory
- update GSL template for jet
- create EMC and GSL versions of yaml files under hosts
- add realtime experiment setup scripts
commit c0cddbe264651ffee5d502b0faa774332bf9d19e
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Fri Jan 26 21:37:38 2024 +0000
Delete files leftover from older gsl_ufs_rt branch
commit 5371b03be790e4694274d307d78555328f4e8cf8
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Wed Jan 17 02:20:37 2024 +0000
Update configuration files for GSL
commit 18db5c8f6c3754eea90b9e418da6f2ec80a6c79b
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Wed Jan 17 01:55:49 2024 +0000
Updated gsl_ufs_rt branch - initial merge of gsl_ufs_dev branch
Squashed commit of the following:
commit 3c0c126a376af31866a93aef4cdd0b4145150c58
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
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 <Judy.K.Henderson@noaa.gov>
Date: Tue Jan 16 16:46:25 2024 +0000
Update link script for ufs_utils.fd
commit 5b21b31900955013b4e8106d3ae906b9da93b361
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Tue Jan 16 16:45:25 2024 +0000
Add GSL archive scripts for initial conditions
commit abb88baf9dd536a3b2ea1e24eaa99cbfe85af799
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
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 <Judy.K.Henderson@noaa.gov>
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 <Judy.K.Henderson@noaa.gov>
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 <Judy.K.Henderson@noaa.gov>
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 <Judy.K.Henderson@noaa.gov>
Date: Thu Jan 11 23:34:36 2024 +0000
Add namelist parameter, nord_tr, for GSL suites
commit c4a41de7ebcda2f80ce69ac94bd2b3a6f5d04ed5
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
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 <Judy.K.Henderson@noaa.gov>
Date: Tue Jan 9 02:26:22 2024 +0000
Add experiment setup script for p8_ugwpv1
commit c5a3697d22fdbb02bb80ddffee2629dddc10c702
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
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 <Judy.K.Henderson@noaa.gov>
Date: Tue Jan 9 02:13:42 2024 +0000
Updated GSL-specific files under ufs_utils.fd_gsl
commit 1b153fc95b93a16eb40b791be7322100fde4a3d4
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date: Tue Jan 2 10:30:33 2024 -0700
Stop Gempak pgrb2 spec from modifying $DATA (#2147)
This PR addresses issue #1224. The following is accomplished:
- Instances where `DATA` is modified, corrections are made to use a locally defined variable such that `DATA` is no longer modified at run-time;
- Shell linter exceptions are addressed accordingly;
- The respective GEMPAK tasks is added to the Rocoto mesh.
Resolves #1224
commit 31ad23527802f7d07171132cc620f7135c4d8cba
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date: Tue Jan 2 10:27:30 2024 -0700
Reorganize NPOESS scripts (#2166)
This PR addresses issue #1226. The following is accomplished:
- Using the GEMPAK j-job script `JGFS_ATMOS_GEMPAK_PGRB2_SPEC`, the structure
of `JGFS_ATMOS_PGRB2_SPEC_NPOESS` is updated;
- Environment variables specific to the script `exgfs_atmos_grib2_special_npoess.sh`
are moved accordingly; this specifically applies to the environment variable `FHOUR`,
`SHOUR`, `FHINC`, `SLEEP_TIME`, and `SLEEP_INT`;
- The `SLEEP_TIME` and `SLEEP_INT` parameters can now be defined at the top-level
(if necessary);
- Restart file checks are move to `exgfs_atmos_grib2_special_npoess.sh`; however,
this may not be necessary (see `TODO` note within draft PR.
Resolves #1226
commit 22bd82fa93b49e5ce98eb3f69123956dd5018049
Author: Kate Friedman <kate.friedman@noaa.gov>
Date: Tue Jan 2 11:55:03 2024 -0500
Orog fix file reorg and fix directory variable standardization (#2181)
This PR makes updates to use the newly reorganized `orog/20231027`
fix file version and standardizes the fix file directory variables.
Changes:
1. Update UFS_UTILS hash to ce385ce
2. Update fix file version file to use new orog timestamp: `orog_ver=20231027`
3. Add ".mx$(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 <40322596+ADCollard@users.noreply.github.com>
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 <jessica.meixner@noaa.gov>
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 <69919478+DavidHuber-NOAA@users.noreply.github.com>
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 <bbakernoaa@users.noreply.github.com>
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 <aerorahul@users.noreply.github.com>
commit e55a05980709288d902ad1bd894164bfa5a18a65
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
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 <terrence.mcguinness@cox.net>
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 <58948505+AndrewEichmann-NOAA@users.noreply.github.com>
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 <69919478+DavidHuber-NOAA@users.noreply.github.com>
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 <kate.friedman@noaa.gov>
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 <kate.friedman@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <terrence.mcguinness@cox.net>
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 <aerorahul@users.noreply.github.com>
Date: Thu Dec 14 16:05:33 2023 -0500
Correct fbwind (#2161)
commit f3f3e05e6325e6c2e8ddab186f1ed2f985fec49a
Author: Kate Friedman <kate.friedman@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <69919478+DavidHuber-NOAA@users.noreply.github.com>
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 <kate.friedman@noaa.gov>
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 <cory.r.martin@noaa.gov>
Date: Thu Dec 7 15:12:05 2023 -0500
Update GDAS hash to most recent stable versions (#2138)
commit 93da9f105502e24f1a1a621f05ea49e1fdfe0102
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date: Thu Dec 7 10:41:05 2023 -0700
Corrected typo in a gempak job gempakncdcupapgif . (#2137)
commit 3483f550db1ae35a680de49f7485ce5a11902dd9
Author: Cory Martin <cory.r.martin@noaa.gov>
Date: Thu Dec 7 12:34:56 2023 -0500
Add support for FGAT and IAU for aerosol DA (#1940)
commit e2664c011bf5fb03a9b1b37878cad423a1fde6f9
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
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 <Walter.Kolczynski@noaa.gov>
commit a29f751aed05312da3d80d396159bb5a906d6ce4
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date: Wed Dec 6 13:45:56 2023 -0700
Adds GEMPAK and related jobs to rocoto task mesh (#2127)
commit 1fc8b5bf55581de18e786611c65bc3f84bb0c082
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
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 <kate.friedman@noaa.gov>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <kate.friedman@noaa.gov>
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 <terrence.mcguinness@cox.net>
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 <69919478+DavidHuber-NOAA@users.noreply.github.com>
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 <jiande.wang@noaa.gov>
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 <58948505+AndrewEichmann-NOAA@users.noreply.github.com>
Date: Wed Nov 29 15:17:36 2023 -0500
Added variables to config.prepoceanobs (#2101)
commit c2d78a61a224678fb804eed19f39d1f07408ae5f
Author: Kate Friedman <kate.friedman@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <kate.friedman@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <kate.friedman@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <kate.friedman@noaa.gov>
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 <kate.friedman@noaa.gov>
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 <jessica.meixner@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <48260754+WenMeng-NOAA@users.noreply.github.com>
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 <Walter.Kolczynski@noaa.gov>
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 <aerorahul@users.noreply.github.com>
Date: Wed Nov 15 16:44:03 2023 -0500
Fix missing _PREV in ocean restart file location (#2070)
commit 255616d37505c785bdddd5d3e39e8399110b626e
Author: mdtoyNOAA <73618848+mdtoyNOAA@users.noreply.github.com>
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 <guillaume.vernieres@noaa.gov>
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 <guoqing.ge@noaa.gov>
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 <kate.friedman@noaa.gov>
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 <kate.friedman@noaa.gov>
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 <aerorahul@users.noreply.github.com>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <kate.friedman@noaa.gov>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <Walter.Kolczynski@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <jiande.wang@noaa.gov>
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 <bbakernoaa@users.noreply.github.com>
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 <69919478+DavidHuber-NOAA@users.noreply.github.com>
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 <terrence.mcguinness@cox.net>
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 <guillaume.vernieres@noaa.gov>
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 <jiande.wang@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <58948505+AndrewEichmann-NOAA@users.noreply.github.com>
Date: Thu Nov 2 16:09:59 2023 -0400
changed optional script name vars for ocean analysis (#2025)
commit 93bc918cdabee771c182c6f33cc54a20b5bb86c6
Author: Kate Friedman <kate.friedman@noaa.gov>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <58948505+AndrewEichmann-NOAA@users.noreply.github.com>
Date: Wed Nov 1 14:19:55 2023 -0400
Updates to prep ocean obs task (#1870)
commit 77be0ec6a3117b9f7e71a19c69ac64c09b521ecd
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <69919478+DavidHuber-NOAA@users.noreply.github.com>
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 <Walter.Kolczynski@noaa.gov>
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 <terrence.mcguinness@cox.net>
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 <terrence.mcguinness@cox.net>
Date: Tue Oct 31 13:57:02 2023 +0000
Allow CI case to exclude running on certain platforms (#2001)
commit 7cc137116f1619bf1e5a12eaacb98d17da97c223
Author: Jeff Whitaker <jswhit@fastmail.fm>
Date: Tue Oct 31 07:54:24 2023 -0600
Add initial C96/1 deg coupled model support (#1991)
commit 7086ddc4bece6fb2a8c1c2e6090800d4293e410e
Author: AndrewEichmann-NOAA <58948505+AndrewEichmann-NOAA@users.noreply.github.com>
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 <guillaume.vernieres@noaa.gov>
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 <108816337+AnilKumar-NOAA@users.noreply.github.com>
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 <26926959+RussTreadon-NOAA@users.noreply.github.com>
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 <69919478+DavidHuber-NOAA@users.noreply.github.com>
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 <jessica.meixner@noaa.gov>
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 <aerorahul@users.noreply.github.com>
Date: Wed Oct 25 16:15:28 2023 -0400
Fix incorrect usage of CFP on WCOSS2 (#1977)
commit 0b5cf9b67a8146d9d4815ea6545f7f2524120d83
Author: Kate Friedman <kate.friedman@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <terrence.mcguinness@cox.net>
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 <terry.mcguinness@noaa.gov>
commit c58deae0cf078d1ee093529064d74f60482aa3f4
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <henry.winterbottom.wxdev@gmail.com>
commit 1b00224e18842cd873eb1779be08f96687e49e1f
Author: Kate Friedman <kate.friedman@noaa.gov>
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 <26926959+RussTreadon-NOAA@users.noreply.github.com>
Date: Tue Oct 24 13:32:52 2023 -0400
Refactor UFSDA ATM var and ens layout (#1945)
commit 8940adddfe9d21189740e71487603fb2acee2336
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Tue Oct 24 11:02:29 2023 -0400
Optimize the checkout script (#1956)
* Multithread the checkout script #1953
commit 4b5cd0bc435fc158258ca38c3d5f44add6b60469
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
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 <Walter.Kolczynski@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <aerorahul@users.noreply.github.com>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <terrence.mcguinness@cox.net>
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 <terry.mcguinness@noaa.gov>
commit ea4dfa5800b5cb529478cc64d329f567393fa37d
Author: Guillaume Vernieres <guillaume.vernieres@noaa.gov>
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 <terrence.mcguinness@…
kayeekayee
added a commit
to kayeekayee/global-workflow
that referenced
this issue
Mar 11, 2024
- based on gsl_ufs_dev from NOAA-GSL/gsl_ufs_dev
29Feb24 global-workflow, 25c026e
UFS: 29Jan24, 625ac02
FV3: 06Jan24, 5e7f196
UPP: 07Nov23, 78f369b
update pointers for ufs_model and ufs_utils
remove GSL directories for ufs_model and ufs_utils
add GSL C3_MYNN xml suite
Squashed commit of the following:
commit 25c026ef03a8d8c0db0b7368d2836f0b2e866eae
Author: jderrico-noaa <janet.m.derrico@noaa.gov>
Date: Thu Feb 29 20:35:11 2024 +0000
update ufs_model pointer
commit a28617a951c46b765aa996bfe4d28b554ec4e0a4
Author: jderrico-noaa <janet.m.derrico@noaa.gov>
Date: Thu Feb 22 06:16:26 2024 +0000
removed unneeded gsl directories
commit 6fb4f90e8572e98c977a1d2ab385f033111f3ea7
Author: jderrico-noaa <janet.m.derrico@noaa.gov>
Date: Thu Feb 22 06:08:13 2024 +0000
update ufs_utils.fd pointer
commit 9264f0c09239d046c5cd862d807e9b82f51dc3bd
Author: jderrico-noaa <janet.m.derrico@noaa.gov>
Date: Wed Feb 21 19:33:26 2024 +0000
update .gitmodules file
commit f8edfa966147506f2c207728039e3a736cb95415
Author: jderrico-noaa <janet.m.derrico@noaa.gov>
Date: Wed Feb 21 19:30:47 2024 +0000
update pointer to ufs_utils.fd
commit 5e0d2ab02d58e6a7a40db55a149a93008b28aa8b
Author: jderrico-noaa <janet.m.derrico@noaa.gov>
Date: Wed Feb 21 19:25:52 2024 +0000
update pointer to ufs_model.fd
commit ebc9e1d02987a1c6aa8cabedf2323642748fab3c
Merge: e7a81511 50cb1e6f
Author: Janet Derrico <143837053+jderrico-noaa@users.noreply.github.com>
Date: Thu Feb 15 13:40:33 2024 -0700
Merge pull request #40 from kayeekayee/gsl_ufs_dev
Merge to 2024 Jan 12 NOAA-EMC/develop and update to 2024 Jan 29 UFS
commit 50cb1e6f0c661e4c6e2ef0be4527cce58379b2c9
Author: kayee.wong <kayee.wong@noaa.gov>
Date: Thu Feb 15 20:30:34 2024 +0000
Add pygraf workflow.
commit 38b726125d49cff6cae4c0e5fff2438fc33143c5
Author: kayee.wong <kayee.wong@noaa.gov>
Date: Wed Feb 14 17:43:15 2024 +0000
Add double quote for the arguments when calling setup_expt.py.
commit 053f2025fb0b0679c7d4f84958973c1534ec050c
Author: kayee.wong <kayee.wong@noaa.gov>
Date: Tue Feb 13 23:57:06 2024 +0000
more fix.
commit 6f80ea2edc5444e275a79b371d02b6e98e963662
Author: kayee.wong <kayee.wong@noaa.gov>
Date: Tue Feb 13 23:50:01 2024 +0000
more bug fix.
commit 56e283f1f666a38a4a3b30e1528e96eeb5c622e7
Author: kayee.wong <kayee.wong@noaa.gov>
Date: Tue Feb 13 23:40:02 2024 +0000
Minor bug fix.
commit 2dcfed06ff6789eb77cf92e22b80f5475923fafc
Author: kayee.wong <kayee.wong@noaa.gov>
Date: Tue Feb 13 23:19:03 2024 +0000
Update parameter for c3 case
Add c3 and mynn template
commit cc46b19ccc7cdb54878340eff79dda9e747abdf7
Author: kayee.wong <kayee.wong@noaa.gov>
Date: Tue Feb 13 20:51:23 2024 +0000
Update INFO.
Add c3 SDF in the build.
commit a444ed48a23f24724853036e522b4437bf412c59
Author: kayee.wong <kayee.wong@noaa.gov>
Date: Tue Feb 13 18:42:33 2024 +0000
Update to UFS 2024 Jan 29 version.
commit 88595707c7521cdce37ae1cf78720a7827242b24
Author: kayee.wong <kayee.wong@noaa.gov>
Date: Tue Feb 13 18:16:46 2024 +0000
Minor bug fix.
commit baa0e9f10b132098d5134efaad712a51ebc26b83
Author: kayee.wong <kayee.wong@noaa.gov>
Date: Tue Feb 13 17:59:27 2024 +0000
Update parameters for setup_expt.py in p8_ugwpv1.sh to resdetatmos and comroot.
commit 5875f06903f82a47fafb05f89f840e3b099d18d8
Author: kayee.wong <kayee.wong@noaa.gov>
Date: Tue Feb 13 17:51:11 2024 +0000
Remove old gsl SDFs.
Remove 'rrtmg_lw_pre' from C3 and MYNN SDFs.
commit 9e0d1342f4e1edce96c9b2baeec55c2cffb964cd
Author: kayee.wong <kayee.wong@noaa.gov>
Date: Thu Feb 8 22:14:01 2024 +0000
Merge to 2024 Jan 12 NOAA-EMC/develop.
Squashed commit of the following:
commit c59047614c29f6ec15a4d4a6fa1855929287debd
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Fri Jan 12 19:21:02 2024 -0500
Update hash to ufs-weather-model. The noahmptable.tbl was reorganized, so update link_workflow.sh to use the same one used in UFSWM RT (#2219)
commit c041968e165c07da785376f1441374687b55d6cc
Author: Kate Friedman <kate.friedman@noaa.gov>
Date: Fri Jan 12 12:09:35 2024 -0500
Add ocean resolution to setup_expt invocation and retire/reduce COMROT/ROTDIR usage (#2214)
Two series of updates:
1) Update setup scripts to now allow users to provide ocean resolution
2) Housekeeping to retire the `COMROT` variable, replacing it with other variables
as needed, and reduce the `ROTDIR` variable usage.
Both updates change options for the workflow setup API.
Refs #2061
commit 997f97816493d9ed0242e169b6dcf84e5c9338d6
Author: AndrewEichmann-NOAA <58948505+AndrewEichmann-NOAA@users.noreply.github.com>
Date: Fri Jan 12 10:46:36 2024 -0500
Allow use of ocean obs prep in WCDA cycling and remove R2D2 (#2215)
Enables use of ocean obs prep task in WCDA cycling and removes R2D2 from same.
Runs task gdasprepoceanobs before gdasocnanalprep -- obtains ocean data nc4 files from DMPDIR, processes them into IODA format and copies them to COM_OBS.
Replaces the current R2D2 processing.
commit 12a5bb192ab6282d44c008c06dc14947abd37249
Merge: 4cb58020 6492c2da
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Fri Jan 12 09:26:27 2024 -0500
Merge pull request #2217 from DavidHuber-NOAA/update/versions
Update and clean up version and module files
commit 6492c2da5f49bd31575d0bef5278c9a7f8ba3412
Author: David Huber <david.huber@noaa.gov>
Date: Thu Jan 11 11:49:08 2024 -0600
Update orion module/version files for met/metplus #2123
commit 94c9937f0bff380b0ebd6acdcfd2509e1ae99389
Author: DavidHuber <david.huber@noaa.gov>
Date: Thu Jan 11 17:42:53 2024 +0000
Comment met/metplus out from Hera modulefile. #2123
commit 8c32f8b7d00bba6e3e954f149e6548fb27713a3c
Merge: a65e4c67 4cb58020
Author: David Huber <david.huber@noaa.gov>
Date: Thu Jan 11 11:34:44 2024 -0600
Merge branch 'develop' of github.com:noaa-emc/global-workflow into develop
commit a65e4c675f21dbe72198d263e85e894e62b41e13
Author: David Huber <david.huber@noaa.gov>
Date: Thu Jan 11 11:34:19 2024 -0600
Initial update of version/module files #2123
commit 4cb580201af68c1c0e2ae19faf0727dcbbe43b4d
Author: souopgui <souopgui@users.noreply.github.com>
Date: Wed Jan 10 08:30:22 2024 -0600
Fix OpenMP over-allocation of resources in exglobal_atmos_products.sh when running MPMD tasks (#2212)
Fix OpenMP over-allocation of resources running MPMD tasks
Co-authored-by: Innocent Souopgui <isouopgui@redlineperf.com>
commit b056b531faee6929687cb8a588ffafa1a66426fb
Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
Date: Mon Jan 8 17:28:05 2024 -0500
Add Hercules as valid machine in CI scripts (#2207)
Few updates to CI scripts to include names for hercules that where missed
the first time.
commit 6574d29a8c26b0695614874c344bccc5182363f4
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Mon Jan 8 17:25:47 2024 -0500
Fix invalid GH action and restart file name (#2210)
Resolves a typo that leads to an invalid workflow yaml and fixes the restart filename in restart detection.
Resolves #2205
commit 69605eac299df381ea9e0e329654487e26380ff5
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Mon Jan 8 17:00:28 2024 -0500
Stop attempting to comment link to RTD for non-PRs (#2209)
Adds a check so comments with a link to documentation are only generated
for PRs.
commit 4e160a895bfb31c281e21557dd86c13954a1a967
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Mon Jan 8 13:10:15 2024 -0500
Enable UPP for GOES processing (#2203)
Wnables the creation of special master grib2 files from UPP for
GOES processing
commit c15875b6dbf685327af9316ee43b3d01f0fc815e
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Mon Jan 8 09:56:06 2024 -0500
Port cycling to Hercules (#2196)
Adds cycled support for Hercules (excluding gsi-monitor).
Partially resolves #1588
GSI monitoring is disabled on Hercules due to missing Perl modules. That will be enabled in a later PR.
commit ef6827dd6abdab2996d1e19f9e0ff5d3071e0fdd
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Mon Jan 8 09:43:12 2024 -0500
Refactor rocoto task XML creation (#2189)
Refactors the rocoto task generation to be recursive.
This will allow nested metatasks to loop over multiple variables, which is needed for GEFS product generation.
As part of this refactor, there is no longer separate arguments to designate metatasks.
Instead, task dicts can include a nested 'task_dict' as well as a 'var_dict' containing the variables to loop over.
The nested task dict can then either have another layer, or be the innermost task.
To accommodate the new recursive nature, some defaults that were previously defined in create_wf_task() had to be pushed down into the function that creates the innermost task.
Also, former keywords have been absorbed by the task dict.
Refs #823
Refs #827
commit 2b81cfac16f103fb29b3aeb9748941787abf7287
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Mon Jan 8 09:41:03 2024 -0500
Update fix versions (#2198)
Updates fix versions for a few components:
- Update cice and mom6 versions to support C96/1p00 marine
- Update wave to change betamax setting for glo_025 waves
Resolves #2004
Resolves #2107
commit e7a81511e37f86e881da020e06b95990b470d952
Merge: af47b77c 75ad3754
Author: Janet Derrico <143837053+jderrico-noaa@users.noreply.github.com>
Date: Thu Feb 1 13:14:02 2024 -0700
Merge pull request #37 from jderrico-noaa/gsl_ufs_dev
Add GSL archive script and correct typos/fixed paths
commit 75ad3754f8bef5411c2570b5e392cd08e95cb6cb
Author: jderrico-noaa <janet.m.derrico@noaa.gov>
Date: Thu Feb 1 20:00:52 2024 +0000
adding consistent [[ ]] for if statements
commit 67b99668c82a5fd8c42479b9b1bfe8b0bad0be25
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Thu Feb 1 19:37:47 2024 +0000
Updated HOMEgfs in GSL XML templates
commit 4d3719c086e7907a6eeff03112042d392e0d8c5e
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Thu Feb 1 17:27:39 2024 +0000
Correct syntax errors in GSL scripts
Add new GSL archive script for archiving grib2 and ICs, but no netcdf files
commit 4309dd0b3b2d5625e7e1740d7cd3e39aacd5bc29
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Mon Jan 29 18:05:45 2024 +0000
Add GSL diag tables to parm/ufs/fv3
Update GSL template for hera
Create EMC and GSL versions of files under workflow/rocoto
- tasks.py, workflow_tasks.py
commit af47b77c7ee59a11c798995b4362b57e9096b090
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Sat Jan 27 02:07:43 2024 +0000
Create GSL version of archive script
commit 529d9f71f97b6e643e76a53bc9871901ae861faf
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Sat Jan 27 01:37:09 2024 +0000
Create GSL version of tracker.sh
- this is a placeholder with changes from last year's HFIP experiment; will likely need to be updated in the future
commit 8457e12c313bee602265b863129734354b019271
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Sat Jan 27 01:27:42 2024 +0000
Link config.base.emc.dyn_hera to config.base.emc.dyn
commit 7a05f5bd947944d8c3be828aeef9cc03bf9e073a
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Sat Jan 27 01:22:54 2024 +0000
Create GSL version of hpssarch_gen.sh
- assume we only run cold starts
- archive only 0p25 grib2 files (no 0p50 opr 1p00)
- assume no pgrb2b or flux files are created so no need to archive to HPSS
commit 98f5d6b16437e2a340bf16f83187e389a53f8bf0
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Sat Jan 27 00:24:06 2024 +0000
Update workflow directory
- add GSL template for jet (based on last year's experiment)
- create EMC and GSL versions of yaml files under hosts; defaults point to GSL files
commit 38a7e5629ceeb23d399643a021e9a0a88468a07c
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Thu Jan 25 18:40:37 2024 +0000
Update atmos_products configuration file for GSL
- set downset to 1 so pgrb2b files are not created
- set FLXGF to "NO" so interpolated sflux.1p00 files are not created
commit fe8a953658d092ce2b597e14f31678624606fd8a
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Thu Jan 25 17:02:25 2024 +0000
Update nodes for gfsfcst task in GSL template for hera to match default configuration in config.ufs
(12x12, 2 threads, 1 write group, 40 write tasks ==> 56 nodes)
Increase walltime to 4:10 for gfsfcst task
commit 9d85b0f6d50e8ed142557fcb87c89d2e5d63c617
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Tue Jan 23 19:08:52 2024 +0000
Added default location for PTMP/STMP in workflow/hosts/hera.yaml
Added GSL XML template for hera
commit 1cf317d327fae78c5469712c9e5a6aa1ffa4b23b
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Wed Jan 17 22:33:13 2024 +0000
Add sjet partition
Make syntax consistent in "if" statements in config.resources
commit 2755e203751f50113849b06769173285e093290b
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Wed Jan 17 22:32:26 2024 +0000
Update configuration files for GSL
- create Hera and Jet versions of config.base.emc.dyn
- correct typo in config.fcst
- create different versions of config.ufs;
default is 12x12, 2 threads, 1 write group/40 write tasks (56 nodes)
commit 3c0c126a376af31866a93aef4cdd0b4145150c58
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
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 <Judy.K.Henderson@noaa.gov>
Date: Tue Jan 16 16:46:25 2024 +0000
Update link script for ufs_utils.fd
commit 5b21b31900955013b4e8106d3ae906b9da93b361
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Tue Jan 16 16:45:25 2024 +0000
Add GSL archive scripts for initial conditions
commit abb88baf9dd536a3b2ea1e24eaa99cbfe85af799
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
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 <Judy.K.Henderson@noaa.gov>
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 <Judy.K.Henderson@noaa.gov>
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 <Judy.K.Henderson@noaa.gov>
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 <Judy.K.Henderson@noaa.gov>
Date: Thu Jan 11 23:34:36 2024 +0000
Add namelist parameter, nord_tr, for GSL suites
commit c4a41de7ebcda2f80ce69ac94bd2b3a6f5d04ed5
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
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 <Judy.K.Henderson@noaa.gov>
Date: Tue Jan 9 02:26:22 2024 +0000
Add experiment setup script for p8_ugwpv1
commit c5a3697d22fdbb02bb80ddffee2629dddc10c702
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
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 <Judy.K.Henderson@noaa.gov>
Date: Tue Jan 9 02:13:42 2024 +0000
Updated GSL-specific files under ufs_utils.fd_gsl
commit 1b153fc95b93a16eb40b791be7322100fde4a3d4
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date: Tue Jan 2 10:30:33 2024 -0700
Stop Gempak pgrb2 spec from modifying $DATA (#2147)
This PR addresses issue #1224. The following is accomplished:
- Instances where `DATA` is modified, corrections are made to use a locally defined variable such that `DATA` is no longer modified at run-time;
- Shell linter exceptions are addressed accordingly;
- The respective GEMPAK tasks is added to the Rocoto mesh.
Resolves #1224
commit 31ad23527802f7d07171132cc620f7135c4d8cba
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date: Tue Jan 2 10:27:30 2024 -0700
Reorganize NPOESS scripts (#2166)
This PR addresses issue #1226. The following is accomplished:
- Using the GEMPAK j-job script `JGFS_ATMOS_GEMPAK_PGRB2_SPEC`, the structure
of `JGFS_ATMOS_PGRB2_SPEC_NPOESS` is updated;
- Environment variables specific to the script `exgfs_atmos_grib2_special_npoess.sh`
are moved accordingly; this specifically applies to the environment variable `FHOUR`,
`SHOUR`, `FHINC`, `SLEEP_TIME`, and `SLEEP_INT`;
- The `SLEEP_TIME` and `SLEEP_INT` parameters can now be defined at the top-level
(if necessary);
- Restart file checks are move to `exgfs_atmos_grib2_special_npoess.sh`; however,
this may not be necessary (see `TODO` note within draft PR.
Resolves #1226
commit 22bd82fa93b49e5ce98eb3f69123956dd5018049
Author: Kate Friedman <kate.friedman@noaa.gov>
Date: Tue Jan 2 11:55:03 2024 -0500
Orog fix file reorg and fix directory variable standardization (#2181)
This PR makes updates to use the newly reorganized `orog/20231027`
fix file version and standardizes the fix file directory variables.
Changes:
1. Update UFS_UTILS hash to ce385ce
2. Update fix file version file to use new orog timestamp: `orog_ver=20231027`
3. Add ".mx$(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 <40322596+ADCollard@users.noreply.github.com>
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 <jessica.meixner@noaa.gov>
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 <69919478+DavidHuber-NOAA@users.noreply.github.com>
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 <bbakernoaa@users.noreply.github.com>
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 <aerorahul@users.noreply.github.com>
commit e55a05980709288d902ad1bd894164bfa5a18a65
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
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 <terrence.mcguinness@cox.net>
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 <58948505+AndrewEichmann-NOAA@users.noreply.github.com>
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 <69919478+DavidHuber-NOAA@users.noreply.github.com>
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 <kate.friedman@noaa.gov>
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 <kate.friedman@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <terrence.mcguinness@cox.net>
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 <aerorahul@users.noreply.github.com>
Date: Thu Dec 14 16:05:33 2023 -0500
Correct fbwind (#2161)
commit f3f3e05e6325e6c2e8ddab186f1ed2f985fec49a
Author: Kate Friedman <kate.friedman@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <69919478+DavidHuber-NOAA@users.noreply.github.com>
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 <kate.friedman@noaa.gov>
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 <cory.r.martin@noaa.gov>
Date: Thu Dec 7 15:12:05 2023 -0500
Update GDAS hash to most recent stable versions (#2138)
commit 93da9f105502e24f1a1a621f05ea49e1fdfe0102
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date: Thu Dec 7 10:41:05 2023 -0700
Corrected typo in a gempak job gempakncdcupapgif . (#2137)
commit 3483f550db1ae35a680de49f7485ce5a11902dd9
Author: Cory Martin <cory.r.martin@noaa.gov>
Date: Thu Dec 7 12:34:56 2023 -0500
Add support for FGAT and IAU for aerosol DA (#1940)
commit e2664c011bf5fb03a9b1b37878cad423a1fde6f9
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
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 <Walter.Kolczynski@noaa.gov>
commit a29f751aed05312da3d80d396159bb5a906d6ce4
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date: Wed Dec 6 13:45:56 2023 -0700
Adds GEMPAK and related jobs to rocoto task mesh (#2127)
commit 1fc8b5bf55581de18e786611c65bc3f84bb0c082
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
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 <kate.friedman@noaa.gov>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <kate.friedman@noaa.gov>
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 <terrence.mcguinness@cox.net>
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 <69919478+DavidHuber-NOAA@users.noreply.github.com>
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 <jiande.wang@noaa.gov>
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 <58948505+AndrewEichmann-NOAA@users.noreply.github.com>
Date: Wed Nov 29 15:17:36 2023 -0500
Added variables to config.prepoceanobs (#2101)
commit c2d78a61a224678fb804eed19f39d1f07408ae5f
Author: Kate Friedman <kate.friedman@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <kate.friedman@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <kate.friedman@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <kate.friedman@noaa.gov>
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 <kate.friedman@noaa.gov>
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 <jessica.meixner@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <48260754+WenMeng-NOAA@users.noreply.github.com>
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 <Walter.Kolczynski@noaa.gov>
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 <aerorahul@users.noreply.github.com>
Date: Wed Nov 15 16:44:03 2023 -0500
Fix missing _PREV in ocean restart file location (#2070)
commit 255616d37505c785bdddd5d3e39e8399110b626e
Author: mdtoyNOAA <73618848+mdtoyNOAA@users.noreply.github.com>
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 <guillaume.vernieres@noaa.gov>
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 <guoqing.ge@noaa.gov>
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 <kate.friedman@noaa.gov>
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 <kate.friedman@noaa.gov>
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 <aerorahul@users.noreply.github.com>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <kate.friedman@noaa.gov>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <Walter.Kolczynski@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <jiande.wang@noaa.gov>
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 <bbakernoaa@users.noreply.github.com>
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 <69919478+DavidHuber-NOAA@users.noreply.github.com>
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 <terrence.mcguinness@cox.net>
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 <guillaume.vernieres@noaa.gov>
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 <jiande.wang@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <58948505+AndrewEichmann-NOAA@users.noreply.github.com>
Date: Thu Nov 2 16:09:59 2023 -0400
changed optional script name vars for ocean analysis (#2025)
commit 93bc918cdabee771c182c6f33cc54a20b5bb86c6
Author: Kate Friedman <kate.friedman@noaa.gov>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <58948505+AndrewEichmann-NOAA@users.noreply.github.com>
Date: Wed Nov 1 14:19:55 2023 -0400
Updates to prep ocean obs task (#1870)
commit 77be0ec6a3117b9f7e71a19c69ac64c09b521ecd
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <69919478+DavidHuber-NOAA@users.noreply.github.com>
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 <Walter.Kolczynski@noaa.gov>
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 <terrence.mcguinness@cox.net>
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 <terrence.mcguinness@cox.net>
Date: Tue Oct 31 13:57:02 2023 +0000
Allow CI case to exclude running on certain platforms (#2001)
commit 7cc137116f1619bf1e5a12eaacb98d17da97c223
Author: Jeff Whitaker <jswhit@fastmail.fm>
Date: Tue Oct 31 07:54:24 2023 -0600
Add initial C96/1 deg coupled model support (#1991)
commit 7086ddc4bece6fb2a8c1c2e6090800d4293e410e
Author: AndrewEichmann-NOAA <58948505+AndrewEichmann-NOAA@users.noreply.github.com>
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 <guillaume.vernieres@noaa.gov>
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 <108816337+AnilKumar-NOAA@users.noreply.github.com>
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 <26926959+RussTreadon-NOAA@users.noreply.github.com>
Date: Thu Oct 26 23:44:27 2023 -0400
Update GDASApp hash (#1975)
Update GDASApp hash to bring recent UFSDA development into g-w…
kayeekayee
added a commit
to kayeekayee/global-workflow
that referenced
this issue
Mar 12, 2024
12Jan24 global-workflow
UFS: 29Jan24, 625ac02
FV3: 29Jan24, bd38c56
UPP: 07Nov23, 78f369b
UFS_UTILS: 22Dev23, ce385ce
update pointers for ufs_model and ufs_utils
add GSL C3_MYNN xml suite
Squashed commit of the following:
commit 25c026ef03a8d8c0db0b7368d2836f0b2e866eae
Author: jderrico-noaa <janet.m.derrico@noaa.gov>
Date: Thu Feb 29 20:35:11 2024 +0000
update ufs_model pointer
commit a28617a951c46b765aa996bfe4d28b554ec4e0a4
Author: jderrico-noaa <janet.m.derrico@noaa.gov>
Date: Thu Feb 22 06:16:26 2024 +0000
removed unneeded gsl directories
commit 6fb4f90e8572e98c977a1d2ab385f033111f3ea7
Author: jderrico-noaa <janet.m.derrico@noaa.gov>
Date: Thu Feb 22 06:08:13 2024 +0000
update ufs_utils.fd pointer
commit 9264f0c09239d046c5cd862d807e9b82f51dc3bd
Author: jderrico-noaa <janet.m.derrico@noaa.gov>
Date: Wed Feb 21 19:33:26 2024 +0000
update .gitmodules file
commit f8edfa966147506f2c207728039e3a736cb95415
Author: jderrico-noaa <janet.m.derrico@noaa.gov>
Date: Wed Feb 21 19:30:47 2024 +0000
update pointer to ufs_utils.fd
commit 5e0d2ab02d58e6a7a40db55a149a93008b28aa8b
Author: jderrico-noaa <janet.m.derrico@noaa.gov>
Date: Wed Feb 21 19:25:52 2024 +0000
update pointer to ufs_model.fd
commit ebc9e1d02987a1c6aa8cabedf2323642748fab3c
Merge: e7a81511 50cb1e6f
Author: Janet Derrico <143837053+jderrico-noaa@users.noreply.github.com>
Date: Thu Feb 15 13:40:33 2024 -0700
Merge pull request #40 from kayeekayee/gsl_ufs_dev
Merge to 2024 Jan 12 NOAA-EMC/develop and update to 2024 Jan 29 UFS
commit 50cb1e6f0c661e4c6e2ef0be4527cce58379b2c9
Author: kayee.wong <kayee.wong@noaa.gov>
Date: Thu Feb 15 20:30:34 2024 +0000
Add pygraf workflow.
commit 38b726125d49cff6cae4c0e5fff2438fc33143c5
Author: kayee.wong <kayee.wong@noaa.gov>
Date: Wed Feb 14 17:43:15 2024 +0000
Add double quote for the arguments when calling setup_expt.py.
commit 053f2025fb0b0679c7d4f84958973c1534ec050c
Author: kayee.wong <kayee.wong@noaa.gov>
Date: Tue Feb 13 23:57:06 2024 +0000
more fix.
commit 6f80ea2edc5444e275a79b371d02b6e98e963662
Author: kayee.wong <kayee.wong@noaa.gov>
Date: Tue Feb 13 23:50:01 2024 +0000
more bug fix.
commit 56e283f1f666a38a4a3b30e1528e96eeb5c622e7
Author: kayee.wong <kayee.wong@noaa.gov>
Date: Tue Feb 13 23:40:02 2024 +0000
Minor bug fix.
commit 2dcfed06ff6789eb77cf92e22b80f5475923fafc
Author: kayee.wong <kayee.wong@noaa.gov>
Date: Tue Feb 13 23:19:03 2024 +0000
Update parameter for c3 case
Add c3 and mynn template
commit cc46b19ccc7cdb54878340eff79dda9e747abdf7
Author: kayee.wong <kayee.wong@noaa.gov>
Date: Tue Feb 13 20:51:23 2024 +0000
Update INFO.
Add c3 SDF in the build.
commit a444ed48a23f24724853036e522b4437bf412c59
Author: kayee.wong <kayee.wong@noaa.gov>
Date: Tue Feb 13 18:42:33 2024 +0000
Update to UFS 2024 Jan 29 version.
commit 88595707c7521cdce37ae1cf78720a7827242b24
Author: kayee.wong <kayee.wong@noaa.gov>
Date: Tue Feb 13 18:16:46 2024 +0000
Minor bug fix.
commit baa0e9f10b132098d5134efaad712a51ebc26b83
Author: kayee.wong <kayee.wong@noaa.gov>
Date: Tue Feb 13 17:59:27 2024 +0000
Update parameters for setup_expt.py in p8_ugwpv1.sh to resdetatmos and comroot.
commit 5875f06903f82a47fafb05f89f840e3b099d18d8
Author: kayee.wong <kayee.wong@noaa.gov>
Date: Tue Feb 13 17:51:11 2024 +0000
Remove old gsl SDFs.
Remove 'rrtmg_lw_pre' from C3 and MYNN SDFs.
commit 9e0d1342f4e1edce96c9b2baeec55c2cffb964cd
Author: kayee.wong <kayee.wong@noaa.gov>
Date: Thu Feb 8 22:14:01 2024 +0000
Merge to 2024 Jan 12 NOAA-EMC/develop.
Squashed commit of the following:
commit c59047614c29f6ec15a4d4a6fa1855929287debd
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Fri Jan 12 19:21:02 2024 -0500
Update hash to ufs-weather-model. The noahmptable.tbl was reorganized, so update link_workflow.sh to use the same one used in UFSWM RT (#2219)
commit c041968e165c07da785376f1441374687b55d6cc
Author: Kate Friedman <kate.friedman@noaa.gov>
Date: Fri Jan 12 12:09:35 2024 -0500
Add ocean resolution to setup_expt invocation and retire/reduce COMROT/ROTDIR usage (#2214)
Two series of updates:
1) Update setup scripts to now allow users to provide ocean resolution
2) Housekeeping to retire the `COMROT` variable, replacing it with other variables
as needed, and reduce the `ROTDIR` variable usage.
Both updates change options for the workflow setup API.
Refs #2061
commit 997f97816493d9ed0242e169b6dcf84e5c9338d6
Author: AndrewEichmann-NOAA <58948505+AndrewEichmann-NOAA@users.noreply.github.com>
Date: Fri Jan 12 10:46:36 2024 -0500
Allow use of ocean obs prep in WCDA cycling and remove R2D2 (#2215)
Enables use of ocean obs prep task in WCDA cycling and removes R2D2 from same.
Runs task gdasprepoceanobs before gdasocnanalprep -- obtains ocean data nc4 files from DMPDIR, processes them into IODA format and copies them to COM_OBS.
Replaces the current R2D2 processing.
commit 12a5bb192ab6282d44c008c06dc14947abd37249
Merge: 4cb58020 6492c2da
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Fri Jan 12 09:26:27 2024 -0500
Merge pull request #2217 from DavidHuber-NOAA/update/versions
Update and clean up version and module files
commit 6492c2da5f49bd31575d0bef5278c9a7f8ba3412
Author: David Huber <david.huber@noaa.gov>
Date: Thu Jan 11 11:49:08 2024 -0600
Update orion module/version files for met/metplus #2123
commit 94c9937f0bff380b0ebd6acdcfd2509e1ae99389
Author: DavidHuber <david.huber@noaa.gov>
Date: Thu Jan 11 17:42:53 2024 +0000
Comment met/metplus out from Hera modulefile. #2123
commit 8c32f8b7d00bba6e3e954f149e6548fb27713a3c
Merge: a65e4c67 4cb58020
Author: David Huber <david.huber@noaa.gov>
Date: Thu Jan 11 11:34:44 2024 -0600
Merge branch 'develop' of github.com:noaa-emc/global-workflow into develop
commit a65e4c675f21dbe72198d263e85e894e62b41e13
Author: David Huber <david.huber@noaa.gov>
Date: Thu Jan 11 11:34:19 2024 -0600
Initial update of version/module files #2123
commit 4cb580201af68c1c0e2ae19faf0727dcbbe43b4d
Author: souopgui <souopgui@users.noreply.github.com>
Date: Wed Jan 10 08:30:22 2024 -0600
Fix OpenMP over-allocation of resources in exglobal_atmos_products.sh when running MPMD tasks (#2212)
Fix OpenMP over-allocation of resources running MPMD tasks
Co-authored-by: Innocent Souopgui <isouopgui@redlineperf.com>
commit b056b531faee6929687cb8a588ffafa1a66426fb
Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
Date: Mon Jan 8 17:28:05 2024 -0500
Add Hercules as valid machine in CI scripts (#2207)
Few updates to CI scripts to include names for hercules that where missed
the first time.
commit 6574d29a8c26b0695614874c344bccc5182363f4
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Mon Jan 8 17:25:47 2024 -0500
Fix invalid GH action and restart file name (#2210)
Resolves a typo that leads to an invalid workflow yaml and fixes the restart filename in restart detection.
Resolves #2205
commit 69605eac299df381ea9e0e329654487e26380ff5
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Mon Jan 8 17:00:28 2024 -0500
Stop attempting to comment link to RTD for non-PRs (#2209)
Adds a check so comments with a link to documentation are only generated
for PRs.
commit 4e160a895bfb31c281e21557dd86c13954a1a967
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Mon Jan 8 13:10:15 2024 -0500
Enable UPP for GOES processing (#2203)
Wnables the creation of special master grib2 files from UPP for
GOES processing
commit c15875b6dbf685327af9316ee43b3d01f0fc815e
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Mon Jan 8 09:56:06 2024 -0500
Port cycling to Hercules (#2196)
Adds cycled support for Hercules (excluding gsi-monitor).
Partially resolves #1588
GSI monitoring is disabled on Hercules due to missing Perl modules. That will be enabled in a later PR.
commit ef6827dd6abdab2996d1e19f9e0ff5d3071e0fdd
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Mon Jan 8 09:43:12 2024 -0500
Refactor rocoto task XML creation (#2189)
Refactors the rocoto task generation to be recursive.
This will allow nested metatasks to loop over multiple variables, which is needed for GEFS product generation.
As part of this refactor, there is no longer separate arguments to designate metatasks.
Instead, task dicts can include a nested 'task_dict' as well as a 'var_dict' containing the variables to loop over.
The nested task dict can then either have another layer, or be the innermost task.
To accommodate the new recursive nature, some defaults that were previously defined in create_wf_task() had to be pushed down into the function that creates the innermost task.
Also, former keywords have been absorbed by the task dict.
Refs #823
Refs #827
commit 2b81cfac16f103fb29b3aeb9748941787abf7287
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Mon Jan 8 09:41:03 2024 -0500
Update fix versions (#2198)
Updates fix versions for a few components:
- Update cice and mom6 versions to support C96/1p00 marine
- Update wave to change betamax setting for glo_025 waves
Resolves #2004
Resolves #2107
commit e7a81511e37f86e881da020e06b95990b470d952
Merge: af47b77c 75ad3754
Author: Janet Derrico <143837053+jderrico-noaa@users.noreply.github.com>
Date: Thu Feb 1 13:14:02 2024 -0700
Merge pull request #37 from jderrico-noaa/gsl_ufs_dev
Add GSL archive script and correct typos/fixed paths
commit 75ad3754f8bef5411c2570b5e392cd08e95cb6cb
Author: jderrico-noaa <janet.m.derrico@noaa.gov>
Date: Thu Feb 1 20:00:52 2024 +0000
adding consistent [[ ]] for if statements
commit 67b99668c82a5fd8c42479b9b1bfe8b0bad0be25
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Thu Feb 1 19:37:47 2024 +0000
Updated HOMEgfs in GSL XML templates
commit 4d3719c086e7907a6eeff03112042d392e0d8c5e
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Thu Feb 1 17:27:39 2024 +0000
Correct syntax errors in GSL scripts
Add new GSL archive script for archiving grib2 and ICs, but no netcdf files
commit 4309dd0b3b2d5625e7e1740d7cd3e39aacd5bc29
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Mon Jan 29 18:05:45 2024 +0000
Add GSL diag tables to parm/ufs/fv3
Update GSL template for hera
Create EMC and GSL versions of files under workflow/rocoto
- tasks.py, workflow_tasks.py
commit af47b77c7ee59a11c798995b4362b57e9096b090
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Sat Jan 27 02:07:43 2024 +0000
Create GSL version of archive script
commit 529d9f71f97b6e643e76a53bc9871901ae861faf
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Sat Jan 27 01:37:09 2024 +0000
Create GSL version of tracker.sh
- this is a placeholder with changes from last year's HFIP experiment; will likely need to be updated in the future
commit 8457e12c313bee602265b863129734354b019271
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Sat Jan 27 01:27:42 2024 +0000
Link config.base.emc.dyn_hera to config.base.emc.dyn
commit 7a05f5bd947944d8c3be828aeef9cc03bf9e073a
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Sat Jan 27 01:22:54 2024 +0000
Create GSL version of hpssarch_gen.sh
- assume we only run cold starts
- archive only 0p25 grib2 files (no 0p50 opr 1p00)
- assume no pgrb2b or flux files are created so no need to archive to HPSS
commit 98f5d6b16437e2a340bf16f83187e389a53f8bf0
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Sat Jan 27 00:24:06 2024 +0000
Update workflow directory
- add GSL template for jet (based on last year's experiment)
- create EMC and GSL versions of yaml files under hosts; defaults point to GSL files
commit 38a7e5629ceeb23d399643a021e9a0a88468a07c
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Thu Jan 25 18:40:37 2024 +0000
Update atmos_products configuration file for GSL
- set downset to 1 so pgrb2b files are not created
- set FLXGF to "NO" so interpolated sflux.1p00 files are not created
commit fe8a953658d092ce2b597e14f31678624606fd8a
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Thu Jan 25 17:02:25 2024 +0000
Update nodes for gfsfcst task in GSL template for hera to match default configuration in config.ufs
(12x12, 2 threads, 1 write group, 40 write tasks ==> 56 nodes)
Increase walltime to 4:10 for gfsfcst task
commit 9d85b0f6d50e8ed142557fcb87c89d2e5d63c617
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Tue Jan 23 19:08:52 2024 +0000
Added default location for PTMP/STMP in workflow/hosts/hera.yaml
Added GSL XML template for hera
commit 1cf317d327fae78c5469712c9e5a6aa1ffa4b23b
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Wed Jan 17 22:33:13 2024 +0000
Add sjet partition
Make syntax consistent in "if" statements in config.resources
commit 2755e203751f50113849b06769173285e093290b
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Wed Jan 17 22:32:26 2024 +0000
Update configuration files for GSL
- create Hera and Jet versions of config.base.emc.dyn
- correct typo in config.fcst
- create different versions of config.ufs;
default is 12x12, 2 threads, 1 write group/40 write tasks (56 nodes)
commit 3c0c126a376af31866a93aef4cdd0b4145150c58
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
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 <Judy.K.Henderson@noaa.gov>
Date: Tue Jan 16 16:46:25 2024 +0000
Update link script for ufs_utils.fd
commit 5b21b31900955013b4e8106d3ae906b9da93b361
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Tue Jan 16 16:45:25 2024 +0000
Add GSL archive scripts for initial conditions
commit abb88baf9dd536a3b2ea1e24eaa99cbfe85af799
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
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 <Judy.K.Henderson@noaa.gov>
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 <Judy.K.Henderson@noaa.gov>
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 <Judy.K.Henderson@noaa.gov>
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 <Judy.K.Henderson@noaa.gov>
Date: Thu Jan 11 23:34:36 2024 +0000
Add namelist parameter, nord_tr, for GSL suites
commit c4a41de7ebcda2f80ce69ac94bd2b3a6f5d04ed5
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
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 <Judy.K.Henderson@noaa.gov>
Date: Tue Jan 9 02:26:22 2024 +0000
Add experiment setup script for p8_ugwpv1
commit c5a3697d22fdbb02bb80ddffee2629dddc10c702
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
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 <Judy.K.Henderson@noaa.gov>
Date: Tue Jan 9 02:13:42 2024 +0000
Updated GSL-specific files under ufs_utils.fd_gsl
commit 1b153fc95b93a16eb40b791be7322100fde4a3d4
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date: Tue Jan 2 10:30:33 2024 -0700
Stop Gempak pgrb2 spec from modifying $DATA (#2147)
This PR addresses issue #1224. The following is accomplished:
- Instances where `DATA` is modified, corrections are made to use a locally defined variable such that `DATA` is no longer modified at run-time;
- Shell linter exceptions are addressed accordingly;
- The respective GEMPAK tasks is added to the Rocoto mesh.
Resolves #1224
commit 31ad23527802f7d07171132cc620f7135c4d8cba
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date: Tue Jan 2 10:27:30 2024 -0700
Reorganize NPOESS scripts (#2166)
This PR addresses issue #1226. The following is accomplished:
- Using the GEMPAK j-job script `JGFS_ATMOS_GEMPAK_PGRB2_SPEC`, the structure
of `JGFS_ATMOS_PGRB2_SPEC_NPOESS` is updated;
- Environment variables specific to the script `exgfs_atmos_grib2_special_npoess.sh`
are moved accordingly; this specifically applies to the environment variable `FHOUR`,
`SHOUR`, `FHINC`, `SLEEP_TIME`, and `SLEEP_INT`;
- The `SLEEP_TIME` and `SLEEP_INT` parameters can now be defined at the top-level
(if necessary);
- Restart file checks are move to `exgfs_atmos_grib2_special_npoess.sh`; however,
this may not be necessary (see `TODO` note within draft PR.
Resolves #1226
commit 22bd82fa93b49e5ce98eb3f69123956dd5018049
Author: Kate Friedman <kate.friedman@noaa.gov>
Date: Tue Jan 2 11:55:03 2024 -0500
Orog fix file reorg and fix directory variable standardization (#2181)
This PR makes updates to use the newly reorganized `orog/20231027`
fix file version and standardizes the fix file directory variables.
Changes:
1. Update UFS_UTILS hash to ce385ce
2. Update fix file version file to use new orog timestamp: `orog_ver=20231027`
3. Add ".mx$(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 <40322596+ADCollard@users.noreply.github.com>
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 <jessica.meixner@noaa.gov>
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 <69919478+DavidHuber-NOAA@users.noreply.github.com>
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 <bbakernoaa@users.noreply.github.com>
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 <aerorahul@users.noreply.github.com>
commit e55a05980709288d902ad1bd894164bfa5a18a65
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
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 <terrence.mcguinness@cox.net>
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 <58948505+AndrewEichmann-NOAA@users.noreply.github.com>
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 <69919478+DavidHuber-NOAA@users.noreply.github.com>
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 <kate.friedman@noaa.gov>
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 <kate.friedman@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <terrence.mcguinness@cox.net>
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 <aerorahul@users.noreply.github.com>
Date: Thu Dec 14 16:05:33 2023 -0500
Correct fbwind (#2161)
commit f3f3e05e6325e6c2e8ddab186f1ed2f985fec49a
Author: Kate Friedman <kate.friedman@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <69919478+DavidHuber-NOAA@users.noreply.github.com>
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 <kate.friedman@noaa.gov>
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 <cory.r.martin@noaa.gov>
Date: Thu Dec 7 15:12:05 2023 -0500
Update GDAS hash to most recent stable versions (#2138)
commit 93da9f105502e24f1a1a621f05ea49e1fdfe0102
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date: Thu Dec 7 10:41:05 2023 -0700
Corrected typo in a gempak job gempakncdcupapgif . (#2137)
commit 3483f550db1ae35a680de49f7485ce5a11902dd9
Author: Cory Martin <cory.r.martin@noaa.gov>
Date: Thu Dec 7 12:34:56 2023 -0500
Add support for FGAT and IAU for aerosol DA (#1940)
commit e2664c011bf5fb03a9b1b37878cad423a1fde6f9
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
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 <Walter.Kolczynski@noaa.gov>
commit a29f751aed05312da3d80d396159bb5a906d6ce4
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date: Wed Dec 6 13:45:56 2023 -0700
Adds GEMPAK and related jobs to rocoto task mesh (#2127)
commit 1fc8b5bf55581de18e786611c65bc3f84bb0c082
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
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 <kate.friedman@noaa.gov>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <kate.friedman@noaa.gov>
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 <terrence.mcguinness@cox.net>
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 <69919478+DavidHuber-NOAA@users.noreply.github.com>
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 <jiande.wang@noaa.gov>
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 <58948505+AndrewEichmann-NOAA@users.noreply.github.com>
Date: Wed Nov 29 15:17:36 2023 -0500
Added variables to config.prepoceanobs (#2101)
commit c2d78a61a224678fb804eed19f39d1f07408ae5f
Author: Kate Friedman <kate.friedman@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <kate.friedman@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <kate.friedman@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <kate.friedman@noaa.gov>
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 <kate.friedman@noaa.gov>
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 <jessica.meixner@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <48260754+WenMeng-NOAA@users.noreply.github.com>
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 <Walter.Kolczynski@noaa.gov>
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 <aerorahul@users.noreply.github.com>
Date: Wed Nov 15 16:44:03 2023 -0500
Fix missing _PREV in ocean restart file location (#2070)
commit 255616d37505c785bdddd5d3e39e8399110b626e
Author: mdtoyNOAA <73618848+mdtoyNOAA@users.noreply.github.com>
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 <guillaume.vernieres@noaa.gov>
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 <guoqing.ge@noaa.gov>
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 <kate.friedman@noaa.gov>
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 <kate.friedman@noaa.gov>
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 <aerorahul@users.noreply.github.com>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <kate.friedman@noaa.gov>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <Walter.Kolczynski@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <jiande.wang@noaa.gov>
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 <bbakernoaa@users.noreply.github.com>
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 <69919478+DavidHuber-NOAA@users.noreply.github.com>
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 <terrence.mcguinness@cox.net>
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 <guillaume.vernieres@noaa.gov>
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 <jiande.wang@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <58948505+AndrewEichmann-NOAA@users.noreply.github.com>
Date: Thu Nov 2 16:09:59 2023 -0400
changed optional script name vars for ocean analysis (#2025)
commit 93bc918cdabee771c182c6f33cc54a20b5bb86c6
Author: Kate Friedman <kate.friedman@noaa.gov>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <58948505+AndrewEichmann-NOAA@users.noreply.github.com>
Date: Wed Nov 1 14:19:55 2023 -0400
Updates to prep ocean obs task (#1870)
commit 77be0ec6a3117b9f7e71a19c69ac64c09b521ecd
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <69919478+DavidHuber-NOAA@users.noreply.github.com>
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 <Walter.Kolczynski@noaa.gov>
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 <terrence.mcguinness@cox.net>
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 <terrence.mcguinness@cox.net>
Date: Tue Oct 31 13:57:02 2023 +0000
Allow CI case to exclude running on certain platforms (#2001)
commit 7cc137116f1619bf1e5a12eaacb98d17da97c223
Author: Jeff Whitaker <jswhit@fastmail.fm>
Date: Tue Oct 31 07:54:24 2023 -0600
Add initial C96/1 deg coupled model support (#1991)
commit 7086ddc4bece6fb2a8c1c2e6090800d4293e410e
Author: AndrewEichmann-NOAA <58948505+AndrewEichmann-NOAA@users.noreply.github.com>
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 <guillaume.vernieres@noaa.gov>
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 <108816337+AnilKumar-NOAA@users.noreply.github.com>
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 <26926959+RussTreadon-NOAA@users.noreply.github.com>
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 962368884991670d3a1e…
kayeekayee
added a commit
to kayeekayee/global-workflow
that referenced
this issue
Mar 16, 2024
12Jan24 global-workflow
UFS: 29Jan24, 625ac02
FV3: 29Jan24, bd38c56
UPP: 07Nov23, 78f369b
UFS_UTILS: 22Dev23, ce385ce
update pointers for ufs_model and ufs_utils
add GSL C3_MYNN xml suite
Change dt_inner=75 for any configuration running aerosol-aware Thompson (ltaerosol=.true.)
Squashed commit of the following:
commit 25c026ef03a8d8c0db0b7368d2836f0b2e866eae
Author: jderrico-noaa <janet.m.derrico@noaa.gov>
Date: Thu Feb 29 20:35:11 2024 +0000
update ufs_model pointer
commit a28617a951c46b765aa996bfe4d28b554ec4e0a4
Author: jderrico-noaa <janet.m.derrico@noaa.gov>
Date: Thu Feb 22 06:16:26 2024 +0000
removed unneeded gsl directories
commit 6fb4f90e8572e98c977a1d2ab385f033111f3ea7
Author: jderrico-noaa <janet.m.derrico@noaa.gov>
Date: Thu Feb 22 06:08:13 2024 +0000
update ufs_utils.fd pointer
commit 9264f0c09239d046c5cd862d807e9b82f51dc3bd
Author: jderrico-noaa <janet.m.derrico@noaa.gov>
Date: Wed Feb 21 19:33:26 2024 +0000
update .gitmodules file
commit f8edfa966147506f2c207728039e3a736cb95415
Author: jderrico-noaa <janet.m.derrico@noaa.gov>
Date: Wed Feb 21 19:30:47 2024 +0000
update pointer to ufs_utils.fd
commit 5e0d2ab02d58e6a7a40db55a149a93008b28aa8b
Author: jderrico-noaa <janet.m.derrico@noaa.gov>
Date: Wed Feb 21 19:25:52 2024 +0000
update pointer to ufs_model.fd
commit ebc9e1d02987a1c6aa8cabedf2323642748fab3c
Merge: e7a81511 50cb1e6f
Author: Janet Derrico <143837053+jderrico-noaa@users.noreply.github.com>
Date: Thu Feb 15 13:40:33 2024 -0700
Merge pull request #40 from kayeekayee/gsl_ufs_dev
Merge to 2024 Jan 12 NOAA-EMC/develop and update to 2024 Jan 29 UFS
commit 50cb1e6f0c661e4c6e2ef0be4527cce58379b2c9
Author: kayee.wong <kayee.wong@noaa.gov>
Date: Thu Feb 15 20:30:34 2024 +0000
Add pygraf workflow.
commit 38b726125d49cff6cae4c0e5fff2438fc33143c5
Author: kayee.wong <kayee.wong@noaa.gov>
Date: Wed Feb 14 17:43:15 2024 +0000
Add double quote for the arguments when calling setup_expt.py.
commit 053f2025fb0b0679c7d4f84958973c1534ec050c
Author: kayee.wong <kayee.wong@noaa.gov>
Date: Tue Feb 13 23:57:06 2024 +0000
more fix.
commit 6f80ea2edc5444e275a79b371d02b6e98e963662
Author: kayee.wong <kayee.wong@noaa.gov>
Date: Tue Feb 13 23:50:01 2024 +0000
more bug fix.
commit 56e283f1f666a38a4a3b30e1528e96eeb5c622e7
Author: kayee.wong <kayee.wong@noaa.gov>
Date: Tue Feb 13 23:40:02 2024 +0000
Minor bug fix.
commit 2dcfed06ff6789eb77cf92e22b80f5475923fafc
Author: kayee.wong <kayee.wong@noaa.gov>
Date: Tue Feb 13 23:19:03 2024 +0000
Update parameter for c3 case
Add c3 and mynn template
commit cc46b19ccc7cdb54878340eff79dda9e747abdf7
Author: kayee.wong <kayee.wong@noaa.gov>
Date: Tue Feb 13 20:51:23 2024 +0000
Update INFO.
Add c3 SDF in the build.
commit a444ed48a23f24724853036e522b4437bf412c59
Author: kayee.wong <kayee.wong@noaa.gov>
Date: Tue Feb 13 18:42:33 2024 +0000
Update to UFS 2024 Jan 29 version.
commit 88595707c7521cdce37ae1cf78720a7827242b24
Author: kayee.wong <kayee.wong@noaa.gov>
Date: Tue Feb 13 18:16:46 2024 +0000
Minor bug fix.
commit baa0e9f10b132098d5134efaad712a51ebc26b83
Author: kayee.wong <kayee.wong@noaa.gov>
Date: Tue Feb 13 17:59:27 2024 +0000
Update parameters for setup_expt.py in p8_ugwpv1.sh to resdetatmos and comroot.
commit 5875f06903f82a47fafb05f89f840e3b099d18d8
Author: kayee.wong <kayee.wong@noaa.gov>
Date: Tue Feb 13 17:51:11 2024 +0000
Remove old gsl SDFs.
Remove 'rrtmg_lw_pre' from C3 and MYNN SDFs.
commit 9e0d1342f4e1edce96c9b2baeec55c2cffb964cd
Author: kayee.wong <kayee.wong@noaa.gov>
Date: Thu Feb 8 22:14:01 2024 +0000
Merge to 2024 Jan 12 NOAA-EMC/develop.
Squashed commit of the following:
commit c59047614c29f6ec15a4d4a6fa1855929287debd
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Fri Jan 12 19:21:02 2024 -0500
Update hash to ufs-weather-model. The noahmptable.tbl was reorganized, so update link_workflow.sh to use the same one used in UFSWM RT (#2219)
commit c041968e165c07da785376f1441374687b55d6cc
Author: Kate Friedman <kate.friedman@noaa.gov>
Date: Fri Jan 12 12:09:35 2024 -0500
Add ocean resolution to setup_expt invocation and retire/reduce COMROT/ROTDIR usage (#2214)
Two series of updates:
1) Update setup scripts to now allow users to provide ocean resolution
2) Housekeeping to retire the `COMROT` variable, replacing it with other variables
as needed, and reduce the `ROTDIR` variable usage.
Both updates change options for the workflow setup API.
Refs #2061
commit 997f97816493d9ed0242e169b6dcf84e5c9338d6
Author: AndrewEichmann-NOAA <58948505+AndrewEichmann-NOAA@users.noreply.github.com>
Date: Fri Jan 12 10:46:36 2024 -0500
Allow use of ocean obs prep in WCDA cycling and remove R2D2 (#2215)
Enables use of ocean obs prep task in WCDA cycling and removes R2D2 from same.
Runs task gdasprepoceanobs before gdasocnanalprep -- obtains ocean data nc4 files from DMPDIR, processes them into IODA format and copies them to COM_OBS.
Replaces the current R2D2 processing.
commit 12a5bb192ab6282d44c008c06dc14947abd37249
Merge: 4cb58020 6492c2da
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Fri Jan 12 09:26:27 2024 -0500
Merge pull request #2217 from DavidHuber-NOAA/update/versions
Update and clean up version and module files
commit 6492c2da5f49bd31575d0bef5278c9a7f8ba3412
Author: David Huber <david.huber@noaa.gov>
Date: Thu Jan 11 11:49:08 2024 -0600
Update orion module/version files for met/metplus #2123
commit 94c9937f0bff380b0ebd6acdcfd2509e1ae99389
Author: DavidHuber <david.huber@noaa.gov>
Date: Thu Jan 11 17:42:53 2024 +0000
Comment met/metplus out from Hera modulefile. #2123
commit 8c32f8b7d00bba6e3e954f149e6548fb27713a3c
Merge: a65e4c67 4cb58020
Author: David Huber <david.huber@noaa.gov>
Date: Thu Jan 11 11:34:44 2024 -0600
Merge branch 'develop' of github.com:noaa-emc/global-workflow into develop
commit a65e4c675f21dbe72198d263e85e894e62b41e13
Author: David Huber <david.huber@noaa.gov>
Date: Thu Jan 11 11:34:19 2024 -0600
Initial update of version/module files #2123
commit 4cb580201af68c1c0e2ae19faf0727dcbbe43b4d
Author: souopgui <souopgui@users.noreply.github.com>
Date: Wed Jan 10 08:30:22 2024 -0600
Fix OpenMP over-allocation of resources in exglobal_atmos_products.sh when running MPMD tasks (#2212)
Fix OpenMP over-allocation of resources running MPMD tasks
Co-authored-by: Innocent Souopgui <isouopgui@redlineperf.com>
commit b056b531faee6929687cb8a588ffafa1a66426fb
Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
Date: Mon Jan 8 17:28:05 2024 -0500
Add Hercules as valid machine in CI scripts (#2207)
Few updates to CI scripts to include names for hercules that where missed
the first time.
commit 6574d29a8c26b0695614874c344bccc5182363f4
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Mon Jan 8 17:25:47 2024 -0500
Fix invalid GH action and restart file name (#2210)
Resolves a typo that leads to an invalid workflow yaml and fixes the restart filename in restart detection.
Resolves #2205
commit 69605eac299df381ea9e0e329654487e26380ff5
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Mon Jan 8 17:00:28 2024 -0500
Stop attempting to comment link to RTD for non-PRs (#2209)
Adds a check so comments with a link to documentation are only generated
for PRs.
commit 4e160a895bfb31c281e21557dd86c13954a1a967
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Mon Jan 8 13:10:15 2024 -0500
Enable UPP for GOES processing (#2203)
Wnables the creation of special master grib2 files from UPP for
GOES processing
commit c15875b6dbf685327af9316ee43b3d01f0fc815e
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Mon Jan 8 09:56:06 2024 -0500
Port cycling to Hercules (#2196)
Adds cycled support for Hercules (excluding gsi-monitor).
Partially resolves #1588
GSI monitoring is disabled on Hercules due to missing Perl modules. That will be enabled in a later PR.
commit ef6827dd6abdab2996d1e19f9e0ff5d3071e0fdd
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Mon Jan 8 09:43:12 2024 -0500
Refactor rocoto task XML creation (#2189)
Refactors the rocoto task generation to be recursive.
This will allow nested metatasks to loop over multiple variables, which is needed for GEFS product generation.
As part of this refactor, there is no longer separate arguments to designate metatasks.
Instead, task dicts can include a nested 'task_dict' as well as a 'var_dict' containing the variables to loop over.
The nested task dict can then either have another layer, or be the innermost task.
To accommodate the new recursive nature, some defaults that were previously defined in create_wf_task() had to be pushed down into the function that creates the innermost task.
Also, former keywords have been absorbed by the task dict.
Refs #823
Refs #827
commit 2b81cfac16f103fb29b3aeb9748941787abf7287
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Mon Jan 8 09:41:03 2024 -0500
Update fix versions (#2198)
Updates fix versions for a few components:
- Update cice and mom6 versions to support C96/1p00 marine
- Update wave to change betamax setting for glo_025 waves
Resolves #2004
Resolves #2107
commit e7a81511e37f86e881da020e06b95990b470d952
Merge: af47b77c 75ad3754
Author: Janet Derrico <143837053+jderrico-noaa@users.noreply.github.com>
Date: Thu Feb 1 13:14:02 2024 -0700
Merge pull request #37 from jderrico-noaa/gsl_ufs_dev
Add GSL archive script and correct typos/fixed paths
commit 75ad3754f8bef5411c2570b5e392cd08e95cb6cb
Author: jderrico-noaa <janet.m.derrico@noaa.gov>
Date: Thu Feb 1 20:00:52 2024 +0000
adding consistent [[ ]] for if statements
commit 67b99668c82a5fd8c42479b9b1bfe8b0bad0be25
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Thu Feb 1 19:37:47 2024 +0000
Updated HOMEgfs in GSL XML templates
commit 4d3719c086e7907a6eeff03112042d392e0d8c5e
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Thu Feb 1 17:27:39 2024 +0000
Correct syntax errors in GSL scripts
Add new GSL archive script for archiving grib2 and ICs, but no netcdf files
commit 4309dd0b3b2d5625e7e1740d7cd3e39aacd5bc29
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Mon Jan 29 18:05:45 2024 +0000
Add GSL diag tables to parm/ufs/fv3
Update GSL template for hera
Create EMC and GSL versions of files under workflow/rocoto
- tasks.py, workflow_tasks.py
commit af47b77c7ee59a11c798995b4362b57e9096b090
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Sat Jan 27 02:07:43 2024 +0000
Create GSL version of archive script
commit 529d9f71f97b6e643e76a53bc9871901ae861faf
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Sat Jan 27 01:37:09 2024 +0000
Create GSL version of tracker.sh
- this is a placeholder with changes from last year's HFIP experiment; will likely need to be updated in the future
commit 8457e12c313bee602265b863129734354b019271
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Sat Jan 27 01:27:42 2024 +0000
Link config.base.emc.dyn_hera to config.base.emc.dyn
commit 7a05f5bd947944d8c3be828aeef9cc03bf9e073a
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Sat Jan 27 01:22:54 2024 +0000
Create GSL version of hpssarch_gen.sh
- assume we only run cold starts
- archive only 0p25 grib2 files (no 0p50 opr 1p00)
- assume no pgrb2b or flux files are created so no need to archive to HPSS
commit 98f5d6b16437e2a340bf16f83187e389a53f8bf0
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Sat Jan 27 00:24:06 2024 +0000
Update workflow directory
- add GSL template for jet (based on last year's experiment)
- create EMC and GSL versions of yaml files under hosts; defaults point to GSL files
commit 38a7e5629ceeb23d399643a021e9a0a88468a07c
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Thu Jan 25 18:40:37 2024 +0000
Update atmos_products configuration file for GSL
- set downset to 1 so pgrb2b files are not created
- set FLXGF to "NO" so interpolated sflux.1p00 files are not created
commit fe8a953658d092ce2b597e14f31678624606fd8a
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Thu Jan 25 17:02:25 2024 +0000
Update nodes for gfsfcst task in GSL template for hera to match default configuration in config.ufs
(12x12, 2 threads, 1 write group, 40 write tasks ==> 56 nodes)
Increase walltime to 4:10 for gfsfcst task
commit 9d85b0f6d50e8ed142557fcb87c89d2e5d63c617
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Tue Jan 23 19:08:52 2024 +0000
Added default location for PTMP/STMP in workflow/hosts/hera.yaml
Added GSL XML template for hera
commit 1cf317d327fae78c5469712c9e5a6aa1ffa4b23b
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Wed Jan 17 22:33:13 2024 +0000
Add sjet partition
Make syntax consistent in "if" statements in config.resources
commit 2755e203751f50113849b06769173285e093290b
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Wed Jan 17 22:32:26 2024 +0000
Update configuration files for GSL
- create Hera and Jet versions of config.base.emc.dyn
- correct typo in config.fcst
- create different versions of config.ufs;
default is 12x12, 2 threads, 1 write group/40 write tasks (56 nodes)
commit 3c0c126a376af31866a93aef4cdd0b4145150c58
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
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 <Judy.K.Henderson@noaa.gov>
Date: Tue Jan 16 16:46:25 2024 +0000
Update link script for ufs_utils.fd
commit 5b21b31900955013b4e8106d3ae906b9da93b361
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Tue Jan 16 16:45:25 2024 +0000
Add GSL archive scripts for initial conditions
commit abb88baf9dd536a3b2ea1e24eaa99cbfe85af799
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
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 <Judy.K.Henderson@noaa.gov>
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 <Judy.K.Henderson@noaa.gov>
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 <Judy.K.Henderson@noaa.gov>
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 <Judy.K.Henderson@noaa.gov>
Date: Thu Jan 11 23:34:36 2024 +0000
Add namelist parameter, nord_tr, for GSL suites
commit c4a41de7ebcda2f80ce69ac94bd2b3a6f5d04ed5
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
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 <Judy.K.Henderson@noaa.gov>
Date: Tue Jan 9 02:26:22 2024 +0000
Add experiment setup script for p8_ugwpv1
commit c5a3697d22fdbb02bb80ddffee2629dddc10c702
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
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 <Judy.K.Henderson@noaa.gov>
Date: Tue Jan 9 02:13:42 2024 +0000
Updated GSL-specific files under ufs_utils.fd_gsl
commit 1b153fc95b93a16eb40b791be7322100fde4a3d4
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date: Tue Jan 2 10:30:33 2024 -0700
Stop Gempak pgrb2 spec from modifying $DATA (#2147)
This PR addresses issue #1224. The following is accomplished:
- Instances where `DATA` is modified, corrections are made to use a locally defined variable such that `DATA` is no longer modified at run-time;
- Shell linter exceptions are addressed accordingly;
- The respective GEMPAK tasks is added to the Rocoto mesh.
Resolves #1224
commit 31ad23527802f7d07171132cc620f7135c4d8cba
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date: Tue Jan 2 10:27:30 2024 -0700
Reorganize NPOESS scripts (#2166)
This PR addresses issue #1226. The following is accomplished:
- Using the GEMPAK j-job script `JGFS_ATMOS_GEMPAK_PGRB2_SPEC`, the structure
of `JGFS_ATMOS_PGRB2_SPEC_NPOESS` is updated;
- Environment variables specific to the script `exgfs_atmos_grib2_special_npoess.sh`
are moved accordingly; this specifically applies to the environment variable `FHOUR`,
`SHOUR`, `FHINC`, `SLEEP_TIME`, and `SLEEP_INT`;
- The `SLEEP_TIME` and `SLEEP_INT` parameters can now be defined at the top-level
(if necessary);
- Restart file checks are move to `exgfs_atmos_grib2_special_npoess.sh`; however,
this may not be necessary (see `TODO` note within draft PR.
Resolves #1226
commit 22bd82fa93b49e5ce98eb3f69123956dd5018049
Author: Kate Friedman <kate.friedman@noaa.gov>
Date: Tue Jan 2 11:55:03 2024 -0500
Orog fix file reorg and fix directory variable standardization (#2181)
This PR makes updates to use the newly reorganized `orog/20231027`
fix file version and standardizes the fix file directory variables.
Changes:
1. Update UFS_UTILS hash to ce385ce
2. Update fix file version file to use new orog timestamp: `orog_ver=20231027`
3. Add ".mx$(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 <40322596+ADCollard@users.noreply.github.com>
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 <jessica.meixner@noaa.gov>
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 <69919478+DavidHuber-NOAA@users.noreply.github.com>
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 <bbakernoaa@users.noreply.github.com>
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 <aerorahul@users.noreply.github.com>
commit e55a05980709288d902ad1bd894164bfa5a18a65
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
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 <terrence.mcguinness@cox.net>
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 <58948505+AndrewEichmann-NOAA@users.noreply.github.com>
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 <69919478+DavidHuber-NOAA@users.noreply.github.com>
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 <kate.friedman@noaa.gov>
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 <kate.friedman@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <terrence.mcguinness@cox.net>
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 <aerorahul@users.noreply.github.com>
Date: Thu Dec 14 16:05:33 2023 -0500
Correct fbwind (#2161)
commit f3f3e05e6325e6c2e8ddab186f1ed2f985fec49a
Author: Kate Friedman <kate.friedman@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <69919478+DavidHuber-NOAA@users.noreply.github.com>
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 <kate.friedman@noaa.gov>
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 <cory.r.martin@noaa.gov>
Date: Thu Dec 7 15:12:05 2023 -0500
Update GDAS hash to most recent stable versions (#2138)
commit 93da9f105502e24f1a1a621f05ea49e1fdfe0102
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date: Thu Dec 7 10:41:05 2023 -0700
Corrected typo in a gempak job gempakncdcupapgif . (#2137)
commit 3483f550db1ae35a680de49f7485ce5a11902dd9
Author: Cory Martin <cory.r.martin@noaa.gov>
Date: Thu Dec 7 12:34:56 2023 -0500
Add support for FGAT and IAU for aerosol DA (#1940)
commit e2664c011bf5fb03a9b1b37878cad423a1fde6f9
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
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 <Walter.Kolczynski@noaa.gov>
commit a29f751aed05312da3d80d396159bb5a906d6ce4
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date: Wed Dec 6 13:45:56 2023 -0700
Adds GEMPAK and related jobs to rocoto task mesh (#2127)
commit 1fc8b5bf55581de18e786611c65bc3f84bb0c082
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
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 <kate.friedman@noaa.gov>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <kate.friedman@noaa.gov>
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 <terrence.mcguinness@cox.net>
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 <69919478+DavidHuber-NOAA@users.noreply.github.com>
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 <jiande.wang@noaa.gov>
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 <58948505+AndrewEichmann-NOAA@users.noreply.github.com>
Date: Wed Nov 29 15:17:36 2023 -0500
Added variables to config.prepoceanobs (#2101)
commit c2d78a61a224678fb804eed19f39d1f07408ae5f
Author: Kate Friedman <kate.friedman@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <kate.friedman@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <kate.friedman@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <kate.friedman@noaa.gov>
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 <kate.friedman@noaa.gov>
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 <jessica.meixner@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <48260754+WenMeng-NOAA@users.noreply.github.com>
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 <Walter.Kolczynski@noaa.gov>
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 <aerorahul@users.noreply.github.com>
Date: Wed Nov 15 16:44:03 2023 -0500
Fix missing _PREV in ocean restart file location (#2070)
commit 255616d37505c785bdddd5d3e39e8399110b626e
Author: mdtoyNOAA <73618848+mdtoyNOAA@users.noreply.github.com>
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 <guillaume.vernieres@noaa.gov>
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 <guoqing.ge@noaa.gov>
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 <kate.friedman@noaa.gov>
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 <kate.friedman@noaa.gov>
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 <aerorahul@users.noreply.github.com>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <kate.friedman@noaa.gov>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <Walter.Kolczynski@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <jiande.wang@noaa.gov>
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 <bbakernoaa@users.noreply.github.com>
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 <69919478+DavidHuber-NOAA@users.noreply.github.com>
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 <terrence.mcguinness@cox.net>
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 <guillaume.vernieres@noaa.gov>
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 <jiande.wang@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <58948505+AndrewEichmann-NOAA@users.noreply.github.com>
Date: Thu Nov 2 16:09:59 2023 -0400
changed optional script name vars for ocean analysis (#2025)
commit 93bc918cdabee771c182c6f33cc54a20b5bb86c6
Author: Kate Friedman <kate.friedman@noaa.gov>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <58948505+AndrewEichmann-NOAA@users.noreply.github.com>
Date: Wed Nov 1 14:19:55 2023 -0400
Updates to prep ocean obs task (#1870)
commit 77be0ec6a3117b9f7e71a19c69ac64c09b521ecd
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <69919478+DavidHuber-NOAA@users.noreply.github.com>
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 <Walter.Kolczynski@noaa.gov>
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 <terrence.mcguinness@cox.net>
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 <terrence.mcguinness@cox.net>
Date: Tue Oct 31 13:57:02 2023 +0000
Allow CI case to exclude running on certain platforms (#2001)
commit 7cc137116f1619bf1e5a12eaacb98d17da97c223
Author: Jeff Whitaker <jswhit@fastmail.fm>
Date: Tue Oct 31 07:54:24 2023 -0600
Add initial C96/1 deg coupled model support (#1991)
commit 7086ddc4bece6fb2a8c1c2e6090800d4293e410e
Author: AndrewEichmann-NOAA <58948505+AndrewEichmann-NOAA@users.noreply.github.com>
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 <guillaume.vernieres@noaa.gov>
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 <108816337+AnilKumar-NOAA@users.noreply.github.com>
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 <26926959+RussTreadon-NOAA@users.noreply.github.com>
Date: Thu Oct 26 23:44:27 2023 -0400
Update GDASApp hash (#1975)
Update GDASApp hash…
kayeekayee
added a commit
to kayeekayee/global-workflow
that referenced
this issue
Mar 20, 2024
12Jan24 global-workflow
UFS: 29Jan24, 625ac02
FV3: 29Jan24, bd38c56 (GSL: 28Feb24 , a439cc7)
UPP: 07Nov23, 78f369b
UFS_UTILS: 22Dev23, ce385ce
update pointers for ufs_model and ufs_utils
add GSL C3_MYNN xml suite
Squashed commit of the following:
commit db6a85e0ce36cec28714a4c9d6e13565253cf7bb
Author: jderrico-noaa <janet.m.derrico@noaa.gov>
Date: Tue Mar 19 19:33:28 2024 +0000
29Jan ufs_model.fd, 29Jan FV3 with C3 files
commit de7b382c4b259d99d39e8857cbcee7efe64c1956
Author: jderrico-noaa <janet.m.derrico@noaa.gov>
Date: Mon Mar 18 16:23:05 2024 +0000
update pointer for atmos_cubed_sphere to Feb 1 hash
commit 0fc27835205aaf57bdba228b1769e0ac7b37712e
Merge: b2c8ef81 db06f7c5
Author: jderrico-noaa <janet.m.derrico@noaa.gov>
Date: Thu Mar 14 00:17:24 2024 +0000
Merge branch 'gsl_ufs_dev' of https://github.com/NOAA-GSL/global-workflow into gsl_ufs_dev
commit b2c8ef81229b5e9b8e7592cb12c2f3e8e3179d92
Author: jderrico-noaa <janet.m.derrico@noaa.gov>
Date: Wed Mar 13 23:51:45 2024 +0000
ccpp pointer updates to framework and physics
commit 484a18df8c9022190c8900c80e40507a6771e314
Author: jderrico-noaa <janet.m.derrico@noaa.gov>
Date: Wed Mar 13 23:43:18 2024 +0000
ccpp pointer update in ufs_model.fd/FV3
commit db06f7c57d4cfc863352a4613c8260b0dffd9afe
Merge: 579f90c1 2dbd12a6
Author: Janet Derrico <143837053+jderrico-noaa@users.noreply.github.com>
Date: Wed Mar 13 15:55:48 2024 -0600
Merge pull request #43 from kayeekayee/gsl_ufs_dev
update GSL C3_MYNN files and change dt_inner=75
commit 2dbd12a695c4349071ee8470e597540e71bc0292
Author: kayee.wong <kayee.wong@noaa.gov>
Date: Wed Mar 13 03:48:51 2024 +0000
update GSL C3_MYNN files
commit 579f90c1e0e2896710046c1885f68560ea435fa6
Author: jderrico-noaa <janet.m.derrico@noaa.gov>
Date: Thu Mar 7 19:20:46 2024 +0000
update ufs_model.fd submodule pointer
commit 2f2622d68eb8444afde9c1ddad470cfee1b63b99
Author: jderrico-noaa <janet.m.derrico@noaa.gov>
Date: Thu Mar 7 19:15:23 2024 +0000
update ufs_model.fd submod pointer
commit 706a0c52bb11af78e016014550ebd6847cc0ee19
Author: jderrico-noaa <janet.m.derrico@noaa.gov>
Date: Thu Mar 7 19:12:35 2024 +0000
update ufs_model.fd/FV3 path
commit 352f188f095e19442ade1f3fd167ff2fed501cd2
Merge: 5a8edc76 96545dcb
Author: jderrico-noaa <janet.m.derrico@noaa.gov>
Date: Thu Mar 7 17:58:38 2024 +0000
update ufs model pointer
commit 5a8edc766f2f4d3e12c692069d46c02fd766c354
Author: jderrico-noaa <janet.m.derrico@noaa.gov>
Date: Thu Mar 7 17:42:00 2024 +0000
update FV3 and UPP
commit 96545dcb63e3f8f7dfc036961d818db15fa1a003
Author: jderrico-noaa <janet.m.derrico@noaa.gov>
Date: Wed Mar 6 10:05:39 2024 -0700
update pointer for ufs_model.fd
commit 25c026ef03a8d8c0db0b7368d2836f0b2e866eae
Author: jderrico-noaa <janet.m.derrico@noaa.gov>
Date: Thu Feb 29 20:35:11 2024 +0000
update ufs_model pointer
commit a28617a951c46b765aa996bfe4d28b554ec4e0a4
Author: jderrico-noaa <janet.m.derrico@noaa.gov>
Date: Thu Feb 22 06:16:26 2024 +0000
removed unneeded gsl directories
commit 6fb4f90e8572e98c977a1d2ab385f033111f3ea7
Author: jderrico-noaa <janet.m.derrico@noaa.gov>
Date: Thu Feb 22 06:08:13 2024 +0000
update ufs_utils.fd pointer
commit 9264f0c09239d046c5cd862d807e9b82f51dc3bd
Author: jderrico-noaa <janet.m.derrico@noaa.gov>
Date: Wed Feb 21 19:33:26 2024 +0000
update .gitmodules file
commit f8edfa966147506f2c207728039e3a736cb95415
Author: jderrico-noaa <janet.m.derrico@noaa.gov>
Date: Wed Feb 21 19:30:47 2024 +0000
update pointer to ufs_utils.fd
commit 5e0d2ab02d58e6a7a40db55a149a93008b28aa8b
Author: jderrico-noaa <janet.m.derrico@noaa.gov>
Date: Wed Feb 21 19:25:52 2024 +0000
update pointer to ufs_model.fd
commit ebc9e1d02987a1c6aa8cabedf2323642748fab3c
Merge: e7a81511 50cb1e6f
Author: Janet Derrico <143837053+jderrico-noaa@users.noreply.github.com>
Date: Thu Feb 15 13:40:33 2024 -0700
Merge pull request #40 from kayeekayee/gsl_ufs_dev
Merge to 2024 Jan 12 NOAA-EMC/develop and update to 2024 Jan 29 UFS
commit 50cb1e6f0c661e4c6e2ef0be4527cce58379b2c9
Author: kayee.wong <kayee.wong@noaa.gov>
Date: Thu Feb 15 20:30:34 2024 +0000
Add pygraf workflow.
commit 38b726125d49cff6cae4c0e5fff2438fc33143c5
Author: kayee.wong <kayee.wong@noaa.gov>
Date: Wed Feb 14 17:43:15 2024 +0000
Add double quote for the arguments when calling setup_expt.py.
commit 053f2025fb0b0679c7d4f84958973c1534ec050c
Author: kayee.wong <kayee.wong@noaa.gov>
Date: Tue Feb 13 23:57:06 2024 +0000
more fix.
commit 6f80ea2edc5444e275a79b371d02b6e98e963662
Author: kayee.wong <kayee.wong@noaa.gov>
Date: Tue Feb 13 23:50:01 2024 +0000
more bug fix.
commit 56e283f1f666a38a4a3b30e1528e96eeb5c622e7
Author: kayee.wong <kayee.wong@noaa.gov>
Date: Tue Feb 13 23:40:02 2024 +0000
Minor bug fix.
commit 2dcfed06ff6789eb77cf92e22b80f5475923fafc
Author: kayee.wong <kayee.wong@noaa.gov>
Date: Tue Feb 13 23:19:03 2024 +0000
Update parameter for c3 case
Add c3 and mynn template
commit cc46b19ccc7cdb54878340eff79dda9e747abdf7
Author: kayee.wong <kayee.wong@noaa.gov>
Date: Tue Feb 13 20:51:23 2024 +0000
Update INFO.
Add c3 SDF in the build.
commit a444ed48a23f24724853036e522b4437bf412c59
Author: kayee.wong <kayee.wong@noaa.gov>
Date: Tue Feb 13 18:42:33 2024 +0000
Update to UFS 2024 Jan 29 version.
commit 88595707c7521cdce37ae1cf78720a7827242b24
Author: kayee.wong <kayee.wong@noaa.gov>
Date: Tue Feb 13 18:16:46 2024 +0000
Minor bug fix.
commit baa0e9f10b132098d5134efaad712a51ebc26b83
Author: kayee.wong <kayee.wong@noaa.gov>
Date: Tue Feb 13 17:59:27 2024 +0000
Update parameters for setup_expt.py in p8_ugwpv1.sh to resdetatmos and comroot.
commit 5875f06903f82a47fafb05f89f840e3b099d18d8
Author: kayee.wong <kayee.wong@noaa.gov>
Date: Tue Feb 13 17:51:11 2024 +0000
Remove old gsl SDFs.
Remove 'rrtmg_lw_pre' from C3 and MYNN SDFs.
commit 9e0d1342f4e1edce96c9b2baeec55c2cffb964cd
Author: kayee.wong <kayee.wong@noaa.gov>
Date: Thu Feb 8 22:14:01 2024 +0000
Merge to 2024 Jan 12 NOAA-EMC/develop.
Squashed commit of the following:
commit c59047614c29f6ec15a4d4a6fa1855929287debd
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Fri Jan 12 19:21:02 2024 -0500
Update hash to ufs-weather-model. The noahmptable.tbl was reorganized, so update link_workflow.sh to use the same one used in UFSWM RT (#2219)
commit c041968e165c07da785376f1441374687b55d6cc
Author: Kate Friedman <kate.friedman@noaa.gov>
Date: Fri Jan 12 12:09:35 2024 -0500
Add ocean resolution to setup_expt invocation and retire/reduce COMROT/ROTDIR usage (#2214)
Two series of updates:
1) Update setup scripts to now allow users to provide ocean resolution
2) Housekeeping to retire the `COMROT` variable, replacing it with other variables
as needed, and reduce the `ROTDIR` variable usage.
Both updates change options for the workflow setup API.
Refs #2061
commit 997f97816493d9ed0242e169b6dcf84e5c9338d6
Author: AndrewEichmann-NOAA <58948505+AndrewEichmann-NOAA@users.noreply.github.com>
Date: Fri Jan 12 10:46:36 2024 -0500
Allow use of ocean obs prep in WCDA cycling and remove R2D2 (#2215)
Enables use of ocean obs prep task in WCDA cycling and removes R2D2 from same.
Runs task gdasprepoceanobs before gdasocnanalprep -- obtains ocean data nc4 files from DMPDIR, processes them into IODA format and copies them to COM_OBS.
Replaces the current R2D2 processing.
commit 12a5bb192ab6282d44c008c06dc14947abd37249
Merge: 4cb58020 6492c2da
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Fri Jan 12 09:26:27 2024 -0500
Merge pull request #2217 from DavidHuber-NOAA/update/versions
Update and clean up version and module files
commit 6492c2da5f49bd31575d0bef5278c9a7f8ba3412
Author: David Huber <david.huber@noaa.gov>
Date: Thu Jan 11 11:49:08 2024 -0600
Update orion module/version files for met/metplus #2123
commit 94c9937f0bff380b0ebd6acdcfd2509e1ae99389
Author: DavidHuber <david.huber@noaa.gov>
Date: Thu Jan 11 17:42:53 2024 +0000
Comment met/metplus out from Hera modulefile. #2123
commit 8c32f8b7d00bba6e3e954f149e6548fb27713a3c
Merge: a65e4c67 4cb58020
Author: David Huber <david.huber@noaa.gov>
Date: Thu Jan 11 11:34:44 2024 -0600
Merge branch 'develop' of github.com:noaa-emc/global-workflow into develop
commit a65e4c675f21dbe72198d263e85e894e62b41e13
Author: David Huber <david.huber@noaa.gov>
Date: Thu Jan 11 11:34:19 2024 -0600
Initial update of version/module files #2123
commit 4cb580201af68c1c0e2ae19faf0727dcbbe43b4d
Author: souopgui <souopgui@users.noreply.github.com>
Date: Wed Jan 10 08:30:22 2024 -0600
Fix OpenMP over-allocation of resources in exglobal_atmos_products.sh when running MPMD tasks (#2212)
Fix OpenMP over-allocation of resources running MPMD tasks
Co-authored-by: Innocent Souopgui <isouopgui@redlineperf.com>
commit b056b531faee6929687cb8a588ffafa1a66426fb
Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
Date: Mon Jan 8 17:28:05 2024 -0500
Add Hercules as valid machine in CI scripts (#2207)
Few updates to CI scripts to include names for hercules that where missed
the first time.
commit 6574d29a8c26b0695614874c344bccc5182363f4
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Mon Jan 8 17:25:47 2024 -0500
Fix invalid GH action and restart file name (#2210)
Resolves a typo that leads to an invalid workflow yaml and fixes the restart filename in restart detection.
Resolves #2205
commit 69605eac299df381ea9e0e329654487e26380ff5
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Mon Jan 8 17:00:28 2024 -0500
Stop attempting to comment link to RTD for non-PRs (#2209)
Adds a check so comments with a link to documentation are only generated
for PRs.
commit 4e160a895bfb31c281e21557dd86c13954a1a967
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Mon Jan 8 13:10:15 2024 -0500
Enable UPP for GOES processing (#2203)
Wnables the creation of special master grib2 files from UPP for
GOES processing
commit c15875b6dbf685327af9316ee43b3d01f0fc815e
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Mon Jan 8 09:56:06 2024 -0500
Port cycling to Hercules (#2196)
Adds cycled support for Hercules (excluding gsi-monitor).
Partially resolves #1588
GSI monitoring is disabled on Hercules due to missing Perl modules. That will be enabled in a later PR.
commit ef6827dd6abdab2996d1e19f9e0ff5d3071e0fdd
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Mon Jan 8 09:43:12 2024 -0500
Refactor rocoto task XML creation (#2189)
Refactors the rocoto task generation to be recursive.
This will allow nested metatasks to loop over multiple variables, which is needed for GEFS product generation.
As part of this refactor, there is no longer separate arguments to designate metatasks.
Instead, task dicts can include a nested 'task_dict' as well as a 'var_dict' containing the variables to loop over.
The nested task dict can then either have another layer, or be the innermost task.
To accommodate the new recursive nature, some defaults that were previously defined in create_wf_task() had to be pushed down into the function that creates the innermost task.
Also, former keywords have been absorbed by the task dict.
Refs #823
Refs #827
commit 2b81cfac16f103fb29b3aeb9748941787abf7287
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Mon Jan 8 09:41:03 2024 -0500
Update fix versions (#2198)
Updates fix versions for a few components:
- Update cice and mom6 versions to support C96/1p00 marine
- Update wave to change betamax setting for glo_025 waves
Resolves #2004
Resolves #2107
commit e7a81511e37f86e881da020e06b95990b470d952
Merge: af47b77c 75ad3754
Author: Janet Derrico <143837053+jderrico-noaa@users.noreply.github.com>
Date: Thu Feb 1 13:14:02 2024 -0700
Merge pull request #37 from jderrico-noaa/gsl_ufs_dev
Add GSL archive script and correct typos/fixed paths
commit 75ad3754f8bef5411c2570b5e392cd08e95cb6cb
Author: jderrico-noaa <janet.m.derrico@noaa.gov>
Date: Thu Feb 1 20:00:52 2024 +0000
adding consistent [[ ]] for if statements
commit 67b99668c82a5fd8c42479b9b1bfe8b0bad0be25
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Thu Feb 1 19:37:47 2024 +0000
Updated HOMEgfs in GSL XML templates
commit 4d3719c086e7907a6eeff03112042d392e0d8c5e
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Thu Feb 1 17:27:39 2024 +0000
Correct syntax errors in GSL scripts
Add new GSL archive script for archiving grib2 and ICs, but no netcdf files
commit 4309dd0b3b2d5625e7e1740d7cd3e39aacd5bc29
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Mon Jan 29 18:05:45 2024 +0000
Add GSL diag tables to parm/ufs/fv3
Update GSL template for hera
Create EMC and GSL versions of files under workflow/rocoto
- tasks.py, workflow_tasks.py
commit af47b77c7ee59a11c798995b4362b57e9096b090
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Sat Jan 27 02:07:43 2024 +0000
Create GSL version of archive script
commit 529d9f71f97b6e643e76a53bc9871901ae861faf
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Sat Jan 27 01:37:09 2024 +0000
Create GSL version of tracker.sh
- this is a placeholder with changes from last year's HFIP experiment; will likely need to be updated in the future
commit 8457e12c313bee602265b863129734354b019271
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Sat Jan 27 01:27:42 2024 +0000
Link config.base.emc.dyn_hera to config.base.emc.dyn
commit 7a05f5bd947944d8c3be828aeef9cc03bf9e073a
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Sat Jan 27 01:22:54 2024 +0000
Create GSL version of hpssarch_gen.sh
- assume we only run cold starts
- archive only 0p25 grib2 files (no 0p50 opr 1p00)
- assume no pgrb2b or flux files are created so no need to archive to HPSS
commit 98f5d6b16437e2a340bf16f83187e389a53f8bf0
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Sat Jan 27 00:24:06 2024 +0000
Update workflow directory
- add GSL template for jet (based on last year's experiment)
- create EMC and GSL versions of yaml files under hosts; defaults point to GSL files
commit 38a7e5629ceeb23d399643a021e9a0a88468a07c
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Thu Jan 25 18:40:37 2024 +0000
Update atmos_products configuration file for GSL
- set downset to 1 so pgrb2b files are not created
- set FLXGF to "NO" so interpolated sflux.1p00 files are not created
commit fe8a953658d092ce2b597e14f31678624606fd8a
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Thu Jan 25 17:02:25 2024 +0000
Update nodes for gfsfcst task in GSL template for hera to match default configuration in config.ufs
(12x12, 2 threads, 1 write group, 40 write tasks ==> 56 nodes)
Increase walltime to 4:10 for gfsfcst task
commit 9d85b0f6d50e8ed142557fcb87c89d2e5d63c617
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Tue Jan 23 19:08:52 2024 +0000
Added default location for PTMP/STMP in workflow/hosts/hera.yaml
Added GSL XML template for hera
commit 1cf317d327fae78c5469712c9e5a6aa1ffa4b23b
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Wed Jan 17 22:33:13 2024 +0000
Add sjet partition
Make syntax consistent in "if" statements in config.resources
commit 2755e203751f50113849b06769173285e093290b
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Wed Jan 17 22:32:26 2024 +0000
Update configuration files for GSL
- create Hera and Jet versions of config.base.emc.dyn
- correct typo in config.fcst
- create different versions of config.ufs;
default is 12x12, 2 threads, 1 write group/40 write tasks (56 nodes)
commit 3c0c126a376af31866a93aef4cdd0b4145150c58
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
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 <Judy.K.Henderson@noaa.gov>
Date: Tue Jan 16 16:46:25 2024 +0000
Update link script for ufs_utils.fd
commit 5b21b31900955013b4e8106d3ae906b9da93b361
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Tue Jan 16 16:45:25 2024 +0000
Add GSL archive scripts for initial conditions
commit abb88baf9dd536a3b2ea1e24eaa99cbfe85af799
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
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 <Judy.K.Henderson@noaa.gov>
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 <Judy.K.Henderson@noaa.gov>
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 <Judy.K.Henderson@noaa.gov>
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 <Judy.K.Henderson@noaa.gov>
Date: Thu Jan 11 23:34:36 2024 +0000
Add namelist parameter, nord_tr, for GSL suites
commit c4a41de7ebcda2f80ce69ac94bd2b3a6f5d04ed5
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
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 <Judy.K.Henderson@noaa.gov>
Date: Tue Jan 9 02:26:22 2024 +0000
Add experiment setup script for p8_ugwpv1
commit c5a3697d22fdbb02bb80ddffee2629dddc10c702
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
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 <Judy.K.Henderson@noaa.gov>
Date: Tue Jan 9 02:13:42 2024 +0000
Updated GSL-specific files under ufs_utils.fd_gsl
commit 1b153fc95b93a16eb40b791be7322100fde4a3d4
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date: Tue Jan 2 10:30:33 2024 -0700
Stop Gempak pgrb2 spec from modifying $DATA (#2147)
This PR addresses issue #1224. The following is accomplished:
- Instances where `DATA` is modified, corrections are made to use a locally defined variable such that `DATA` is no longer modified at run-time;
- Shell linter exceptions are addressed accordingly;
- The respective GEMPAK tasks is added to the Rocoto mesh.
Resolves #1224
commit 31ad23527802f7d07171132cc620f7135c4d8cba
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date: Tue Jan 2 10:27:30 2024 -0700
Reorganize NPOESS scripts (#2166)
This PR addresses issue #1226. The following is accomplished:
- Using the GEMPAK j-job script `JGFS_ATMOS_GEMPAK_PGRB2_SPEC`, the structure
of `JGFS_ATMOS_PGRB2_SPEC_NPOESS` is updated;
- Environment variables specific to the script `exgfs_atmos_grib2_special_npoess.sh`
are moved accordingly; this specifically applies to the environment variable `FHOUR`,
`SHOUR`, `FHINC`, `SLEEP_TIME`, and `SLEEP_INT`;
- The `SLEEP_TIME` and `SLEEP_INT` parameters can now be defined at the top-level
(if necessary);
- Restart file checks are move to `exgfs_atmos_grib2_special_npoess.sh`; however,
this may not be necessary (see `TODO` note within draft PR.
Resolves #1226
commit 22bd82fa93b49e5ce98eb3f69123956dd5018049
Author: Kate Friedman <kate.friedman@noaa.gov>
Date: Tue Jan 2 11:55:03 2024 -0500
Orog fix file reorg and fix directory variable standardization (#2181)
This PR makes updates to use the newly reorganized `orog/20231027`
fix file version and standardizes the fix file directory variables.
Changes:
1. Update UFS_UTILS hash to ce385ce
2. Update fix file version file to use new orog timestamp: `orog_ver=20231027`
3. Add ".mx$(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 <40322596+ADCollard@users.noreply.github.com>
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 <jessica.meixner@noaa.gov>
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 <69919478+DavidHuber-NOAA@users.noreply.github.com>
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 <bbakernoaa@users.noreply.github.com>
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 <aerorahul@users.noreply.github.com>
commit e55a05980709288d902ad1bd894164bfa5a18a65
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
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 <terrence.mcguinness@cox.net>
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 <58948505+AndrewEichmann-NOAA@users.noreply.github.com>
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 <69919478+DavidHuber-NOAA@users.noreply.github.com>
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 <kate.friedman@noaa.gov>
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 <kate.friedman@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <terrence.mcguinness@cox.net>
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 <aerorahul@users.noreply.github.com>
Date: Thu Dec 14 16:05:33 2023 -0500
Correct fbwind (#2161)
commit f3f3e05e6325e6c2e8ddab186f1ed2f985fec49a
Author: Kate Friedman <kate.friedman@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <69919478+DavidHuber-NOAA@users.noreply.github.com>
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 <kate.friedman@noaa.gov>
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 <cory.r.martin@noaa.gov>
Date: Thu Dec 7 15:12:05 2023 -0500
Update GDAS hash to most recent stable versions (#2138)
commit 93da9f105502e24f1a1a621f05ea49e1fdfe0102
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date: Thu Dec 7 10:41:05 2023 -0700
Corrected typo in a gempak job gempakncdcupapgif . (#2137)
commit 3483f550db1ae35a680de49f7485ce5a11902dd9
Author: Cory Martin <cory.r.martin@noaa.gov>
Date: Thu Dec 7 12:34:56 2023 -0500
Add support for FGAT and IAU for aerosol DA (#1940)
commit e2664c011bf5fb03a9b1b37878cad423a1fde6f9
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
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 <Walter.Kolczynski@noaa.gov>
commit a29f751aed05312da3d80d396159bb5a906d6ce4
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date: Wed Dec 6 13:45:56 2023 -0700
Adds GEMPAK and related jobs to rocoto task mesh (#2127)
commit 1fc8b5bf55581de18e786611c65bc3f84bb0c082
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
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 <kate.friedman@noaa.gov>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <kate.friedman@noaa.gov>
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 <terrence.mcguinness@cox.net>
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 <69919478+DavidHuber-NOAA@users.noreply.github.com>
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 <jiande.wang@noaa.gov>
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 <58948505+AndrewEichmann-NOAA@users.noreply.github.com>
Date: Wed Nov 29 15:17:36 2023 -0500
Added variables to config.prepoceanobs (#2101)
commit c2d78a61a224678fb804eed19f39d1f07408ae5f
Author: Kate Friedman <kate.friedman@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <kate.friedman@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <kate.friedman@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <kate.friedman@noaa.gov>
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 <kate.friedman@noaa.gov>
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 <jessica.meixner@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <48260754+WenMeng-NOAA@users.noreply.github.com>
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 <Walter.Kolczynski@noaa.gov>
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 <aerorahul@users.noreply.github.com>
Date: Wed Nov 15 16:44:03 2023 -0500
Fix missing _PREV in ocean restart file location (#2070)
commit 255616d37505c785bdddd5d3e39e8399110b626e
Author: mdtoyNOAA <73618848+mdtoyNOAA@users.noreply.github.com>
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 <guillaume.vernieres@noaa.gov>
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 <guoqing.ge@noaa.gov>
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 <kate.friedman@noaa.gov>
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 <kate.friedman@noaa.gov>
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 <aerorahul@users.noreply.github.com>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <kate.friedman@noaa.gov>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <Walter.Kolczynski@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <jiande.wang@noaa.gov>
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 <bbakernoaa@users.noreply.github.com>
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 <69919478+DavidHuber-NOAA@users.noreply.github.com>
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 <terrence.mcguinness@cox.net>
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 <guillaume.vernieres@noaa.gov>
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 <jiande.wang@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <58948505+AndrewEichmann-NOAA@users.noreply.github.com>
Date: Thu Nov 2 16:09:59 2023 -0400
changed optional script name vars for ocean analysis (#2025)
commit 93bc918cdabee771c182c6f33cc54a20b5bb86c6
Author: Kate Friedman <kate.friedman@noaa.gov>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <58948505+AndrewEichmann-NOAA@users.noreply.github.com>
Date: Wed Nov 1 14:19:55 2023 -0400
Updates to prep ocean obs task (#1870)
commit 77be0ec6a3117b9f7e71a19c69ac64c09b521ecd
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <69919478+DavidHuber-NOAA@users.noreply.github.com>
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 <Walter.Kolczynski@noaa.gov>
Date: Tu…
kayeekayee
added a commit
to kayeekayee/global-workflow
that referenced
this issue
Mar 20, 2024
12Jan24 global-workflow
UFS: 29Jan24, 625ac02
FV3: 29Jan24, bd38c56 (GSL: 28Feb24 , a439cc7)
UPP: 07Nov23, 78f369b
UFS_UTILS: 22Dev23, ce385ce
update pointers for ufs_model and ufs_utils
add GSL C3_MYNN xml suite
Change dt_inner=75 for any configuration running aerosol-aware Thompson (ltaerosol=.true.)
Squashed commit of the following:
commit db6a85e0ce36cec28714a4c9d6e13565253cf7bb
Author: jderrico-noaa <janet.m.derrico@noaa.gov>
Date: Tue Mar 19 19:33:28 2024 +0000
29Jan ufs_model.fd, 29Jan FV3 with C3 files
commit de7b382c4b259d99d39e8857cbcee7efe64c1956
Author: jderrico-noaa <janet.m.derrico@noaa.gov>
Date: Mon Mar 18 16:23:05 2024 +0000
update pointer for atmos_cubed_sphere to Feb 1 hash
commit 0fc27835205aaf57bdba228b1769e0ac7b37712e
Merge: b2c8ef81 db06f7c5
Author: jderrico-noaa <janet.m.derrico@noaa.gov>
Date: Thu Mar 14 00:17:24 2024 +0000
Merge branch 'gsl_ufs_dev' of https://github.com/NOAA-GSL/global-workflow into gsl_ufs_dev
commit b2c8ef81229b5e9b8e7592cb12c2f3e8e3179d92
Author: jderrico-noaa <janet.m.derrico@noaa.gov>
Date: Wed Mar 13 23:51:45 2024 +0000
ccpp pointer updates to framework and physics
commit 484a18df8c9022190c8900c80e40507a6771e314
Author: jderrico-noaa <janet.m.derrico@noaa.gov>
Date: Wed Mar 13 23:43:18 2024 +0000
ccpp pointer update in ufs_model.fd/FV3
commit db06f7c57d4cfc863352a4613c8260b0dffd9afe
Merge: 579f90c1 2dbd12a6
Author: Janet Derrico <143837053+jderrico-noaa@users.noreply.github.com>
Date: Wed Mar 13 15:55:48 2024 -0600
Merge pull request #43 from kayeekayee/gsl_ufs_dev
update GSL C3_MYNN files and change dt_inner=75
commit 2dbd12a695c4349071ee8470e597540e71bc0292
Author: kayee.wong <kayee.wong@noaa.gov>
Date: Wed Mar 13 03:48:51 2024 +0000
update GSL C3_MYNN files
commit 579f90c1e0e2896710046c1885f68560ea435fa6
Author: jderrico-noaa <janet.m.derrico@noaa.gov>
Date: Thu Mar 7 19:20:46 2024 +0000
update ufs_model.fd submodule pointer
commit 2f2622d68eb8444afde9c1ddad470cfee1b63b99
Author: jderrico-noaa <janet.m.derrico@noaa.gov>
Date: Thu Mar 7 19:15:23 2024 +0000
update ufs_model.fd submod pointer
commit 706a0c52bb11af78e016014550ebd6847cc0ee19
Author: jderrico-noaa <janet.m.derrico@noaa.gov>
Date: Thu Mar 7 19:12:35 2024 +0000
update ufs_model.fd/FV3 path
commit 352f188f095e19442ade1f3fd167ff2fed501cd2
Merge: 5a8edc76 96545dcb
Author: jderrico-noaa <janet.m.derrico@noaa.gov>
Date: Thu Mar 7 17:58:38 2024 +0000
update ufs model pointer
commit 5a8edc766f2f4d3e12c692069d46c02fd766c354
Author: jderrico-noaa <janet.m.derrico@noaa.gov>
Date: Thu Mar 7 17:42:00 2024 +0000
update FV3 and UPP
commit 96545dcb63e3f8f7dfc036961d818db15fa1a003
Author: jderrico-noaa <janet.m.derrico@noaa.gov>
Date: Wed Mar 6 10:05:39 2024 -0700
update pointer for ufs_model.fd
commit 25c026ef03a8d8c0db0b7368d2836f0b2e866eae
Author: jderrico-noaa <janet.m.derrico@noaa.gov>
Date: Thu Feb 29 20:35:11 2024 +0000
update ufs_model pointer
commit a28617a951c46b765aa996bfe4d28b554ec4e0a4
Author: jderrico-noaa <janet.m.derrico@noaa.gov>
Date: Thu Feb 22 06:16:26 2024 +0000
removed unneeded gsl directories
commit 6fb4f90e8572e98c977a1d2ab385f033111f3ea7
Author: jderrico-noaa <janet.m.derrico@noaa.gov>
Date: Thu Feb 22 06:08:13 2024 +0000
update ufs_utils.fd pointer
commit 9264f0c09239d046c5cd862d807e9b82f51dc3bd
Author: jderrico-noaa <janet.m.derrico@noaa.gov>
Date: Wed Feb 21 19:33:26 2024 +0000
update .gitmodules file
commit f8edfa966147506f2c207728039e3a736cb95415
Author: jderrico-noaa <janet.m.derrico@noaa.gov>
Date: Wed Feb 21 19:30:47 2024 +0000
update pointer to ufs_utils.fd
commit 5e0d2ab02d58e6a7a40db55a149a93008b28aa8b
Author: jderrico-noaa <janet.m.derrico@noaa.gov>
Date: Wed Feb 21 19:25:52 2024 +0000
update pointer to ufs_model.fd
commit ebc9e1d02987a1c6aa8cabedf2323642748fab3c
Merge: e7a81511 50cb1e6f
Author: Janet Derrico <143837053+jderrico-noaa@users.noreply.github.com>
Date: Thu Feb 15 13:40:33 2024 -0700
Merge pull request #40 from kayeekayee/gsl_ufs_dev
Merge to 2024 Jan 12 NOAA-EMC/develop and update to 2024 Jan 29 UFS
commit 50cb1e6f0c661e4c6e2ef0be4527cce58379b2c9
Author: kayee.wong <kayee.wong@noaa.gov>
Date: Thu Feb 15 20:30:34 2024 +0000
Add pygraf workflow.
commit 38b726125d49cff6cae4c0e5fff2438fc33143c5
Author: kayee.wong <kayee.wong@noaa.gov>
Date: Wed Feb 14 17:43:15 2024 +0000
Add double quote for the arguments when calling setup_expt.py.
commit 053f2025fb0b0679c7d4f84958973c1534ec050c
Author: kayee.wong <kayee.wong@noaa.gov>
Date: Tue Feb 13 23:57:06 2024 +0000
more fix.
commit 6f80ea2edc5444e275a79b371d02b6e98e963662
Author: kayee.wong <kayee.wong@noaa.gov>
Date: Tue Feb 13 23:50:01 2024 +0000
more bug fix.
commit 56e283f1f666a38a4a3b30e1528e96eeb5c622e7
Author: kayee.wong <kayee.wong@noaa.gov>
Date: Tue Feb 13 23:40:02 2024 +0000
Minor bug fix.
commit 2dcfed06ff6789eb77cf92e22b80f5475923fafc
Author: kayee.wong <kayee.wong@noaa.gov>
Date: Tue Feb 13 23:19:03 2024 +0000
Update parameter for c3 case
Add c3 and mynn template
commit cc46b19ccc7cdb54878340eff79dda9e747abdf7
Author: kayee.wong <kayee.wong@noaa.gov>
Date: Tue Feb 13 20:51:23 2024 +0000
Update INFO.
Add c3 SDF in the build.
commit a444ed48a23f24724853036e522b4437bf412c59
Author: kayee.wong <kayee.wong@noaa.gov>
Date: Tue Feb 13 18:42:33 2024 +0000
Update to UFS 2024 Jan 29 version.
commit 88595707c7521cdce37ae1cf78720a7827242b24
Author: kayee.wong <kayee.wong@noaa.gov>
Date: Tue Feb 13 18:16:46 2024 +0000
Minor bug fix.
commit baa0e9f10b132098d5134efaad712a51ebc26b83
Author: kayee.wong <kayee.wong@noaa.gov>
Date: Tue Feb 13 17:59:27 2024 +0000
Update parameters for setup_expt.py in p8_ugwpv1.sh to resdetatmos and comroot.
commit 5875f06903f82a47fafb05f89f840e3b099d18d8
Author: kayee.wong <kayee.wong@noaa.gov>
Date: Tue Feb 13 17:51:11 2024 +0000
Remove old gsl SDFs.
Remove 'rrtmg_lw_pre' from C3 and MYNN SDFs.
commit 9e0d1342f4e1edce96c9b2baeec55c2cffb964cd
Author: kayee.wong <kayee.wong@noaa.gov>
Date: Thu Feb 8 22:14:01 2024 +0000
Merge to 2024 Jan 12 NOAA-EMC/develop.
Squashed commit of the following:
commit c59047614c29f6ec15a4d4a6fa1855929287debd
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Fri Jan 12 19:21:02 2024 -0500
Update hash to ufs-weather-model. The noahmptable.tbl was reorganized, so update link_workflow.sh to use the same one used in UFSWM RT (#2219)
commit c041968e165c07da785376f1441374687b55d6cc
Author: Kate Friedman <kate.friedman@noaa.gov>
Date: Fri Jan 12 12:09:35 2024 -0500
Add ocean resolution to setup_expt invocation and retire/reduce COMROT/ROTDIR usage (#2214)
Two series of updates:
1) Update setup scripts to now allow users to provide ocean resolution
2) Housekeeping to retire the `COMROT` variable, replacing it with other variables
as needed, and reduce the `ROTDIR` variable usage.
Both updates change options for the workflow setup API.
Refs #2061
commit 997f97816493d9ed0242e169b6dcf84e5c9338d6
Author: AndrewEichmann-NOAA <58948505+AndrewEichmann-NOAA@users.noreply.github.com>
Date: Fri Jan 12 10:46:36 2024 -0500
Allow use of ocean obs prep in WCDA cycling and remove R2D2 (#2215)
Enables use of ocean obs prep task in WCDA cycling and removes R2D2 from same.
Runs task gdasprepoceanobs before gdasocnanalprep -- obtains ocean data nc4 files from DMPDIR, processes them into IODA format and copies them to COM_OBS.
Replaces the current R2D2 processing.
commit 12a5bb192ab6282d44c008c06dc14947abd37249
Merge: 4cb58020 6492c2da
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Fri Jan 12 09:26:27 2024 -0500
Merge pull request #2217 from DavidHuber-NOAA/update/versions
Update and clean up version and module files
commit 6492c2da5f49bd31575d0bef5278c9a7f8ba3412
Author: David Huber <david.huber@noaa.gov>
Date: Thu Jan 11 11:49:08 2024 -0600
Update orion module/version files for met/metplus #2123
commit 94c9937f0bff380b0ebd6acdcfd2509e1ae99389
Author: DavidHuber <david.huber@noaa.gov>
Date: Thu Jan 11 17:42:53 2024 +0000
Comment met/metplus out from Hera modulefile. #2123
commit 8c32f8b7d00bba6e3e954f149e6548fb27713a3c
Merge: a65e4c67 4cb58020
Author: David Huber <david.huber@noaa.gov>
Date: Thu Jan 11 11:34:44 2024 -0600
Merge branch 'develop' of github.com:noaa-emc/global-workflow into develop
commit a65e4c675f21dbe72198d263e85e894e62b41e13
Author: David Huber <david.huber@noaa.gov>
Date: Thu Jan 11 11:34:19 2024 -0600
Initial update of version/module files #2123
commit 4cb580201af68c1c0e2ae19faf0727dcbbe43b4d
Author: souopgui <souopgui@users.noreply.github.com>
Date: Wed Jan 10 08:30:22 2024 -0600
Fix OpenMP over-allocation of resources in exglobal_atmos_products.sh when running MPMD tasks (#2212)
Fix OpenMP over-allocation of resources running MPMD tasks
Co-authored-by: Innocent Souopgui <isouopgui@redlineperf.com>
commit b056b531faee6929687cb8a588ffafa1a66426fb
Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
Date: Mon Jan 8 17:28:05 2024 -0500
Add Hercules as valid machine in CI scripts (#2207)
Few updates to CI scripts to include names for hercules that where missed
the first time.
commit 6574d29a8c26b0695614874c344bccc5182363f4
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Mon Jan 8 17:25:47 2024 -0500
Fix invalid GH action and restart file name (#2210)
Resolves a typo that leads to an invalid workflow yaml and fixes the restart filename in restart detection.
Resolves #2205
commit 69605eac299df381ea9e0e329654487e26380ff5
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Mon Jan 8 17:00:28 2024 -0500
Stop attempting to comment link to RTD for non-PRs (#2209)
Adds a check so comments with a link to documentation are only generated
for PRs.
commit 4e160a895bfb31c281e21557dd86c13954a1a967
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Mon Jan 8 13:10:15 2024 -0500
Enable UPP for GOES processing (#2203)
Wnables the creation of special master grib2 files from UPP for
GOES processing
commit c15875b6dbf685327af9316ee43b3d01f0fc815e
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Mon Jan 8 09:56:06 2024 -0500
Port cycling to Hercules (#2196)
Adds cycled support for Hercules (excluding gsi-monitor).
Partially resolves #1588
GSI monitoring is disabled on Hercules due to missing Perl modules. That will be enabled in a later PR.
commit ef6827dd6abdab2996d1e19f9e0ff5d3071e0fdd
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Mon Jan 8 09:43:12 2024 -0500
Refactor rocoto task XML creation (#2189)
Refactors the rocoto task generation to be recursive.
This will allow nested metatasks to loop over multiple variables, which is needed for GEFS product generation.
As part of this refactor, there is no longer separate arguments to designate metatasks.
Instead, task dicts can include a nested 'task_dict' as well as a 'var_dict' containing the variables to loop over.
The nested task dict can then either have another layer, or be the innermost task.
To accommodate the new recursive nature, some defaults that were previously defined in create_wf_task() had to be pushed down into the function that creates the innermost task.
Also, former keywords have been absorbed by the task dict.
Refs #823
Refs #827
commit 2b81cfac16f103fb29b3aeb9748941787abf7287
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Mon Jan 8 09:41:03 2024 -0500
Update fix versions (#2198)
Updates fix versions for a few components:
- Update cice and mom6 versions to support C96/1p00 marine
- Update wave to change betamax setting for glo_025 waves
Resolves #2004
Resolves #2107
commit e7a81511e37f86e881da020e06b95990b470d952
Merge: af47b77c 75ad3754
Author: Janet Derrico <143837053+jderrico-noaa@users.noreply.github.com>
Date: Thu Feb 1 13:14:02 2024 -0700
Merge pull request #37 from jderrico-noaa/gsl_ufs_dev
Add GSL archive script and correct typos/fixed paths
commit 75ad3754f8bef5411c2570b5e392cd08e95cb6cb
Author: jderrico-noaa <janet.m.derrico@noaa.gov>
Date: Thu Feb 1 20:00:52 2024 +0000
adding consistent [[ ]] for if statements
commit 67b99668c82a5fd8c42479b9b1bfe8b0bad0be25
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Thu Feb 1 19:37:47 2024 +0000
Updated HOMEgfs in GSL XML templates
commit 4d3719c086e7907a6eeff03112042d392e0d8c5e
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Thu Feb 1 17:27:39 2024 +0000
Correct syntax errors in GSL scripts
Add new GSL archive script for archiving grib2 and ICs, but no netcdf files
commit 4309dd0b3b2d5625e7e1740d7cd3e39aacd5bc29
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Mon Jan 29 18:05:45 2024 +0000
Add GSL diag tables to parm/ufs/fv3
Update GSL template for hera
Create EMC and GSL versions of files under workflow/rocoto
- tasks.py, workflow_tasks.py
commit af47b77c7ee59a11c798995b4362b57e9096b090
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Sat Jan 27 02:07:43 2024 +0000
Create GSL version of archive script
commit 529d9f71f97b6e643e76a53bc9871901ae861faf
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Sat Jan 27 01:37:09 2024 +0000
Create GSL version of tracker.sh
- this is a placeholder with changes from last year's HFIP experiment; will likely need to be updated in the future
commit 8457e12c313bee602265b863129734354b019271
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Sat Jan 27 01:27:42 2024 +0000
Link config.base.emc.dyn_hera to config.base.emc.dyn
commit 7a05f5bd947944d8c3be828aeef9cc03bf9e073a
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Sat Jan 27 01:22:54 2024 +0000
Create GSL version of hpssarch_gen.sh
- assume we only run cold starts
- archive only 0p25 grib2 files (no 0p50 opr 1p00)
- assume no pgrb2b or flux files are created so no need to archive to HPSS
commit 98f5d6b16437e2a340bf16f83187e389a53f8bf0
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Sat Jan 27 00:24:06 2024 +0000
Update workflow directory
- add GSL template for jet (based on last year's experiment)
- create EMC and GSL versions of yaml files under hosts; defaults point to GSL files
commit 38a7e5629ceeb23d399643a021e9a0a88468a07c
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Thu Jan 25 18:40:37 2024 +0000
Update atmos_products configuration file for GSL
- set downset to 1 so pgrb2b files are not created
- set FLXGF to "NO" so interpolated sflux.1p00 files are not created
commit fe8a953658d092ce2b597e14f31678624606fd8a
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Thu Jan 25 17:02:25 2024 +0000
Update nodes for gfsfcst task in GSL template for hera to match default configuration in config.ufs
(12x12, 2 threads, 1 write group, 40 write tasks ==> 56 nodes)
Increase walltime to 4:10 for gfsfcst task
commit 9d85b0f6d50e8ed142557fcb87c89d2e5d63c617
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Tue Jan 23 19:08:52 2024 +0000
Added default location for PTMP/STMP in workflow/hosts/hera.yaml
Added GSL XML template for hera
commit 1cf317d327fae78c5469712c9e5a6aa1ffa4b23b
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Wed Jan 17 22:33:13 2024 +0000
Add sjet partition
Make syntax consistent in "if" statements in config.resources
commit 2755e203751f50113849b06769173285e093290b
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Wed Jan 17 22:32:26 2024 +0000
Update configuration files for GSL
- create Hera and Jet versions of config.base.emc.dyn
- correct typo in config.fcst
- create different versions of config.ufs;
default is 12x12, 2 threads, 1 write group/40 write tasks (56 nodes)
commit 3c0c126a376af31866a93aef4cdd0b4145150c58
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
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 <Judy.K.Henderson@noaa.gov>
Date: Tue Jan 16 16:46:25 2024 +0000
Update link script for ufs_utils.fd
commit 5b21b31900955013b4e8106d3ae906b9da93b361
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Tue Jan 16 16:45:25 2024 +0000
Add GSL archive scripts for initial conditions
commit abb88baf9dd536a3b2ea1e24eaa99cbfe85af799
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
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 <Judy.K.Henderson@noaa.gov>
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 <Judy.K.Henderson@noaa.gov>
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 <Judy.K.Henderson@noaa.gov>
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 <Judy.K.Henderson@noaa.gov>
Date: Thu Jan 11 23:34:36 2024 +0000
Add namelist parameter, nord_tr, for GSL suites
commit c4a41de7ebcda2f80ce69ac94bd2b3a6f5d04ed5
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
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 <Judy.K.Henderson@noaa.gov>
Date: Tue Jan 9 02:26:22 2024 +0000
Add experiment setup script for p8_ugwpv1
commit c5a3697d22fdbb02bb80ddffee2629dddc10c702
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
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 <Judy.K.Henderson@noaa.gov>
Date: Tue Jan 9 02:13:42 2024 +0000
Updated GSL-specific files under ufs_utils.fd_gsl
commit 1b153fc95b93a16eb40b791be7322100fde4a3d4
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date: Tue Jan 2 10:30:33 2024 -0700
Stop Gempak pgrb2 spec from modifying $DATA (#2147)
This PR addresses issue #1224. The following is accomplished:
- Instances where `DATA` is modified, corrections are made to use a locally defined variable such that `DATA` is no longer modified at run-time;
- Shell linter exceptions are addressed accordingly;
- The respective GEMPAK tasks is added to the Rocoto mesh.
Resolves #1224
commit 31ad23527802f7d07171132cc620f7135c4d8cba
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date: Tue Jan 2 10:27:30 2024 -0700
Reorganize NPOESS scripts (#2166)
This PR addresses issue #1226. The following is accomplished:
- Using the GEMPAK j-job script `JGFS_ATMOS_GEMPAK_PGRB2_SPEC`, the structure
of `JGFS_ATMOS_PGRB2_SPEC_NPOESS` is updated;
- Environment variables specific to the script `exgfs_atmos_grib2_special_npoess.sh`
are moved accordingly; this specifically applies to the environment variable `FHOUR`,
`SHOUR`, `FHINC`, `SLEEP_TIME`, and `SLEEP_INT`;
- The `SLEEP_TIME` and `SLEEP_INT` parameters can now be defined at the top-level
(if necessary);
- Restart file checks are move to `exgfs_atmos_grib2_special_npoess.sh`; however,
this may not be necessary (see `TODO` note within draft PR.
Resolves #1226
commit 22bd82fa93b49e5ce98eb3f69123956dd5018049
Author: Kate Friedman <kate.friedman@noaa.gov>
Date: Tue Jan 2 11:55:03 2024 -0500
Orog fix file reorg and fix directory variable standardization (#2181)
This PR makes updates to use the newly reorganized `orog/20231027`
fix file version and standardizes the fix file directory variables.
Changes:
1. Update UFS_UTILS hash to ce385ce
2. Update fix file version file to use new orog timestamp: `orog_ver=20231027`
3. Add ".mx$(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 <40322596+ADCollard@users.noreply.github.com>
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 <jessica.meixner@noaa.gov>
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 <69919478+DavidHuber-NOAA@users.noreply.github.com>
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 <bbakernoaa@users.noreply.github.com>
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 <aerorahul@users.noreply.github.com>
commit e55a05980709288d902ad1bd894164bfa5a18a65
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
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 <terrence.mcguinness@cox.net>
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 <58948505+AndrewEichmann-NOAA@users.noreply.github.com>
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 <69919478+DavidHuber-NOAA@users.noreply.github.com>
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 <kate.friedman@noaa.gov>
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 <kate.friedman@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <terrence.mcguinness@cox.net>
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 <aerorahul@users.noreply.github.com>
Date: Thu Dec 14 16:05:33 2023 -0500
Correct fbwind (#2161)
commit f3f3e05e6325e6c2e8ddab186f1ed2f985fec49a
Author: Kate Friedman <kate.friedman@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <69919478+DavidHuber-NOAA@users.noreply.github.com>
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 <kate.friedman@noaa.gov>
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 <cory.r.martin@noaa.gov>
Date: Thu Dec 7 15:12:05 2023 -0500
Update GDAS hash to most recent stable versions (#2138)
commit 93da9f105502e24f1a1a621f05ea49e1fdfe0102
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date: Thu Dec 7 10:41:05 2023 -0700
Corrected typo in a gempak job gempakncdcupapgif . (#2137)
commit 3483f550db1ae35a680de49f7485ce5a11902dd9
Author: Cory Martin <cory.r.martin@noaa.gov>
Date: Thu Dec 7 12:34:56 2023 -0500
Add support for FGAT and IAU for aerosol DA (#1940)
commit e2664c011bf5fb03a9b1b37878cad423a1fde6f9
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
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 <Walter.Kolczynski@noaa.gov>
commit a29f751aed05312da3d80d396159bb5a906d6ce4
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date: Wed Dec 6 13:45:56 2023 -0700
Adds GEMPAK and related jobs to rocoto task mesh (#2127)
commit 1fc8b5bf55581de18e786611c65bc3f84bb0c082
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
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 <kate.friedman@noaa.gov>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <kate.friedman@noaa.gov>
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 <terrence.mcguinness@cox.net>
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 <69919478+DavidHuber-NOAA@users.noreply.github.com>
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 <jiande.wang@noaa.gov>
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 <58948505+AndrewEichmann-NOAA@users.noreply.github.com>
Date: Wed Nov 29 15:17:36 2023 -0500
Added variables to config.prepoceanobs (#2101)
commit c2d78a61a224678fb804eed19f39d1f07408ae5f
Author: Kate Friedman <kate.friedman@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <kate.friedman@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <kate.friedman@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <kate.friedman@noaa.gov>
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 <kate.friedman@noaa.gov>
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 <jessica.meixner@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <48260754+WenMeng-NOAA@users.noreply.github.com>
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 <Walter.Kolczynski@noaa.gov>
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 <aerorahul@users.noreply.github.com>
Date: Wed Nov 15 16:44:03 2023 -0500
Fix missing _PREV in ocean restart file location (#2070)
commit 255616d37505c785bdddd5d3e39e8399110b626e
Author: mdtoyNOAA <73618848+mdtoyNOAA@users.noreply.github.com>
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 <guillaume.vernieres@noaa.gov>
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 <guoqing.ge@noaa.gov>
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 <kate.friedman@noaa.gov>
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 <kate.friedman@noaa.gov>
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 <aerorahul@users.noreply.github.com>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <kate.friedman@noaa.gov>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <Walter.Kolczynski@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <jiande.wang@noaa.gov>
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 <bbakernoaa@users.noreply.github.com>
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 <69919478+DavidHuber-NOAA@users.noreply.github.com>
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 <terrence.mcguinness@cox.net>
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 <guillaume.vernieres@noaa.gov>
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 <jiande.wang@noaa.gov>
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 <Walter.Kolczynski@noaa.gov>
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 <58948505+AndrewEichmann-NOAA@users.noreply.github.com>
Date: Thu Nov 2 16:09:59 2023 -0400
changed optional script name vars for ocean analysis (#2025)
commit 93bc918cdabee771c182c6f33cc54a20b5bb86c6
Author: Kate Friedman <kate.friedman@noaa.gov>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <58948505+AndrewEichmann-NOAA@users.noreply.github.com>
Date: Wed Nov 1 14:19:55 2023 -0400
Updates to prep ocean obs task (#1870)
commit 77be0ec6a3117b9f7e71a19c69ac64c09b521ecd
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
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 <69919478+DavidHuber-NOAA@users.noreply.github.com>
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 67c050c201f92e8…
WalterKolczynski-NOAA
removed
the
blocked
WalterKolczynski-NOAA
added a commit
to WalterKolczynski-NOAA/global-workflow
that referenced
this issue
Apr 24, 2024
Lustre has a defect under Rocky 9 that results in symlink sometimes failing when the link name is not explicit. This updates all link creation to use explicit names. `config.base` is updated to turn off two monitor jobs on Hercules because the executables are not yet built there. This, combined with the previous change, should make workflow available for use on Hercules. Also removes the redundant utility names for NCP, NLN, etc. in the gdas scripts that are already defined in `config.base`. Resolves NOAA-EMC#2131 Resolves NOAA-EMC#2522
10 tasks
WalterKolczynski-NOAA
added a commit
to WalterKolczynski-NOAA/global-workflow
that referenced
this issue
Apr 24, 2024
Lustre has a defect under Rocky 9 that results in symlink sometimes failing when the link name is not explicit. This updates all link creation to use explicit names. `config.base` is updated to turn off two monitor jobs on Hercules because the executables are not yet built there. This, combined with the previous change, should make workflow available for use on Hercules. Also removes the redundant utility names for NCP, NLN, etc. in the gdas scripts that are already defined in `config.base`. Resolves NOAA-EMC#2131 Resolves NOAA-EMC#2522
WalterKolczynski-NOAA
added a commit
to WalterKolczynski-NOAA/global-workflow
that referenced
this issue
Apr 30, 2024
Lustre has a defect under Rocky 9 that results in symlink sometimes failing when the link name is not explicit. This updates all link creation to use explicit names. `config.base` is updated to turn off two monitor jobs on Hercules because the executables are not yet built there. This, combined with the previous change, should make workflow available for use on Hercules. Also removes the redundant utility names for NCP, NLN, etc. in the gdas scripts that are already defined in `config.base`. Resolves NOAA-EMC#2131 Resolves NOAA-EMC#2522
WalterKolczynski-NOAA
added a commit
that referenced
this issue
Apr 30, 2024
Lustre has a defect under Rocky 9 that results in symlink sometimes failing when the link name is not explicit. This updates all link creation to use explicit names. `config.base` is updated to turn off two monitor jobs on Hercules because the executables are not yet built there. This, combined with the previous change, should make workflow available for use on Hercules. Also removes the redundant utility names for NCP, NLN, etc. in the gdas scripts that are already defined in `config.base`. Resolves #2131 Resolves #2522
kayeekayee
added a commit
to kayeekayee/global-workflow
that referenced
this issue
Aug 28, 2024
…l 19 UFS (c127601)
Squashed commit of the following:
commit d599fff4aedd41ae587dbe02226acb12ff48efc1
Author: HelinWei-NOAA <48133472+HelinWei-NOAA@users.noreply.github.com>
Date: Mon Aug 5 05:31:31 2024 -0400
Change land surface for HR4 (#2787)
Resets the default value of opt_diag to 2 corresponding to the land
surface upgrades in ufs-weather-model for HR4.
Resolves #2786
commit 6d7f7e860a0c7062f90bf09fdf9a5d19dc77cfdb
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Fri Aug 2 15:41:29 2024 -0400
Run METplus serially and correct the name of prod tasks (#2804)
Adds 2 hot fixes:
- METplus v9.1.3 has a bug in it that sometimes attempts to create
multiple copies of the same directory when running in parallel, causing
a Python error and downstream problems. This PR makes METplus run in
serial mode, preventing such issues.
- Corrects the name of the atmos_prod, ocean_prod, and ice_prod tasks in
workflow/rocoto/tasks.py (was accidentally changed to e.g. atmosprod)
commit 0706c59ac53cc3bbfbaa56cbd7fa75ab51117830
Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
Date: Fri Aug 2 15:03:45 2024 -0400
Update Java Agent launching script for Jenkins connections (#2762)
Made updates to the Jenkins Launching Script for robustness and less
ambiguous documentation:
- Clearer distinction between required user token for the remote api and
the systems token for launching
- Added pre-checks: `gh` is authenticating, named compliant token and
secret file exists
- More robust Jason based parser of the remote api response for checking
the state of the Node connection
- For `cron` use a 5 minute pause and recheck was added before
re-launching of the java agent
- Added concise header documentation of requirements and purpose
---------
Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
commit b73b1fd203496db97f8067652659573a632bcc67
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Fri Aug 2 07:59:06 2024 -0400
Fix erroneous cdump addition (#2803)
commit 49877046ac3306f6b78ca0ab5d5089ba1aa3e3e3
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Thu Aug 1 20:26:13 2024 -0400
Update ocean post-processing triggers (#2784)
This PR:
- replaces `check_netcdf.sh` checker for ocean post-processing with with
ocean output at the next forecast hour or finishing of the forecast job
for ocean prod
- removes no longer needed `ush/check_netcdf.sh`
commit aa2af1ca8d59424a60a1730722bf528775d9e606
Author: GeorgeGayno-NOAA <52789452+GeorgeGayno-NOAA@users.noreply.github.com>
Date: Thu Aug 1 16:46:10 2024 -0400
Update the gfs_utils repository hash (#2801)
# Description
Point to the latest hash of the gfs-utils repository, which contains the
bug fix to gaussian_sfcanl.
Resolves #2669.
Refs: https://github.com/NOAA-EMC/gfs-utils/pull/73
commit d3d85f0e0d573f16a71ca44778021dfc0ccf50c8
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Thu Aug 1 08:12:14 2024 -0400
Add fixes for metplus jobs when gfs_cyc=2 or 4 (#2791)
Changes how METplus jobs run so that they run on the last GFS cycle for
a given `PDY`.
This is a departure from operations where the METplus jobs run on the
00Z cycle for the previous 3 cycles and 00Z (i.e. `${PDYm1}06` through
`${PDY}00`). With this PR, for gfs_cyc=4, METplus jobs will run on
`${PDY}18` for cycles 00-18. See
https://github.com/NOAA-EMC/EMC_verif-global/pull/131 for more details.
commit 1cf8b448af562dbb7af198399c78c585977e81da
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Tue Jul 30 10:38:49 2024 -0400
Simplify resource-related variables, remove CDUMP where unneeded (#2727)
This overhauls resource-related variables to use a common set of
variables for each job. In the process, this also removed the use of
CDUMP in most cases.
Resolves #1299 #2693
commit 61875f25c9e971f82ae499b5b612d7f095deebd4
Author: Eric Sinsky - NOAA <48259628+EricSinsky-NOAA@users.noreply.github.com>
Date: Mon Jul 29 14:40:03 2024 -0400
Remove f000 from atmos rocoto tasks for replay cases (#2778)
The main purpose of this PR is to remove the f000 from
atmosphere-related rocoto tasks when `REPLAY_ICS` is set to `YES`. In
cases where `REPLAY_ICS` is `YES` and `OFFSET_START_HOUR `is greater
than `0`, it becomes necessary to have the first lead hour set to
`OFFSET_START_HOUR ` for the atmosphere-related rocoto tasks. For
example, when `OFFSET_START_HOUR ` is set to `3`, then the minimum lead
time for the atmos_prod and atmos_ensstat rocoto tasks needs to be 3 and
the minimum lead time for the ocean_prod rocoto task needs to be 6
(assuming `FHOUT_OCN` is 6). This PR makes this rocoto workflow set up
possible by removing 0 from fhrs for atmosphere-related tasks in
`gefs_tasks.py` when replaying.
This PR also moves where f000 is being removed for the ocean_prod and
ice_prod tasks. The if-block that performs this f000 removal has been
moved from `tasks.py` to `gefs_tasks.py` and `gfs_tasks.py`.
---------
Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com>
commit f156a7894d639f177e3e2588f98eec1f6f59aa68
Author: Jessica Meixner <jessica.meixner@noaa.gov>
Date: Fri Jul 26 14:18:32 2024 -0500
HR4 GWD update (#2732)
This update is a combination of the gravity wave drag (GWD) versions
from the NOAA/GSL and NOAA/PSL
commit a7f6b32ed63efa0de21bfb0ce63364a5b22b9891
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Thu Jul 25 14:26:52 2024 -0400
Temporarily disable METplus jobs (#2796)
commit 848659691fdbf47e7ccdbbb2ebf22a6e470633a2
Author: Guillaume Vernieres <guillaume.vernieres@noaa.gov>
Date: Wed Jul 24 15:00:35 2024 -0400
Refactoring of the marine B-matrix job (#2749)
Refactor the functionality of B-matrix generation from the GDASApp
Resolves #2743
commit 65a7ab75dc0e4baba06a02e11ed0455787056a68
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Tue Jul 23 08:35:48 2024 -0400
Replace Jinja namespaces with replace_tmpl filter and disable ACCOUNT_SERVICE option (#2775)
Removes the namespace-based construction of EnKF member COM directories
in the enkf archive template.
commit c45b9611f3e701b819bd33dc5af29033f060bb91
Author: Eric Sinsky - NOAA <48259628+EricSinsky-NOAA@users.noreply.github.com>
Date: Tue Jul 23 00:33:16 2024 -0400
Add task to process reforecast variables to save on WCOSS2 (#2680)
# Description
This PR adds an optional task to the global-workflow to process a subset
of ocean, ice, wave and atmosphere products to be saved on WCOSS2 for
the GEFSv13 reforecast. This task is designed to process GEFS variables
so that specific reforecast product requirements are met. A new variable
in `config.base` called `DO_EXTRACTVARS` enables this task, which is
currently called `extractvars`. `DO_EXTRACTVARS` is set to `NO` by
default and is specifically a task designed to be executed for the
GEFSv13 reforecast.
Refs #1878
# Type of change
- New feature (adds functionality)
# Change characteristics
- Is this a breaking change (a change in existing functionality)? NO
- Does this change require a documentation update? NO
# How has this been tested?
This has been cloned and tested on WCOSS2. This will need to be tested
on Hera and other platforms on which the reforecast may be running.
# Checklist
- [ ] Any dependent changes have been merged and published
- [x] My code follows the style guidelines of this project
- [x] I have performed a self-review of my own code
- [ ] I have commented my code, particularly in hard-to-understand areas
- [x] My changes generate no new warnings
- [x] New and existing tests pass with my changes
- [ ] I have made corresponding changes to the documentation if
necessary
---------
Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com>
commit 71dc33c6ca991c16ce743760d99feaaf60f2218a
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Mon Jul 22 14:51:53 2024 -0400
Set METplus process count in config.metp; add verif-global support for Rocky 9 (#2774)
Fix metp* resources and check that they completed properly; add support for Orion Rocky 9
commit 56df67a90fe090c425199f1285e5aac722c398b1
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Mon Jul 22 09:28:18 2024 -0400
Hotfix: Update jcb to avoid git-lfs files (#2782)
Removes git-lfs files from the `GDASApp` `jcb` submodule, allowing it to
be cloned on Hera.
This hotfix points to a non-authoritative branch of the GDASApp
(https://github.com/DavidHuber-NOAA/GDASApp/tree/hotfix/update_jcb) and
should be updated ASAP back to the authoritative repository.
commit fc668aa422ebbad76ceda1b3bbf8dc0ea432defd
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Tue Jul 16 09:44:00 2024 -0400
Address issues in creating XML for GFS forecast-only with app S2SWA (#2757)
This bugfix PR:
- fixes an issue where a user is unable to generate the XML for a GFS
forecast-only experiment with APP=S2SWA
Specifically, the changes are related to defining `aero_fcst_cdumps`.
Following `setup_expt.py`, the user will have to set
`AERO_FCST_CDUMPS="gdas|gfs|both" depending on their use case in
`config.base`.
commit e0878dba0e53706a7f53429b61aee2936e2c21bf
Author: Kate Friedman <kate.friedman@noaa.gov>
Date: Mon Jul 15 10:25:11 2024 -0400
Updated prepobs and fit2obs versions for Orion Rocky9 (#2758)
Update prepobs to v1.0.2 and fit2obs to v1.1.2
These versions now support Orion Rocky9. Updates are included
for new install locations on WCOSS2, Hera, Orion/Hercules, and Jet.
commit 4968f3a8de9a5f90651cacd74e38f97bc80b7bbb
Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
Date: Thu Jul 11 17:48:47 2024 +0000
CI maintenance updates and adding CI Unit Tests (#2740)
This PR has a few maintenance updates to the CI pipeline and adds a test
directory with Unit Tests
**Major Maintenance updates:**
- Added try blocks with appropriate messaging to GitHub PR of failure
for:
- - **scm** checkout
- - build fail (with error logs sent as gists)
- - create experiment fails with `stderr` sent to GitHub PR messaging
- Pre-stage FAILS from the above are now captured these fails allow
FINALIZE to update the label to FAIL (i.e. no more "hanging" CI state
labels in GitHub - see image below)
**Minor Maintenance updates:**
- Fix for STALLED cases reviled from PR 2700 (just needed a lambda
specifier)
- Fixed path to experiment directory in PR message (had dropped EXPDIR
in path)
- Needed `latin-1` decoder in reading log files for publishing
**Added python Unit Tests for CI functionality:**
- Installed **Rocoto** and **wxfow** in GitHub Runner for testing key CI
utility codes
- Cashed the install of Rocoto in the GitHub Runners to greatly reduce
stetup time for running the unit tests
- Unit Tests Python scripts added
- `test_rocostat.py`: rocoto_statcount() rocoto_summary()
rocoto_stalled()
- `test_setup.py`: setup_expt() test_setup_xml()
- `test_create_experment`: test_create_experiment()
- - Runs all PR cases that do not have ICs in the GItHub Runner
- Reporting mechanism in the Actions tab for Python Unit Testing results
- Test case data for STALLED and RUNNING stored on S3 and pulled using
wget during runtime of tests
commit 5ef4db74649b8be03402c17aa29c024e71699a7b
Author: AndrewEichmann-NOAA <58948505+AndrewEichmann-NOAA@users.noreply.github.com>
Date: Thu Jul 11 08:59:24 2024 -0400
Adds contents of constructor and initialize methods to marine LETKF class (#2635)
Adds contents of constructor and initialize methods to marine LETKF class
Partially addresses https://github.com/NOAA-EMC/GDASApp/issues/1091
---------
Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com>
Co-authored-by: Cory Martin <cory.r.martin@noaa.gov>
commit 8998ec7b74123e953b97a93fa14cc78d471a1aee
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Tue Jul 9 08:31:57 2024 -0400
Fix GDAS group B restart archiving (#2735)
Archives the GDAS restartb dataset at a 6-hour offset from restarta
This allows cycled experiments to restart from the archives.
The tabbing for the master archive templates was also added to
improve readability.
Resolves #2722
commit 3ca74771255727033b9dc043c652ac585178629c
Author: AndrewEichmann-NOAA <58948505+AndrewEichmann-NOAA@users.noreply.github.com>
Date: Tue Jul 9 08:28:54 2024 -0400
Add fcst dependency to ocnanalprep (#2728)
Add previous cycle's `fcst` as a dependency to `ocnanalprep`
This ensures that the availability of restart files to the latter. This addresses a
seldomly-encountered race condition where `ocnanalprep` fails due to the
lack of the files.
commit 58fca1668aecd6fb1afd12a441256ad35900e075
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Fri Jul 5 15:02:23 2024 -0400
Update (partially) global-workflow for orion+rocky9 (#2741)
This PR:
- updates a few submodules (GSI, GSI-utils, GSI-monitor, UFS_utils,
GFS-utils) to include recent update to their modulefiles for
Orion+Rocky9 upgrade
- updates the modulefiles in global-workflow to load modules from
Orion+Rocky9 paths
- updates modulefiles for `gwsetup` and `gwci` as well.
- removes NCL and GEMPAK from Orion. NCL is not used and GEMPAK is not
installed.
- adds `parm/config.gfs/config.resources.ORION` to address GSI
performance degradation after Rocky 9 upgrade.
This PR:
- does not update the build for UPP. Standalone UPP is not available via
ufs-weather-model as of #2729
- will need a follow-up update for `prepobs` and `fit2obs` updated
locations when they are installed in `glopara` space on Orion.
# Type of change
- Maintenance (code refactor, clean-up, new CI test, etc.)
# Change characteristics
- Is this a breaking change (a change in existing functionality)? NO
- Does this change require a documentation update? NO
# How has this been tested?
This PR is not sufficient for Orion.
This PR must be tested on other platforms (Hera, WCOSS2) as this PR
updates submodules.
# Checklist
- [ ] Any dependent changes have been merged and published
- [ ] My code follows the style guidelines of this project
- [ ] I have performed a self-review of my own code
- [ ] I have commented my code, particularly in hard-to-understand areas
- [ ] My changes generate no new warnings
- [ ] New and existing tests pass with my changes
- [ ] I have made corresponding changes to the documentation if
necessary
---------
Co-authored-by: Kate Friedman <kate.friedman@noaa.gov>
commit d65d3d257b38225fac74e86b770f43e1f8ae2d5a
Author: Jessica Meixner <jessica.meixner@noaa.gov>
Date: Wed Jul 3 21:07:49 2024 -0400
Update ufs model hash to 20240625 (#2729)
Updates UFS weather model hash to hash from 2024-06-24 which has orion
porting updates + a few namelist updates.
commit 2bd106a013805ba4e16dbdc456d6731f8f36ec85
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Wed Jul 3 11:32:40 2024 -0400
Hotfix for undefined CLUSTERS (#2748)
Defines `CLUSTERS` as an empty string for all hosts except Gaea and uses
the native `dict` `get` method to prevent grabbing an unset entry.
commit 7dc6651a3b92194d963675bdc0a9ec3c28499abf
Author: GwenChen-NOAA <95313292+GwenChen-NOAA@users.noreply.github.com>
Date: Wed Jul 3 09:56:08 2024 -0400
Update gempak job to run one fcst hour per task (#2671)
This PR updates gempak jobs (gfs, gdas, and goes) from processing all
forecast hours at once to one forecast hour at a time. This will reduce
the job runtime to less than 5 min, so restart capability is not needed.
Resolves #1250
Ref #2666 #2667
---------
Co-authored-by: Walter.Kolczynski <Walter.Kolczynski@noaa.gov>
commit 8215ae654202186a4f753c3abe937b7b9b91a9c7
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Tue Jul 2 16:22:11 2024 -0400
Hotfix for clusters from #2701 (#2747)
Fixes an issue created from #2701 that added `CLUSTERS` to the
`gaea.yaml`.
commit 11943e36ba12b3df49c51942da780698fab02d38
Author: DavidBurrows-NCO <82525974+DavidBurrows-NCO@users.noreply.github.com>
Date: Tue Jul 2 12:58:10 2024 -0400
Fix xml file setup and complete C48 ATM and S2SW runs for CI on Gaea (#2701)
This PR sets up the ability on Gaea for auto generation of a clean xml
file, i.e., an xml file that does not need any alterations before
running rocoto.
Refs #2572
Refs #2664
commit de8706702ead0630beb54d868f83aa2cb23f8f79
Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com>
Date: Mon Jul 1 09:29:14 2024 -0400
Update for JCB policies and stage DA job files with Jinja2-templates (#2700)
This PR updates the `gdas.cd` hash to bring in new JCB conventions.
Resolves #2699
From #2654
This PR will move much of the staging code that take place in the python
initialization subroutines of the variational and ensemble DA jobs into
Jinja2-templated YAML files to be passed into the wxflow file handler.
Much of the staging has already been done this way, but this PR simply
expands that strategy.
The old Python routines that were doing this staging are now removed.
This is part of a broader refactoring of the pygfs tasking.
wxflow PR [#30](https://github.com/NOAA-EMC/wxflow/pull/30) is a
companion to this PR.
Co-authored-by: danholdaway <danholdaway@users.noreply.github.com>
Co-authored-by: DavidNew-NOAA <david.new@noaa.gov>
Co-authored-by: DavidNew-NOAA <134300700+DavidNew-NOAA@users.noreply.github.com>
Co-authored-by: Dan Holdaway <27729500+danholdaway@users.noreply.github.com>
commit c49e4eee1a2ca818b3ecdcb9ea41c3f3e91d585b
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Fri Jun 28 14:56:19 2024 -0400
Revert PR 2681 (#2739)
This PR:
- reverts #2681 in part
- keeps some changes for `RUN`.
- is a hotfix
- should be merged ASAP after consensus w/ @guillaumevernieres
@CatherineThomas-NOAA @WalterKolczynski-NOAA
commit 9476c1237af4adbc95f90bd1bdd34b6b99f2f8a3
Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
Date: Wed Jun 26 15:46:08 2024 -0400
updated Finalize in Jenkinsfile and added try block around scm checkout (#2692)
We are updating the Jenkins Pipeline with a try block around checkout to
capture errors for the user.
Also cleaned up Finalize and added section to clean out workspace on
success.
commit 968568f682bac7564095440bdb7813abefd76821
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Wed Jun 26 13:27:19 2024 -0400
Activate snow DA test on WCOSS (#2720)
Activate the snow DA test on WCOSS.
commit 7706760bb8adbdf78cb640b02739023c886e7699
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Wed Jun 26 10:02:22 2024 -0400
Cleanup of stale RUNDIRS from an experiment (#2719)
This PR:
- removes stale temporary scratch run directories from `$DATAROOT/`
every 3 days.
- should help to scrub failed attempts.
- removes an unused variable `RUNDIR` defined in `config.base`
commit 8962991691b5f0857b813bddfd28aa1034d4bd2b
Author: Jessica Meixner <jessica.meixner@noaa.gov>
Date: Wed Jun 26 09:43:48 2024 -0400
Update logic for MOM6 number of layers/exception values (#2681)
Updates the logic to be by run instead of for DO_JEDIOCNVAR to determine
how many layers and sets the exception value for MOM6 to be 1e-34 for
all scenarios. Note, we will no longer have zeros in the ocean grib
output and the DA will also run without issues.
Fixes https://github.com/NOAA-EMC/global-workflow/issues/2615
commit 12431f76bdce807067929415007592cffc8a2457
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date: Wed Jun 26 07:42:35 2024 -0600
Update wave jobs to use COMIN/COMOUT (#2643)
NCO has requested that each COM variable specify whether it is an input
or an output.
This completes that process for the global-workflow wave
model and products tasks.
Refs #2451
commit b902c0bac126c323a07186ad8881384b032b6fda
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Tue Jun 25 07:48:46 2024 -0400
Assign machine- and RUN-specific resources (#2672)
Redefine resource variables based explicitly on RUN or CDUMP
Additionally, machine-specific resources are moved out of
config.resources and placed in respective config.resources.{machine}
files.
Resolves #177 #2672
commit 4e1b937b67ed220120e81925c4507f03b9b8965f
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Mon Jun 24 10:50:52 2024 -0400
Add minimum software requirements (#2712)
Adds a table to HPC documentation stating the minimum support versions
commit f43a86276aaef91efa28faadc71a3cf50e749efe
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Fri Jun 21 13:44:29 2024 -0400
Fix and simplify online archiving and reenable METplus jobs (#2687)
This fixes the online archiving portion of the `*arch` and `*earc00`
jobs, a prerequisite for running METplus. This also reenables
METplus by default.
The approach previously taken created `FileHandler` dictionaries at
varying levels within the resulting yaml, which was not properly parsed
by `exglobal_archive.py`. This approach creates a single `FileHandler`
dictionary and is much less complicated overall.
Resolves #2673 #2647
commit 8993b42cb91144c0ab0501dc7841ea8d675c4701
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Wed Jun 19 21:51:22 2024 -0400
Eliminate post groups (#2667)
Eliminates the post groups used for upp and products jobs so that each
task only processes one forecast hour. This is more efficient and
greatly simplifies downstream dependencies that depend on a specific
forecast hour.
Resolves #2666
Refs #2642
commit 0b810c888239853fedd0e4584fe62536c6aaacdf
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date: Tue Jun 18 20:32:48 2024 -0600
Removes misleading "No such file or directory" syntax errors from output files (#2688)
This PR addresses issue #1252. The following is accomplished:
- Prior to removing files, the existence of a file is checked prior to
attempting to remove; this is performed as noted
[here](https://github.com/NOAA-EMC/global-workflow/issues/1252#issue-1538627369);
this PR only addresses the the `chgrp` issue.
Refs #1252
---------
Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
commit 3270ac3bf00c3ebc8166c70d84647ec44431fbae
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date: Tue Jun 18 12:17:59 2024 -0600
Hotfix for bug in template names. (#2697)
This PR is a hotfix for an incorrectly named (e.g., non-existent) `COM/`
template.
Resolves #2696
Refs #2451
commit 35d4d99eaac669721add9ddcc793153e5ab3b30a
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date: Tue Jun 18 08:06:53 2024 -0600
Update archive job to use COMIN/COMOUT (#2668)
NCO has requested that each COM variable specify whether it is an input
or an output. This completes that process for the global-workflow
archive task.
Refs #2451
---------
Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com>
Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
commit 47b3a581c8257fa24411fb400df8bb0e1e04972a
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Mon Jun 17 22:55:38 2024 -0400
Turn on high-frequency output in extended test (#2679)
Turns on high-frequency (hourly) output in the extended products test to
exercise that aspect of the code. This test only runs on WCOSS.
Also adds the hooks to optionally turn on the metplus jobs, but that is
deferred as they are not currently working correctly.
commit 38f2df9fb0c074b1f80d3c637080be79be693161
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Mon Jun 17 17:12:55 2024 +0000
Optimize wavepostpnt (#2657)
Optimize the gfswavepostpnt, gfswavepostbndpntbll, and gfswavepostbndpnt jobs
This is done by
1) reducing the number of calls to `sed`, `awk`, `grep`, and `cat` by
- performing operations on all files at once instead of looping over
each file
- removing piped `cat` calls (e.g. `cat <file> | sed 'something'`)
- combining `sed` and `grep` calls when possible
- adding logic to `awk` calls instead of handling that logic in bash
2) minimizing as much as possible the amount of data on disk that has to
be read in (e.g. limiting sed to read only the line numbers it needs)
---------
Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
commit 5af325a6a4e0a14d180514a418603ca79fada487
Author: Dan Holdaway <27729500+danholdaway@users.noreply.github.com>
Date: Fri Jun 14 18:05:23 2024 -0400
Update GDASapp hash to move JCB into GDASapp (#2665)
This PR moves JCB into GDASapp. The PR
also bumps up the hash of GDASapp to what is in `feature/move_jcb`,
which at time of writing is develop plus the absorption of JCB into
GDASapp.
Note that I also took the changes from
https://github.com/NOAA-EMC/global-workflow/pull/2641 to follow the
testing @RussTreadon-NOAA has done.
commit 6c93b4554e235fcb4d0004e99a4c4498d55d461b
Author: Yaping Wang <49168260+ypwang19@users.noreply.github.com>
Date: Fri Jun 14 10:18:17 2024 -0500
Add observation preparation job for aerosols DA to workflow (#2624)
Add a prepaeroobs job to prepare aerosol obs files for DA.
This job does quality control of the VIIRS aerosol raw observations and
convert them to ioda format.
Resolves #2623
---------
Co-authored-by: ypwang19 <yaping.wang@users.noreply.github.com>
Co-authored-by: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
Co-authored-by: Cory Martin <cory.r.martin@noaa.gov>
Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
commit 5a5fc2be7555f094a0f90fd3a3df22d071ccdfd4
Author: Jessica Meixner <jessica.meixner@noaa.gov>
Date: Fri Jun 14 11:04:41 2024 -0400
Remove ocean daily files (#2689)
This PR removes the ocn_daily files that are produced by the ocean
component. These files can be recreated by averaging data that exists in
the 6 hour aveaged files if needed.
Fixes https://github.com/NOAA-EMC/global-workflow/issues/2675
Fixes https://github.com/NOAA-EMC/global-workflow/issues/2659 (by
removing them and making this obsolete)
commit 603a4a8052a5c43ce5986f028c3fcfd5fd248ad4
Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
Date: Thu Jun 13 12:22:03 2024 -0400
Update Jenkinsfile
needed a comma
commit dc21eac6c3941d7f30803891d91d82f4cc1f8183
Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
Date: Thu Jun 13 11:41:14 2024 -0400
Add Hercules-EMC to the Jenkins configurable parameter list (#2685)
This quick-fix PR is to update the Jenkins Pipeline's configurable
parameter list to include the **Hercules-EMC** node.
This allows Jenkins users to restart Jobs in the controller when no
updates have been made.
commit ebacebfbe458634b8c80af6a735d6b6d01e4e406
Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com>
Date: Thu Jun 13 11:20:24 2024 -0400
Update gdas.cd and gsi_utils hashes (#2641)
This PR updates the `sorc/gdas.cd` and `sorc/gsi_utils` hashes. The
updated hashes bring in bug fixes, new UFS DA functionality, and a Gaea
build for gsi_utils.
Resolves #2640
commit 34155fb4767769600a1ff95f0a65e37081addc2a
Author: Neil Barton <103681022+NeilBarton-NOAA@users.noreply.github.com>
Date: Thu Jun 13 11:18:22 2024 -0400
Add ability to use GEFS replay ICs (#2559)
The PR allows the use of ICs from PSL's replay analysis. These replay
ICs will be used for GEFS reforecasting and SFS. Two main changes are
associated with these updates: (1) replay ICs being valid at 3Z, and (2)
the use of warm starts.
Resolves #1838
---------
Co-authored-by: Jessica Meixner <Jessica.Meixner@noaa.gov>
Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com>
commit 6c19a0e3fc4400e1d39288be4ee4fc244b74f699
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date: Wed Jun 12 19:25:42 2024 -0600
Replace `sleep` with `wait_for_file` (#2586)
This PR addresses issue #2444. The following is accomplished:
- All `sleep` statements are replaced with `wait_for_file` for the
relevant scripts beneath `scripts` and `ush`;
- Indentation and shell-norms are updated where applicable.
Note: The WAFS scripts are not updated as per @aerorahul direction.
Resolves #2444
---------
Co-authored-by: henrywinterbottom-wxdev <henry.winterbottom.wxdev@gmail.com>
Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
commit 5b2a3d449a0835cec2663aabb06f1c47a3faf84e
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Wed Jun 12 13:31:55 2024 -0400
Add COM template for JEDI obs (#2678)
Adds a COM template to define a path to store obs processed for JEDI.
This will allow UFSDA to stop writing to COM_OBS, which should be
read-only as it belongs to obsproc in operations.
No functional change yet.
commit 2e6f1fcde9935619352b1b26cba42ec0f4d845ed
Author: Guoqing Ge <guoqing.ge@noaa.gov>
Date: Wed Jun 12 09:06:23 2024 -0600
Link both global-nest fix files and non-nest ones at the same time (#2632)
This PR enables linking both global-nest fix files and non-nest ones at
the same time and users can run both nesting and non-nesting experiments
at the same time without worries about what fix files to be linked.
Resolves #2631
commit 61de004d4f9e9edf8a31bb173f2719b46451a36a
Author: Jessica Meixner <jessica.meixner@noaa.gov>
Date: Wed Jun 12 11:03:13 2024 -0400
Update ufs-weather-model (#2663)
Updates ufs-weather-model, this updates RDHPCS to the newer spack-stack
allowing some temporary fixes to be reverted.
* removes upp submodule
* uses upp from the ufs-weather-model
* restores the build and link that were hacked during the Hera Rocky 8
transition to allow for UPP submodule
* Removes forecast directories in clean-up
Resolves #2617
Resolves #2437
---------
Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com>
commit 15eaf35fb13f361be400be38a5f7ca7b5461ab1d
Author: Eric Sinsky - NOAA <48259628+EricSinsky-NOAA@users.noreply.github.com>
Date: Wed Jun 12 01:15:37 2024 -0400
Add ability to process ocean/ice products specific to GEFS (#2561)
This PR begins to add the capability to produce GEFSv13 ocean and ice
products in the global-workflow according to stakeholder requirements.
The following features are added.
- An oceanice prod yaml file has been added to address the ocean and ice
products specific to GEFSv13.
- The rocoto dependencies and config.base for GEFS have also been
modified to allow for 24-hour averaged ocean and ice output.
- Various scripts have been modified to allow for ocean and ice output
frequencies of 24 hours.
- `FHOUT_OCNICE` has been split into two variables called `FHOUT_OCN`
and `FHOUT_ICE`. The same has been done for `FHOUT_OCNICE_GFS`.
Refs #1878
commit 6691e7489650e0b738c176fbd096109288dc09b6
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date: Tue Jun 11 21:15:07 2024 -0600
Update cleanup job to use COMIN/COMOUT (#2649)
NCO has requested that each COM variable specify whether it is an input
or an output. This completes that process for the global-workflow
clean-up task.
Refs #2451
---------
Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
commit 23a8d8835dd4c5d69ca20f5ff23705f30f17b4b0
Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
Date: Tue Jun 11 16:17:25 2024 -0400
Add overwrite to creat experiment in BASH CI (#2676)
This is a quick hotfix to the CI BASH driver script adding `--overwrite`
to create experiment script to avoid errors from restarting an
experiment.
commit e7909af8d9e1f34140388a3f8556d8e582c58fe5
Author: emilyhcliu <36091766+emilyhcliu@users.noreply.github.com>
Date: Mon Jun 10 15:11:27 2024 -0400
Add handling to select CRTM cloud optical table based on cloud scheme and update calcanal_gfs.py (#2645)
This PR proposes updates for the following two scripts:
1. In **scripts/exglobal_atmos_analysis.sh** --- Add handling to select
CRTM cloud optical table based on cloud microphysical scheme indicated
by `imp_physics'
The default scheme in the GFS forecast model is Thompson scheme
(imp_physics = 8).
2. In **/ush/calcanl_gfs.py** --- Increase the MPI number declared in
the script due to increased variables to interplate increments and
calculate analysis in the netcdf_io routines in GSI-utils.
Here is the related [PR #46 for
GSI-utils](https://github.com/NOAA-EMC/GSI-utils/pull/46).
---------
Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com>
Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
commit 9caa51de8fb7be07d2e61775da01937d576964f6
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date: Thu Jun 6 22:15:23 2024 -0600
Update RDHPCS Hera resource for `eupd` task (#2636)
As per @wx20jjung, the resource for the `eupd` task have been updated
for RDHPCS Hera to account for memory issues for C384 `gdaseupd` job
fails.
Resolves #2454
---------
Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
commit acf3aaa2b1d3e3024b0b5d2fe23eee8c317a980b
Author: DavidNew-NOAA <134300700+DavidNew-NOAA@users.noreply.github.com>
Date: Thu Jun 6 11:49:03 2024 -0400
Parameterize some things in config.atmanl and config.atmensanl (#2661)
This PR adds some parameters in config.atmanl and config.atmensanl that
can be altered with the defaults.yaml. The motivation is to make these
files match those in the GDASApp JJOB tests (example:
https://github.com/NOAA-EMC/GDASApp/blob/develop/test/atm/global-workflow/config.atmanl),
so we can just use the Global Workflow config.atmanl and
config.atmensanl in the tests rather than custom ones in GDASApp that
have to be separately updated every time the ones in the Global Workflow
are updated.
commit 54ea0b73a07921be5fbb07fe41e976888bd3e549
Author: Guillaume Vernieres <guillaume.vernieres@noaa.gov>
Date: Thu Jun 6 01:36:02 2024 -0400
Add links to the ocean insitu obs processing tools (#2644)
Add links to the marine bufr to ioda converters for the marine insitu
observations.
- fixes https://github.com/NOAA-EMC/GDASApp/issues/1106
- waiting for https://github.com/NOAA-EMC/GDASApp/pull/1135
commit 205d0c2b13e2d7755cec75bf8c978ab20d453862
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Wed Jun 5 17:31:30 2024 +0000
Update S4 point of contact in docs (#2660)
Update the point of contact for global workflow issues on S4.
commit aa23ccf1d0d229f9ff1398d84af1fa7ee5bed262
Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com>
Date: Wed Jun 5 12:50:14 2024 -0400
Enable wcoss2 ufsda build and module load (#2620)
This PR enables ufsda (`sorc/gdas.cd`) to be built and run on WCOSS2.
Resolves #2602
Resolves #2579
commit 67b833e0c7bc390865d453588b4609a1a7ede981
Author: Jessica Meixner <jessica.meixner@noaa.gov>
Date: Tue Jun 4 13:33:43 2024 -0400
Update ufs-weather-model (#2646)
Updates UFS model to the commit https://github.com/ufs-community/ufs-weather-model/commit/5bec704243286421fc613838fc67a2129e96acd6
This should resolve the issue and allow C768 runs on Hera and allow for CICE
to run on WCOSS2 (due to library updates to allow linking).
From what I can tell, all updates needed were done by
@HenryWinterbottom-NOAA which were updates for CICE
Fixes #2490
commit c44d0ac86cfdf78eb87492431bf6d825e8bae637
Author: GwenChen-NOAA <95313292+GwenChen-NOAA@users.noreply.github.com>
Date: Tue Jun 4 10:29:49 2024 -0400
Update wmo parm files to fix WMO header (#2652)
This PR updates wmo parm files to switch WMO header of precipitation
type products (CRAIN, CFRZR, CICEP, and CSNOW) from time averaged to
instantaneous.
Resolves #2566
commit 237d6dd213e8b1455d2f45dc5978fb2d3de93e60
Author: Cory Martin <cory.r.martin@noaa.gov>
Date: Tue Jun 4 13:55:33 2024 +0000
Add IAU to snow DA (and its test) (#2610)
This PR enables IAU for the snow DA which is necessary for GFSv17.
A snow analysis is created for the center of the window regardless, and
an additional at the beginning of the window is added if IAU is on. The
former is needed for UPP and the latter, to initialize the model.
The increment is valid throughout the window for 3DVar, so the same
increment is added to both forecasts.
Additionally, the input file that goes into global_cycle has been
updated to be the output of the JEDI snow analysis instead of the
forecast (@jiaruidong2017 I recall discussing this, can you confirm this
is right or am I mistaken)
This PR also makes the CI test for snow DA (and aerosol DA) include IAU
rather than without IAU,.
---------
Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com>
Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
commit c92bf415060750127c9c05a62a1d2851c489551a
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Sat Jun 1 05:11:07 2024 +0000
Archiving cleanup (#2621)
1) Adds a lot of comments to the jinja templates for archiving
2) Rearranges the gdas and enkf templates to a more logical order
3) Fixes a couple of bugs in the enkf archiving of increments and
analyses
4) Disables archiving for the half cycle
5) Removes the `FITSARC` key from `config.base` and `arcdir.yaml.j2`,
instead relying on `DO_FIT2OBS`
6) Updates wxflow to add the option to not allow undefined variables
when parsing jinja templates and invokes this feature when running
archives
Resolves #2612
commit 12aa1e9cd2d159e2b303d2b33d6c79c365688eec
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Fri May 31 04:57:08 2024 -0400
Switch to Rocky 9 built external packages on Hercules (#2608)
The workflow was updated to use modules built on Rocky 9, but the
external packages (like prepobs) were still pointing to the versions
built on CentOS (Orion). This transitions to packages built on Rocky 9.
Updating of the tracker package has been deferred until later. As such,
the tracker jobs have been disabled by returning immediately if they are
on Hercules. Since these jobs are small, resource-wise, it should not
meaningfully impact turnover time.
commit 4422550c01c9214a2b3b8890bdcc898123ee216a
Author: Guoqing Ge <guoqing.ge@noaa.gov>
Date: Thu May 30 08:05:23 2024 -0600
Add the capability to use slurm reservation nodes (#2627)
Add the capability to use slurm reservation nodes
Add "ACCOUNT_SERVICE" for jobs to run in PARTITION_SERVICE
Resolves #2626
commit a54153fd9d26126206bc07a1da4e80f50c0c5910
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Wed May 29 23:24:07 2024 -0400
Update forecast job to use COMIN/COMOUT (#2622)
NCO has requested that each COM variable specify whether it is an input
or an output. This completes that process for the forecast job.
Refs #2451
---------
Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
commit d69a8af95d492982b918670322ed5c41ab074335
Author: Jessica Meixner <jessica.meixner@noaa.gov>
Date: Wed May 29 21:29:03 2024 -0400
Update to add 1-deg global wave grid (#2619)
This PR adds options to use a global 1 deg grid, intended for testing
with the SFS application.
Requires new fix file changes NOAA-EMC/global-workflow#2618
commit 0b4670ecf83b99b72835c8380573b2bca7cf5324
Author: Jessica Meixner <jessica.meixner@noaa.gov>
Date: Wed May 29 17:17:21 2024 -0400
Add C384mx025_3DVarAOWCDA yamls (#2625)
Adds the C384mx025_3DVarAOWCDA yaml files for one experiment into a new GFSv17 folder.
commit 2e885d05c64b947f00a3cf055a1277fbfac195c9
Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
Date: Wed May 29 13:00:51 2024 -0400
Script to keep Jenkins Agent persistent from cron (#2634)
This "persistent" Java Agent launch script can be ran from a cron job:
- Uses Jenkins Remote API to check the status of the Node connection
using curl for a given machine.
- If it is not connected a new agent is launched for that node.
Resolves #2633
commit bb58e064d8e82ce51802bd6064cfa84cae2cc4d5
Author: GwenChen-NOAA <95313292+GwenChen-NOAA@users.noreply.github.com>
Date: Tue May 28 17:17:11 2024 -0400
Change GRIB2 parameter names and vertical levels for ocean/ice post (#2611)
Based on users' feedback, this PR do the following:
1. Change GRIB2 parameter names DLWRF -> NLWRF and DSWRF -> NSWRF
2. Change the vertical level of ocean 3D variables (WTMP, SALIN, UOGRD,
and VOGRD) from "%g m below water surface" to "%g m below sea level"
3. Round up depth numbers to integer (e.g. 4481.0625 -> 4481 m)
Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com>
commit e53c5e8e0abbc0edf95970a71df0e6e8a2be9f31
Author: DavidNew-NOAA <134300700+DavidNew-NOAA@users.noreply.github.com>
Date: Tue May 28 17:16:23 2024 -0400
Add atmensanlfv3inc job (#2592)
This PR creates the atmensanlfv3inc job, the ensemble version of
atmanlfv3inc, created in GW PR #2420. Its GDASApp companion PR is
#[1104](https://github.com/NOAA-EMC/GDASApp/pull/1104), and its JCB-GDAS
companion PR is #[3](https://github.com/NOAA-EMC/jcb-gdas/pull/3).
commit 50c2b8951b29a3c883a778becbf8582f9519eb48
Author: Anil Kumar <108816337+AnilKumar-NOAA@users.noreply.github.com>
Date: Tue May 28 13:23:53 2024 -0400
Global-workflow (AR) Generic updates for Gaea C5 (#2515)
- Port global-workflow’s build and run capability to Gaea-C5
- Building global-workflow on Gaea-C5
- Setting up experiments with global-workflow on Gaea-C5
---------
Co-authored-by: AnilKumar-NOAA <Anil.Kumar@gaea53.ncrc.gov>
Co-authored-by: DavidBurrows-NCO <82525974+DavidBurrows-NCO@users.noreply.github.com>
commit b6ca771a0c584cbfcbbf9be739765d5f3815df97
Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
Date: Fri May 24 10:52:45 2024 -0400
Update STMP and PTMP settings in host file for Orion and Hercules (#2614)
- Updating STMP and PTMP settings in host file for Orion and Hercules
because they are cross mounted.
- Also took the opportunity to finally update **SLURM_ACCOUNT** to
**HPC_ACCOUT** in CI over rides.
- Added a refactor of the `rocotostat.py` tool that is more pythonic and
as a execute retry feature because the `rocotostat` utility on Orion has
been failing sometimes.
commit 7d2c539f45194cd4e5b21bfd4b83a9480189cd0f
Author: Guillaume Vernieres <guillaume.vernieres@noaa.gov>
Date: Tue May 21 23:50:50 2024 -0400
Sea-ice analysis insertion (#2584)
Allows cycling and restarting CICE with the sea-ice analysis if the
marine DA is switched on.
Resolves #2568
Resolves NOAA-EMC/GDASApp#1103
commit 5369a1ff3a3969149fcf32810fad0e50216752b7
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Tue May 21 22:12:29 2024 +0000
Refactored archiving (#2491)
This provides a new pygfs task, archive.py, that provides all of the
tools necessary to archive data to the local (`ARCDIR`) and backup
(`ATARDIR`) archive directories. YAML-Jinja2 templates are provided to
define the file to be archived or tarred to replace the
`hpssarch_gen.sh`, `exglobal_earc`, and `exglobal_archive.sh` scripts
and make it easier to add new data and explicitly handle optional and
required files.
For `ATARDIR` archiving, a master jinja template is provided for each
`RUN` (i.e. master_gdas.yaml.j2, master_gfs.yaml.j2,
master_enkf.yaml.j2). The master_enkf.yaml.j2 template is used for both
`enkfgdas` and `enkfgfs` `RUN`s. These templates then include the
appropriate `RUN`-specific jinja templates (e.g. gdas.yaml.j2) based on
experiment, cycle, and coupled parameters. Each of these templates
corresponds to a single tarball to populate and are tabbed 4 spaces so
they are defined within the master `datasets` dictionary.
Future developers should not have to make modifications to archive.py
unless archiving is being enabled for a new `RUN` (e.g. `gefs`) and then
only a single `elif` needs to be added to the configure method to
specify the master `ATARDIR` template to archive (e.g.
`master_gefs.yaml.j2`). If a new component is coming online that needs
to be archived to `ATARDIR` (e.g. SNOW), then create a new template for
each `RUN` that it needs to be archived for (e.g. `gdassnow.yaml.j2`)
and reference the template in the appropriate master templates, e.g.
`master_gdas.yaml:`
```jinja
{% if DO_SNOW %}
{% include "gdassnow.yaml.j2" %}
{% endif %}
```
A few other issues were addressed along the way:
1. Aerosols have been reenabled. Aerosol forecasts should only be
performed during gdas cycles, but analyses can be performed for both gfs
and gdas cycles. This was accomplished by setting separate
`AERO_<job>_CDUMP` variables to parse on for both `ANL` and `FCST` jobs.
2. Fixed the name of the `cice6_rst_ok` variable in `forecast_det.sh`.
This prevented restarts from being used for cice-enable experiments.
This feature was not tested.
3. Create a temporary fix for the `wgrib` utility. For spack-stack
1.6.0, the `grib-util` module file does not declare `WGRIB`. An issue is
open (https://github.com/JCSDA/spack-stack/issues/1097) to fix this in
existing installations. Once complete, this temporary fix should be
removed.
4. The number of `earc` jobs has been reduced for lower resolution
experiments. Both C48 and C96 experiments will now only have two earc
jobs (one for the non-member files to archive and another for the member
files). C192 will have up to 3 earc jobs (one non-member, one for
members 1-40 and another for members 41-80, if needed).
Resolves #2345
Resolves #2318
---------
Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
commit 9aad86f27d37d19165b9a0b64cf70c7a4dd6362c
Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
Date: Fri May 17 12:57:59 2024 -0400
Add remove RUNDIRS step in CI before creating experements (#2607)
As had been done in Bash CI we need to remove the RUNDIR in Jenkins
before a creating an experiment in the event that case had beem
previously ran.
commit bb930050b3cd51d28ecba6b231c8675f6d11856c
Author: AndrewEichmann-NOAA <58948505+AndrewEichmann-NOAA@users.noreply.github.com>
Date: Thu May 16 12:28:30 2024 -0400
Adds jjob and other necessities for marine LETKF task (#2564)
Adds jjob, rocoto script, config file, and other necessities for new
marine LETKF task.
Partially addresses NOAA-EMC/GDASApp#1091
commit 2c50fbde4d6cc3e53c55dca56925353a02fd1730
Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
Date: Thu May 16 12:12:06 2024 -0400
Updating CI Machine configs with redundant PTMP (#2605)
Quick fix adding PTMP as STMP in Machine configs for CI for completeness
commit ef340ff33a6f89adf70838206ba3fd56a953fa7a
Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
Date: Thu May 16 11:37:30 2024 -0400
Fix race condition in CI between Orion and Hercules (#2604)
Hotfix to solve race conditions in the CI system due to cross-mounted
file systems between Orion and Hercules
commit e8b17e27f719df280170dc3f5bd9f19917cefaf2
Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
Date: Wed May 15 17:16:30 2024 -0400
Remove existing EXPDIRs and COMROTs when CI is re-run (#2601)
Quick hotfix for having default for re-runing jobs to start clean with
new EXPDIRs and COMROTs
commit b5d113efb1970ede5cd1d3d4dff8d96320519c41
Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
Date: Wed May 15 16:52:49 2024 -0400
Moving logic for skipping hosts in pr cases (#2573)
This PR removes the logic of skipping hosts for pr cases from
`create_experiment.py` and moves it to a test in the cron bash driver
using a `parse_yaml.py` python tool.
The Jenkins pipeline was not effected as it uses the
`get_host_case_list.py` utility to form the cases on a per host bases.
Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com>
commit 3cd0c68c0de9900bc7b73e1ed7621573dff5e916
Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com>
Date: Wed May 15 13:13:30 2024 -0400
Update gsi_utils.fd hash (#2598)
This PR updates the `gsi_utils.fd` hash to bring in updates which add
safeguards to
-
`src/EnKF/gfs/src/getsigensmeanp_smooth.fd/getsigensmeanp_smooth_ncep.f90`
- `src/EnKF/gfs/src/recentersigp.fd/recentersigp.f90`
The safeguards are described in GSI-utils PR
[#41](https://github.com/NOAA-EMC/GSI-utils/pull/41) and the associated
issue.
Resolves #2597
commit d5366c66bd67f89d118b18956fe230207cbf0aea
Author: Kate Friedman <kate.friedman@noaa.gov>
Date: Wed May 15 13:12:56 2024 -0400
Update CICE and MOM6 fix versions (#2600)
This PR updates the CICE (`cice_ver`) and MOM6 (`mom6_ver`) fix versions
to the newer `20240416` timestamps, which includes updates and fixes to
the `100` (1-deg) resolution files.
Resolves #2480
Resolves #2483
Resolves #2595
commit 6ca106e6c0466d7165fc37b147e0e2735a1d6a0b
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Mon May 13 22:57:38 2024 +0000
Limit gfswavepostpnt to 40 PEs/node (#2588)
This fixes the slow runtime of the gfswavepostpnt job on Hercules. The
job is very I/O intensive and does not scale well to large nodes, so
limit the number of jobs/node to 40.
Resolves #2587
commit 4fb7c12c325702a47f27c802a5067efd33d0327c
Author: Fanglin Yang <fanglin.yang@noaa.gov>
Date: Mon May 13 16:37:51 2024 -0400
Update damping and time-step (#2575)
Updates the model to use explicit Rayleigh damping for u/v and implicit
damping to w. This improves model stability and allows for longer
timesteps. Also unifies the GDAS and GFS to use the same damping.
Results from a test at the C1152 resolution (coupled model) can be found
at https://www.emc.ncep.noaa.gov/gmb/wx24fy/C1152/newdamp/
Resolves #2574
Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Co-authored-by: Lisa Bengtsson <lbengtss@Orion-login-1.HPC.MsState.Edu>
Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com>
commit 6a9c1372ecce9e50e4f6e10e56f6e504cde1afe6
Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
Date: Fri May 10 14:17:13 2024 -0400
Do not use BUILT_semphore to force rebuilds when re-run (#2593)
Remove the placement of the `BUILT_semaphore` file after the build in
the Jenkins Pipeline and force it to rebuild any changes after a PR is
re-ran.
commit 2346c6161f75ae02369cbf30f30c6150d3e12b66
Author: Innocent Souopgui <162634017+InnocentSouopgui-NOAA@users.noreply.github.com>
Date: Thu May 9 21:17:06 2024 -0500
Migration to Rocky8 spack-stack installations on Jet (#2458)
# Description
Migrates Global Workflow to Rocky8 spack-stack installations on Jet.
Jet has moved from CentOS7 to Rocky8.
Resolves #2377
Refs NOAA-EMC/UPP#919
Refs NOAA-EMC/gfs-utils#60
Refs NOAA-EMC/GSI#732
Refs NOAA-EMC/GSI-Monitor#130
Refs NOAA-EMC/GSI-utils#33
commit c7b3973014480a20dd8e24edaeb83a9e9e68159f
Author: Jessica Meixner <jessica.meixner@noaa.gov>
Date: Thu May 9 11:36:58 2024 -0400
Updates for cold start half cycle, then continuing with IAU for WCDA (#2560)
This PR allows us to run C384 S2S with IAU, but starting with the first
half-cycle as a cold-start. This will be necessary for cycled testing as
we build towards the full system for GFSv17. This updates the copying of
the restarts for RUN=gdas for both ocean and ice copying what the atm
model is doing. It also reduced the amount of restart files from 4 to 3.
Other updates:
* Add DOJEDI ocean triggers for archiving certain files update from:
@CatherineThomas-NOAA
* Adds COPY_FINAL_RESTARTS option to turn on/off copying the last
restart file to COM. Defaults to off...
* Defines model_start_date_current_cycle & model_start_date_next_cycle
to help with knowing which IC to grab.
Refs #2546
Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com>
commit b405b7d3d11d384ce9fe3b9cd2180f315f7b38f2
Author: Dan Holdaway <27729500+danholdaway@users.noreply.github.com>
Date: Wed May 8 20:52:48 2024 -0400
Use JCB for assembling JEDI YAML files for atmospheric GDAS (#2477)
Change the JEDI YAML assembly for the atmospheric GDAS to use the JEDI
Configuration Builder (JCB) tool so that YAMLs can be made more portable
and invoke the observation chronicle mechanism.
Resolves #2476
Co-authored-by: danholdaway <danholdaway@users.noreply.github.com>
Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
commit 0cf0349c1f88048806e68ab58e93a3261b7a0e95
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Wed May 8 02:04:16 2024 -0400
Add CI test for products (#2567)
Adds a new version of the atm3DVar test that runs the full forecast
length and produces most of the secondary products. For now, this test
will only run on WCOSS due to gempak failures on other machines as well
as computational needs. On other machines, the original version will run
(the original version will not run on WCOSS). AWIPS remains off for now
in this extended test due to a bug involving tocgrib2 and the convective
precip fields (see #2566).
The new test runs for 4½ cycles and the full 384-hr forecast length to
ensure all gempak scripts are exercised. Since the cycle throttle is 3
and the bulk of the time is in the free forecast, the cycles run mostly
concurrently so it doesn't extend the total test time too much beyond
that of a single 384-hr forecast.
Fixes a bug in NPOESS that was introduced when the post filenames were
reverted to the previous format for the GOES products until the final
filenames are determined (#2499).
Also removes the AWIPS g2 job from the rocoto mesh to complete the
retirement of grib1 products.
Resolves #2132
Resolves #2445
commit 9b6f8404ac4507d14adc404b77cfdf002b55e832
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Tue May 7 00:14:36 2024 -0400
Add task to prepare emissions for GEFS (#2562)
This PR:
- introduces a task to prepare emissions for a forecast into the GEFS
application.
- adds configuration, j-job, rocoto job, ex-script and the python class
for this job
- updates GEFS workflow to be able to generate the XML to call this job.
- updates the `fcst` and `efcs` job dependencies in the GEFS application
to depend on `prep_emissions` if aerosols are turned ON.
- provides a placeholder for @bbakernoaa to work on the details for
preparing emissions.
Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
commit 233c18815d2e8e6b344f161fd0c102a4fbdfb66d
Author: Dan Holdaway <27729500+danholdaway@users.noreply.github.com>
Date: Mon May 6 18:11:35 2024 -0400
Single Executable for main GDAS JEDI applications (#2565)
Changes that accompany GDAS PR (NOAA-EMC/GDASApp/pull/1075) that allows
building of a single gdas executable, which should be more compliant
with NCO requirements.
Addresses https://github.com/NOAA-EMC/GDASApp/issues/1085
commit a005244bbfb2f1c525bca60d966f8095aa1acb8e
Author: Guoqing Ge <guoqing.ge@noaa.gov>
Date: Thu May 2 20:32:53 2024 -0600
Add nest capability (#2545)
This PR adds the global nesting capability to the global workflow so
that one can run a regional domain nested in a global run.
Resolves #2544
Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com>
commit cb87daaced9fddd17f8370a1842d7e4ddab24e8f
Author: DavidBurrows-NCO <82525974+DavidBurrows-NCO@users.noreply.github.com>
Date: Thu May 2 15:30:53 2024 -0400
Update gfs_utils for Gaea (#2556)
What: add build capability to the gfs_utils submod within the global
workflow on Gaea
Refs #2535
Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com>
commit 707a1cc5124bcd8e006839a17f76ceb88f45f902
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date: Wed May 1 18:13:02 2024 -0600
Updated GEMPAK version and APRUN launcher. (#2555)
This PR addresses issue #2248 and #2513. The following is accomplished:
- Updates the parallel executable for GEMPAK applications;
- Updates the GEMPAK version for RDHPCS Hera.
Describe your changes. Focus on the *what* and *why*. The *how* will be
evident from the changes. In particular, be sure to note any interface
changes, such as command line syntax, that will need to be communicated
to users.
At the end of your description, please be sure to add the issue this PR
solves using the word "Resolves". If there are any issues that are
related but not yet resolved (including in other repos), you may use
"Refs".
Resolves #2248
Resolves #2513
Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Co-authored-by: henrywinterbottom-wxdev <henry.winterbottom.wxdev@gmail.com>
commit f151cbf394e998ca0fdae893ca174499468d0c85
Author: Travis Elless <113720457+TravisElless-NOAA@users.noreply.github.com>
Date: Wed May 1 11:01:18 2024 -0400
Utilize scale-dependent localization for atmospheric analysis (#2542)
The plan for GFSv17 is to use a scale-dependent localization for the
atmospheric analysis. This PR adds the necessary parameters to allow
this feature to be used by default.
commit 53b6764392cb4c0f3b4506ccd3f8cba5c5d2c56e
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Tue Apr 30 16:37:54 2024 -0400
Remove implicit symlink names (#2527)
Lustre has a defect under Rocky 9 that results in symlink sometimes
failing when the link name is not explicit. This updates all link
creation to use explicit names.
`config.base` is updated to turn off two monitor jobs on Hercules
because the executables are not yet built there. This, combined with the
previous change, should make workflow available for use on Hercules.
Also removes the redundant utility names for NCP, NLN, etc. in the gdas
scripts that are already defined in `config.base`.
Resolves #2131
Resolves #2522
commit 762f040a2045db17cdacd9026df9c4b8fd520156
Author: AndrewEichmann-NOAA <58948505+AndrewEichmann-NOAA@users.noreply.github.com>
Date: Mon Apr 29 22:26:28 2024 -0400
Fixes sea ice archiving (#2541)
Removes/changes sea ice output files that are failing to be added to
list for archiving, causing `gdasarch` to fail in WCDA cycling.
Resolves https://github.com/NOAA-EMC/GDASApp/issues/1044
commit 2ecf4f86e0cbe59407ba2c4e105ee7292f1eda01
Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com>
Date: Mon Apr 29 22:25:57 2024 -0400
Link ensemble analysis increment files to COMROOT for warm_start (#2553)
Scripting is added to `setup_expt.py` to link ensemble analysis
increment files to COMROOT for warm_start experiments.
Resolves #2552
commit 3a7abe1d63c573006e0e656237f1220002c3f579
Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
Date: Tue Apr 30 02:25:28 2024 +0000
Launch Multiple Platforms to Jenkins with polling (#2548)
When launching Jenkins CI Tests all requested RDHPCS machines can now be
selected via the Ready label at once.
This is all that is required sense polling also works now on the
controller end.
Killing the jobs still needs to be done directly on the Jenkins
Controller.
Do not try to update the CI process using Labels. It is for launching
only.
Jenkins will update the labels as the states change.
NOTE: When a case fails the label will be update to a **Fail** for that
system but will continue to report failures of subsequent cases until
otherwise stopped in the Jenkins Controller directly.
Do not update any labels to **Ready** until a push has been made to the
repo of the PR, and
The job has been completed or stopped directly on the controller first.
You can do this at anytime without having to wait until the other
machines are completed.
Co-authored-by: tmcguinness <terry.mcguinness@noaa.gov>
Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com>
commit 4b96c1237c562b67650c2d2fa015984c95b228eb
Author: Jessica Meixner <jessica.meixner@noaa.gov>
Date: Sat Apr 27 19:03:26 2024 -0400
Turn C48mx500_3DVarAOWCDA back on (#2543)
This PR turns the C48mx500_3DVarAOWCDA test back on. This required a few
bugfixes in GDAS app which have now been merged.
Resolves #2438
Resolves #2528
co-authors: @guillaumevernieres and @aerorahul who provided the bug
fixes.
commit 48489b4e7758e80660941279652431e49fdd3cfa
Author: Guoqing Ge <guoqing.ge@noaa.gov>
Date: Sat Apr 27 00:23:00 2024 -0600
Add option to link different orog/ugwd fix files for global nest (#2532)
The global nest runs use a different set of tiles and need a different
set of orog and ugwd fix files.
The PR add an option to link correct fix files for global nest.
Resolves #2530
Resolves #2529
commit 7911f12ef0213f487a0681b260e4c982c946c17c
Author: GwenChen-NOAA <95313292+GwenChen-NOAA@users.noreply.github.com>
Date: Fri Apr 26 16:20:44 2024 -0400
Retire AWIPS GRIB1 products (#2547)
This PR retires AWIPS GRIB1 products by deleting the files that are responsible for it.
This PR does not remove the awips_g2 tasks from rocoto task list. It will be addressed in a follow up PR by workflow developers
Refs #2445
commit 93c853d464908a88222d5a6eeca686cd1a413c0e
Author: James Jung <Jim.Jung@noaa.gov>
Date: Fri Apr 26 13:16:47 2024 -0400
Add CADS use flexibility (#2540)
The current design requires a script change to turn CADS on/off for
specific instruments. The new design moves the on/off (true/false) flags
to the config.anal file.
Resolves #2538
commit 11bf141319ef2a29398742007a29d79bbf4439d5
Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
Date: Thu Apr 25 23:35:57 2024 +0000
Hot fix for bash CI on WCOSS2 (#2536)
A couple of minor hotfixes need for bash CI to work on WCOSS2.
PR tested in bash on WCOSS with these changes
Co-authored-by: tmcguinness <terry.mcguinness@noaa.gov>
commit f11bf3dc2bc062c070b901ce3aa808bd6b69a007
Author: Walter Kolczynski - NOAA <Walter…
kayeekayee
added a commit
to kayeekayee/global-workflow
that referenced
this issue
Sep 2, 2024
- based on gsl_ufs_dev from KaYee's fork
global-workflow: 07Aug24,37c53ac [dev_07Aug2024_37c53ac]
UFS: 19Jul24, c127601
FV3: 19Jul24, 2527c11
UPP: 23Apr24, be0410e
CCPP-PHYSICS: 19Jul24, 46df080
UFS_UTILS: 26Jun24, 3ef2e6b
Squashed commit of the following:
commit 70b557836379bb7e545fcc6642e28d66cfc17735
Merge: 5edbd123e 37c53ac69
Author: Janet Derrico <143837053+jderrico-noaa@users.noreply.github.com>
Date: Wed Aug 7 11:02:24 2024 -0600
Merge branch 'NOAA-EMC:develop' into develop
commit 37c53ac692274eb5e9f9a3220033406e8c4b4a04
Author: Kate Friedman <kate.friedman@noaa.gov>
Date: Wed Aug 7 08:11:21 2024 -0400
Revert MSU FIX_DIRs back to glopara (#2811)
commit 876dfee26ad67e1f729bbf52b3167d48ea5a7517
Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
Date: Tue Aug 6 14:47:36 2024 -0400
Bugfix for updating label states in Jenkins (#2808)
Quick bug fix for updating state labels in CI during finalize.
(did not reference GitHub CLI executable correctly in the pipeline
script)
commit 8fee36f0307b0c08080e3a8fa8fa6703e7da5fce
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Tue Aug 6 11:02:45 2024 -0400
Clean-up temporary rundirs - take 2. (#2753)
This PR:
- is a follow-up to a previous PR that aggressively pruned run
directories.
- removes run directories for the current cycle in the clean-up if the
cycle is successful. If the cycle is not successful, cleanup is not
called and all run directories for the cycle are safe from being purged.
- also updates the PR template to list/query for any updates to
submodules.
---------
Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Co-authored-by: David Huber <david.huber@noaa.gov>
Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
commit d599fff4aedd41ae587dbe02226acb12ff48efc1
Author: HelinWei-NOAA <48133472+HelinWei-NOAA@users.noreply.github.com>
Date: Mon Aug 5 05:31:31 2024 -0400
Change land surface for HR4 (#2787)
Resets the default value of opt_diag to 2 corresponding to the land
surface upgrades in ufs-weather-model for HR4.
Resolves #2786
commit 6d7f7e860a0c7062f90bf09fdf9a5d19dc77cfdb
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Fri Aug 2 15:41:29 2024 -0400
Run METplus serially and correct the name of prod tasks (#2804)
Adds 2 hot fixes:
- METplus v9.1.3 has a bug in it that sometimes attempts to create
multiple copies of the same directory when running in parallel, causing
a Python error and downstream problems. This PR makes METplus run in
serial mode, preventing such issues.
- Corrects the name of the atmos_prod, ocean_prod, and ice_prod tasks in
workflow/rocoto/tasks.py (was accidentally changed to e.g. atmosprod)
commit 0706c59ac53cc3bbfbaa56cbd7fa75ab51117830
Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
Date: Fri Aug 2 15:03:45 2024 -0400
Update Java Agent launching script for Jenkins connections (#2762)
Made updates to the Jenkins Launching Script for robustness and less
ambiguous documentation:
- Clearer distinction between required user token for the remote api and
the systems token for launching
- Added pre-checks: `gh` is authenticating, named compliant token and
secret file exists
- More robust Jason based parser of the remote api response for checking
the state of the Node connection
- For `cron` use a 5 minute pause and recheck was added before
re-launching of the java agent
- Added concise header documentation of requirements and purpose
---------
Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
commit b73b1fd203496db97f8067652659573a632bcc67
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Fri Aug 2 07:59:06 2024 -0400
Fix erroneous cdump addition (#2803)
commit 49877046ac3306f6b78ca0ab5d5089ba1aa3e3e3
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Thu Aug 1 20:26:13 2024 -0400
Update ocean post-processing triggers (#2784)
This PR:
- replaces `check_netcdf.sh` checker for ocean post-processing with with
ocean output at the next forecast hour or finishing of the forecast job
for ocean prod
- removes no longer needed `ush/check_netcdf.sh`
commit aa2af1ca8d59424a60a1730722bf528775d9e606
Author: GeorgeGayno-NOAA <52789452+GeorgeGayno-NOAA@users.noreply.github.com>
Date: Thu Aug 1 16:46:10 2024 -0400
Update the gfs_utils repository hash (#2801)
# Description
Point to the latest hash of the gfs-utils repository, which contains the
bug fix to gaussian_sfcanl.
Resolves #2669.
Refs: https://github.com/NOAA-EMC/gfs-utils/pull/73
commit d3d85f0e0d573f16a71ca44778021dfc0ccf50c8
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Thu Aug 1 08:12:14 2024 -0400
Add fixes for metplus jobs when gfs_cyc=2 or 4 (#2791)
Changes how METplus jobs run so that they run on the last GFS cycle for
a given `PDY`.
This is a departure from operations where the METplus jobs run on the
00Z cycle for the previous 3 cycles and 00Z (i.e. `${PDYm1}06` through
`${PDY}00`). With this PR, for gfs_cyc=4, METplus jobs will run on
`${PDY}18` for cycles 00-18. See
https://github.com/NOAA-EMC/EMC_verif-global/pull/131 for more details.
commit 1cf8b448af562dbb7af198399c78c585977e81da
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Tue Jul 30 10:38:49 2024 -0400
Simplify resource-related variables, remove CDUMP where unneeded (#2727)
This overhauls resource-related variables to use a common set of
variables for each job. In the process, this also removed the use of
CDUMP in most cases.
Resolves #1299 #2693
commit 61875f25c9e971f82ae499b5b612d7f095deebd4
Author: Eric Sinsky - NOAA <48259628+EricSinsky-NOAA@users.noreply.github.com>
Date: Mon Jul 29 14:40:03 2024 -0400
Remove f000 from atmos rocoto tasks for replay cases (#2778)
The main purpose of this PR is to remove the f000 from
atmosphere-related rocoto tasks when `REPLAY_ICS` is set to `YES`. In
cases where `REPLAY_ICS` is `YES` and `OFFSET_START_HOUR `is greater
than `0`, it becomes necessary to have the first lead hour set to
`OFFSET_START_HOUR ` for the atmosphere-related rocoto tasks. For
example, when `OFFSET_START_HOUR ` is set to `3`, then the minimum lead
time for the atmos_prod and atmos_ensstat rocoto tasks needs to be 3 and
the minimum lead time for the ocean_prod rocoto task needs to be 6
(assuming `FHOUT_OCN` is 6). This PR makes this rocoto workflow set up
possible by removing 0 from fhrs for atmosphere-related tasks in
`gefs_tasks.py` when replaying.
This PR also moves where f000 is being removed for the ocean_prod and
ice_prod tasks. The if-block that performs this f000 removal has been
moved from `tasks.py` to `gefs_tasks.py` and `gfs_tasks.py`.
---------
Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com>
commit f156a7894d639f177e3e2588f98eec1f6f59aa68
Author: Jessica Meixner <jessica.meixner@noaa.gov>
Date: Fri Jul 26 14:18:32 2024 -0500
HR4 GWD update (#2732)
This update is a combination of the gravity wave drag (GWD) versions
from the NOAA/GSL and NOAA/PSL
commit a7f6b32ed63efa0de21bfb0ce63364a5b22b9891
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Thu Jul 25 14:26:52 2024 -0400
Temporarily disable METplus jobs (#2796)
commit 848659691fdbf47e7ccdbbb2ebf22a6e470633a2
Author: Guillaume Vernieres <guillaume.vernieres@noaa.gov>
Date: Wed Jul 24 15:00:35 2024 -0400
Refactoring of the marine B-matrix job (#2749)
Refactor the functionality of B-matrix generation from the GDASApp
Resolves #2743
commit 65a7ab75dc0e4baba06a02e11ed0455787056a68
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Tue Jul 23 08:35:48 2024 -0400
Replace Jinja namespaces with replace_tmpl filter and disable ACCOUNT_SERVICE option (#2775)
Removes the namespace-based construction of EnKF member COM directories
in the enkf archive template.
commit c45b9611f3e701b819bd33dc5af29033f060bb91
Author: Eric Sinsky - NOAA <48259628+EricSinsky-NOAA@users.noreply.github.com>
Date: Tue Jul 23 00:33:16 2024 -0400
Add task to process reforecast variables to save on WCOSS2 (#2680)
# Description
This PR adds an optional task to the global-workflow to process a subset
of ocean, ice, wave and atmosphere products to be saved on WCOSS2 for
the GEFSv13 reforecast. This task is designed to process GEFS variables
so that specific reforecast product requirements are met. A new variable
in `config.base` called `DO_EXTRACTVARS` enables this task, which is
currently called `extractvars`. `DO_EXTRACTVARS` is set to `NO` by
default and is specifically a task designed to be executed for the
GEFSv13 reforecast.
Refs #1878
# Type of change
- New feature (adds functionality)
# Change characteristics
- Is this a breaking change (a change in existing functionality)? NO
- Does this change require a documentation update? NO
# How has this been tested?
This has been cloned and tested on WCOSS2. This will need to be tested
on Hera and other platforms on which the reforecast may be running.
# Checklist
- [ ] Any dependent changes have been merged and published
- [x] My code follows the style guidelines of this project
- [x] I have performed a self-review of my own code
- [ ] I have commented my code, particularly in hard-to-understand areas
- [x] My changes generate no new warnings
- [x] New and existing tests pass with my changes
- [ ] I have made corresponding changes to the documentation if
necessary
---------
Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com>
commit 71dc33c6ca991c16ce743760d99feaaf60f2218a
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Mon Jul 22 14:51:53 2024 -0400
Set METplus process count in config.metp; add verif-global support for Rocky 9 (#2774)
Fix metp* resources and check that they completed properly; add support for Orion Rocky 9
commit 56df67a90fe090c425199f1285e5aac722c398b1
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Mon Jul 22 09:28:18 2024 -0400
Hotfix: Update jcb to avoid git-lfs files (#2782)
Removes git-lfs files from the `GDASApp` `jcb` submodule, allowing it to
be cloned on Hera.
This hotfix points to a non-authoritative branch of the GDASApp
(https://github.com/DavidHuber-NOAA/GDASApp/tree/hotfix/update_jcb) and
should be updated ASAP back to the authoritative repository.
commit fc668aa422ebbad76ceda1b3bbf8dc0ea432defd
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Tue Jul 16 09:44:00 2024 -0400
Address issues in creating XML for GFS forecast-only with app S2SWA (#2757)
This bugfix PR:
- fixes an issue where a user is unable to generate the XML for a GFS
forecast-only experiment with APP=S2SWA
Specifically, the changes are related to defining `aero_fcst_cdumps`.
Following `setup_expt.py`, the user will have to set
`AERO_FCST_CDUMPS="gdas|gfs|both" depending on their use case in
`config.base`.
commit e0878dba0e53706a7f53429b61aee2936e2c21bf
Author: Kate Friedman <kate.friedman@noaa.gov>
Date: Mon Jul 15 10:25:11 2024 -0400
Updated prepobs and fit2obs versions for Orion Rocky9 (#2758)
Update prepobs to v1.0.2 and fit2obs to v1.1.2
These versions now support Orion Rocky9. Updates are included
for new install locations on WCOSS2, Hera, Orion/Hercules, and Jet.
commit 4968f3a8de9a5f90651cacd74e38f97bc80b7bbb
Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
Date: Thu Jul 11 17:48:47 2024 +0000
CI maintenance updates and adding CI Unit Tests (#2740)
This PR has a few maintenance updates to the CI pipeline and adds a test
directory with Unit Tests
**Major Maintenance updates:**
- Added try blocks with appropriate messaging to GitHub PR of failure
for:
- - **scm** checkout
- - build fail (with error logs sent as gists)
- - create experiment fails with `stderr` sent to GitHub PR messaging
- Pre-stage FAILS from the above are now captured these fails allow
FINALIZE to update the label to FAIL (i.e. no more "hanging" CI state
labels in GitHub - see image below)
**Minor Maintenance updates:**
- Fix for STALLED cases reviled from PR 2700 (just needed a lambda
specifier)
- Fixed path to experiment directory in PR message (had dropped EXPDIR
in path)
- Needed `latin-1` decoder in reading log files for publishing
**Added python Unit Tests for CI functionality:**
- Installed **Rocoto** and **wxfow** in GitHub Runner for testing key CI
utility codes
- Cashed the install of Rocoto in the GitHub Runners to greatly reduce
stetup time for running the unit tests
- Unit Tests Python scripts added
- `test_rocostat.py`: rocoto_statcount() rocoto_summary()
rocoto_stalled()
- `test_setup.py`: setup_expt() test_setup_xml()
- `test_create_experment`: test_create_experiment()
- - Runs all PR cases that do not have ICs in the GItHub Runner
- Reporting mechanism in the Actions tab for Python Unit Testing results
- Test case data for STALLED and RUNNING stored on S3 and pulled using
wget during runtime of tests
commit 5ef4db74649b8be03402c17aa29c024e71699a7b
Author: AndrewEichmann-NOAA <58948505+AndrewEichmann-NOAA@users.noreply.github.com>
Date: Thu Jul 11 08:59:24 2024 -0400
Adds contents of constructor and initialize methods to marine LETKF class (#2635)
Adds contents of constructor and initialize methods to marine LETKF class
Partially addresses https://github.com/NOAA-EMC/GDASApp/issues/1091
---------
Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com>
Co-authored-by: Cory Martin <cory.r.martin@noaa.gov>
commit 8998ec7b74123e953b97a93fa14cc78d471a1aee
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Tue Jul 9 08:31:57 2024 -0400
Fix GDAS group B restart archiving (#2735)
Archives the GDAS restartb dataset at a 6-hour offset from restarta
This allows cycled experiments to restart from the archives.
The tabbing for the master archive templates was also added to
improve readability.
Resolves #2722
commit 3ca74771255727033b9dc043c652ac585178629c
Author: AndrewEichmann-NOAA <58948505+AndrewEichmann-NOAA@users.noreply.github.com>
Date: Tue Jul 9 08:28:54 2024 -0400
Add fcst dependency to ocnanalprep (#2728)
Add previous cycle's `fcst` as a dependency to `ocnanalprep`
This ensures that the availability of restart files to the latter. This addresses a
seldomly-encountered race condition where `ocnanalprep` fails due to the
lack of the files.
commit 58fca1668aecd6fb1afd12a441256ad35900e075
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Fri Jul 5 15:02:23 2024 -0400
Update (partially) global-workflow for orion+rocky9 (#2741)
This PR:
- updates a few submodules (GSI, GSI-utils, GSI-monitor, UFS_utils,
GFS-utils) to include recent update to their modulefiles for
Orion+Rocky9 upgrade
- updates the modulefiles in global-workflow to load modules from
Orion+Rocky9 paths
- updates modulefiles for `gwsetup` and `gwci` as well.
- removes NCL and GEMPAK from Orion. NCL is not used and GEMPAK is not
installed.
- adds `parm/config.gfs/config.resources.ORION` to address GSI
performance degradation after Rocky 9 upgrade.
This PR:
- does not update the build for UPP. Standalone UPP is not available via
ufs-weather-model as of #2729
- will need a follow-up update for `prepobs` and `fit2obs` updated
locations when they are installed in `glopara` space on Orion.
# Type of change
- Maintenance (code refactor, clean-up, new CI test, etc.)
# Change characteristics
- Is this a breaking change (a change in existing functionality)? NO
- Does this change require a documentation update? NO
# How has this been tested?
This PR is not sufficient for Orion.
This PR must be tested on other platforms (Hera, WCOSS2) as this PR
updates submodules.
# Checklist
- [ ] Any dependent changes have been merged and published
- [ ] My code follows the style guidelines of this project
- [ ] I have performed a self-review of my own code
- [ ] I have commented my code, particularly in hard-to-understand areas
- [ ] My changes generate no new warnings
- [ ] New and existing tests pass with my changes
- [ ] I have made corresponding changes to the documentation if
necessary
---------
Co-authored-by: Kate Friedman <kate.friedman@noaa.gov>
commit d65d3d257b38225fac74e86b770f43e1f8ae2d5a
Author: Jessica Meixner <jessica.meixner@noaa.gov>
Date: Wed Jul 3 21:07:49 2024 -0400
Update ufs model hash to 20240625 (#2729)
Updates UFS weather model hash to hash from 2024-06-24 which has orion
porting updates + a few namelist updates.
commit 2bd106a013805ba4e16dbdc456d6731f8f36ec85
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Wed Jul 3 11:32:40 2024 -0400
Hotfix for undefined CLUSTERS (#2748)
Defines `CLUSTERS` as an empty string for all hosts except Gaea and uses
the native `dict` `get` method to prevent grabbing an unset entry.
commit 7dc6651a3b92194d963675bdc0a9ec3c28499abf
Author: GwenChen-NOAA <95313292+GwenChen-NOAA@users.noreply.github.com>
Date: Wed Jul 3 09:56:08 2024 -0400
Update gempak job to run one fcst hour per task (#2671)
This PR updates gempak jobs (gfs, gdas, and goes) from processing all
forecast hours at once to one forecast hour at a time. This will reduce
the job runtime to less than 5 min, so restart capability is not needed.
Resolves #1250
Ref #2666 #2667
---------
Co-authored-by: Walter.Kolczynski <Walter.Kolczynski@noaa.gov>
commit 8215ae654202186a4f753c3abe937b7b9b91a9c7
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Tue Jul 2 16:22:11 2024 -0400
Hotfix for clusters from #2701 (#2747)
Fixes an issue created from #2701 that added `CLUSTERS` to the
`gaea.yaml`.
commit 11943e36ba12b3df49c51942da780698fab02d38
Author: DavidBurrows-NCO <82525974+DavidBurrows-NCO@users.noreply.github.com>
Date: Tue Jul 2 12:58:10 2024 -0400
Fix xml file setup and complete C48 ATM and S2SW runs for CI on Gaea (#2701)
This PR sets up the ability on Gaea for auto generation of a clean xml
file, i.e., an xml file that does not need any alterations before
running rocoto.
Refs #2572
Refs #2664
commit de8706702ead0630beb54d868f83aa2cb23f8f79
Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com>
Date: Mon Jul 1 09:29:14 2024 -0400
Update for JCB policies and stage DA job files with Jinja2-templates (#2700)
This PR updates the `gdas.cd` hash to bring in new JCB conventions.
Resolves #2699
From #2654
This PR will move much of the staging code that take place in the python
initialization subroutines of the variational and ensemble DA jobs into
Jinja2-templated YAML files to be passed into the wxflow file handler.
Much of the staging has already been done this way, but this PR simply
expands that strategy.
The old Python routines that were doing this staging are now removed.
This is part of a broader refactoring of the pygfs tasking.
wxflow PR [#30](https://github.com/NOAA-EMC/wxflow/pull/30) is a
companion to this PR.
Co-authored-by: danholdaway <danholdaway@users.noreply.github.com>
Co-authored-by: DavidNew-NOAA <david.new@noaa.gov>
Co-authored-by: DavidNew-NOAA <134300700+DavidNew-NOAA@users.noreply.github.com>
Co-authored-by: Dan Holdaway <27729500+danholdaway@users.noreply.github.com>
commit c49e4eee1a2ca818b3ecdcb9ea41c3f3e91d585b
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Fri Jun 28 14:56:19 2024 -0400
Revert PR 2681 (#2739)
This PR:
- reverts #2681 in part
- keeps some changes for `RUN`.
- is a hotfix
- should be merged ASAP after consensus w/ @guillaumevernieres
@CatherineThomas-NOAA @WalterKolczynski-NOAA
commit 9476c1237af4adbc95f90bd1bdd34b6b99f2f8a3
Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
Date: Wed Jun 26 15:46:08 2024 -0400
updated Finalize in Jenkinsfile and added try block around scm checkout (#2692)
We are updating the Jenkins Pipeline with a try block around checkout to
capture errors for the user.
Also cleaned up Finalize and added section to clean out workspace on
success.
commit 968568f682bac7564095440bdb7813abefd76821
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Wed Jun 26 13:27:19 2024 -0400
Activate snow DA test on WCOSS (#2720)
Activate the snow DA test on WCOSS.
commit 7706760bb8adbdf78cb640b02739023c886e7699
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Wed Jun 26 10:02:22 2024 -0400
Cleanup of stale RUNDIRS from an experiment (#2719)
This PR:
- removes stale temporary scratch run directories from `$DATAROOT/`
every 3 days.
- should help to scrub failed attempts.
- removes an unused variable `RUNDIR` defined in `config.base`
commit 8962991691b5f0857b813bddfd28aa1034d4bd2b
Author: Jessica Meixner <jessica.meixner@noaa.gov>
Date: Wed Jun 26 09:43:48 2024 -0400
Update logic for MOM6 number of layers/exception values (#2681)
Updates the logic to be by run instead of for DO_JEDIOCNVAR to determine
how many layers and sets the exception value for MOM6 to be 1e-34 for
all scenarios. Note, we will no longer have zeros in the ocean grib
output and the DA will also run without issues.
Fixes https://github.com/NOAA-EMC/global-workflow/issues/2615
commit 12431f76bdce807067929415007592cffc8a2457
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date: Wed Jun 26 07:42:35 2024 -0600
Update wave jobs to use COMIN/COMOUT (#2643)
NCO has requested that each COM variable specify whether it is an input
or an output.
This completes that process for the global-workflow wave
model and products tasks.
Refs #2451
commit b902c0bac126c323a07186ad8881384b032b6fda
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Tue Jun 25 07:48:46 2024 -0400
Assign machine- and RUN-specific resources (#2672)
Redefine resource variables based explicitly on RUN or CDUMP
Additionally, machine-specific resources are moved out of
config.resources and placed in respective config.resources.{machine}
files.
Resolves #177 #2672
commit 5edbd123e2878a07f5cce8e3c7ea6147f286633a
Merge: 09333c01d 4e1b937b6
Author: Janet Derrico <143837053+jderrico-noaa@users.noreply.github.com>
Date: Mon Jun 24 12:44:05 2024 -0600
Merge branch 'NOAA-EMC:develop' into develop
commit 4e1b937b67ed220120e81925c4507f03b9b8965f
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Mon Jun 24 10:50:52 2024 -0400
Add minimum software requirements (#2712)
Adds a table to HPC documentation stating the minimum support versions
commit f43a86276aaef91efa28faadc71a3cf50e749efe
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Fri Jun 21 13:44:29 2024 -0400
Fix and simplify online archiving and reenable METplus jobs (#2687)
This fixes the online archiving portion of the `*arch` and `*earc00`
jobs, a prerequisite for running METplus. This also reenables
METplus by default.
The approach previously taken created `FileHandler` dictionaries at
varying levels within the resulting yaml, which was not properly parsed
by `exglobal_archive.py`. This approach creates a single `FileHandler`
dictionary and is much less complicated overall.
Resolves #2673 #2647
commit 8993b42cb91144c0ab0501dc7841ea8d675c4701
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Wed Jun 19 21:51:22 2024 -0400
Eliminate post groups (#2667)
Eliminates the post groups used for upp and products jobs so that each
task only processes one forecast hour. This is more efficient and
greatly simplifies downstream dependencies that depend on a specific
forecast hour.
Resolves #2666
Refs #2642
commit 0b810c888239853fedd0e4584fe62536c6aaacdf
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date: Tue Jun 18 20:32:48 2024 -0600
Removes misleading "No such file or directory" syntax errors from output files (#2688)
This PR addresses issue #1252. The following is accomplished:
- Prior to removing files, the existence of a file is checked prior to
attempting to remove; this is performed as noted
[here](https://github.com/NOAA-EMC/global-workflow/issues/1252#issue-1538627369);
this PR only addresses the the `chgrp` issue.
Refs #1252
---------
Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
commit 3270ac3bf00c3ebc8166c70d84647ec44431fbae
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date: Tue Jun 18 12:17:59 2024 -0600
Hotfix for bug in template names. (#2697)
This PR is a hotfix for an incorrectly named (e.g., non-existent) `COM/`
template.
Resolves #2696
Refs #2451
commit 35d4d99eaac669721add9ddcc793153e5ab3b30a
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date: Tue Jun 18 08:06:53 2024 -0600
Update archive job to use COMIN/COMOUT (#2668)
NCO has requested that each COM variable specify whether it is an input
or an output. This completes that process for the global-workflow
archive task.
Refs #2451
---------
Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com>
Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
commit 47b3a581c8257fa24411fb400df8bb0e1e04972a
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Mon Jun 17 22:55:38 2024 -0400
Turn on high-frequency output in extended test (#2679)
Turns on high-frequency (hourly) output in the extended products test to
exercise that aspect of the code. This test only runs on WCOSS.
Also adds the hooks to optionally turn on the metplus jobs, but that is
deferred as they are not currently working correctly.
commit 38f2df9fb0c074b1f80d3c637080be79be693161
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Mon Jun 17 17:12:55 2024 +0000
Optimize wavepostpnt (#2657)
Optimize the gfswavepostpnt, gfswavepostbndpntbll, and gfswavepostbndpnt jobs
This is done by
1) reducing the number of calls to `sed`, `awk`, `grep`, and `cat` by
- performing operations on all files at once instead of looping over
each file
- removing piped `cat` calls (e.g. `cat <file> | sed 'something'`)
- combining `sed` and `grep` calls when possible
- adding logic to `awk` calls instead of handling that logic in bash
2) minimizing as much as possible the amount of data on disk that has to
be read in (e.g. limiting sed to read only the line numbers it needs)
---------
Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
commit 5af325a6a4e0a14d180514a418603ca79fada487
Author: Dan Holdaway <27729500+danholdaway@users.noreply.github.com>
Date: Fri Jun 14 18:05:23 2024 -0400
Update GDASapp hash to move JCB into GDASapp (#2665)
This PR moves JCB into GDASapp. The PR
also bumps up the hash of GDASapp to what is in `feature/move_jcb`,
which at time of writing is develop plus the absorption of JCB into
GDASapp.
Note that I also took the changes from
https://github.com/NOAA-EMC/global-workflow/pull/2641 to follow the
testing @RussTreadon-NOAA has done.
commit 6c93b4554e235fcb4d0004e99a4c4498d55d461b
Author: Yaping Wang <49168260+ypwang19@users.noreply.github.com>
Date: Fri Jun 14 10:18:17 2024 -0500
Add observation preparation job for aerosols DA to workflow (#2624)
Add a prepaeroobs job to prepare aerosol obs files for DA.
This job does quality control of the VIIRS aerosol raw observations and
convert them to ioda format.
Resolves #2623
---------
Co-authored-by: ypwang19 <yaping.wang@users.noreply.github.com>
Co-authored-by: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
Co-authored-by: Cory Martin <cory.r.martin@noaa.gov>
Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
commit 5a5fc2be7555f094a0f90fd3a3df22d071ccdfd4
Author: Jessica Meixner <jessica.meixner@noaa.gov>
Date: Fri Jun 14 11:04:41 2024 -0400
Remove ocean daily files (#2689)
This PR removes the ocn_daily files that are produced by the ocean
component. These files can be recreated by averaging data that exists in
the 6 hour aveaged files if needed.
Fixes https://github.com/NOAA-EMC/global-workflow/issues/2675
Fixes https://github.com/NOAA-EMC/global-workflow/issues/2659 (by
removing them and making this obsolete)
commit 603a4a8052a5c43ce5986f028c3fcfd5fd248ad4
Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
Date: Thu Jun 13 12:22:03 2024 -0400
Update Jenkinsfile
needed a comma
commit dc21eac6c3941d7f30803891d91d82f4cc1f8183
Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
Date: Thu Jun 13 11:41:14 2024 -0400
Add Hercules-EMC to the Jenkins configurable parameter list (#2685)
This quick-fix PR is to update the Jenkins Pipeline's configurable
parameter list to include the **Hercules-EMC** node.
This allows Jenkins users to restart Jobs in the controller when no
updates have been made.
commit ebacebfbe458634b8c80af6a735d6b6d01e4e406
Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com>
Date: Thu Jun 13 11:20:24 2024 -0400
Update gdas.cd and gsi_utils hashes (#2641)
This PR updates the `sorc/gdas.cd` and `sorc/gsi_utils` hashes. The
updated hashes bring in bug fixes, new UFS DA functionality, and a Gaea
build for gsi_utils.
Resolves #2640
commit 34155fb4767769600a1ff95f0a65e37081addc2a
Author: Neil Barton <103681022+NeilBarton-NOAA@users.noreply.github.com>
Date: Thu Jun 13 11:18:22 2024 -0400
Add ability to use GEFS replay ICs (#2559)
The PR allows the use of ICs from PSL's replay analysis. These replay
ICs will be used for GEFS reforecasting and SFS. Two main changes are
associated with these updates: (1) replay ICs being valid at 3Z, and (2)
the use of warm starts.
Resolves #1838
---------
Co-authored-by: Jessica Meixner <Jessica.Meixner@noaa.gov>
Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com>
commit 6c19a0e3fc4400e1d39288be4ee4fc244b74f699
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date: Wed Jun 12 19:25:42 2024 -0600
Replace `sleep` with `wait_for_file` (#2586)
This PR addresses issue #2444. The following is accomplished:
- All `sleep` statements are replaced with `wait_for_file` for the
relevant scripts beneath `scripts` and `ush`;
- Indentation and shell-norms are updated where applicable.
Note: The WAFS scripts are not updated as per @aerorahul direction.
Resolves #2444
---------
Co-authored-by: henrywinterbottom-wxdev <henry.winterbottom.wxdev@gmail.com>
Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
commit 5b2a3d449a0835cec2663aabb06f1c47a3faf84e
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Wed Jun 12 13:31:55 2024 -0400
Add COM template for JEDI obs (#2678)
Adds a COM template to define a path to store obs processed for JEDI.
This will allow UFSDA to stop writing to COM_OBS, which should be
read-only as it belongs to obsproc in operations.
No functional change yet.
commit 2e6f1fcde9935619352b1b26cba42ec0f4d845ed
Author: Guoqing Ge <guoqing.ge@noaa.gov>
Date: Wed Jun 12 09:06:23 2024 -0600
Link both global-nest fix files and non-nest ones at the same time (#2632)
This PR enables linking both global-nest fix files and non-nest ones at
the same time and users can run both nesting and non-nesting experiments
at the same time without worries about what fix files to be linked.
Resolves #2631
commit 61de004d4f9e9edf8a31bb173f2719b46451a36a
Author: Jessica Meixner <jessica.meixner@noaa.gov>
Date: Wed Jun 12 11:03:13 2024 -0400
Update ufs-weather-model (#2663)
Updates ufs-weather-model, this updates RDHPCS to the newer spack-stack
allowing some temporary fixes to be reverted.
* removes upp submodule
* uses upp from the ufs-weather-model
* restores the build and link that were hacked during the Hera Rocky 8
transition to allow for UPP submodule
* Removes forecast directories in clean-up
Resolves #2617
Resolves #2437
---------
Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com>
commit 15eaf35fb13f361be400be38a5f7ca7b5461ab1d
Author: Eric Sinsky - NOAA <48259628+EricSinsky-NOAA@users.noreply.github.com>
Date: Wed Jun 12 01:15:37 2024 -0400
Add ability to process ocean/ice products specific to GEFS (#2561)
This PR begins to add the capability to produce GEFSv13 ocean and ice
products in the global-workflow according to stakeholder requirements.
The following features are added.
- An oceanice prod yaml file has been added to address the ocean and ice
products specific to GEFSv13.
- The rocoto dependencies and config.base for GEFS have also been
modified to allow for 24-hour averaged ocean and ice output.
- Various scripts have been modified to allow for ocean and ice output
frequencies of 24 hours.
- `FHOUT_OCNICE` has been split into two variables called `FHOUT_OCN`
and `FHOUT_ICE`. The same has been done for `FHOUT_OCNICE_GFS`.
Refs #1878
commit 6691e7489650e0b738c176fbd096109288dc09b6
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date: Tue Jun 11 21:15:07 2024 -0600
Update cleanup job to use COMIN/COMOUT (#2649)
NCO has requested that each COM variable specify whether it is an input
or an output. This completes that process for the global-workflow
clean-up task.
Refs #2451
---------
Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
commit 23a8d8835dd4c5d69ca20f5ff23705f30f17b4b0
Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
Date: Tue Jun 11 16:17:25 2024 -0400
Add overwrite to creat experiment in BASH CI (#2676)
This is a quick hotfix to the CI BASH driver script adding `--overwrite`
to create experiment script to avoid errors from restarting an
experiment.
commit e7909af8d9e1f34140388a3f8556d8e582c58fe5
Author: emilyhcliu <36091766+emilyhcliu@users.noreply.github.com>
Date: Mon Jun 10 15:11:27 2024 -0400
Add handling to select CRTM cloud optical table based on cloud scheme and update calcanal_gfs.py (#2645)
This PR proposes updates for the following two scripts:
1. In **scripts/exglobal_atmos_analysis.sh** --- Add handling to select
CRTM cloud optical table based on cloud microphysical scheme indicated
by `imp_physics'
The default scheme in the GFS forecast model is Thompson scheme
(imp_physics = 8).
2. In **/ush/calcanl_gfs.py** --- Increase the MPI number declared in
the script due to increased variables to interplate increments and
calculate analysis in the netcdf_io routines in GSI-utils.
Here is the related [PR #46 for
GSI-utils](https://github.com/NOAA-EMC/GSI-utils/pull/46).
---------
Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com>
Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
commit 9caa51de8fb7be07d2e61775da01937d576964f6
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date: Thu Jun 6 22:15:23 2024 -0600
Update RDHPCS Hera resource for `eupd` task (#2636)
As per @wx20jjung, the resource for the `eupd` task have been updated
for RDHPCS Hera to account for memory issues for C384 `gdaseupd` job
fails.
Resolves #2454
---------
Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
commit acf3aaa2b1d3e3024b0b5d2fe23eee8c317a980b
Author: DavidNew-NOAA <134300700+DavidNew-NOAA@users.noreply.github.com>
Date: Thu Jun 6 11:49:03 2024 -0400
Parameterize some things in config.atmanl and config.atmensanl (#2661)
This PR adds some parameters in config.atmanl and config.atmensanl that
can be altered with the defaults.yaml. The motivation is to make these
files match those in the GDASApp JJOB tests (example:
https://github.com/NOAA-EMC/GDASApp/blob/develop/test/atm/global-workflow/config.atmanl),
so we can just use the Global Workflow config.atmanl and
config.atmensanl in the tests rather than custom ones in GDASApp that
have to be separately updated every time the ones in the Global Workflow
are updated.
commit 54ea0b73a07921be5fbb07fe41e976888bd3e549
Author: Guillaume Vernieres <guillaume.vernieres@noaa.gov>
Date: Thu Jun 6 01:36:02 2024 -0400
Add links to the ocean insitu obs processing tools (#2644)
Add links to the marine bufr to ioda converters for the marine insitu
observations.
- fixes https://github.com/NOAA-EMC/GDASApp/issues/1106
- waiting for https://github.com/NOAA-EMC/GDASApp/pull/1135
commit 205d0c2b13e2d7755cec75bf8c978ab20d453862
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Wed Jun 5 17:31:30 2024 +0000
Update S4 point of contact in docs (#2660)
Update the point of contact for global workflow issues on S4.
commit aa23ccf1d0d229f9ff1398d84af1fa7ee5bed262
Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com>
Date: Wed Jun 5 12:50:14 2024 -0400
Enable wcoss2 ufsda build and module load (#2620)
This PR enables ufsda (`sorc/gdas.cd`) to be built and run on WCOSS2.
Resolves #2602
Resolves #2579
commit 67b833e0c7bc390865d453588b4609a1a7ede981
Author: Jessica Meixner <jessica.meixner@noaa.gov>
Date: Tue Jun 4 13:33:43 2024 -0400
Update ufs-weather-model (#2646)
Updates UFS model to the commit https://github.com/ufs-community/ufs-weather-model/commit/5bec704243286421fc613838fc67a2129e96acd6
This should resolve the issue and allow C768 runs on Hera and allow for CICE
to run on WCOSS2 (due to library updates to allow linking).
From what I can tell, all updates needed were done by
@HenryWinterbottom-NOAA which were updates for CICE
Fixes #2490
commit c44d0ac86cfdf78eb87492431bf6d825e8bae637
Author: GwenChen-NOAA <95313292+GwenChen-NOAA@users.noreply.github.com>
Date: Tue Jun 4 10:29:49 2024 -0400
Update wmo parm files to fix WMO header (#2652)
This PR updates wmo parm files to switch WMO header of precipitation
type products (CRAIN, CFRZR, CICEP, and CSNOW) from time averaged to
instantaneous.
Resolves #2566
commit 237d6dd213e8b1455d2f45dc5978fb2d3de93e60
Author: Cory Martin <cory.r.martin@noaa.gov>
Date: Tue Jun 4 13:55:33 2024 +0000
Add IAU to snow DA (and its test) (#2610)
This PR enables IAU for the snow DA which is necessary for GFSv17.
A snow analysis is created for the center of the window regardless, and
an additional at the beginning of the window is added if IAU is on. The
former is needed for UPP and the latter, to initialize the model.
The increment is valid throughout the window for 3DVar, so the same
increment is added to both forecasts.
Additionally, the input file that goes into global_cycle has been
updated to be the output of the JEDI snow analysis instead of the
forecast (@jiaruidong2017 I recall discussing this, can you confirm this
is right or am I mistaken)
This PR also makes the CI test for snow DA (and aerosol DA) include IAU
rather than without IAU,.
---------
Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com>
Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
commit c92bf415060750127c9c05a62a1d2851c489551a
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Sat Jun 1 05:11:07 2024 +0000
Archiving cleanup (#2621)
1) Adds a lot of comments to the jinja templates for archiving
2) Rearranges the gdas and enkf templates to a more logical order
3) Fixes a couple of bugs in the enkf archiving of increments and
analyses
4) Disables archiving for the half cycle
5) Removes the `FITSARC` key from `config.base` and `arcdir.yaml.j2`,
instead relying on `DO_FIT2OBS`
6) Updates wxflow to add the option to not allow undefined variables
when parsing jinja templates and invokes this feature when running
archives
Resolves #2612
commit 12aa1e9cd2d159e2b303d2b33d6c79c365688eec
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Fri May 31 04:57:08 2024 -0400
Switch to Rocky 9 built external packages on Hercules (#2608)
The workflow was updated to use modules built on Rocky 9, but the
external packages (like prepobs) were still pointing to the versions
built on CentOS (Orion). This transitions to packages built on Rocky 9.
Updating of the tracker package has been deferred until later. As such,
the tracker jobs have been disabled by returning immediately if they are
on Hercules. Since these jobs are small, resource-wise, it should not
meaningfully impact turnover time.
commit 4422550c01c9214a2b3b8890bdcc898123ee216a
Author: Guoqing Ge <guoqing.ge@noaa.gov>
Date: Thu May 30 08:05:23 2024 -0600
Add the capability to use slurm reservation nodes (#2627)
Add the capability to use slurm reservation nodes
Add "ACCOUNT_SERVICE" for jobs to run in PARTITION_SERVICE
Resolves #2626
commit a54153fd9d26126206bc07a1da4e80f50c0c5910
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Wed May 29 23:24:07 2024 -0400
Update forecast job to use COMIN/COMOUT (#2622)
NCO has requested that each COM variable specify whether it is an input
or an output. This completes that process for the forecast job.
Refs #2451
---------
Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
commit d69a8af95d492982b918670322ed5c41ab074335
Author: Jessica Meixner <jessica.meixner@noaa.gov>
Date: Wed May 29 21:29:03 2024 -0400
Update to add 1-deg global wave grid (#2619)
This PR adds options to use a global 1 deg grid, intended for testing
with the SFS application.
Requires new fix file changes NOAA-EMC/global-workflow#2618
commit 0b4670ecf83b99b72835c8380573b2bca7cf5324
Author: Jessica Meixner <jessica.meixner@noaa.gov>
Date: Wed May 29 17:17:21 2024 -0400
Add C384mx025_3DVarAOWCDA yamls (#2625)
Adds the C384mx025_3DVarAOWCDA yaml files for one experiment into a new GFSv17 folder.
commit 2e885d05c64b947f00a3cf055a1277fbfac195c9
Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
Date: Wed May 29 13:00:51 2024 -0400
Script to keep Jenkins Agent persistent from cron (#2634)
This "persistent" Java Agent launch script can be ran from a cron job:
- Uses Jenkins Remote API to check the status of the Node connection
using curl for a given machine.
- If it is not connected a new agent is launched for that node.
Resolves #2633
commit bb58e064d8e82ce51802bd6064cfa84cae2cc4d5
Author: GwenChen-NOAA <95313292+GwenChen-NOAA@users.noreply.github.com>
Date: Tue May 28 17:17:11 2024 -0400
Change GRIB2 parameter names and vertical levels for ocean/ice post (#2611)
Based on users' feedback, this PR do the following:
1. Change GRIB2 parameter names DLWRF -> NLWRF and DSWRF -> NSWRF
2. Change the vertical level of ocean 3D variables (WTMP, SALIN, UOGRD,
and VOGRD) from "%g m below water surface" to "%g m below sea level"
3. Round up depth numbers to integer (e.g. 4481.0625 -> 4481 m)
Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com>
commit e53c5e8e0abbc0edf95970a71df0e6e8a2be9f31
Author: DavidNew-NOAA <134300700+DavidNew-NOAA@users.noreply.github.com>
Date: Tue May 28 17:16:23 2024 -0400
Add atmensanlfv3inc job (#2592)
This PR creates the atmensanlfv3inc job, the ensemble version of
atmanlfv3inc, created in GW PR #2420. Its GDASApp companion PR is
#[1104](https://github.com/NOAA-EMC/GDASApp/pull/1104), and its JCB-GDAS
companion PR is #[3](https://github.com/NOAA-EMC/jcb-gdas/pull/3).
commit 50c2b8951b29a3c883a778becbf8582f9519eb48
Author: Anil Kumar <108816337+AnilKumar-NOAA@users.noreply.github.com>
Date: Tue May 28 13:23:53 2024 -0400
Global-workflow (AR) Generic updates for Gaea C5 (#2515)
- Port global-workflow’s build and run capability to Gaea-C5
- Building global-workflow on Gaea-C5
- Setting up experiments with global-workflow on Gaea-C5
---------
Co-authored-by: AnilKumar-NOAA <Anil.Kumar@gaea53.ncrc.gov>
Co-authored-by: DavidBurrows-NCO <82525974+DavidBurrows-NCO@users.noreply.github.com>
commit b6ca771a0c584cbfcbbf9be739765d5f3815df97
Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
Date: Fri May 24 10:52:45 2024 -0400
Update STMP and PTMP settings in host file for Orion and Hercules (#2614)
- Updating STMP and PTMP settings in host file for Orion and Hercules
because they are cross mounted.
- Also took the opportunity to finally update **SLURM_ACCOUNT** to
**HPC_ACCOUT** in CI over rides.
- Added a refactor of the `rocotostat.py` tool that is more pythonic and
as a execute retry feature because the `rocotostat` utility on Orion has
been failing sometimes.
commit 7d2c539f45194cd4e5b21bfd4b83a9480189cd0f
Author: Guillaume Vernieres <guillaume.vernieres@noaa.gov>
Date: Tue May 21 23:50:50 2024 -0400
Sea-ice analysis insertion (#2584)
Allows cycling and restarting CICE with the sea-ice analysis if the
marine DA is switched on.
Resolves #2568
Resolves NOAA-EMC/GDASApp#1103
commit 5369a1ff3a3969149fcf32810fad0e50216752b7
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Tue May 21 22:12:29 2024 +0000
Refactored archiving (#2491)
This provides a new pygfs task, archive.py, that provides all of the
tools necessary to archive data to the local (`ARCDIR`) and backup
(`ATARDIR`) archive directories. YAML-Jinja2 templates are provided to
define the file to be archived or tarred to replace the
`hpssarch_gen.sh`, `exglobal_earc`, and `exglobal_archive.sh` scripts
and make it easier to add new data and explicitly handle optional and
required files.
For `ATARDIR` archiving, a master jinja template is provided for each
`RUN` (i.e. master_gdas.yaml.j2, master_gfs.yaml.j2,
master_enkf.yaml.j2). The master_enkf.yaml.j2 template is used for both
`enkfgdas` and `enkfgfs` `RUN`s. These templates then include the
appropriate `RUN`-specific jinja templates (e.g. gdas.yaml.j2) based on
experiment, cycle, and coupled parameters. Each of these templates
corresponds to a single tarball to populate and are tabbed 4 spaces so
they are defined within the master `datasets` dictionary.
Future developers should not have to make modifications to archive.py
unless archiving is being enabled for a new `RUN` (e.g. `gefs`) and then
only a single `elif` needs to be added to the configure method to
specify the master `ATARDIR` template to archive (e.g.
`master_gefs.yaml.j2`). If a new component is coming online that needs
to be archived to `ATARDIR` (e.g. SNOW), then create a new template for
each `RUN` that it needs to be archived for (e.g. `gdassnow.yaml.j2`)
and reference the template in the appropriate master templates, e.g.
`master_gdas.yaml:`
```jinja
{% if DO_SNOW %}
{% include "gdassnow.yaml.j2" %}
{% endif %}
```
A few other issues were addressed along the way:
1. Aerosols have been reenabled. Aerosol forecasts should only be
performed during gdas cycles, but analyses can be performed for both gfs
and gdas cycles. This was accomplished by setting separate
`AERO_<job>_CDUMP` variables to parse on for both `ANL` and `FCST` jobs.
2. Fixed the name of the `cice6_rst_ok` variable in `forecast_det.sh`.
This prevented restarts from being used for cice-enable experiments.
This feature was not tested.
3. Create a temporary fix for the `wgrib` utility. For spack-stack
1.6.0, the `grib-util` module file does not declare `WGRIB`. An issue is
open (https://github.com/JCSDA/spack-stack/issues/1097) to fix this in
existing installations. Once complete, this temporary fix should be
removed.
4. The number of `earc` jobs has been reduced for lower resolution
experiments. Both C48 and C96 experiments will now only have two earc
jobs (one for the non-member files to archive and another for the member
files). C192 will have up to 3 earc jobs (one non-member, one for
members 1-40 and another for members 41-80, if needed).
Resolves #2345
Resolves #2318
---------
Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
commit 9aad86f27d37d19165b9a0b64cf70c7a4dd6362c
Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
Date: Fri May 17 12:57:59 2024 -0400
Add remove RUNDIRS step in CI before creating experements (#2607)
As had been done in Bash CI we need to remove the RUNDIR in Jenkins
before a creating an experiment in the event that case had beem
previously ran.
commit 09333c01dbafddb2d2fe7e181b479af3cc6d3621
Merge: f7e9f4489 bb930050b
Author: Janet Derrico <143837053+jderrico-noaa@users.noreply.github.com>
Date: Thu May 16 14:33:19 2024 -0600
Merge branch 'NOAA-EMC:develop' into develop
commit bb930050b3cd51d28ecba6b231c8675f6d11856c
Author: AndrewEichmann-NOAA <58948505+AndrewEichmann-NOAA@users.noreply.github.com>
Date: Thu May 16 12:28:30 2024 -0400
Adds jjob and other necessities for marine LETKF task (#2564)
Adds jjob, rocoto script, config file, and other necessities for new
marine LETKF task.
Partially addresses NOAA-EMC/GDASApp#1091
commit 2c50fbde4d6cc3e53c55dca56925353a02fd1730
Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
Date: Thu May 16 12:12:06 2024 -0400
Updating CI Machine configs with redundant PTMP (#2605)
Quick fix adding PTMP as STMP in Machine configs for CI for completeness
commit ef340ff33a6f89adf70838206ba3fd56a953fa7a
Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
Date: Thu May 16 11:37:30 2024 -0400
Fix race condition in CI between Orion and Hercules (#2604)
Hotfix to solve race conditions in the CI system due to cross-mounted
file systems between Orion and Hercules
commit e8b17e27f719df280170dc3f5bd9f19917cefaf2
Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
Date: Wed May 15 17:16:30 2024 -0400
Remove existing EXPDIRs and COMROTs when CI is re-run (#2601)
Quick hotfix for having default for re-runing jobs to start clean with
new EXPDIRs and COMROTs
commit b5d113efb1970ede5cd1d3d4dff8d96320519c41
Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
Date: Wed May 15 16:52:49 2024 -0400
Moving logic for skipping hosts in pr cases (#2573)
This PR removes the logic of skipping hosts for pr cases from
`create_experiment.py` and moves it to a test in the cron bash driver
using a `parse_yaml.py` python tool.
The Jenkins pipeline was not effected as it uses the
`get_host_case_list.py` utility to form the cases on a per host bases.
Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com>
commit 3cd0c68c0de9900bc7b73e1ed7621573dff5e916
Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com>
Date: Wed May 15 13:13:30 2024 -0400
Update gsi_utils.fd hash (#2598)
This PR updates the `gsi_utils.fd` hash to bring in updates which add
safeguards to
-
`src/EnKF/gfs/src/getsigensmeanp_smooth.fd/getsigensmeanp_smooth_ncep.f90`
- `src/EnKF/gfs/src/recentersigp.fd/recentersigp.f90`
The safeguards are described in GSI-utils PR
[#41](https://github.com/NOAA-EMC/GSI-utils/pull/41) and the associated
issue.
Resolves #2597
commit d5366c66bd67f89d118b18956fe230207cbf0aea
Author: Kate Friedman <kate.friedman@noaa.gov>
Date: Wed May 15 13:12:56 2024 -0400
Update CICE and MOM6 fix versions (#2600)
This PR updates the CICE (`cice_ver`) and MOM6 (`mom6_ver`) fix versions
to the newer `20240416` timestamps, which includes updates and fixes to
the `100` (1-deg) resolution files.
Resolves #2480
Resolves #2483
Resolves #2595
commit 6ca106e6c0466d7165fc37b147e0e2735a1d6a0b
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Mon May 13 22:57:38 2024 +0000
Limit gfswavepostpnt to 40 PEs/node (#2588)
This fixes the slow runtime of the gfswavepostpnt job on Hercules. The
job is very I/O intensive and does not scale well to large nodes, so
limit the number of jobs/node to 40.
Resolves #2587
commit 4fb7c12c325702a47f27c802a5067efd33d0327c
Author: Fanglin Yang <fanglin.yang@noaa.gov>
Date: Mon May 13 16:37:51 2024 -0400
Update damping and time-step (#2575)
Updates the model to use explicit Rayleigh damping for u/v and implicit
damping to w. This improves model stability and allows for longer
timesteps. Also unifies the GDAS and GFS to use the same damping.
Results from a test at the C1152 resolution (coupled model) can be found
at https://www.emc.ncep.noaa.gov/gmb/wx24fy/C1152/newdamp/
Resolves #2574
Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Co-authored-by: Lisa Bengtsson <lbengtss@Orion-login-1.HPC.MsState.Edu>
Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com>
commit 6a9c1372ecce9e50e4f6e10e56f6e504cde1afe6
Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
Date: Fri May 10 14:17:13 2024 -0400
Do not use BUILT_semphore to force rebuilds when re-run (#2593)
Remove the placement of the `BUILT_semaphore` file after the build in
the Jenkins Pipeline and force it to rebuild any changes after a PR is
re-ran.
commit 2346c6161f75ae02369cbf30f30c6150d3e12b66
Author: Innocent Souopgui <162634017+InnocentSouopgui-NOAA@users.noreply.github.com>
Date: Thu May 9 21:17:06 2024 -0500
Migration to Rocky8 spack-stack installations on Jet (#2458)
# Description
Migrates Global Workflow to Rocky8 spack-stack installations on Jet.
Jet has moved from CentOS7 to Rocky8.
Resolves #2377
Refs NOAA-EMC/UPP#919
Refs NOAA-EMC/gfs-utils#60
Refs NOAA-EMC/GSI#732
Refs NOAA-EMC/GSI-Monitor#130
Refs NOAA-EMC/GSI-utils#33
commit c7b3973014480a20dd8e24edaeb83a9e9e68159f
Author: Jessica Meixner <jessica.meixner@noaa.gov>
Date: Thu May 9 11:36:58 2024 -0400
Updates for cold start half cycle, then continuing with IAU for WCDA (#2560)
This PR allows us to run C384 S2S with IAU, but starting with the first
half-cycle as a cold-start. This will be necessary for cycled testing as
we build towards the full system for GFSv17. This updates the copying of
the restarts for RUN=gdas for both ocean and ice copying what the atm
model is doing. It also reduced the amount of restart files from 4 to 3.
Other updates:
* Add DOJEDI ocean triggers for archiving certain files update from:
@CatherineThomas-NOAA
* Adds COPY_FINAL_RESTARTS option to turn on/off copying the last
restart file to COM. Defaults to off...
* Defines model_start_date_current_cycle & model_start_date_next_cycle
to help with knowing which IC to grab.
Refs #2546
Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com>
commit b405b7d3d11d384ce9fe3b9cd2180f315f7b38f2
Author: Dan Holdaway <27729500+danholdaway@users.noreply.github.com>
Date: Wed May 8 20:52:48 2024 -0400
Use JCB for assembling JEDI YAML files for atmospheric GDAS (#2477)
Change the JEDI YAML assembly for the atmospheric GDAS to use the JEDI
Configuration Builder (JCB) tool so that YAMLs can be made more portable
and invoke the observation chronicle mechanism.
Resolves #2476
Co-authored-by: danholdaway <danholdaway@users.noreply.github.com>
Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
commit 0cf0349c1f88048806e68ab58e93a3261b7a0e95
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Wed May 8 02:04:16 2024 -0400
Add CI test for products (#2567)
Adds a new version of the atm3DVar test that runs the full forecast
length and produces most of the secondary products. For now, this test
will only run on WCOSS due to gempak failures on other machines as well
as computational needs. On other machines, the original version will run
(the original version will not run on WCOSS). AWIPS remains off for now
in this extended test due to a bug involving tocgrib2 and the convective
precip fields (see #2566).
The new test runs for 4½ cycles and the full 384-hr forecast length to
ensure all gempak scripts are exercised. Since the cycle throttle is 3
and the bulk of the time is in the free forecast, the cycles run mostly
concurrently so it doesn't extend the total test time too much beyond
that of a single 384-hr forecast.
Fixes a bug in NPOESS that was introduced when the post filenames were
reverted to the previous format for the GOES products until the final
filenames are determined (#2499).
Also removes the AWIPS g2 job from the rocoto mesh to complete the
retirement of grib1 products.
Resolves #2132
Resolves #2445
commit 9b6f8404ac4507d14adc404b77cfdf002b55e832
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Tue May 7 00:14:36 2024 -0400
Add task to prepare emissions for GEFS (#2562)
This PR:
- introduces a task to prepare emissions for a forecast into the GEFS
application.
- adds configuration, j-job, rocoto job, ex-script and the python class
for this job
- updates GEFS workflow to be able to generate the XML to call this job.
- updates the `fcst` and `efcs` job dependencies in the GEFS application
to depend on `prep_emissions` if aerosols are turned ON.
- provides a placeholder for @bbakernoaa to work on the details for
preparing emissions.
Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
commit 233c18815d2e8e6b344f161fd0c102a4fbdfb66d
Author: Dan Holdaway <27729500+danholdaway@users.noreply.github.com>
Date: Mon May 6 18:11:35 2024 -0400
Single Executable for main GDAS JEDI applications (#2565)
Changes that accompany GDAS PR (NOAA-EMC/GDASApp/pull/1075) that allows
building of a single gdas executable, which should be more compliant
with NCO requirements.
Addresses https://github.com/NOAA-EMC/GDASApp/issues/1085
commit a005244bbfb2f1c525bca60d966f8095aa1acb8e
Author: Guoqing Ge <guoqing.ge@noaa.gov>
Date: Thu May 2 20:32:53 2024 -0600
Add nest capability (#2545)
This PR adds the global nesting capability to the global workflow so
that one can run a regional domain nested in a global run.
Resolves #2544
Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com>
commit cb87daaced9fddd17f8370a1842d7e4ddab24e8f
Author: DavidBurrows-NCO <82525974+DavidBurrows-NCO@users.noreply.github.com>
Date: Thu May 2 15:30:53 2024 -0400
Update gfs_utils for Gaea (#2556)
What: add build capability to the gfs_utils submod within the global
workflow on Gaea
Refs #2535
Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com>
commit 707a1cc5124bcd8e006839a17f76ceb88f45f902
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date: Wed May 1 18:13:02 2024 -0600
Updated GEMPAK version and APRUN launcher. (#2555)
This PR addresses issue #2248 and #2513. The following is accomplished:
- Updates the parallel executable for GEMPAK applications;
- Updates the GEMPAK version for RDHPCS Hera.
Describe your changes. Focus on the *what* and *why*. The *how* will be
evident from the changes. In particular, be sure to note any interface
changes, such as command line syntax, that will need to be communicated
to users.
At the end of your description, please be sure to add the issue this PR
solves using the word "Resolves". If there are any issues that are
related but not yet resolved (including in other repos), you may use
"Refs".
Resolves #2248
Resolves #2513
Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Co-authored-by: henrywinterbottom-wxdev <henry.winterbottom.wxdev@gmail.com>
commit f151cbf394e998ca0fdae893ca174499468d0c85
Author: Travis Elless <113720457+TravisElless-NOAA@users.noreply.github.com>
Date: Wed May 1 11:01:18 2024 -0400
Utilize scale-dependent localization for atmospheric analysis (#2542)
The plan for GFSv17 is to use a scale-dependent localization for the
atmospheric analysis. This PR adds the necessary parameters to allow
this feature to be used by default.
commit 53b6764392cb4c0f3b4506ccd3f8cba5c5d2c56e
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Tue Apr 30 16:37:54 2024 -0400
Remove implicit symlink names (#2527)
Lustre has a defect under Rocky 9 that results in symlink sometimes
failing when the link name is not explicit. This updates all link
creation to use explicit names.
`config.base` is updated to turn off two monitor jobs on Hercules
because the executables are not yet built there. This, combined with the
previous change, should make workflow available for use on Hercules.
Also removes the redundant utility names for NCP, NLN, etc. in the gdas
scripts that are already defined in `config.base`.
Resolves #2131
Resolves #2522
commit f7e9f4489fc0b10830f621fdf149e8e3149d6a51
Merge: 67a4810c4 762f040a2
Author: Janet Derrico <143837053+jderrico-noaa@users.noreply.github.com>
Date: Tue Apr 30 12:24:48 2024 -0600
Merge branch 'NOAA-EMC:develop' into develop
commit 762f040a2045db17cdacd9026df9c4b8fd520156
Author: AndrewEichmann-NOAA <58948505+AndrewEichmann-NOAA@users.noreply.github.com>
Date: Mon Apr 29 22:26:28 2024 -0400
Fixes sea ice archiving (#2541)
Removes/changes sea ice output files that are failing to be added to
list for archiving, causing `gdasarch` to fail in WCDA cycling.
Resolves https://github.com/NOAA-EMC/GDASApp/issues/1044
commit 2ecf4f86e0cbe59407ba2c4e105ee7292f1eda01
Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com>
Date: Mon Apr 29 22:25:57 2024 -0400
Link ensemble analysis increment files to COMROOT for warm_start (#2553)
Scripting is added to `setup_expt.py` to link ensemble analysis
increment files to COMROOT for warm_start experiments.
Resolves #2552
commit 3a7abe1d63c573006e0e656237f1220002c3f579
Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
Date: Tue Apr 30 02:25:28 2024 +0000
Launch Multiple Platforms to Jenkins with polling (#2548)
When launching Jenkins CI Tests all requested RDHPCS machines can now be
selected via the Ready label at once.
This is all that is required sense polling also works now on the
controller end.
Killing the jobs still needs to be done directly on the Jenkins
Controller.
Do not try to update the CI process using Labels. It is for launching
only.
Jenkins will update the labels as the states change.
NOTE: When a case fails the label will be update to a **Fail** for that
system but will continue to report failures of subsequent cases until
otherwise stopped in the Jenkins Controller directly.
Do not update any labels to …
kayeekayee
added a commit
to kayeekayee/global-workflow
that referenced
this issue
Sep 18, 2024
- based on gsl_ufs_dev from KaYee's fork
global-workflow: 07Aug24,37c53ac [develop_07Aug2024_37c53ac]
UFS: 19Jul24, c127601
FV3: 19Jul24, 2527c11
UPP: 23Apr24, be0410e
CCPP-PHYSICS: 19Jul24, 46df080
UFS_UTILS: 26Jun24, 3ef2e6b
Squashed commit of the following:
commit 70b557836379bb7e545fcc6642e28d66cfc17735
Merge: 5edbd123e 37c53ac69
Author: Janet Derrico <143837053+jderrico-noaa@users.noreply.github.com>
Date: Wed Aug 7 11:02:24 2024 -0600
Merge branch 'NOAA-EMC:develop' into develop
commit 37c53ac692274eb5e9f9a3220033406e8c4b4a04
Author: Kate Friedman <kate.friedman@noaa.gov>
Date: Wed Aug 7 08:11:21 2024 -0400
Revert MSU FIX_DIRs back to glopara (#2811)
commit 876dfee26ad67e1f729bbf52b3167d48ea5a7517
Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
Date: Tue Aug 6 14:47:36 2024 -0400
Bugfix for updating label states in Jenkins (#2808)
Quick bug fix for updating state labels in CI during finalize.
(did not reference GitHub CLI executable correctly in the pipeline
script)
commit 8fee36f0307b0c08080e3a8fa8fa6703e7da5fce
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Tue Aug 6 11:02:45 2024 -0400
Clean-up temporary rundirs - take 2. (#2753)
This PR:
- is a follow-up to a previous PR that aggressively pruned run
directories.
- removes run directories for the current cycle in the clean-up if the
cycle is successful. If the cycle is not successful, cleanup is not
called and all run directories for the cycle are safe from being purged.
- also updates the PR template to list/query for any updates to
submodules.
---------
Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Co-authored-by: David Huber <david.huber@noaa.gov>
Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
commit d599fff4aedd41ae587dbe02226acb12ff48efc1
Author: HelinWei-NOAA <48133472+HelinWei-NOAA@users.noreply.github.com>
Date: Mon Aug 5 05:31:31 2024 -0400
Change land surface for HR4 (#2787)
Resets the default value of opt_diag to 2 corresponding to the land
surface upgrades in ufs-weather-model for HR4.
Resolves #2786
commit 6d7f7e860a0c7062f90bf09fdf9a5d19dc77cfdb
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Fri Aug 2 15:41:29 2024 -0400
Run METplus serially and correct the name of prod tasks (#2804)
Adds 2 hot fixes:
- METplus v9.1.3 has a bug in it that sometimes attempts to create
multiple copies of the same directory when running in parallel, causing
a Python error and downstream problems. This PR makes METplus run in
serial mode, preventing such issues.
- Corrects the name of the atmos_prod, ocean_prod, and ice_prod tasks in
workflow/rocoto/tasks.py (was accidentally changed to e.g. atmosprod)
commit 0706c59ac53cc3bbfbaa56cbd7fa75ab51117830
Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
Date: Fri Aug 2 15:03:45 2024 -0400
Update Java Agent launching script for Jenkins connections (#2762)
Made updates to the Jenkins Launching Script for robustness and less
ambiguous documentation:
- Clearer distinction between required user token for the remote api and
the systems token for launching
- Added pre-checks: `gh` is authenticating, named compliant token and
secret file exists
- More robust Jason based parser of the remote api response for checking
the state of the Node connection
- For `cron` use a 5 minute pause and recheck was added before
re-launching of the java agent
- Added concise header documentation of requirements and purpose
---------
Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
commit b73b1fd203496db97f8067652659573a632bcc67
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Fri Aug 2 07:59:06 2024 -0400
Fix erroneous cdump addition (#2803)
commit 49877046ac3306f6b78ca0ab5d5089ba1aa3e3e3
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Thu Aug 1 20:26:13 2024 -0400
Update ocean post-processing triggers (#2784)
This PR:
- replaces `check_netcdf.sh` checker for ocean post-processing with with
ocean output at the next forecast hour or finishing of the forecast job
for ocean prod
- removes no longer needed `ush/check_netcdf.sh`
commit aa2af1ca8d59424a60a1730722bf528775d9e606
Author: GeorgeGayno-NOAA <52789452+GeorgeGayno-NOAA@users.noreply.github.com>
Date: Thu Aug 1 16:46:10 2024 -0400
Update the gfs_utils repository hash (#2801)
# Description
Point to the latest hash of the gfs-utils repository, which contains the
bug fix to gaussian_sfcanl.
Resolves #2669.
Refs: https://github.com/NOAA-EMC/gfs-utils/pull/73
commit d3d85f0e0d573f16a71ca44778021dfc0ccf50c8
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Thu Aug 1 08:12:14 2024 -0400
Add fixes for metplus jobs when gfs_cyc=2 or 4 (#2791)
Changes how METplus jobs run so that they run on the last GFS cycle for
a given `PDY`.
This is a departure from operations where the METplus jobs run on the
00Z cycle for the previous 3 cycles and 00Z (i.e. `${PDYm1}06` through
`${PDY}00`). With this PR, for gfs_cyc=4, METplus jobs will run on
`${PDY}18` for cycles 00-18. See
https://github.com/NOAA-EMC/EMC_verif-global/pull/131 for more details.
commit 1cf8b448af562dbb7af198399c78c585977e81da
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Tue Jul 30 10:38:49 2024 -0400
Simplify resource-related variables, remove CDUMP where unneeded (#2727)
This overhauls resource-related variables to use a common set of
variables for each job. In the process, this also removed the use of
CDUMP in most cases.
Resolves #1299 #2693
commit 61875f25c9e971f82ae499b5b612d7f095deebd4
Author: Eric Sinsky - NOAA <48259628+EricSinsky-NOAA@users.noreply.github.com>
Date: Mon Jul 29 14:40:03 2024 -0400
Remove f000 from atmos rocoto tasks for replay cases (#2778)
The main purpose of this PR is to remove the f000 from
atmosphere-related rocoto tasks when `REPLAY_ICS` is set to `YES`. In
cases where `REPLAY_ICS` is `YES` and `OFFSET_START_HOUR `is greater
than `0`, it becomes necessary to have the first lead hour set to
`OFFSET_START_HOUR ` for the atmosphere-related rocoto tasks. For
example, when `OFFSET_START_HOUR ` is set to `3`, then the minimum lead
time for the atmos_prod and atmos_ensstat rocoto tasks needs to be 3 and
the minimum lead time for the ocean_prod rocoto task needs to be 6
(assuming `FHOUT_OCN` is 6). This PR makes this rocoto workflow set up
possible by removing 0 from fhrs for atmosphere-related tasks in
`gefs_tasks.py` when replaying.
This PR also moves where f000 is being removed for the ocean_prod and
ice_prod tasks. The if-block that performs this f000 removal has been
moved from `tasks.py` to `gefs_tasks.py` and `gfs_tasks.py`.
---------
Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com>
commit f156a7894d639f177e3e2588f98eec1f6f59aa68
Author: Jessica Meixner <jessica.meixner@noaa.gov>
Date: Fri Jul 26 14:18:32 2024 -0500
HR4 GWD update (#2732)
This update is a combination of the gravity wave drag (GWD) versions
from the NOAA/GSL and NOAA/PSL
commit a7f6b32ed63efa0de21bfb0ce63364a5b22b9891
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Thu Jul 25 14:26:52 2024 -0400
Temporarily disable METplus jobs (#2796)
commit 848659691fdbf47e7ccdbbb2ebf22a6e470633a2
Author: Guillaume Vernieres <guillaume.vernieres@noaa.gov>
Date: Wed Jul 24 15:00:35 2024 -0400
Refactoring of the marine B-matrix job (#2749)
Refactor the functionality of B-matrix generation from the GDASApp
Resolves #2743
commit 65a7ab75dc0e4baba06a02e11ed0455787056a68
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Tue Jul 23 08:35:48 2024 -0400
Replace Jinja namespaces with replace_tmpl filter and disable ACCOUNT_SERVICE option (#2775)
Removes the namespace-based construction of EnKF member COM directories
in the enkf archive template.
commit c45b9611f3e701b819bd33dc5af29033f060bb91
Author: Eric Sinsky - NOAA <48259628+EricSinsky-NOAA@users.noreply.github.com>
Date: Tue Jul 23 00:33:16 2024 -0400
Add task to process reforecast variables to save on WCOSS2 (#2680)
# Description
This PR adds an optional task to the global-workflow to process a subset
of ocean, ice, wave and atmosphere products to be saved on WCOSS2 for
the GEFSv13 reforecast. This task is designed to process GEFS variables
so that specific reforecast product requirements are met. A new variable
in `config.base` called `DO_EXTRACTVARS` enables this task, which is
currently called `extractvars`. `DO_EXTRACTVARS` is set to `NO` by
default and is specifically a task designed to be executed for the
GEFSv13 reforecast.
Refs #1878
# Type of change
- New feature (adds functionality)
# Change characteristics
- Is this a breaking change (a change in existing functionality)? NO
- Does this change require a documentation update? NO
# How has this been tested?
This has been cloned and tested on WCOSS2. This will need to be tested
on Hera and other platforms on which the reforecast may be running.
# Checklist
- [ ] Any dependent changes have been merged and published
- [x] My code follows the style guidelines of this project
- [x] I have performed a self-review of my own code
- [ ] I have commented my code, particularly in hard-to-understand areas
- [x] My changes generate no new warnings
- [x] New and existing tests pass with my changes
- [ ] I have made corresponding changes to the documentation if
necessary
---------
Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com>
commit 71dc33c6ca991c16ce743760d99feaaf60f2218a
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Mon Jul 22 14:51:53 2024 -0400
Set METplus process count in config.metp; add verif-global support for Rocky 9 (#2774)
Fix metp* resources and check that they completed properly; add support for Orion Rocky 9
commit 56df67a90fe090c425199f1285e5aac722c398b1
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Mon Jul 22 09:28:18 2024 -0400
Hotfix: Update jcb to avoid git-lfs files (#2782)
Removes git-lfs files from the `GDASApp` `jcb` submodule, allowing it to
be cloned on Hera.
This hotfix points to a non-authoritative branch of the GDASApp
(https://github.com/DavidHuber-NOAA/GDASApp/tree/hotfix/update_jcb) and
should be updated ASAP back to the authoritative repository.
commit fc668aa422ebbad76ceda1b3bbf8dc0ea432defd
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Tue Jul 16 09:44:00 2024 -0400
Address issues in creating XML for GFS forecast-only with app S2SWA (#2757)
This bugfix PR:
- fixes an issue where a user is unable to generate the XML for a GFS
forecast-only experiment with APP=S2SWA
Specifically, the changes are related to defining `aero_fcst_cdumps`.
Following `setup_expt.py`, the user will have to set
`AERO_FCST_CDUMPS="gdas|gfs|both" depending on their use case in
`config.base`.
commit e0878dba0e53706a7f53429b61aee2936e2c21bf
Author: Kate Friedman <kate.friedman@noaa.gov>
Date: Mon Jul 15 10:25:11 2024 -0400
Updated prepobs and fit2obs versions for Orion Rocky9 (#2758)
Update prepobs to v1.0.2 and fit2obs to v1.1.2
These versions now support Orion Rocky9. Updates are included
for new install locations on WCOSS2, Hera, Orion/Hercules, and Jet.
commit 4968f3a8de9a5f90651cacd74e38f97bc80b7bbb
Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
Date: Thu Jul 11 17:48:47 2024 +0000
CI maintenance updates and adding CI Unit Tests (#2740)
This PR has a few maintenance updates to the CI pipeline and adds a test
directory with Unit Tests
**Major Maintenance updates:**
- Added try blocks with appropriate messaging to GitHub PR of failure
for:
- - **scm** checkout
- - build fail (with error logs sent as gists)
- - create experiment fails with `stderr` sent to GitHub PR messaging
- Pre-stage FAILS from the above are now captured these fails allow
FINALIZE to update the label to FAIL (i.e. no more "hanging" CI state
labels in GitHub - see image below)
**Minor Maintenance updates:**
- Fix for STALLED cases reviled from PR 2700 (just needed a lambda
specifier)
- Fixed path to experiment directory in PR message (had dropped EXPDIR
in path)
- Needed `latin-1` decoder in reading log files for publishing
**Added python Unit Tests for CI functionality:**
- Installed **Rocoto** and **wxfow** in GitHub Runner for testing key CI
utility codes
- Cashed the install of Rocoto in the GitHub Runners to greatly reduce
stetup time for running the unit tests
- Unit Tests Python scripts added
- `test_rocostat.py`: rocoto_statcount() rocoto_summary()
rocoto_stalled()
- `test_setup.py`: setup_expt() test_setup_xml()
- `test_create_experment`: test_create_experiment()
- - Runs all PR cases that do not have ICs in the GItHub Runner
- Reporting mechanism in the Actions tab for Python Unit Testing results
- Test case data for STALLED and RUNNING stored on S3 and pulled using
wget during runtime of tests
commit 5ef4db74649b8be03402c17aa29c024e71699a7b
Author: AndrewEichmann-NOAA <58948505+AndrewEichmann-NOAA@users.noreply.github.com>
Date: Thu Jul 11 08:59:24 2024 -0400
Adds contents of constructor and initialize methods to marine LETKF class (#2635)
Adds contents of constructor and initialize methods to marine LETKF class
Partially addresses https://github.com/NOAA-EMC/GDASApp/issues/1091
---------
Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com>
Co-authored-by: Cory Martin <cory.r.martin@noaa.gov>
commit 8998ec7b74123e953b97a93fa14cc78d471a1aee
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Tue Jul 9 08:31:57 2024 -0400
Fix GDAS group B restart archiving (#2735)
Archives the GDAS restartb dataset at a 6-hour offset from restarta
This allows cycled experiments to restart from the archives.
The tabbing for the master archive templates was also added to
improve readability.
Resolves #2722
commit 3ca74771255727033b9dc043c652ac585178629c
Author: AndrewEichmann-NOAA <58948505+AndrewEichmann-NOAA@users.noreply.github.com>
Date: Tue Jul 9 08:28:54 2024 -0400
Add fcst dependency to ocnanalprep (#2728)
Add previous cycle's `fcst` as a dependency to `ocnanalprep`
This ensures that the availability of restart files to the latter. This addresses a
seldomly-encountered race condition where `ocnanalprep` fails due to the
lack of the files.
commit 58fca1668aecd6fb1afd12a441256ad35900e075
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Fri Jul 5 15:02:23 2024 -0400
Update (partially) global-workflow for orion+rocky9 (#2741)
This PR:
- updates a few submodules (GSI, GSI-utils, GSI-monitor, UFS_utils,
GFS-utils) to include recent update to their modulefiles for
Orion+Rocky9 upgrade
- updates the modulefiles in global-workflow to load modules from
Orion+Rocky9 paths
- updates modulefiles for `gwsetup` and `gwci` as well.
- removes NCL and GEMPAK from Orion. NCL is not used and GEMPAK is not
installed.
- adds `parm/config.gfs/config.resources.ORION` to address GSI
performance degradation after Rocky 9 upgrade.
This PR:
- does not update the build for UPP. Standalone UPP is not available via
ufs-weather-model as of #2729
- will need a follow-up update for `prepobs` and `fit2obs` updated
locations when they are installed in `glopara` space on Orion.
# Type of change
- Maintenance (code refactor, clean-up, new CI test, etc.)
# Change characteristics
- Is this a breaking change (a change in existing functionality)? NO
- Does this change require a documentation update? NO
# How has this been tested?
This PR is not sufficient for Orion.
This PR must be tested on other platforms (Hera, WCOSS2) as this PR
updates submodules.
# Checklist
- [ ] Any dependent changes have been merged and published
- [ ] My code follows the style guidelines of this project
- [ ] I have performed a self-review of my own code
- [ ] I have commented my code, particularly in hard-to-understand areas
- [ ] My changes generate no new warnings
- [ ] New and existing tests pass with my changes
- [ ] I have made corresponding changes to the documentation if
necessary
---------
Co-authored-by: Kate Friedman <kate.friedman@noaa.gov>
commit d65d3d257b38225fac74e86b770f43e1f8ae2d5a
Author: Jessica Meixner <jessica.meixner@noaa.gov>
Date: Wed Jul 3 21:07:49 2024 -0400
Update ufs model hash to 20240625 (#2729)
Updates UFS weather model hash to hash from 2024-06-24 which has orion
porting updates + a few namelist updates.
commit 2bd106a013805ba4e16dbdc456d6731f8f36ec85
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Wed Jul 3 11:32:40 2024 -0400
Hotfix for undefined CLUSTERS (#2748)
Defines `CLUSTERS` as an empty string for all hosts except Gaea and uses
the native `dict` `get` method to prevent grabbing an unset entry.
commit 7dc6651a3b92194d963675bdc0a9ec3c28499abf
Author: GwenChen-NOAA <95313292+GwenChen-NOAA@users.noreply.github.com>
Date: Wed Jul 3 09:56:08 2024 -0400
Update gempak job to run one fcst hour per task (#2671)
This PR updates gempak jobs (gfs, gdas, and goes) from processing all
forecast hours at once to one forecast hour at a time. This will reduce
the job runtime to less than 5 min, so restart capability is not needed.
Resolves #1250
Ref #2666 #2667
---------
Co-authored-by: Walter.Kolczynski <Walter.Kolczynski@noaa.gov>
commit 8215ae654202186a4f753c3abe937b7b9b91a9c7
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Tue Jul 2 16:22:11 2024 -0400
Hotfix for clusters from #2701 (#2747)
Fixes an issue created from #2701 that added `CLUSTERS` to the
`gaea.yaml`.
commit 11943e36ba12b3df49c51942da780698fab02d38
Author: DavidBurrows-NCO <82525974+DavidBurrows-NCO@users.noreply.github.com>
Date: Tue Jul 2 12:58:10 2024 -0400
Fix xml file setup and complete C48 ATM and S2SW runs for CI on Gaea (#2701)
This PR sets up the ability on Gaea for auto generation of a clean xml
file, i.e., an xml file that does not need any alterations before
running rocoto.
Refs #2572
Refs #2664
commit de8706702ead0630beb54d868f83aa2cb23f8f79
Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com>
Date: Mon Jul 1 09:29:14 2024 -0400
Update for JCB policies and stage DA job files with Jinja2-templates (#2700)
This PR updates the `gdas.cd` hash to bring in new JCB conventions.
Resolves #2699
From #2654
This PR will move much of the staging code that take place in the python
initialization subroutines of the variational and ensemble DA jobs into
Jinja2-templated YAML files to be passed into the wxflow file handler.
Much of the staging has already been done this way, but this PR simply
expands that strategy.
The old Python routines that were doing this staging are now removed.
This is part of a broader refactoring of the pygfs tasking.
wxflow PR [#30](https://github.com/NOAA-EMC/wxflow/pull/30) is a
companion to this PR.
Co-authored-by: danholdaway <danholdaway@users.noreply.github.com>
Co-authored-by: DavidNew-NOAA <david.new@noaa.gov>
Co-authored-by: DavidNew-NOAA <134300700+DavidNew-NOAA@users.noreply.github.com>
Co-authored-by: Dan Holdaway <27729500+danholdaway@users.noreply.github.com>
commit c49e4eee1a2ca818b3ecdcb9ea41c3f3e91d585b
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Fri Jun 28 14:56:19 2024 -0400
Revert PR 2681 (#2739)
This PR:
- reverts #2681 in part
- keeps some changes for `RUN`.
- is a hotfix
- should be merged ASAP after consensus w/ @guillaumevernieres
@CatherineThomas-NOAA @WalterKolczynski-NOAA
commit 9476c1237af4adbc95f90bd1bdd34b6b99f2f8a3
Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
Date: Wed Jun 26 15:46:08 2024 -0400
updated Finalize in Jenkinsfile and added try block around scm checkout (#2692)
We are updating the Jenkins Pipeline with a try block around checkout to
capture errors for the user.
Also cleaned up Finalize and added section to clean out workspace on
success.
commit 968568f682bac7564095440bdb7813abefd76821
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Wed Jun 26 13:27:19 2024 -0400
Activate snow DA test on WCOSS (#2720)
Activate the snow DA test on WCOSS.
commit 7706760bb8adbdf78cb640b02739023c886e7699
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Wed Jun 26 10:02:22 2024 -0400
Cleanup of stale RUNDIRS from an experiment (#2719)
This PR:
- removes stale temporary scratch run directories from `$DATAROOT/`
every 3 days.
- should help to scrub failed attempts.
- removes an unused variable `RUNDIR` defined in `config.base`
commit 8962991691b5f0857b813bddfd28aa1034d4bd2b
Author: Jessica Meixner <jessica.meixner@noaa.gov>
Date: Wed Jun 26 09:43:48 2024 -0400
Update logic for MOM6 number of layers/exception values (#2681)
Updates the logic to be by run instead of for DO_JEDIOCNVAR to determine
how many layers and sets the exception value for MOM6 to be 1e-34 for
all scenarios. Note, we will no longer have zeros in the ocean grib
output and the DA will also run without issues.
Fixes https://github.com/NOAA-EMC/global-workflow/issues/2615
commit 12431f76bdce807067929415007592cffc8a2457
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date: Wed Jun 26 07:42:35 2024 -0600
Update wave jobs to use COMIN/COMOUT (#2643)
NCO has requested that each COM variable specify whether it is an input
or an output.
This completes that process for the global-workflow wave
model and products tasks.
Refs #2451
commit b902c0bac126c323a07186ad8881384b032b6fda
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Tue Jun 25 07:48:46 2024 -0400
Assign machine- and RUN-specific resources (#2672)
Redefine resource variables based explicitly on RUN or CDUMP
Additionally, machine-specific resources are moved out of
config.resources and placed in respective config.resources.{machine}
files.
Resolves #177 #2672
commit 5edbd123e2878a07f5cce8e3c7ea6147f286633a
Merge: 09333c01d 4e1b937b6
Author: Janet Derrico <143837053+jderrico-noaa@users.noreply.github.com>
Date: Mon Jun 24 12:44:05 2024 -0600
Merge branch 'NOAA-EMC:develop' into develop
commit 4e1b937b67ed220120e81925c4507f03b9b8965f
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Mon Jun 24 10:50:52 2024 -0400
Add minimum software requirements (#2712)
Adds a table to HPC documentation stating the minimum support versions
commit f43a86276aaef91efa28faadc71a3cf50e749efe
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Fri Jun 21 13:44:29 2024 -0400
Fix and simplify online archiving and reenable METplus jobs (#2687)
This fixes the online archiving portion of the `*arch` and `*earc00`
jobs, a prerequisite for running METplus. This also reenables
METplus by default.
The approach previously taken created `FileHandler` dictionaries at
varying levels within the resulting yaml, which was not properly parsed
by `exglobal_archive.py`. This approach creates a single `FileHandler`
dictionary and is much less complicated overall.
Resolves #2673 #2647
commit 8993b42cb91144c0ab0501dc7841ea8d675c4701
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Wed Jun 19 21:51:22 2024 -0400
Eliminate post groups (#2667)
Eliminates the post groups used for upp and products jobs so that each
task only processes one forecast hour. This is more efficient and
greatly simplifies downstream dependencies that depend on a specific
forecast hour.
Resolves #2666
Refs #2642
commit 0b810c888239853fedd0e4584fe62536c6aaacdf
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date: Tue Jun 18 20:32:48 2024 -0600
Removes misleading "No such file or directory" syntax errors from output files (#2688)
This PR addresses issue #1252. The following is accomplished:
- Prior to removing files, the existence of a file is checked prior to
attempting to remove; this is performed as noted
[here](https://github.com/NOAA-EMC/global-workflow/issues/1252#issue-1538627369);
this PR only addresses the the `chgrp` issue.
Refs #1252
---------
Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
commit 3270ac3bf00c3ebc8166c70d84647ec44431fbae
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date: Tue Jun 18 12:17:59 2024 -0600
Hotfix for bug in template names. (#2697)
This PR is a hotfix for an incorrectly named (e.g., non-existent) `COM/`
template.
Resolves #2696
Refs #2451
commit 35d4d99eaac669721add9ddcc793153e5ab3b30a
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date: Tue Jun 18 08:06:53 2024 -0600
Update archive job to use COMIN/COMOUT (#2668)
NCO has requested that each COM variable specify whether it is an input
or an output. This completes that process for the global-workflow
archive task.
Refs #2451
---------
Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com>
Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
commit 47b3a581c8257fa24411fb400df8bb0e1e04972a
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Mon Jun 17 22:55:38 2024 -0400
Turn on high-frequency output in extended test (#2679)
Turns on high-frequency (hourly) output in the extended products test to
exercise that aspect of the code. This test only runs on WCOSS.
Also adds the hooks to optionally turn on the metplus jobs, but that is
deferred as they are not currently working correctly.
commit 38f2df9fb0c074b1f80d3c637080be79be693161
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Mon Jun 17 17:12:55 2024 +0000
Optimize wavepostpnt (#2657)
Optimize the gfswavepostpnt, gfswavepostbndpntbll, and gfswavepostbndpnt jobs
This is done by
1) reducing the number of calls to `sed`, `awk`, `grep`, and `cat` by
- performing operations on all files at once instead of looping over
each file
- removing piped `cat` calls (e.g. `cat <file> | sed 'something'`)
- combining `sed` and `grep` calls when possible
- adding logic to `awk` calls instead of handling that logic in bash
2) minimizing as much as possible the amount of data on disk that has to
be read in (e.g. limiting sed to read only the line numbers it needs)
---------
Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
commit 5af325a6a4e0a14d180514a418603ca79fada487
Author: Dan Holdaway <27729500+danholdaway@users.noreply.github.com>
Date: Fri Jun 14 18:05:23 2024 -0400
Update GDASapp hash to move JCB into GDASapp (#2665)
This PR moves JCB into GDASapp. The PR
also bumps up the hash of GDASapp to what is in `feature/move_jcb`,
which at time of writing is develop plus the absorption of JCB into
GDASapp.
Note that I also took the changes from
https://github.com/NOAA-EMC/global-workflow/pull/2641 to follow the
testing @RussTreadon-NOAA has done.
commit 6c93b4554e235fcb4d0004e99a4c4498d55d461b
Author: Yaping Wang <49168260+ypwang19@users.noreply.github.com>
Date: Fri Jun 14 10:18:17 2024 -0500
Add observation preparation job for aerosols DA to workflow (#2624)
Add a prepaeroobs job to prepare aerosol obs files for DA.
This job does quality control of the VIIRS aerosol raw observations and
convert them to ioda format.
Resolves #2623
---------
Co-authored-by: ypwang19 <yaping.wang@users.noreply.github.com>
Co-authored-by: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
Co-authored-by: Cory Martin <cory.r.martin@noaa.gov>
Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
commit 5a5fc2be7555f094a0f90fd3a3df22d071ccdfd4
Author: Jessica Meixner <jessica.meixner@noaa.gov>
Date: Fri Jun 14 11:04:41 2024 -0400
Remove ocean daily files (#2689)
This PR removes the ocn_daily files that are produced by the ocean
component. These files can be recreated by averaging data that exists in
the 6 hour aveaged files if needed.
Fixes https://github.com/NOAA-EMC/global-workflow/issues/2675
Fixes https://github.com/NOAA-EMC/global-workflow/issues/2659 (by
removing them and making this obsolete)
commit 603a4a8052a5c43ce5986f028c3fcfd5fd248ad4
Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
Date: Thu Jun 13 12:22:03 2024 -0400
Update Jenkinsfile
needed a comma
commit dc21eac6c3941d7f30803891d91d82f4cc1f8183
Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
Date: Thu Jun 13 11:41:14 2024 -0400
Add Hercules-EMC to the Jenkins configurable parameter list (#2685)
This quick-fix PR is to update the Jenkins Pipeline's configurable
parameter list to include the **Hercules-EMC** node.
This allows Jenkins users to restart Jobs in the controller when no
updates have been made.
commit ebacebfbe458634b8c80af6a735d6b6d01e4e406
Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com>
Date: Thu Jun 13 11:20:24 2024 -0400
Update gdas.cd and gsi_utils hashes (#2641)
This PR updates the `sorc/gdas.cd` and `sorc/gsi_utils` hashes. The
updated hashes bring in bug fixes, new UFS DA functionality, and a Gaea
build for gsi_utils.
Resolves #2640
commit 34155fb4767769600a1ff95f0a65e37081addc2a
Author: Neil Barton <103681022+NeilBarton-NOAA@users.noreply.github.com>
Date: Thu Jun 13 11:18:22 2024 -0400
Add ability to use GEFS replay ICs (#2559)
The PR allows the use of ICs from PSL's replay analysis. These replay
ICs will be used for GEFS reforecasting and SFS. Two main changes are
associated with these updates: (1) replay ICs being valid at 3Z, and (2)
the use of warm starts.
Resolves #1838
---------
Co-authored-by: Jessica Meixner <Jessica.Meixner@noaa.gov>
Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com>
commit 6c19a0e3fc4400e1d39288be4ee4fc244b74f699
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date: Wed Jun 12 19:25:42 2024 -0600
Replace `sleep` with `wait_for_file` (#2586)
This PR addresses issue #2444. The following is accomplished:
- All `sleep` statements are replaced with `wait_for_file` for the
relevant scripts beneath `scripts` and `ush`;
- Indentation and shell-norms are updated where applicable.
Note: The WAFS scripts are not updated as per @aerorahul direction.
Resolves #2444
---------
Co-authored-by: henrywinterbottom-wxdev <henry.winterbottom.wxdev@gmail.com>
Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
commit 5b2a3d449a0835cec2663aabb06f1c47a3faf84e
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Wed Jun 12 13:31:55 2024 -0400
Add COM template for JEDI obs (#2678)
Adds a COM template to define a path to store obs processed for JEDI.
This will allow UFSDA to stop writing to COM_OBS, which should be
read-only as it belongs to obsproc in operations.
No functional change yet.
commit 2e6f1fcde9935619352b1b26cba42ec0f4d845ed
Author: Guoqing Ge <guoqing.ge@noaa.gov>
Date: Wed Jun 12 09:06:23 2024 -0600
Link both global-nest fix files and non-nest ones at the same time (#2632)
This PR enables linking both global-nest fix files and non-nest ones at
the same time and users can run both nesting and non-nesting experiments
at the same time without worries about what fix files to be linked.
Resolves #2631
commit 61de004d4f9e9edf8a31bb173f2719b46451a36a
Author: Jessica Meixner <jessica.meixner@noaa.gov>
Date: Wed Jun 12 11:03:13 2024 -0400
Update ufs-weather-model (#2663)
Updates ufs-weather-model, this updates RDHPCS to the newer spack-stack
allowing some temporary fixes to be reverted.
* removes upp submodule
* uses upp from the ufs-weather-model
* restores the build and link that were hacked during the Hera Rocky 8
transition to allow for UPP submodule
* Removes forecast directories in clean-up
Resolves #2617
Resolves #2437
---------
Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com>
commit 15eaf35fb13f361be400be38a5f7ca7b5461ab1d
Author: Eric Sinsky - NOAA <48259628+EricSinsky-NOAA@users.noreply.github.com>
Date: Wed Jun 12 01:15:37 2024 -0400
Add ability to process ocean/ice products specific to GEFS (#2561)
This PR begins to add the capability to produce GEFSv13 ocean and ice
products in the global-workflow according to stakeholder requirements.
The following features are added.
- An oceanice prod yaml file has been added to address the ocean and ice
products specific to GEFSv13.
- The rocoto dependencies and config.base for GEFS have also been
modified to allow for 24-hour averaged ocean and ice output.
- Various scripts have been modified to allow for ocean and ice output
frequencies of 24 hours.
- `FHOUT_OCNICE` has been split into two variables called `FHOUT_OCN`
and `FHOUT_ICE`. The same has been done for `FHOUT_OCNICE_GFS`.
Refs #1878
commit 6691e7489650e0b738c176fbd096109288dc09b6
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date: Tue Jun 11 21:15:07 2024 -0600
Update cleanup job to use COMIN/COMOUT (#2649)
NCO has requested that each COM variable specify whether it is an input
or an output. This completes that process for the global-workflow
clean-up task.
Refs #2451
---------
Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
commit 23a8d8835dd4c5d69ca20f5ff23705f30f17b4b0
Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
Date: Tue Jun 11 16:17:25 2024 -0400
Add overwrite to creat experiment in BASH CI (#2676)
This is a quick hotfix to the CI BASH driver script adding `--overwrite`
to create experiment script to avoid errors from restarting an
experiment.
commit e7909af8d9e1f34140388a3f8556d8e582c58fe5
Author: emilyhcliu <36091766+emilyhcliu@users.noreply.github.com>
Date: Mon Jun 10 15:11:27 2024 -0400
Add handling to select CRTM cloud optical table based on cloud scheme and update calcanal_gfs.py (#2645)
This PR proposes updates for the following two scripts:
1. In **scripts/exglobal_atmos_analysis.sh** --- Add handling to select
CRTM cloud optical table based on cloud microphysical scheme indicated
by `imp_physics'
The default scheme in the GFS forecast model is Thompson scheme
(imp_physics = 8).
2. In **/ush/calcanl_gfs.py** --- Increase the MPI number declared in
the script due to increased variables to interplate increments and
calculate analysis in the netcdf_io routines in GSI-utils.
Here is the related [PR #46 for
GSI-utils](https://github.com/NOAA-EMC/GSI-utils/pull/46).
---------
Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com>
Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
commit 9caa51de8fb7be07d2e61775da01937d576964f6
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date: Thu Jun 6 22:15:23 2024 -0600
Update RDHPCS Hera resource for `eupd` task (#2636)
As per @wx20jjung, the resource for the `eupd` task have been updated
for RDHPCS Hera to account for memory issues for C384 `gdaseupd` job
fails.
Resolves #2454
---------
Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
commit acf3aaa2b1d3e3024b0b5d2fe23eee8c317a980b
Author: DavidNew-NOAA <134300700+DavidNew-NOAA@users.noreply.github.com>
Date: Thu Jun 6 11:49:03 2024 -0400
Parameterize some things in config.atmanl and config.atmensanl (#2661)
This PR adds some parameters in config.atmanl and config.atmensanl that
can be altered with the defaults.yaml. The motivation is to make these
files match those in the GDASApp JJOB tests (example:
https://github.com/NOAA-EMC/GDASApp/blob/develop/test/atm/global-workflow/config.atmanl),
so we can just use the Global Workflow config.atmanl and
config.atmensanl in the tests rather than custom ones in GDASApp that
have to be separately updated every time the ones in the Global Workflow
are updated.
commit 54ea0b73a07921be5fbb07fe41e976888bd3e549
Author: Guillaume Vernieres <guillaume.vernieres@noaa.gov>
Date: Thu Jun 6 01:36:02 2024 -0400
Add links to the ocean insitu obs processing tools (#2644)
Add links to the marine bufr to ioda converters for the marine insitu
observations.
- fixes https://github.com/NOAA-EMC/GDASApp/issues/1106
- waiting for https://github.com/NOAA-EMC/GDASApp/pull/1135
commit 205d0c2b13e2d7755cec75bf8c978ab20d453862
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Wed Jun 5 17:31:30 2024 +0000
Update S4 point of contact in docs (#2660)
Update the point of contact for global workflow issues on S4.
commit aa23ccf1d0d229f9ff1398d84af1fa7ee5bed262
Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com>
Date: Wed Jun 5 12:50:14 2024 -0400
Enable wcoss2 ufsda build and module load (#2620)
This PR enables ufsda (`sorc/gdas.cd`) to be built and run on WCOSS2.
Resolves #2602
Resolves #2579
commit 67b833e0c7bc390865d453588b4609a1a7ede981
Author: Jessica Meixner <jessica.meixner@noaa.gov>
Date: Tue Jun 4 13:33:43 2024 -0400
Update ufs-weather-model (#2646)
Updates UFS model to the commit https://github.com/ufs-community/ufs-weather-model/commit/5bec704243286421fc613838fc67a2129e96acd6
This should resolve the issue and allow C768 runs on Hera and allow for CICE
to run on WCOSS2 (due to library updates to allow linking).
From what I can tell, all updates needed were done by
@HenryWinterbottom-NOAA which were updates for CICE
Fixes #2490
commit c44d0ac86cfdf78eb87492431bf6d825e8bae637
Author: GwenChen-NOAA <95313292+GwenChen-NOAA@users.noreply.github.com>
Date: Tue Jun 4 10:29:49 2024 -0400
Update wmo parm files to fix WMO header (#2652)
This PR updates wmo parm files to switch WMO header of precipitation
type products (CRAIN, CFRZR, CICEP, and CSNOW) from time averaged to
instantaneous.
Resolves #2566
commit 237d6dd213e8b1455d2f45dc5978fb2d3de93e60
Author: Cory Martin <cory.r.martin@noaa.gov>
Date: Tue Jun 4 13:55:33 2024 +0000
Add IAU to snow DA (and its test) (#2610)
This PR enables IAU for the snow DA which is necessary for GFSv17.
A snow analysis is created for the center of the window regardless, and
an additional at the beginning of the window is added if IAU is on. The
former is needed for UPP and the latter, to initialize the model.
The increment is valid throughout the window for 3DVar, so the same
increment is added to both forecasts.
Additionally, the input file that goes into global_cycle has been
updated to be the output of the JEDI snow analysis instead of the
forecast (@jiaruidong2017 I recall discussing this, can you confirm this
is right or am I mistaken)
This PR also makes the CI test for snow DA (and aerosol DA) include IAU
rather than without IAU,.
---------
Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com>
Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
commit c92bf415060750127c9c05a62a1d2851c489551a
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Sat Jun 1 05:11:07 2024 +0000
Archiving cleanup (#2621)
1) Adds a lot of comments to the jinja templates for archiving
2) Rearranges the gdas and enkf templates to a more logical order
3) Fixes a couple of bugs in the enkf archiving of increments and
analyses
4) Disables archiving for the half cycle
5) Removes the `FITSARC` key from `config.base` and `arcdir.yaml.j2`,
instead relying on `DO_FIT2OBS`
6) Updates wxflow to add the option to not allow undefined variables
when parsing jinja templates and invokes this feature when running
archives
Resolves #2612
commit 12aa1e9cd2d159e2b303d2b33d6c79c365688eec
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Fri May 31 04:57:08 2024 -0400
Switch to Rocky 9 built external packages on Hercules (#2608)
The workflow was updated to use modules built on Rocky 9, but the
external packages (like prepobs) were still pointing to the versions
built on CentOS (Orion). This transitions to packages built on Rocky 9.
Updating of the tracker package has been deferred until later. As such,
the tracker jobs have been disabled by returning immediately if they are
on Hercules. Since these jobs are small, resource-wise, it should not
meaningfully impact turnover time.
commit 4422550c01c9214a2b3b8890bdcc898123ee216a
Author: Guoqing Ge <guoqing.ge@noaa.gov>
Date: Thu May 30 08:05:23 2024 -0600
Add the capability to use slurm reservation nodes (#2627)
Add the capability to use slurm reservation nodes
Add "ACCOUNT_SERVICE" for jobs to run in PARTITION_SERVICE
Resolves #2626
commit a54153fd9d26126206bc07a1da4e80f50c0c5910
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Wed May 29 23:24:07 2024 -0400
Update forecast job to use COMIN/COMOUT (#2622)
NCO has requested that each COM variable specify whether it is an input
or an output. This completes that process for the forecast job.
Refs #2451
---------
Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
commit d69a8af95d492982b918670322ed5c41ab074335
Author: Jessica Meixner <jessica.meixner@noaa.gov>
Date: Wed May 29 21:29:03 2024 -0400
Update to add 1-deg global wave grid (#2619)
This PR adds options to use a global 1 deg grid, intended for testing
with the SFS application.
Requires new fix file changes NOAA-EMC/global-workflow#2618
commit 0b4670ecf83b99b72835c8380573b2bca7cf5324
Author: Jessica Meixner <jessica.meixner@noaa.gov>
Date: Wed May 29 17:17:21 2024 -0400
Add C384mx025_3DVarAOWCDA yamls (#2625)
Adds the C384mx025_3DVarAOWCDA yaml files for one experiment into a new GFSv17 folder.
commit 2e885d05c64b947f00a3cf055a1277fbfac195c9
Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
Date: Wed May 29 13:00:51 2024 -0400
Script to keep Jenkins Agent persistent from cron (#2634)
This "persistent" Java Agent launch script can be ran from a cron job:
- Uses Jenkins Remote API to check the status of the Node connection
using curl for a given machine.
- If it is not connected a new agent is launched for that node.
Resolves #2633
commit bb58e064d8e82ce51802bd6064cfa84cae2cc4d5
Author: GwenChen-NOAA <95313292+GwenChen-NOAA@users.noreply.github.com>
Date: Tue May 28 17:17:11 2024 -0400
Change GRIB2 parameter names and vertical levels for ocean/ice post (#2611)
Based on users' feedback, this PR do the following:
1. Change GRIB2 parameter names DLWRF -> NLWRF and DSWRF -> NSWRF
2. Change the vertical level of ocean 3D variables (WTMP, SALIN, UOGRD,
and VOGRD) from "%g m below water surface" to "%g m below sea level"
3. Round up depth numbers to integer (e.g. 4481.0625 -> 4481 m)
Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com>
commit e53c5e8e0abbc0edf95970a71df0e6e8a2be9f31
Author: DavidNew-NOAA <134300700+DavidNew-NOAA@users.noreply.github.com>
Date: Tue May 28 17:16:23 2024 -0400
Add atmensanlfv3inc job (#2592)
This PR creates the atmensanlfv3inc job, the ensemble version of
atmanlfv3inc, created in GW PR #2420. Its GDASApp companion PR is
#[1104](https://github.com/NOAA-EMC/GDASApp/pull/1104), and its JCB-GDAS
companion PR is #[3](https://github.com/NOAA-EMC/jcb-gdas/pull/3).
commit 50c2b8951b29a3c883a778becbf8582f9519eb48
Author: Anil Kumar <108816337+AnilKumar-NOAA@users.noreply.github.com>
Date: Tue May 28 13:23:53 2024 -0400
Global-workflow (AR) Generic updates for Gaea C5 (#2515)
- Port global-workflow’s build and run capability to Gaea-C5
- Building global-workflow on Gaea-C5
- Setting up experiments with global-workflow on Gaea-C5
---------
Co-authored-by: AnilKumar-NOAA <Anil.Kumar@gaea53.ncrc.gov>
Co-authored-by: DavidBurrows-NCO <82525974+DavidBurrows-NCO@users.noreply.github.com>
commit b6ca771a0c584cbfcbbf9be739765d5f3815df97
Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
Date: Fri May 24 10:52:45 2024 -0400
Update STMP and PTMP settings in host file for Orion and Hercules (#2614)
- Updating STMP and PTMP settings in host file for Orion and Hercules
because they are cross mounted.
- Also took the opportunity to finally update **SLURM_ACCOUNT** to
**HPC_ACCOUT** in CI over rides.
- Added a refactor of the `rocotostat.py` tool that is more pythonic and
as a execute retry feature because the `rocotostat` utility on Orion has
been failing sometimes.
commit 7d2c539f45194cd4e5b21bfd4b83a9480189cd0f
Author: Guillaume Vernieres <guillaume.vernieres@noaa.gov>
Date: Tue May 21 23:50:50 2024 -0400
Sea-ice analysis insertion (#2584)
Allows cycling and restarting CICE with the sea-ice analysis if the
marine DA is switched on.
Resolves #2568
Resolves NOAA-EMC/GDASApp#1103
commit 5369a1ff3a3969149fcf32810fad0e50216752b7
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Tue May 21 22:12:29 2024 +0000
Refactored archiving (#2491)
This provides a new pygfs task, archive.py, that provides all of the
tools necessary to archive data to the local (`ARCDIR`) and backup
(`ATARDIR`) archive directories. YAML-Jinja2 templates are provided to
define the file to be archived or tarred to replace the
`hpssarch_gen.sh`, `exglobal_earc`, and `exglobal_archive.sh` scripts
and make it easier to add new data and explicitly handle optional and
required files.
For `ATARDIR` archiving, a master jinja template is provided for each
`RUN` (i.e. master_gdas.yaml.j2, master_gfs.yaml.j2,
master_enkf.yaml.j2). The master_enkf.yaml.j2 template is used for both
`enkfgdas` and `enkfgfs` `RUN`s. These templates then include the
appropriate `RUN`-specific jinja templates (e.g. gdas.yaml.j2) based on
experiment, cycle, and coupled parameters. Each of these templates
corresponds to a single tarball to populate and are tabbed 4 spaces so
they are defined within the master `datasets` dictionary.
Future developers should not have to make modifications to archive.py
unless archiving is being enabled for a new `RUN` (e.g. `gefs`) and then
only a single `elif` needs to be added to the configure method to
specify the master `ATARDIR` template to archive (e.g.
`master_gefs.yaml.j2`). If a new component is coming online that needs
to be archived to `ATARDIR` (e.g. SNOW), then create a new template for
each `RUN` that it needs to be archived for (e.g. `gdassnow.yaml.j2`)
and reference the template in the appropriate master templates, e.g.
`master_gdas.yaml:`
```jinja
{% if DO_SNOW %}
{% include "gdassnow.yaml.j2" %}
{% endif %}
```
A few other issues were addressed along the way:
1. Aerosols have been reenabled. Aerosol forecasts should only be
performed during gdas cycles, but analyses can be performed for both gfs
and gdas cycles. This was accomplished by setting separate
`AERO_<job>_CDUMP` variables to parse on for both `ANL` and `FCST` jobs.
2. Fixed the name of the `cice6_rst_ok` variable in `forecast_det.sh`.
This prevented restarts from being used for cice-enable experiments.
This feature was not tested.
3. Create a temporary fix for the `wgrib` utility. For spack-stack
1.6.0, the `grib-util` module file does not declare `WGRIB`. An issue is
open (https://github.com/JCSDA/spack-stack/issues/1097) to fix this in
existing installations. Once complete, this temporary fix should be
removed.
4. The number of `earc` jobs has been reduced for lower resolution
experiments. Both C48 and C96 experiments will now only have two earc
jobs (one for the non-member files to archive and another for the member
files). C192 will have up to 3 earc jobs (one non-member, one for
members 1-40 and another for members 41-80, if needed).
Resolves #2345
Resolves #2318
---------
Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
commit 9aad86f27d37d19165b9a0b64cf70c7a4dd6362c
Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
Date: Fri May 17 12:57:59 2024 -0400
Add remove RUNDIRS step in CI before creating experements (#2607)
As had been done in Bash CI we need to remove the RUNDIR in Jenkins
before a creating an experiment in the event that case had beem
previously ran.
commit 09333c01dbafddb2d2fe7e181b479af3cc6d3621
Merge: f7e9f4489 bb930050b
Author: Janet Derrico <143837053+jderrico-noaa@users.noreply.github.com>
Date: Thu May 16 14:33:19 2024 -0600
Merge branch 'NOAA-EMC:develop' into develop
commit bb930050b3cd51d28ecba6b231c8675f6d11856c
Author: AndrewEichmann-NOAA <58948505+AndrewEichmann-NOAA@users.noreply.github.com>
Date: Thu May 16 12:28:30 2024 -0400
Adds jjob and other necessities for marine LETKF task (#2564)
Adds jjob, rocoto script, config file, and other necessities for new
marine LETKF task.
Partially addresses NOAA-EMC/GDASApp#1091
commit 2c50fbde4d6cc3e53c55dca56925353a02fd1730
Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
Date: Thu May 16 12:12:06 2024 -0400
Updating CI Machine configs with redundant PTMP (#2605)
Quick fix adding PTMP as STMP in Machine configs for CI for completeness
commit ef340ff33a6f89adf70838206ba3fd56a953fa7a
Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
Date: Thu May 16 11:37:30 2024 -0400
Fix race condition in CI between Orion and Hercules (#2604)
Hotfix to solve race conditions in the CI system due to cross-mounted
file systems between Orion and Hercules
commit e8b17e27f719df280170dc3f5bd9f19917cefaf2
Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
Date: Wed May 15 17:16:30 2024 -0400
Remove existing EXPDIRs and COMROTs when CI is re-run (#2601)
Quick hotfix for having default for re-runing jobs to start clean with
new EXPDIRs and COMROTs
commit b5d113efb1970ede5cd1d3d4dff8d96320519c41
Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
Date: Wed May 15 16:52:49 2024 -0400
Moving logic for skipping hosts in pr cases (#2573)
This PR removes the logic of skipping hosts for pr cases from
`create_experiment.py` and moves it to a test in the cron bash driver
using a `parse_yaml.py` python tool.
The Jenkins pipeline was not effected as it uses the
`get_host_case_list.py` utility to form the cases on a per host bases.
Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com>
commit 3cd0c68c0de9900bc7b73e1ed7621573dff5e916
Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com>
Date: Wed May 15 13:13:30 2024 -0400
Update gsi_utils.fd hash (#2598)
This PR updates the `gsi_utils.fd` hash to bring in updates which add
safeguards to
-
`src/EnKF/gfs/src/getsigensmeanp_smooth.fd/getsigensmeanp_smooth_ncep.f90`
- `src/EnKF/gfs/src/recentersigp.fd/recentersigp.f90`
The safeguards are described in GSI-utils PR
[#41](https://github.com/NOAA-EMC/GSI-utils/pull/41) and the associated
issue.
Resolves #2597
commit d5366c66bd67f89d118b18956fe230207cbf0aea
Author: Kate Friedman <kate.friedman@noaa.gov>
Date: Wed May 15 13:12:56 2024 -0400
Update CICE and MOM6 fix versions (#2600)
This PR updates the CICE (`cice_ver`) and MOM6 (`mom6_ver`) fix versions
to the newer `20240416` timestamps, which includes updates and fixes to
the `100` (1-deg) resolution files.
Resolves #2480
Resolves #2483
Resolves #2595
commit 6ca106e6c0466d7165fc37b147e0e2735a1d6a0b
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Mon May 13 22:57:38 2024 +0000
Limit gfswavepostpnt to 40 PEs/node (#2588)
This fixes the slow runtime of the gfswavepostpnt job on Hercules. The
job is very I/O intensive and does not scale well to large nodes, so
limit the number of jobs/node to 40.
Resolves #2587
commit 4fb7c12c325702a47f27c802a5067efd33d0327c
Author: Fanglin Yang <fanglin.yang@noaa.gov>
Date: Mon May 13 16:37:51 2024 -0400
Update damping and time-step (#2575)
Updates the model to use explicit Rayleigh damping for u/v and implicit
damping to w. This improves model stability and allows for longer
timesteps. Also unifies the GDAS and GFS to use the same damping.
Results from a test at the C1152 resolution (coupled model) can be found
at https://www.emc.ncep.noaa.gov/gmb/wx24fy/C1152/newdamp/
Resolves #2574
Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Co-authored-by: Lisa Bengtsson <lbengtss@Orion-login-1.HPC.MsState.Edu>
Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com>
commit 6a9c1372ecce9e50e4f6e10e56f6e504cde1afe6
Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
Date: Fri May 10 14:17:13 2024 -0400
Do not use BUILT_semphore to force rebuilds when re-run (#2593)
Remove the placement of the `BUILT_semaphore` file after the build in
the Jenkins Pipeline and force it to rebuild any changes after a PR is
re-ran.
commit 2346c6161f75ae02369cbf30f30c6150d3e12b66
Author: Innocent Souopgui <162634017+InnocentSouopgui-NOAA@users.noreply.github.com>
Date: Thu May 9 21:17:06 2024 -0500
Migration to Rocky8 spack-stack installations on Jet (#2458)
# Description
Migrates Global Workflow to Rocky8 spack-stack installations on Jet.
Jet has moved from CentOS7 to Rocky8.
Resolves #2377
Refs NOAA-EMC/UPP#919
Refs NOAA-EMC/gfs-utils#60
Refs NOAA-EMC/GSI#732
Refs NOAA-EMC/GSI-Monitor#130
Refs NOAA-EMC/GSI-utils#33
commit c7b3973014480a20dd8e24edaeb83a9e9e68159f
Author: Jessica Meixner <jessica.meixner@noaa.gov>
Date: Thu May 9 11:36:58 2024 -0400
Updates for cold start half cycle, then continuing with IAU for WCDA (#2560)
This PR allows us to run C384 S2S with IAU, but starting with the first
half-cycle as a cold-start. This will be necessary for cycled testing as
we build towards the full system for GFSv17. This updates the copying of
the restarts for RUN=gdas for both ocean and ice copying what the atm
model is doing. It also reduced the amount of restart files from 4 to 3.
Other updates:
* Add DOJEDI ocean triggers for archiving certain files update from:
@CatherineThomas-NOAA
* Adds COPY_FINAL_RESTARTS option to turn on/off copying the last
restart file to COM. Defaults to off...
* Defines model_start_date_current_cycle & model_start_date_next_cycle
to help with knowing which IC to grab.
Refs #2546
Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com>
commit b405b7d3d11d384ce9fe3b9cd2180f315f7b38f2
Author: Dan Holdaway <27729500+danholdaway@users.noreply.github.com>
Date: Wed May 8 20:52:48 2024 -0400
Use JCB for assembling JEDI YAML files for atmospheric GDAS (#2477)
Change the JEDI YAML assembly for the atmospheric GDAS to use the JEDI
Configuration Builder (JCB) tool so that YAMLs can be made more portable
and invoke the observation chronicle mechanism.
Resolves #2476
Co-authored-by: danholdaway <danholdaway@users.noreply.github.com>
Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
commit 0cf0349c1f88048806e68ab58e93a3261b7a0e95
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Wed May 8 02:04:16 2024 -0400
Add CI test for products (#2567)
Adds a new version of the atm3DVar test that runs the full forecast
length and produces most of the secondary products. For now, this test
will only run on WCOSS due to gempak failures on other machines as well
as computational needs. On other machines, the original version will run
(the original version will not run on WCOSS). AWIPS remains off for now
in this extended test due to a bug involving tocgrib2 and the convective
precip fields (see #2566).
The new test runs for 4½ cycles and the full 384-hr forecast length to
ensure all gempak scripts are exercised. Since the cycle throttle is 3
and the bulk of the time is in the free forecast, the cycles run mostly
concurrently so it doesn't extend the total test time too much beyond
that of a single 384-hr forecast.
Fixes a bug in NPOESS that was introduced when the post filenames were
reverted to the previous format for the GOES products until the final
filenames are determined (#2499).
Also removes the AWIPS g2 job from the rocoto mesh to complete the
retirement of grib1 products.
Resolves #2132
Resolves #2445
commit 9b6f8404ac4507d14adc404b77cfdf002b55e832
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Tue May 7 00:14:36 2024 -0400
Add task to prepare emissions for GEFS (#2562)
This PR:
- introduces a task to prepare emissions for a forecast into the GEFS
application.
- adds configuration, j-job, rocoto job, ex-script and the python class
for this job
- updates GEFS workflow to be able to generate the XML to call this job.
- updates the `fcst` and `efcs` job dependencies in the GEFS application
to depend on `prep_emissions` if aerosols are turned ON.
- provides a placeholder for @bbakernoaa to work on the details for
preparing emissions.
Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
commit 233c18815d2e8e6b344f161fd0c102a4fbdfb66d
Author: Dan Holdaway <27729500+danholdaway@users.noreply.github.com>
Date: Mon May 6 18:11:35 2024 -0400
Single Executable for main GDAS JEDI applications (#2565)
Changes that accompany GDAS PR (NOAA-EMC/GDASApp/pull/1075) that allows
building of a single gdas executable, which should be more compliant
with NCO requirements.
Addresses https://github.com/NOAA-EMC/GDASApp/issues/1085
commit a005244bbfb2f1c525bca60d966f8095aa1acb8e
Author: Guoqing Ge <guoqing.ge@noaa.gov>
Date: Thu May 2 20:32:53 2024 -0600
Add nest capability (#2545)
This PR adds the global nesting capability to the global workflow so
that one can run a regional domain nested in a global run.
Resolves #2544
Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com>
commit cb87daaced9fddd17f8370a1842d7e4ddab24e8f
Author: DavidBurrows-NCO <82525974+DavidBurrows-NCO@users.noreply.github.com>
Date: Thu May 2 15:30:53 2024 -0400
Update gfs_utils for Gaea (#2556)
What: add build capability to the gfs_utils submod within the global
workflow on Gaea
Refs #2535
Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com>
commit 707a1cc5124bcd8e006839a17f76ceb88f45f902
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date: Wed May 1 18:13:02 2024 -0600
Updated GEMPAK version and APRUN launcher. (#2555)
This PR addresses issue #2248 and #2513. The following is accomplished:
- Updates the parallel executable for GEMPAK applications;
- Updates the GEMPAK version for RDHPCS Hera.
Describe your changes. Focus on the *what* and *why*. The *how* will be
evident from the changes. In particular, be sure to note any interface
changes, such as command line syntax, that will need to be communicated
to users.
At the end of your description, please be sure to add the issue this PR
solves using the word "Resolves". If there are any issues that are
related but not yet resolved (including in other repos), you may use
"Refs".
Resolves #2248
Resolves #2513
Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Co-authored-by: henrywinterbottom-wxdev <henry.winterbottom.wxdev@gmail.com>
commit f151cbf394e998ca0fdae893ca174499468d0c85
Author: Travis Elless <113720457+TravisElless-NOAA@users.noreply.github.com>
Date: Wed May 1 11:01:18 2024 -0400
Utilize scale-dependent localization for atmospheric analysis (#2542)
The plan for GFSv17 is to use a scale-dependent localization for the
atmospheric analysis. This PR adds the necessary parameters to allow
this feature to be used by default.
commit 53b6764392cb4c0f3b4506ccd3f8cba5c5d2c56e
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Tue Apr 30 16:37:54 2024 -0400
Remove implicit symlink names (#2527)
Lustre has a defect under Rocky 9 that results in symlink sometimes
failing when the link name is not explicit. This updates all link
creation to use explicit names.
`config.base` is updated to turn off two monitor jobs on Hercules
because the executables are not yet built there. This, combined with the
previous change, should make workflow available for use on Hercules.
Also removes the redundant utility names for NCP, NLN, etc. in the gdas
scripts that are already defined in `config.base`.
Resolves #2131
Resolves #2522
commit f7e9f4489fc0b10830f621fdf149e8e3149d6a51
Merge: 67a4810c4 762f040a2
Author: Janet Derrico <143837053+jderrico-noaa@users.noreply.github.com>
Date: Tue Apr 30 12:24:48 2024 -0600
Merge branch 'NOAA-EMC:develop' into develop
commit 762f040a2045db17cdacd9026df9c4b8fd520156
Author: AndrewEichmann-NOAA <58948505+AndrewEichmann-NOAA@users.noreply.github.com>
Date: Mon Apr 29 22:26:28 2024 -0400
Fixes sea ice archiving (#2541)
Removes/changes sea ice output files that are failing to be added to
list for archiving, causing `gdasarch` to fail in WCDA cycling.
Resolves https://github.com/NOAA-EMC/GDASApp/issues/1044
commit 2ecf4f86e0cbe59407ba2c4e105ee7292f1eda01
Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com>
Date: Mon Apr 29 22:25:57 2024 -0400
Link ensemble analysis increment files to COMROOT for warm_start (#2553)
Scripting is added to `setup_expt.py` to link ensemble analysis
increment files to COMROOT for warm_start experiments.
Resolves #2552
commit 3a7abe1d63c573006e0e656237f1220002c3f579
Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
Date: Tue Apr 30 02:25:28 2024 +0000
Launch Multiple Platforms to Jenkins with polling (#2548)
When launching Jenkins CI Tests all requested RDHPCS machines can now be
selected via the Ready label at once.
This is all that is required sense polling also works now on the
controller end.
Killing the jobs still needs to be done directly on the Jenkins
Controller.
Do not try to update the CI process using Labels. It is for launching
only.
Jenkins will update the labels as the states change.
NOTE: When a case fails the label will be update to a **Fail** for that
system but will continue to report failures of subsequent cases until
otherwise stopped in the Jenkins Controller directly.
Do not update any labels…
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What new functionality do you need?
When the workflow is ready, CI should be set up on Hercules as it is on Orion.
Depends on completion of #1588
What are the requirements for the new functionality?
Full CI capability from Orion is duplicated for Hercules.
Acceptance Criteria
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