Makefiles need to support debug and clean #300
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WalterKolczynski-NOAA
added
the
production update
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Assigned to Arun since this will require management of several projects. |
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I'm also fairly certain some of these makefiles are not used in production. |
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The following make files: Are not used in production. If having these makefiles in the source code are going to be an issue, we'll have to figure out something in the wave model repo to deal with this. |
12 tasks
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@JessicaMeixner-NOAA |
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Updated issue main comment to list component POCs and add checkmarks next to each file. |
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@WenMeng-NOAA why dont we just use a txt control file to begin with ? |
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I would not like to remove a regression test system from a repository. Since these are not part of the UFS build system it should hopefully not be an issue for operations. @JessicaMeixner-NOAA just out of curiosity and perhaps an action item for future ww3, these tests should probably have a debug build option ( not an issue for NWS as we do not use OASIS) |
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@arunchawla-NOAA valid point, I added a WW3 issue NOAA-EMC/WW3#635 I think this might become a moot point with the move to cmake, but I don't know the full details so I made an issue just incase. |
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@arunchawla-NOAA The txt control is not in human-friendly format for defining variables output from UPP. The parm/makefile isn't in UPP source code part and isn't involved in UPP build time and run time. It's not a traditional makefile for compiling fortran code. I would think no debug target needed. |
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thanks @WenMeng-NOAA so this is not used in operations right ? You only need it to set the configuration for an operational system. Am I reading that correctly ? If that is the case then that is the reason we can use |
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@arunchawla-NOAA That's right. This script is handy for updating operational UPP control files, e.g. GFS, GEFS, RRFS, HAFS. |
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Do I need to update the latest UFS_UTILS tag that supports GFS v16. I can do that under: ufs-community/UFS_UTILS#629. Some of the programs listed are not used by global-workflow, so I can simply remove them. The head of 'develop' uses CMake and includes a 'debug' option. So if this can wait until the "next major upgrade" do I need to do anything? |
9 tasks
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PR #905 adds a debug option at the gw-level for UFS via the UFS's build script. I assume that takes care of most of the UFS concerns (we build WW3 pre/post separately, so that may still need to be addressed). |
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@WalterKolczynski-NOAA yes, WW3 pre/post will need a debug type option built into the scripts. It's capable of being built in debug mode, but needs the easy functionality like what was just added for UFS. |
WalterKolczynski-NOAA
pushed a commit
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Jul 15, 2022
…ld system, pull sfcanl out from anal. (#905) `ncdiag` is no longer being built within the GSI. It is available as a module on all systems; Hera, Orion and WCOSS2. This PR: - loads ncdiag module - finds the `ncdiag_cat_serial.x` executable from that module (once loaded) - updates hashes for GSI, GSI-utils and GSI-monitor. No code changes were made in these repos. Only location of `ncdiag` changed. In addition, this PR: - Uses the ufs-weather-model compilation script. The global workflow is duplicating and missing configuration options set in the ufs-weather-model. This also enables a "debug" mode of compiling the model (#300). - Fixes #906 - Fixes an improper link to `fix_gsi`. It was being linked to a non-existing directory. - separates out the creation of Gaussian surface analysis from the GSI atmospheric analysis. This capability is pulled from PR #871. It was necessary to pull these changes from PR #871 since the `j-jobs`, `ex-scripts` from the GSI have been brought to global-workflow and the companion PR for PR #871 in the [GSI PR 415](NOAA-EMC/GSI#415) were already merged prior to the updates needed for `ncio` and `ncdiag`. I realize all these changes could have been streamlined into smaller atomic PR's. **Note:** This PR also requires a documentation update as a new job `sfcanl` has been added to the workflow.
jkhender
added a commit
to jkhender/global-workflow
that referenced
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Nov 18, 2022
commit 71a16e84a4ce59869879dd6c20007d0271521e7b
Author: Judy.K.Henderson <Judy.K.Henderson@noaa.gov>
Date: Fri Nov 18 01:46:14 2022 +0000
Squashed commit of the following:
commit a658e75e579ebc4f454377e5a9cf4c1fc54e4e3d
Author: Jessica Meixner <jessica.meixner@noaa.gov>
Date: Wed Aug 3 18:34:34 2022 +0000
Updates for P8 (#946)
These are the final updates for Prototype 8. These changes include:
* Updating to the latest ufs-weather-model hash (in progress, waiting for PR) which will update the calculation of 2m T
* A small update to the organic carbon coefficients for p8, raises them from 0.3 -> 0.4 for oc1 and oc2
* Uses 10km input files for aerosols
* Sets do_gsl_drag_tofd=false by default, which helps with stability of the model
Closes #937
commit b2155ad3dc999a2f41aeace58f3b199a8ddde65c
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Wed Aug 3 10:04:06 2022 -0400
Fix GLDAS j-job link (#954)
The cd was misplaced when checking for the existence of gldas.fd to
create the link for the j-job, so the directory was never found and
the job never linked.
commit 395720cef000ef221c49c93d4f68417b7fda64b6
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Mon Aug 1 17:38:50 2022 -0400
Add ocean post to archive dependencies (#949)
The archive job was not waiting for ocean post to complete because
there was no dependency.
Fixes #948
commit 145b67f70f44abbb713e19073016bacfbfcb8184
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Fri Jul 29 13:42:38 2022 -0400
Initial commit of directory comparison tools (#934)
Adds a new `test/` directory to the top level. Inside are miscellaneous scripts I have used to test bitwise identicality of experiments.
Main scripts:
- `diff_ROTDIR.sh`: Compares two output directories
- `diff_UFS_rundir.sh`: Compares two UFS run directories
Other scripts and file are helpers to these two main scripts.
May eventually form starting point of a global workflow regression test (#267)
Refs #267
commit e480093446797e556bc1371f9f80610a7c9a6d4b
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Fri Jul 29 13:42:02 2022 -0400
Add preamble, convert to bash, and remove env (#929)
This is the first in a wave of commits to improve and standardize the scripts within global workflow. In this commit, all scripts run during execution are converted to bash and a preamble is added to every script that is not sourced by another script.
Every script executed during a forecast cycle is converted to bash. This was mostly straightforward, though there were a couple Korne-shell conventions (primarily using `typeset` to format strings) that had to be replaced with bash-compatable alternatives like `printf`. This in turn required a few modification to prevent zero-padded numbers from being treated as octals (other may have been pre-existing bugs).
The preamble contains a number of feature to standardize code and improve script flow and debugging.
- First, it uses two variables, `$STRICT` and `$TRACE` to control the behavior of `set`. When `$STRICT` is `"YES"`, error on undefined variables (`set -u`) and exit on non-zero return (`set -e`) are turned on. When `$TRACE` is `"YES"`, command trace (`set -x`) is turned on and a useful string is set to `$PS4` that gives the name and line number of the script. Both `$STRICT` and `$TRACE` default to `"YES"`. They also set up commands, `$ERR_EXIT_ON` and `$TRACE_ON`, that will restore the setting of each in the event a script needs to temporarily turn them off.
- Second, the preamble sets up primative timing of scripts using Posix `date`.
- Third, it echos the script is beginning and at what time.
- Finally, it also establishes a postamble function and sets it to run as a trap of EXIT. The postamble will use the end time to calculate the run time of the script, then print that the script has ended at what time, how long has elapsed, and the exit code. By setting this up as a trap instead of just calling it at the end of the script, it ensures the postamble is called even if the script exits early because there is an error.
- In response to this standardization, parts of scripts that performed these preamble functions (announcing start/end, `set -x`, etc) have been deleted. For some scripts where temporarily turning off `-x` or `-e` is needed, they now use `$ERR_EXIT_ON` and `$TRACE_ON` to return to the correct state afterwards, instead of blindly turning the setting back on.
- Additionally, some modifications were needed to comply with `set -eu`. Mostly taking care of undefined variables, but also a couple instances where a non-zero return code had to be dealt with.
If users wish to use their own preamble script instead, the default script can be overridden by setting `$PREAMBLE_SCRIPT` before the run begins.
Instance where scripts would print the full list of environment variables have been removed. These can be spot added back in to debug as necessary. Alternatively, a future PR will add them back in in a standardized way.
`rstprod.sh` is added to the link list from gsi_monitor.fd, as it is needed for the radmon scripts.
The placeholders for AWIPS and GEMPAK in the Hera and Orion environment scripts were replaced with the correct definitions. There were also other modifications to AWIPS and GEMPAK scripts to get it working for development (AWIPS still isn't and will be fixed in the future).
GSI scripts that were brought in recently had all of their backticks replaced with `$( )` as was done with all other script previously.
Refs: #397
commit 949513642d33cb3976d0f8e7dd273aedec505a17
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Thu Jul 28 18:36:58 2022 -0400
minimal intervention to create a data-atmosphere xml (#936)
commit e4b01b99f50c674635477ff3e2e962b9d5ed54aa
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Thu Jul 28 18:28:28 2022 -0400
Remove Cray, Dell, WCOSS1 from module-setup.sh.inc (#943)
This file was missed in the initial cleanup.
commit 1ed89c7d202974bd4ccd2b048fedc56382edc9ec
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Thu Jul 28 15:35:37 2022 -0400
bring GDASApp jjobs and exscripts to global-workflow (#941)
commit f04f3ba4dfd5b358aea425f65f82d40917597776
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Tue Jul 26 22:07:42 2022 -0400
change gdasechgres dependency to just gdasefcs01 instead of gdasefmn (#933)
Replaces the dependency of `gdasechgres` on `gdasefmn` with `gdasefcs01`.
Presently, `gdasechgres` has 2 dependencies:
- `gdasfcst` - deterministic forecast
- `gdasefmn` - ensemble forecasts (all of them).
The work done in `gdasechgres` actually depends only on the `mem001/atmos/gdas.tHHz.atmf006.nc`.
This file is used as a template as well as obtaining `hgtsfc`.
As such, there is no reason to depend on the entire ensemble of forecasts to be complete before `gdasechgres` can start.
commit 490de7bae1322cbaa8ee3d52406034c8edf62dd3
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Tue Jul 26 22:05:59 2022 -0400
Remove obsolete platforms (WCOSS1, Dell, Cray, Theia) references. (#922)
Removes code related to decommissioned HPC platforms WCOSS 1 (Dell & Cray) and Theia. Some references remain in scripts outside the global-workflow repo that are cloned as part of `checkout.sh`. Scripts from the `driver` directory that were hard-wired for one of the WCOSS1 platforms are also removed.
Additionally, this commit also switches to using serial netCDF for resolutions C48. C96, C192. Running with parallel netCDF (on Hera) gave errors when testing at C96 for the deterministic forecast. If someone gives a very compelling reason to use parallel netCDF at these resolutions as default, I would be very interested in what they have to say.
Closes #680
commit 4eb296f7e82459b1d8188636ca3db60b5fa10091
Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com>
Date: Tue Jul 26 14:50:30 2022 -0400
Optimize DA clone, build, and link (#931)
The PR contains changes to optimize the DA clone, build, and link. Changes are made to `checkout.sh`, `build_all.sh`, and `link_workflow.sh` in the g-w `sorc/` directory. These changes are in g-w branch `feature/clone`
Two arguments are added to `checkout.sh` to allow the user to specify which DA package to build the global workflow with. These options are
- `-g`: clone from the [GSI](https://github.com/NOAA-EMC/GSI) repo and build the g-w for GSI-based DA
- `-u`: clone from the [GDASApp](https://github.com/NOAA-EMC/GDASApp) repo and build the g-w for UFS-based DA
If no option is specified, `checkout.sh` does not clone any DA and DA related repos. This is the default behavior of `checkout.sh`. (_DA related_ repos include [GLDAS](https://github.com/NOAA-EMC/GLDAS), [GSI-utils](https://github.com/NOAA-EMC/GSI-utils), and [GSI-Monitor](https://github.com/NOAA-EMC/GSI-Monitor).)
`build_all.sh` is modified to detect which repos and have been cloned and to build accordingly. `link_workflow.sh` is modified to detect which directories are present and link/copy accordingly.
Closes #930
commit 2cad536551180d25bfcfc2b5d35fe1089de7f3c3
Author: Kate Friedman <kate.friedman@noaa.gov>
Date: Tue Jul 26 13:25:37 2022 -0400
WCOSS2 gempak ush scripts updates and cleanup of old release notes (#920)
* WCOSS2 updates to gempak ush scripts
- Add /gempak subfolder where needed in gempak ush scripts.
- Remove unneeded commented out path settings from older iterations.
* Removing older release notes
- Cleaning out older GFS version release notes; includes current GFSv16.2.1 release notes, will commit GFSv16.3
release notes with implementation this fall.
- Will then keep only the latest release notes moving forward.
Refs: #419
commit ffcd5bbde7947902a73eebff7dfe04c2ab045b0a
Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com>
Date: Fri Jul 22 16:00:51 2022 -0400
Add GDASapp (first wave of JEDI changes) (#871)
Merge changes associated with g-w issue #521 from g-w branch feature/ufsda_gdasapp into develop. feature/ufsda_gdasapp contains g-w extensions for JEDI based atmospheric DA.
Specifically, this PR adds the option to add JEDI based variational and/or ensemble DA jobs to replace GSI based DA jobs. The toggling on/off of JEDI_VAR and JEDI_ENS jobs is controlled via two new variables added to `config.base.emc.dyn` and `config.base.nco.static`
```
# DA engine
export DO_JEDIVAR="NO"
export DO_JEDIENS="NO"
```
When both variables are `NO`, the global workflow uses GSI based DA jobs. Thus, the PR does not alter the default behavior of the develop global workflow.
When `DO_JEDIVAR=YES`, GSI jobs `anal` and `analdiag` are replaced by JEDI_VAR jobs `atmanalprep`, `atmanalrun`, and `atmanalpost`. When `DO_JEDIENS=YES`, GSI jobs `eobs`, `ediag`, and `eupd` are replaced by JEDI_ENS jobs `atmensanalprep`, `atmensanalrun`, and `atmensanalpost`.
`checkout.sh`, `build_all.sh`, and `link_workflow.sh` are updated to clone, build, and install the GDASapp in the global workflow.
Local directory `sorc/gdas.cd` contains the GDASApp superstructure plus the relevant components of JEDI needed to run GDASApp.
Closes #521
commit 98f4d16e9bba86d2c433aa0521d960b566062a1f
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Thu Jul 21 16:02:31 2022 -0400
Add postsnd job when bufrsnd it on (#926)
In the workflow refactoring, the addition of postsnd to the task list when
bufrsnd is true was inadvertently left out. It is now added back in.
commit e2869a1247ad2ba72c1bfe82f7682323d5128f4c
Author: Kate Friedman <kate.friedman@noaa.gov>
Date: Tue Jul 19 16:16:20 2022 -0400
Updated GFS transfer*list files from operations (develop) (#918)
Updated transfer list files from WCOSS2 ops.
- In move to WCOSS2 the transfer*list files were moved into a new
transfer folder under the upper-level parm folder.
- The transfer*list files were updated to clean out unneeded paths
and the beginning of the paths were updated from:
`com/gfs/_ENVIR_`
to:
`_COMROOT_/gfs/_SHORTVER_`
Refs: #419
commit 1651014250a748c8c2e2878663c3e8376639044a
Author: ChunxiZhang-NOAA <49283036+ChunxiZhang-NOAA@users.noreply.github.com>
Date: Tue Jul 19 11:18:33 2022 -0400
Fix history type of cldfra in the diag_tables (#915)
The history type of the new cloud fraction field (cldfra) is changed so it is written to the correct output file.
Fixes #914
commit 5c9639dba419ef51608aa8962b54ae69c8ad8c60
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Tue Jul 19 11:11:38 2022 -0400
Combine ecflow and rocoto workflow generation (#916)
Consolidates the workflow generation systems for ecflow and rocoto. Further unification will be made to make a choice to use one or the other. At this time, they are separate and need separate input criteria.
Moves `ush/rocoto` to `workflow/` at the top level. Further refining will be performed as needed based on use and need.
commit b690ed6c7c1a250171484aba267d0724d8c12d11
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Mon Jul 18 19:33:36 2022 -0400
Remove new GSI scripts from gitignore (#917)
When the scripts were moved over from GSI into global workflow, they
were never removed from the .gitignore. This has now been addressed.
Follow-up to PR #904
commit aa2542eb4c95827bc1fc7a4a76d4d0f5bc701f74
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Mon Jul 18 13:49:09 2022 -0400
Add ecFlow generator to `develop` (#912)
* merge workflow_generator from dev_v16 at 7b7947e2 and move workflow_generator to ush/ecflow
commit 5a58fa8a2f75590a671b45bf75a431f2acf2340b
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Mon Jul 18 13:02:59 2022 -0400
Update gsi-utils hash to include bugfix in handling 3D sfc files (#913)
Update GSI-Utils hash to include bugfix that processed 3D fields in surface netCDF files.
Fixes #909
commit e8361cc343743bb5087e75f89406c1265404e359
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Mon Jul 18 12:44:25 2022 -0400
Combine setup_workflows scripts (#859)
`setup_workflow.py` and `setup_workflow_fcstonly.py` are used for setting up the XML for cycled and forecast only configurations.
They share large parts of the tasks and dependencies.
This PR unifies the ones listed above and makes room for extending for incoming applications.
The above two scripts are being replaced by `setup_xml.py`.
The usage is:
```
$> setup_xml.py /path/to/experiment_directory
```
This PR also removes the handicap of defining hundreds of entities for task resources. Instead the task resources are placed with the task itself.
This PR also does the following:
- moves the declaration of `DOBNDPNT_WAVE="NO"` from `config.wave` to `config.base`
- reduces timestep at `C48` from `1200s` to `450s` in `config.fv3`. Several ensemble members failed. Inspecting `config.fv3.nco.static`, the value there is `450s`
- `eobs` job times out with a wallclock time of `15m`. It is increased to `45m` to play it safe.
commit 13385d9c9018def1fbce6772e53665ccb90b2a2a
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Fri Jul 15 14:02:12 2022 -0400
Load `ncdiag` module instead of building it in the GSI, use UFSWM build system, pull sfcanl out from anal. (#905)
`ncdiag` is no longer being built within the GSI. It is available as a module on all systems; Hera, Orion and WCOSS2.
This PR:
- loads ncdiag module
- finds the `ncdiag_cat_serial.x` executable from that module (once loaded)
- updates hashes for GSI, GSI-utils and GSI-monitor. No code changes were made in these repos. Only location of `ncdiag` changed.
In addition, this PR:
- Uses the ufs-weather-model compilation script. The global workflow is duplicating and missing configuration options set in the ufs-weather-model. This also enables a "debug" mode of compiling the model (#300).
- Fixes #906
- Fixes an improper link to `fix_gsi`. It was being linked to a non-existing directory.
- separates out the creation of Gaussian surface analysis from the GSI atmospheric analysis. This capability is pulled from PR #871. It was necessary to pull these changes from PR #871 since the `j-jobs`, `ex-scripts` from the GSI have been brought to global-workflow and the companion PR for PR #871 in the [GSI PR 415](https://github.com/NOAA-EMC/GSI/pull/415) were already merged prior to the updates needed for `ncio` and `ncdiag`.
I realize all these changes could have been streamlined into smaller atomic PR's.
**Note:** This PR also requires a documentation update as a new job `sfcanl` has been added to the workflow.
commit b61c2375a05daff20805d0216ade8201192c0199
Author: Fanglin Yang <fanglin.yang@noaa.gov>
Date: Thu Jul 14 20:07:54 2022 -0400
Update ice climo, fix option for non-fractional grid, and add cloud fraction for Thompson (#902)
Updates the ice climatology from CFSR to IMS_NIC blended.
Fixes issue in the diag table where the cloud fraction entry for Thompson was not included.
Adds new coupled mode setting for when fractional grid is not used.
Fixes #886
Co-authored-by: Chunxi.Zhang-NOAA <Chunxi.Zhang@noaa.gov>
commit 680270975e2eb2f09c58a6112a87c0ecaec9e2a5
Author: Barry Baker <bbakernoaa@users.noreply.github.com>
Date: Thu Jul 14 17:03:34 2022 -0400
Update aerosol variable names and dust alpha (#888)
The names of some aerosol fields have changed and needed to be updated.
The dust alpha parameter is updated to improve model performance.
A typo in the scavenging parameter definition where a string was terminated with a 'smart-quote' instead of a standard one is corrected.
commit 06b25267b7839808508eed9e91dcd2b76a33c3ca
Author: Jessica Meixner <jessica.meixner@noaa.gov>
Date: Thu Jul 14 18:52:56 2022 +0000
Allow for wave mesh to be different than the ocean/ice mesh (#897)
This PR updates the configuration to allow for the wave mesh to be different from the ocean/ice mesh. This PR also changes the default wave grid back to gwes_30m and updates the load-balancing for this change. The ufs-weather-model is updated to use the code that allows for the wave mesh to be different from the ocean/ice mesh.
commit 4f3e14b59ff6c83fbaaf6888c3a3068eae3d77d7
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Wed Jul 13 15:53:18 2022 -0400
Migrate `jobs/`, `scripts/` and `ush/` from GSI to global-workflow (#904)
This PR moves the `jobs/`, `scripts/` and `ush/` from NOAA-EMC/GSI into the global-workflow.
History is preserved.
Corresponding GSI PR https://github.com/NOAA-EMC/GSI/pull/436
commit 46f7589807bcb070c8f86601b74f1a84701b669a
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Wed Jul 13 15:51:56 2022 -0400
build GSI utilities from GSI-utils repo (#889)
**Description**
The GSI Utilities have been moved to https://github.com/NOAA-EMC/GSI-utils
This PR:
- checks out GSI utilities from the above repo
- builds the utilities from the above repo
- does not build the utilities from the GSI repo. In a subsequent PR when the GSI removes the utilities, that option will become redundant.
- updates gsi-monitor hash and uses `build.sh` from that repository
- creates links appropriately.
commit aac2f3a6980cb61a0dbe272b667f602e3051cb16
Author: Jessica Meixner <jessica.meixner@noaa.gov>
Date: Mon Jul 11 06:57:25 2022 +0000
Replace print_esmf with esmf_logkind (#898)
Removes print_esmf as it no longer a variable and add the esmf_logkind variable to config.fcst instead which is the equivalent new variable. The change has already been made in nems_configure.sh, so the setting only needed to be changed in the config file.
commit 4448dd48b2aeebdf4257a2ab08bd147fcb511f92
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Fri Jul 8 13:03:29 2022 -0400
Restore cycling capability (#895)
Restores the ability to run in cycled mode. This requires GSI to be built with ncio/1.1.2, so the build script now sets 1.1.2 as the ncio version until either the GSI default version is updated or module version files are added to global-workflow (Issue #671).
Two new variables, COMIN_OBS and COMIN_GES_OBS, had to be added to the config file in the wake of GSI updates for WCOSS2 to ensure the correct paths are used instead of trying to use the non-functional compath.py.
Note that, for now, in order to use cycling, the microphysics setting (imp_physics) must be changed in config.base from Thompson (8) back to GFDL (11), along with a corresponding CCPP suite (like FV3_GFS_v16).
Fixes #711
commit a39bd6364971894eee4349b028ebf54ab496dee0
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Tue Jul 5 16:10:46 2022 -0400
Merge `ecf` changes from `WCOSS2` into `develop` (#885)
* moved ecflow/ecf to ecf and with updates from feature/ops-wcoss2
commit 3076e13ca5976206f1cdab58cca1b6f80fbb7716
Author: Fanglin Yang <fanglin.yang@noaa.gov>
Date: Fri Jul 1 10:33:39 2022 -0400
Fix settings of dt_inner and lheatstrg (#883)
For Thompson microphysics, currently dt_inner is set to half of physics timestep. It should be set to the same as the physics timestep if semi-Lag sedimentation is applied to rain and graupel.
Canopy heat storage is incorrectly turned off for NOAH LSM, and on for NOAH-MP LSM. This setting needs to be reversed.
Fixes #884
commit 3b9636c4eadc8c31548e170baeefd358483ec71c
Author: Ali.Abdolali <37336972+aliabdolali@users.noreply.github.com>
Date: Wed Jun 29 18:22:06 2022 +0000
Update buoy locations (#881)
Updates buoy locations for those that were incorrect or have been moved.
commit f0f1025d07a1af216e2125111ae7bd9ac43213c2
Author: Barry Baker <bbakernoaa@users.noreply.github.com>
Date: Tue Jun 28 12:05:31 2022 -0400
Update dust input files to not include _FillValue = NaN (#873)
There is an issue with the FENGSHA dust inputs and having the netcdf attribute _FillValue == NaN. This is in relation to ufs-community/ufs-weather-model#1259, ufs-community/ufs-weather-model#1192 and #872
Some dust emissions files have also been updated. File changes only include the netcdf attribute _FillValue changing from NaN -> something appropriate for each variable.
Fixes #873
commit 4c8b388ae4fd1fb618021b5c11d5e9c82c2ee2f7
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Mon Jun 27 18:14:39 2022 -0400
Replace --aerosols with new apps (#854)
Removes the --aerosols option for setup_expt and replaces it with new apps for aerosols to match the idiom for other components. Currently, ATMA and S2SWA are supported.
commit 65cdcce2f841f5e3e4926d4dab73fd5a8a97bd84
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Mon Jun 27 17:47:46 2022 -0400
Update component versions (#851)
Updates the version of components except UFS and verify to the current tip of their respective develop branches.
Verify is not yet updated because we are currently on a branch that hasn't been merged to develop yet in order to use the module/py environment fix.
GSI will still need to be updated further before use after the resolution of NOAA-EMC/GSI/issues/348
Also updated the GSI and UPP build scripts to take in debug (`-d`), operations (`-o`), and verbose (`-v`) options and apply them as appropriate to the component build scripts. The ops flag for GSI still needs work, as I encountered issues using the [build_4nco_global.sh](https://github.com/NOAA-EMC/GSI/blob/develop/ush/build_4nco_global.sh) or [prune_4nco_global.sh](https://github.com/NOAA-EMC/GSI/blob/develop/ush/prune_4nco_global.sh) scripts.
Also fixes a typo in the `parm/post` file list.
Updates are in preparation for the [COM reorg](https://github.com/NOAA-EMC/global-workflow/issues/761)
commit 2dc2af0e84f52864a719d71d3dbf14f6368f4c0f
Author: Jessica Meixner <jessica.meixner@noaa.gov>
Date: Fri Jun 24 18:49:39 2022 +0000
Update caculation of restart based on if a wave IC exists (#875)
Inspect and assert wave initial conditions exist during a RERUN. Take appropriate action.
commit b41a36a10b2f949b0c005e48b978261b3d66eb12
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Thu Jun 16 22:38:28 2022 -0400
update from dev_v16 utils.f90. See issue #713 (#868)
commit a2b9f483c4aaad37e5d26362186b28a782c0541f
Author: Barry Baker <bbakernoaa@users.noreply.github.com>
Date: Tue Jun 14 23:51:47 2022 -0400
Update GOCART settings for p8/p81 (#818)
Wet scavenging coefficients for GOCART are updated.
Fixes a bug where when running atm-aerosol, aerosol settings were not properly read.
Changes the location of aerosol emissions data on Hera now that Raffaele has moved to a new position.
Dust inputs for the fengsha dust emission scheme are updated. These updates include a newer soil database (SOILGRIDSv2) and updates for the drag partition and threshold velocity. It also appropriately scales the emissions by modifying the alpha value found in the dust component configuration file.
Fixes #814
Fixes #815
Fixes #816
Fixes #816
commit 027eab90e2cb94a1055f9bc54245e7d5979aca3b
Author: Kate Friedman <kate.friedman@noaa.gov>
Date: Fri Jun 10 09:10:24 2022 -0400
Retire VSDB (#848)
Remove VSDB variables, script blocks, and scripts from global-workflow develop.
Refs: #844
commit d6705e2564a698eeddf2424bd580482546658788
Author: Kate Friedman <kate.friedman@noaa.gov>
Date: Fri Jun 10 09:05:36 2022 -0400
Add "atmos" COMPONENT subfolder to DMPDIR paths (develop) (#847)
- add atmos to WAVICEFILE DMPDIR path in JGLOBAL_WAVE_PREP
- add COMPONENT to all DMPDIR paths (COMPONENT=atmos already set)
- add "atmos" to all DMPDIR paths in config.anal
- add COMPONENT to COMIN_OBS default that uses DMPDIR in drive_makeprepbufr.sh
- add COMPONENT to SOURCE_DIR default that uses DMPDIR in getdump.sh
- add "atmos" to prep job dependency on updated.status.tm00.bufr_d in setup_workflow.py
Refs: #802
commit 59604d60a787fc758380a1ef513601d6ffa97566
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Fri Jun 10 03:29:16 2022 -0400
Move remaining global post scripts over from UPP (#771)
Several scripts currently located under NOAA-EMC/UPP are only used for global, so they have been moved within global-workflow so they can be managed by the global-workflow team. Scripts are just copied from the current tip of UPP develop, other than some changes to standardize style and indentation.
Also coming over are four parm files that are used to produce GFS products. As a result, we are no longer linking the entire upp parm directory; instead we are creating individual links for the files we use that still reside in upp.
Fixes #630
Fixes #769
commit d78c942a271e669b1fd5adf4f99af108c9f884fe
Author: Jessica Meixner <jessica.meixner@noaa.gov>
Date: Tue Jun 7 14:56:26 2022 +0000
update readme for new linking procedure (#843)
commit 3194f52d1625379e067fd16e84016d45ba5560fc
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Tue Jun 7 01:35:15 2022 -0400
Consolidate post scripts to eliminate coupled mode of link script (#766)
The two scripts that had modified versions for the coupled model have been joined with changes to the original scripts, eliminating the need for a special coupled mode for the link script. As part of this, those two scripts are no longer copied from UPP and are now part of the global-workflow repository.
Fixes: #679
Fixes: #746
Refs: #270
commit d1d2606406aa2deb8d95f348b471770f4388777c
Author: Jessica Meixner <jessica.meixner@noaa.gov>
Date: Mon Jun 6 04:49:38 2022 +0000
Updates for wave mesh cap (#831)
Updates to work with the new WW3 mesh cap, including pointing to the new ufs-weather-model tag for p8c slong with associated namelist changes. There is a new setting in config.ww3, `waveMULTIGRID`, that controls whether WW3 uses generic shell (shel) or multigrid.
The build script for WW3 pre/post has been updated to use the app to determine whether the regular switch file (for ATMW) or the meshcap version (other) is used. In light of this, `build_all.sh` now passes the app to WW3 pre/post as it does with the UFS build.
A large section of the wave prep script that was a hold-over from running WW3 offline from the atmosphere dealing with pre-processing winds was removed. Another large section was moved out of prep and into a new `parsing_namelists_WW3.sh` script that is called during the forecast job (similar to those for some other components).
The ability to set `esmf_logkind` for the UFS model is restored (defaults to ESMF_LOGKIND_MULTI).
The jlog files were removed for the non-pdgen wave script and ush files.
Resources for the coupled model are rebalanced.
Fixes #736
commit 7173fa58f0da831ad181a3afdaf3c861afa49e49
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Wed Jun 1 17:05:21 2022 -0400
Extend `rocoto.py` for handling offsets in data dependencies. (#835)
Extend rocoto.py data_dep to handle offset to cyclestr in any number of instances. Remove hack in aerosol_init dependency generation.
commit a9998af41cb8c2825f34745091a41ea400815d8d
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Wed Jun 1 14:11:49 2022 -0400
Refactor checkout script (#809)
The checkout script is refactored. First, the repetitive checkout code is abstracted into a function that is called for each component. Second, if the clone already exists, checkout will still checkout the requested commit. Third, a new option (-c) is added that will delete any existing clones a create a fresh clone. These last two options allow updating of versions without needing to manually delete directories (and remembering which are created by checkout)
Additionally, a usage statement and code documentation are added.
There is no change to the existing command-line options, only new options. No change is necessary by users (although the checkout order and print messages have changed). The new syntax is as follows:
```
checkout.sh [-c][-h][-m ufs_hash][-o]
-c:
Create a fresh clone (delete existing directories)
-h:
Print this help message and exit
-m ufs_hash:
Check out this UFS hash instead of the default
-o:
Check out operational-only code (GTG and WAFS). Only authorized users can check out GTG.
```
Fixes #808
commit 85bca2479420927d29a1a9db41b542568d527c13
Author: Jessica Meixner <jessica.meixner@noaa.gov>
Date: Wed Jun 1 15:05:07 2022 +0000
Update IC location for hera because climate moved from (#829)
The location of the coupled ICs on Hera is changing, so need to update the path in the config.
commit dbd9fa93ced07f39accf7ff4eec2859f0ed5d35f
Author: ChunxiZhang-NOAA <49283036+ChunxiZhang-NOAA@users.noreply.github.com>
Date: Mon May 30 21:50:56 2022 -0400
Updated SDFs and namelist settings for P8c (#795)
Updates the model version in preparation for prototype 8c, along with commensurate setting updates. Some CCPP suites are removed from the UFS build as they are no longer available.
Also updates the coupled initial conditions, and there is a simultaneous update to fixed orography files.
Refs: #736
commit 05accc1c72b1311ae9689bef5e7a1291dc12a96a
Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com>
Date: Mon May 23 17:36:51 2022 -0400
Correct incorrect increment prefix variable (#805)
One instance of the increment prefix variable in `ush/forecast_postdet.sh` used `PREFIX_INC` instead of the `PREFIX_ATMINC` used elsewhere.
Fixes #804
commit ac7cb1000d5c1d31babd36f4c3e17f643f30fd4d
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Sun May 22 16:50:30 2022 -0400
Remove separate UPP clone (#803)
Now that UPP is cloned within UFS, there is no need to create an independent clone in global-workflow. Scripts are updated to use the UPP within UFS. In addition to removing redundancy, this will avoid version mismatch issues when UFS and global-workflow checkout different versions. The upp directory is now linked from within UFS to sorc as upp.fd (instead of the gfs_post.fd the clone was placed in). Additionally, the build script is renamed to build_upp.sh.
Fixes #770
Moots #797
commit 58728fb2c689c11335f4bf8ac371e18070c6fbd2
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Fri May 20 10:14:58 2022 -0400
Fix build script options (#801)
There was an issue where if build_all.sh was called with only options that are not used by partial_build.sh, partial_build.sh would see those options because $@ was not overwritten. The script have been updated to consume those options so they are no longer present if $@ isn't overwritten in the new script call.
Also fixed the getopts statement in partial_build.sh so we handle errors instead of bash (bash would report the wrong script if the script is sourced)
Fixes #800
commit fa12db279cf829b861d08c06e3e3534a335e9fd7
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Wed May 18 01:04:32 2022 -0400
Refactor some build scripts (#794)
Refactors the build_ufs script to allow the build of any UFS app to support future expansion of global-workflow capability. The default should be sufficient for most users, as S2SWA can be used for ATM, ATMA, S2S, and S2SW as well. The new format of the command is now:
```
build_ufs.sh [-a UFS_app][-v]
-a UFS_app:
Specify the UFS application to build. The default if none is provided is S2SWA
-v:
Turn on verbose mode (BUILD_VERBOSE)
```
build_all.sh is similarly refactored to include the same options. Also, a new `-c build_config` option is added to specify an alternative list of programs to build.
```
build_all.sh [-a UFS_app][-c build_config][-h][-v]
-a UFS_app:
Build a specific UFS app instead of the default
-c build_config:
Selectively build based on the provided config instead of the default config
-h:
Print usage message and exit
-v:
Run all scripts in verbose mode
```
partial_build.sh is also updated to take the new `-c` option to specify a build config.
```
partial_build.sh [-c config_file][-h][-v]
-c config_file:
Selectively build based on the provided config. The default if none is specified is gfs_build.cfg
-h:
Print usage message and exit
-v:
Run in verbose mode
```
In addition to the above, build_all and partial_build had their indentation redone and their usage/help statement updated/added. Also, the build configuration file was renamed to from fv3gfs_build.cfg to gfs_build.cfg.
Fixes #745
Fixes #751
commit 2abee02765a3bae48f2b4e6a900400d6731eda06
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Wed May 18 01:02:57 2022 -0400
Add continuous aerosols support (#693)
Adds support for continuous aerosols when running with GOCART (using the forecast aerosol tracers from the previous cycle as initial tracer fields). This adds a new task to the workflow mesh in forecast-only mode. The new task does not run in the first cycle, though it will appear in rocotostat/rocotoviewer. In subsequent cycles, the task will launch as soon as the needed restart files from the previous cycle are available and gfs_init has completed. There is currently no mechanism to have aerosol_init run for the first cycle (for instance, continuing from a previous experiment); users would have to run the scripts off-line to add aerosols to the initial conditions.
To support the introduction of the necessary python scripts, a new python environment is added to provide necessary libraries. This virtual environment is temporarily being housed in personal space, but an issue has been opened with hpc-stack to add it to the standard stack installations. The introduction of miniconda also caused the conversion of all of the rocoto entry scripts (the ones rocoto calls to run the job) to bash. Most of them had been in korne.
To make sure the needed restart files are produced, config.fcst now makes sure the forecast cadence is included in the list of restart times. This may need more testing to ensure it works properly with other restart lists. As part of this, STEP_GFS was updated to properly determine the step from gfs_cyc instead of being a set value.
Closes #366
Fixes #516
Fixes #630
commit 69b39ee5af8cfbb5cbf5cf62c92d01958b697652
Author: Kate Friedman <kate.friedman@noaa.gov>
Date: Thu May 12 12:18:50 2022 -0400
Add --init to GSI submodule command (#781)
Needed to obtain libsrc submodule during checkout and allows the GSI to build correctly since this GSI hash still needs the libsrc submodule during build.
Refs: #780
commit b09f92c21028ea37e4663ce4c304935a2dc45b33
Author: lgannoaa <37596169+lgannoaa@users.noreply.github.com>
Date: Thu May 12 08:20:16 2022 -0400
Update field_table to be consistent with UFS (#778)
Changes the fixed surface value of hydrometeor number concentrations and sub-grid TKE to 0. Also renames the field table. Both changes are consistent with changes made in UFS.
Fixes #676
commit d72a62d6c0ab2e9f53ca3e6133148f29982f9d32
Author: lgannoaa <37596169+lgannoaa@users.noreply.github.com>
Date: Thu May 12 08:15:23 2022 -0400
Remove special MOD_PATH from build scripts (#775)
We always use pre-installed libraries and special MOD_PATHs are no longer necessary, so these are removed from build scripts. MOD_PATH. This also moots MOD_PATHs that were hard-coded to Hera locations in some scripts. The MOD_PATH in build_ufs.sh remains as it is still needed and is a relative path into the UFS repo.
Fixes #298
commit 2adf123814a2f29e9cca54a11fbb2807b3f6cf1b
Author: Kate Friedman <kate.friedman@noaa.gov>
Date: Wed May 4 12:31:20 2022 -0400
Revert g2tmpl back to 1.10.0 (#773)
Resolves bug with mismatch between hpc-ips and g2tmpl versions on the WCOSS-Dells. Also revert back to 1.10.0 on Hera and Orion to be consistent.
Refs: #772
commit b90f4e99bc42f9a8afbeaa9479e674fb75e096ea
Author: lgannoaa <37596169+lgannoaa@users.noreply.github.com>
Date: Tue May 3 09:45:19 2022 -0400
Remove git submodule update for upp checkout (#768)
UPP no longer has a CMakeModules submodule, so the submodule update
is removed from the checkout script.
Fixes: #767
commit ad2b14d9b1ed0fe89fe59bfb96cc03630e8457de
Author: lgannoaa <37596169+lgannoaa@users.noreply.github.com>
Date: Tue May 3 09:44:57 2022 -0400
Remove duplicate file linking for Thompson MP (#765)
Files for Thompson MP were being copied twice by the link script: once by checking imp_physics, then again checking the CCPP Suite. This is now reduced to one check.
Fixes: #675
commit a9fc0033b908aefb42d5b2d191c65af5cb7660c4
Author: Kate Friedman <kate.friedman@noaa.gov>
Date: Thu Apr 28 15:17:22 2022 -0400
Remove unneeded/outdated modulefiles (#762)
Remove unneeded modulefiles for WCOSS-Cray and GSI monitoring.
commit 3333dee304b6b53d3d716c60d0c87ad06d629c1c
Author: lgannoaa <37596169+lgannoaa@users.noreply.github.com>
Date: Thu Apr 28 14:35:57 2022 -0400
Remove prepbufr_pre-qc from archive lists (#753)
The prepbuft_pre-qc file does not need to be archived, so it no longer is.
Fixes #361
commit 88b1b1591d3201709f5f981908aaf7890d3021bd
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Tue Apr 26 20:40:41 2022 -0400
Convert module files from Tcl to Lua (#756)
Converts all module files from Tcl format to Lua. As a side effect, this change enforces using the files as modules rather than improperly sourcing them instead of loading.
Fixes #670
commit ca80aeb86cb221263611605ba23858448bce0bad
Author: lgannoaa <37596169+lgannoaa@users.noreply.github.com>
Date: Mon Apr 25 06:23:06 2022 -0400
Ensure hourly files when GLDAS is on (#740)
GLDAS requires hourly output, so make sure FHOUT is 1 when GLDAS is on.
Fixes #695
commit 9d00239088651b73a9667b70bd6247b34e35046f
Author: lgannoaa <37596169+lgannoaa@users.noreply.github.com>
Date: Tue Apr 19 21:22:22 2022 -0400
Update cyclone tracker to handle return code correctly #642
Updates the cyclone tracker call to correctly exit with an error code if the tracker script reports one.
Fixes #507
commit 33d3dd14d6df8109274dde4606bb7a50e4638fa2
Author: Jessica Meixner <jessica.meixner@noaa.gov>
Date: Tue Apr 19 21:18:56 2022 -0400
Update ww3 pre and post exe build to use cmake (#731)
Updates the WW3 pre/post build system to use cmake.
Fixes #688
commit 39facec1e03a404f84fd05b8739cd8e4010a0779
Author: Kate Friedman <kate.friedman@noaa.gov>
Date: Tue Apr 12 11:36:30 2022 -0400
Add WCOSS2 GFSv16.2 operational def files into develop (#717)
Add WCOSS2 operational GFS def files.
Refs: #399
commit 0a85223e48a1a8dcced163791d8e7ae5a42a4fab
Author: Xianwu Xue - NOAA <48287866+XianwuXue-NOAA@users.noreply.github.com>
Date: Tue Apr 12 11:34:17 2022 -0400
Initialize "err" to avoid potential task fail (#715)
If not initialize err, and change "set -x" to "set -xue", then the waveinit task will fail with error message:
"line 234: err: unbound variable"
On branch bugfix/issue_714
Changes to be committed:
modified: scripts/exgfs_wave_init.sh
Refs: #714
commit fc6e1c3316397432d2da218b3c4fc0ea1fe70644
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Tue Apr 5 11:07:21 2022 -0400
config.base should not exist in the repository unless it is in ops. template only exists in the repo, the experiment directory should not contain the templated config.base.emc.dyn (#707)
commit cabf437044cb937caf7a7830068fd9e413c5921f
Author: Jessica Meixner <jessica.meixner@noaa.gov>
Date: Wed Mar 30 21:28:50 2022 -0400
Update model and settings for Prototype P8b (#681)
Updates model and setting defaults for prototype 8b.
The UFS version is updated to a recent version of UFS (tag Prototype-P8b). As part of this, the print_esmf option is removed from the model configure file and replaced with a new setting in nems.configure. We have not made this option user-configurable at this point, but that may come in the future.
The default CCPP suites have been updated for all modes to either FV3_GFS_v17_p8 or FV3_GFS_v17_coupled_p8. This involves changing the microphysics to Thompson and changes the gravity wave drag version (knob_ugwp_version) to 0. This change breaks cycled mode for the time being. A future PR will revert the defaults to ones that allow cycled to run along with a more robust system for changing settings.
Tiled fix files are now used for all modes instead of just coupled.
Cellular automata now defaults on ON.
There are also other miscellaneous settings that have had their defaults changed.
Fixes #641, #687
commit e3f707cb9c05b45e9d4019679e406f54008279a5
Author: XuLi-NOAA <55100838+XuLi-NOAA@users.noreply.github.com>
Date: Thu Mar 24 05:43:31 2022 -0400
Modify eobs for EnKF thinning
In the Hybrid EnKF GSI, the thinning box size, dmesh, is different for the full resolution analysis and EnKF respectively. There are set in GSI scripts for the full resolution analysis, and reset in global workflow in config.eobs.
Only two thinning box sizes, dmesh(1) & dmesh(2), are defined in GSI scripts before, recently, two more, dmesh(3) & dmesh(4) are added. Accordingly, these two need to be added in config.eobs as well.
Specifically, add dmesh(3)=225.0,demsh(4)=100.0 to config.eobs.
Fixes #595
commit c32eea459af3177cee28e151b43fe5e12bdfc412
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Tue Mar 22 11:18:10 2022 -0400
Update ocean resolution for C48 (#651)
The ocean resolution for C48 was set as 1-deg, but the fractional
grid fix files available at C48 are for a 4-deg ocean grid. The
ocean resolution is now set to this value when FV3 is C48.
Also commented out a currently redundant block setting OCNRES in
config.ocn. The one in ecfs has to stay as it recalculates the
ocean resolution based on the EnKF resolution.
Fixes #650
commit d758e8b227fca7b5a3320adc43c29ba492c3bfe9
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Thu Mar 10 05:54:49 2022 -0500
Add single forecast GOCART support (#659)
Adds support for running single coupled free forecasts with GOCART aerosols. Support for continuous aerosol fields from cycle to cycle will be added in a future PR.
To turn on aerosols, there is a new --aerosols option for setup_expt.py. The option takes no arguments. When it is used, aerosols will be turned on by setting DO_AERO="YES" in config.base.
GOCART output files are placed in the chem directory in COM.
There is a new tarball archived, chem.tar, that contains the GOCART output.
Partially addresses #516
Fixes #403
commit a0e23e254c7c881b20d66c1c53cd36de509e6d69
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Tue Mar 1 10:50:39 2022 -0500
Specify memory for init job (#669)
The init job has been failing on HPC using slurm due to out-of-memory errors. Now the init job specifies the amount of memory needed.
Fixes #631
commit 6874e8939211fdc07143450bfd1b6a2863172e10
Author: arun chawla <49994787+arunchawla-NOAA@users.noreply.github.com>
Date: Fri Feb 25 16:39:45 2022 -0500
Cleanup of utils directory (#660)
Removes all of the old, unused GSM scripts and code from the utils directory. Those codes that might still be used have been moved to a new GSM-utils repo.
Fixes #618
commit e3d64abc9c02aecb9d5d38755f6524bf9e277e66
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Thu Feb 24 22:49:45 2022 -0500
Fix bug with partition_batch on WCOSS (#668)
partition_batch was not being defined for WCOSS machines, but was
being used in a substitution for config.base.
Fixes #667
commit 9d75d8d78037c7a74d1a9c61a88d9d6a7e9b3be9
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Mon Feb 21 02:10:00 2022 -0500
Split output filetype variable into atm and sfc (#602)
The determination of the FV3 output filetype was a bit unwieldy as it
contained two different settings (one for the atmosphere and one for
the surface) that were not necessarily changed at the same time. They
were also being determined in a different location than other settings
based on the model resolution.
Now the old OUTPUT_FILETYPES variable has been split into two different
variables, OUTPUT_FILETYPES_ATM and OUTPUT_FILETYPES_SFC. The determi-
nation was also moved into the config.fv3 file, where other resolution-
dependent computational settings are set.
This has resulted in some functional change on WCOSS Dell, as the EnKF
was using different chunking settings and never used parallel output
for the surface likely because wasn't being run at a low enough resolu-
tion to consider it. However, there is no reason to believe the two
forecast modes should have different chunk or output settings. So, I've
used the EnKF chunking settings and the free forecast switchover point
for the surface output mode.
The new filetype settings are now also divorced from the OUTPUT_FILE
setting. However, that setting will soon be unnecessary as nemsio
is removed from the code as an option (see Issue #601).
Fixes #600
Refs #601
commit cb8b5adf16200e7b01b8236a960efce5b6d8ce5d
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Thu Feb 17 15:55:24 2022 -0500
Correct MODE comparisons for forecast only (#658)
When the setup_expt scripts were combined, the forecast mode became a mandatory
argument. The value of this option is then directly used for the MODE variable,
but the argument name (forecast-only) does not match what was previously used
for MODE in the forecast-only script (free) and some scripts were still testing
against the old value instead of the new one. Those comparisons have now been
updated to use the new MODE name.
Fixes #657
commit f8867d3f0b1f3b5d238dced412996c56e30d31a1
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Thu Feb 10 20:23:54 2022 -0500
Add LOCALARCH option (#628)
Adds the option to archive output locally during archive jobs. This is intended for systems that do not have access to HPSS (e.g. Orion and soon S4), but can be used on any machine. To enable, the LOCALARCH setting in config.base should be set to "YES" (HPSSARCH must be "NO"). When enabled, the tarballs normally created on HPSS will instead be created in the local directory specified by $ATARDIR.
Defaults have been added to setup_expt.py to point to a local ATARDIR and LOCALARCH (currently =NO).
Fixes #624.
commit 2950c7b97f99341caa738526138022987f665627
Author: Jessica Meixner <jessica.meixner@noaa.gov>
Date: Thu Feb 10 18:07:43 2022 -0500
Turn on fractional grid by default for uncoupled forecasts (#638)
Updates input.nml so that there is more consistency between the cpl and standalone atm input.nml. In particular this addresses the fact that frac_grid was only being set if cpl was true.
Fixes #571
commit 64b1c1e5ce37fba48dd717bd11356a6f57d9def4
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Wed Feb 9 17:02:39 2022 -0500
Specify warm start as .true. or .false. (#644)
Corrects the assignment of EXP_WARM_START to either .true. or .false. depending on the value passed to setup_expt.py via `--start`.
Fixes #643
commit e537f0cecabc8e16e26b14e606558de906b19e3f
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Tue Feb 8 23:33:21 2022 -0500
Archive TC tracking logs if produced (#627)
The archive job was failing if there were no tropical cyclone files (such as when there are no cyclones). This adds a check for the TC tracking logs in case they are not produced to prevent the gfsarch job from failing on cycles when there were no TCs to track.
Fixes #625.
commit 32f93becde5ffa07c162252b95417845f2ab5159
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Tue Feb 8 20:59:37 2022 -0500
Fix separate threading for GFS and GDAS forecasts. (#621)
Fix separate threading options for GDAS and GFS forecasts (#610). This is performed by keeping nth_fcst_gfs separate from nth_fcst and declaring the new variable npe_node_fcst_gfs.
Fixes #610
commit 9bb09a92c55d4534feca5d521fbbd1c664730317
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Tue Feb 8 20:58:05 2022 -0500
Updated the RadMon and OznMon links. #596 (#597)
commit 97ebc4d4e6483b135468d85cd9ed974f88955914
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Thu Feb 3 02:56:34 2022 -0500
Unify `setup_expt.py` and `setup_expt_fcstonly.py` (#537)
`setup_expt.py` and `setup_expt_fcstonly.py` are unified under the former name.
The user is now required to provide a `mode` as the first positional argument to `setup.py`. Valid options are `cycled` and `forecast-only`.
```
❯ python3 setup_expt.py -h
usage: setup_expt.py [-h] {cycled,forecast-only} ...
Setup files and directories to start a GFS parallel. Create EXPDIR, copy config files. Create COMROT experiment directory structure, link
initial condition files from $ICSDIR to $COMROT
positional arguments:
{cycled,forecast-only}
cycled arguments for cycled mode
forecast-only arguments for forecast-only mode
optional arguments:
-h, --help show this help message and exit
```
Upon choosing one of these modes, options specific to the mode can be realized as follows for the `forecast-only` and `cycled` modes respectively.
```
❯ python3 setup_expt.py forecast-only -h feature/unify-setups
usage: setup_expt.py forecast-only [-h] [--pslot PSLOT] [--resdet RESDET] [--comrot COMROT] [--expdir EXPDIR] --idate IDATE --edate EDATE
[--icsdir ICSDIR] [--configdir CONFIGDIR] [--cdump CDUMP] [--gfs_cyc {0,1,2,4}] [--start {warm,cold}]
[--app {ATM,ATMW,S2S,S2SW}]
optional arguments:
-h, --help show this help message and exit
--pslot PSLOT parallel experiment name
--resdet RESDET resolution of the deterministic model forecast
--comrot COMROT full path to COMROT
--expdir EXPDIR full path to EXPDIR
--idate IDATE starting date of experiment, initial conditions must exist!
--edate EDATE end date experiment
--icsdir ICSDIR full path to initial condition directory
--configdir CONFIGDIR
full path to directory containing the config files
--cdump CDUMP CDUMP to start the experiment
--gfs_cyc {0,1,2,4} GFS cycles to run
--start {warm,cold} restart mode: warm or cold
--app {ATM,ATMW,S2S,S2SW}
UFS application
```
```
❯ python3 setup_expt.py cycled -h feature/unify-setups
usage: setup_expt.py cycled [-h] [--pslot PSLOT] [--resdet RESDET] [--comrot COMROT] [--expdir EXPDIR] --idate IDATE --edate EDATE
[--icsdir ICSDIR] [--configdir CONFIGDIR] [--cdump CDUMP] [--gfs_cyc {0,1,2,4}] [--start {warm,cold}]
[--resens RESENS] [--nens NENS] [--app {ATM,ATMW}]
optional arguments:
-h, --help show this help message and exit
--pslot PSLOT parallel experiment name
--resdet RESDET resolution of the deterministic model forecast
--comrot COMROT full path to COMROT
--expdir EXPDIR full path to EXPDIR
--idate IDATE starting date of experiment, initial conditions must exist!
--edate EDATE end date experiment
--icsdir ICSDIR full path to initial condition directory
--configdir CONFIGDIR
full path to directory containing the config files
--cdump CDUMP CDUMP to start the experiment
--gfs_cyc {0,1,2,4} GFS cycles to run
--start {warm,cold} restart mode: warm or cold
--resens RESENS resolution of the ensemble model forecast
--nens NENS number of ensemble members
--app {ATM,ATMW} UFS application
```
Note, `cycled` mode presents some extra options e.g. `nens` as well as a reduced list of the UFS weather model applications.
The functionality of `--icsdir` had been broken for cycled and was hard-coded in free forecast. The functionality has now been repaired for cycled. If you provide one, $COMROT will be populated with appropriate links. If none is specified, no links will be created in $COMROT. In coupled mode free-forecast, ICs are copied *to* icsdir from the central maintained prototype location. Coupled users will now need to set this explicitly. For non-coupled forecast-only, this setting currently does nothing.
The default value for `--configdir` has been updated to the appropriate location in the workflow. Most users will no longer need to set it unless they want to point to a different config source.
The default values for `--comrot` and `--expdir` are updated from None to $HOME to facilitate offline testing of workflow creation.
There are some irrelevant sections such as `gfs_cyc` in forecast-only that is still preserved in this PR. It will be cleaned up in subsequent PR's.
Another unnecessary complication is the argument of `--start`. The logic presented here would ideally be selected at runtime based on the type of IC's populated in comrot. It is left unchanged.
commit d7319f19aceca6ae6d7ce9b06c6eb731832d1de1
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Wed Feb 2 11:19:43 2022 -0500
Stop archiving gfsarch.log as it is being written (#581)
The gfs archive job was failing because it was attempting to archive its own log file into gfsa.tar while it was being written. To exclude that file pattern, bash extended globbing is turned on, which allows the use of a negating group.
Fixes: #558
commit 1b300dbf98eccdf03117b3795a2d8da3310a6126
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Wed Feb 2 11:18:55 2022 -0500
Fix build on non-WCOSS2 machines (#612)
The UFS_UTILS and GLDAS versions are updated to correct build problems on development machines. Each had been using a beta version of ESMF that was removed from the hpc-stack installation without warning. Additionally, GLDAS had introduced bugs into their build scripts during the WCOSS2 port. These issues are now all corrected in the new versions.
Also updates the UFS_UTILS repository to its new location under UFS instead of EMC.
Fixes #476, #561
commit d3028b9d8268028226f9c27800fcd6655e9e4bb8
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Wed Jan 19 14:29:51 2022 -0500
Fix setting of OUTPUT_FILETYPES (#589)
The setting of OUTPUT_FILETYPES was being overwritten by the FV3 model configure parsing script, so the settings determined in the config.fcst file was being ignored. Now that block is removed and config.fcst is updated to make sure it is set for any machine.
Fixes #588
commit 13421b01a07e5d1cca32ee7579a4094d8209b072
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Wed Jan 19 12:16:29 2022 -0500
Update PR template
commit 322a61a61238e8486cb42d7d26282b2728d0c32f
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Wed Jan 19 12:13:33 2022 -0500
Move PR template MD file. Update issue templates
commit 7a52fc8d8bbfc5896b7d03004d5189b2a6b24013
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Wed Jan 19 11:32:51 2022 -0500
rename pull_request_template.md
commit 88ec66eb834e9a78c94feae4f37f774c7807aa3c
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Wed Jan 19 10:34:54 2022 -0500
make changes to the templates
commit 66d84e21ad7ae3fafb4ad5097faf86dfa1b99b60
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Wed Jan 19 10:08:45 2022 -0500
Fix lfrac entry in diag table (#570)
Land fraction was listed in the wrong module, keeping it from being
written to output.
Refs: #562
commit e2657adbdadaac7089591390428324c6aec260a9
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Tue Jan 18 17:04:04 2022 -0500
Update NCO_bug_report.md
commit a9d6851a0c3b6051cb1c7c7ec482fc50d762bef4
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Tue Jan 18 16:59:18 2022 -0500
Update bug report issue template
commit 2fab8b4213645b79b3fea8127e7d4ab21044188e
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Tue Jan 18 15:13:53 2022 -0500
Add templates for Github (#560)
Adds GitHub templates for new issues and PRs to standardize and make sure all the needed information is included.
commit 03be05309b184421c473f1b43082b766b114fd46
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Tue Jan 18 10:02:02 2022 -0500
Fix toggle for building workflow_utils (#580)
The fv3gfs_build.cfg did not have a space between the periods and
the setting for workflow_utils, which means the setting was ignored
and the default of yes was always used.
Fixes: #577
commit aadd3bae3d4fdc7827a93ab51b336a7f6b2fdb02
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Tue Jan 18 10:01:24 2022 -0500
Remove redundant toggle for gldas build (#579)
The build cfg files controlling which components are built and the
partial_build.sh script all have two instances trying to set the
value for gldas. This means one of the settings did nothing when
changed.
Fixes: #578
commit 86d4b305a070c080dcfd44a3f9a31ca2280759fa
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Fri Jan 14 01:05:59 2022 -0500
Update config missed in last GSI update (#569)
When the GSI version was updated in PR #530, updates to the config.anal file were mistakenly omitted. That file is now updated following ops (PR #451, #489).
Refs: PR #530
commit 33308ea3b477db17a5db455a4c4887e3d5cbc711
Author: Jessica Meixner <jessica.meixner@noaa.gov>
Date: Thu Jan 6 00:44:43 2022 -0500
Updates for P8a (#538)
Updates ufs-weather-model to the 2021 Dec 23 commit and the matching UPP hash. Coupled settings are updated to run the P8a mini prototype.
Updates include:
…
WalterKolczynski-NOAA
added
nco-bug
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The only ones that don't have |
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Even if the cmake builds support using debug, we need to make sure the individual |
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@WalterKolczynski-NOAA @aerorahul I checked that all
Is it safe to assume that the other sources listed here are beyond the scope of this PR? |
7 tasks
aerorahul
pushed a commit
that referenced
this issue
Mar 1, 2024
This PR addresses issue #300 that allows building in `debug` mode. Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com>
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@KateFriedman-NOAA Would you please update the bugzilla spreadsheet and issue? |
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I have updated our bugzilla spreadsheet to mark it as RESOLVED. I have also updated the actual bugzilla to note our work, provide links to the associated global-workflow issue/PR, and change the status to RESOLVED/FIXED for NCO to review for closure when the time comes. |
kayeekayee
added a commit
to kayeekayee/global-workflow
that referenced
this issue
Mar 15, 2024
UFS: 21Feb24, 6988662 FV3: 14Feb24, 0fe9ba3 UPP: 23Jan23, 945cb2c UFS_UTILS: 22Feb24, d805336 Squashed commit of the following: commit 732a874 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Mon Mar 4 16:04:26 2024 -0500 Reformat snowDA templates to jinja2 (NOAA-EMC#2371) # Description This PR: - replaces use of non-jinja2 templates in the yaml templates. Specifically `$( )` in favor of pure jinja2. - uses jinja2's built-in capability to include templates within templates, thereby allowing to assemble a completely rendered template before passing it to for e.g. yaml loader. - requires updates to `wxflow` and `gdasapp` - Changes in `wxflow` in `parse_j2yaml` are **not** backwards compatible Additionally, this PR: - renames `config.base.emc.dyn` to `config.base`. Resolves NOAA-EMC#2347 commit d1fa411 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Sat Mar 2 04:54:26 2024 +0000 Reduce Jenkins messaging to GitHub (NOAA-EMC#2370) This PR updates the Jenkins Pipeline code with safeguards against the errors caused when Jenkins fails to authenticate with GitHub to message or update a label. This was achieved simply by: - Reducing the number out messages sent to the GitHub PR - Putting try blocks around most of the update label calls Co-authored-by: tmcguinness <terry.mcguinness@noaa.gov> commit 52fa3cb Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Fri Mar 1 12:36:27 2024 -0700 Adding debug option for all build scripts (NOAA-EMC#2326) This PR addresses issue NOAA-EMC#300 that allows building in `debug` mode. Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit 91738cb Author: DWesl <22566757+DWesl@users.noreply.github.com> Date: Fri Mar 1 13:46:42 2024 -0500 Sort list of coupler restart files for restart time determination (NOAA-EMC#2360) The loop in the following conditional seems to assume the list is sorted, so make that explicit in the array construction. commit 23c2552 Author: Neil Barton <103681022+NeilBarton-NOAA@users.noreply.github.com> Date: Fri Mar 1 13:45:39 2024 -0500 Update stage IC to handle ocean perturbations (NOAA-EMC#2364) This PR adds the option to stage ocean perturbation files for ensemble forecasts. These perturbation files are used in GEFS forecasts. A new variable is introduced in config.base to use the ocean perturbation files. This PR does not include using these perturbation files. A future PR will address this. commit 8efe05f Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Fri Mar 1 07:41:56 2024 -0500 Turn on C48mx500_3DVarAOWCDA test on hera (NOAA-EMC#2363) This PR activates the C48mx500_3DVarAOWCDA test on hera. This required an update of the gdas app. commit 5166593 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Thu Feb 29 20:14:41 2024 +0000 Move Jenkinsfile into ci subdirectory (NOAA-EMC#2355) Just moves the Jenkinsfile into the ci directory Co-authored-by: tmcguinness <terry.mcguinness@noaa.gov> commit b7af315 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Feb 28 22:20:58 2024 +0000 Fix rocoto forecast hour determination for GEFS (NOAA-EMC#2351) The function that generates the list of forecast hours for rocoto was trying to use variables that are not defined for GEFS, causing workflow generation to fail. The function is updated to not try to load these variables before loading the ones actually used for GFS/ GEFS. Also turns GEFS CI test back on and adds an entry to stage C192 ICs (note: these have not been placed in the centralized location.) commit d3a4927 Author: Cory Martin <cory.r.martin@noaa.gov> Date: Wed Feb 28 09:38:49 2024 -0500 Rename the land DA jobs to snow DA to better reflect what they are doing (NOAA-EMC#2330) This PR renames all of the land DA jobs to snow DA to better reflect that this is a JEDI-based snow analysis capability and not a more generic land surface analysis. commit 2693810 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Tue Feb 27 01:25:51 2024 -0500 Update ufs-waether-model hash (NOAA-EMC#2338) Routine update of ufs-weather-model hash. Other small updates: * removes comment referencing closed issue. * Updates the CICE diag frequency to once per day as recommend here: NOAA-EMC#1810 (comment) * Updated amount of time for C384 gdas forecast as it was running out of time * Removed unused variable wave_sys_ver commit 9608852 Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com> Date: Mon Feb 26 14:10:01 2024 -0500 Update JEDI ATM to use .nc for obs and generalize x,y layout (NOAA-EMC#2336) # Description The changes in this PR are twofold 1. replace `.nc4` suffix for JEDI ATM observation related files with `.nc` 2. use templated variables to specify `{layout_x, layout_y}` for JEDI ATM variational and local ensemble apps The first change conforms with the Unidata recommendation that netCDF files end with the suffix `.nc`. The second change replaces hardwired JEDI ATM var and ens `{layout_x, layout_y}` in `config.resources` with a more flexible approach. Resolves NOAA-EMC#2335 commit c5c8466 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Mon Feb 26 10:18:50 2024 -0500 Remove FIX* variables for fix subfolders (NOAA-EMC#2337) Remove `FIX*` variables for fix subfolders and replace them with the remaining `FIXgfs` variable and the subfolder name (e.g. `${FIXam}` -> `${FIXgfs}/am`). The UFS_UTILS and GDASApp repos were similarly updated. This PR includes a new UFS_UTILS hash. The updated GDASAPP hash was already committed within the spack-stack/1.6.0 PR NOAA-EMC#2239. Resolves NOAA-EMC#2184 commit 950c38a Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Fri Feb 23 21:15:46 2024 +0000 Fix several Jenkins issues (NOAA-EMC#2334) Jenkins Updates Resolving final kinks: - Removed all `git` shell commands and now exclusively use Software Control Manger (**scm**) plugin. - Add feature for skipping hosts per configuration specified in case yaml files. - Solved and tested false positive builds and experiments. - Tested archiving of task error log on case fail - First case fail quits pipeline and cancels all pending scheduled jobs - Duel build per yaml configuration arguments supported - All designated case files in PR directory pass on intended host (fully tested on Hera) Remaining updates: - Fist build fail short circuit when building sub-modules and archiving build error log. - Re-build/no-build built in logic for Replay and Rerunning previously failed experiments. commit c67393a Merge: 6f9afff 79d305e Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Fri Feb 23 14:18:15 2024 +0000 Merge pull request NOAA-EMC#2239 from DavidHuber-NOAA/ss160 Update to spack-stack 1.6.0 Includes all submodules except the UFS, which will be updated at a later time. commit 79d305e Author: David Huber <david.huber@noaa.gov> Date: Thu Feb 22 14:53:57 2024 -0600 Disable snow DA tests commit 0459203 Author: David Huber <david.huber@noaa.gov> Date: Thu Feb 22 12:55:51 2024 -0600 Update GDASApp hash to current develop commit 5c96eb2 Author: David Huber <david.huber@noaa.gov> Date: Thu Feb 22 12:37:47 2024 -0600 Update GDAS hash to allow modified snow DA analysis commit 79144f2 Merge: abbb0b8 6f9afff Author: DavidHuber <david.huber@noaa.gov> Date: Thu Feb 22 15:14:39 2024 +0000 Merge remote-tracking branch 'origin/develop' into ss160 commit abbb0b8 Merge: 4ad837e 4529e8c Author: DavidHuber <david.huber@noaa.gov> Date: Thu Feb 22 15:11:03 2024 +0000 Merge remote-tracking branch 'henry/feature/gwdev_issue_2129' into ss160 commit 4ad837e Merge: 516b2a2 7ca45db Author: DavidHuber <david.huber@noaa.gov> Date: Thu Feb 22 15:10:24 2024 +0000 Merge remote-tracking branch 'henry/feature/gfsv17_issue_2125' into ss160 commit 516b2a2 Author: DavidHuber <david.huber@noaa.gov> Date: Thu Feb 22 14:19:16 2024 +0000 Updated GDAS to include rocoto/1.3.6 on Hera. commit 6f9afff Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Wed Feb 21 13:09:44 2024 -0500 Add some flexibility for ocean/ice output (NOAA-EMC#2327) This adds functionality to have ocean/ice output frequency be separate from the atm model. One time was created because there's an assumption in the post that these are the same. This could be further modified to remove this assumption. Refs NOAA-EMC#1629 commit f6d3015 Author: David Huber <david.huber@noaa.gov> Date: Tue Feb 20 09:53:08 2024 -0600 Update GDASApp hash to include SS/1.6.0 support. commit 0bf340b Author: David Huber <david.huber@noaa.gov> Date: Tue Feb 20 09:07:32 2024 -0600 Construct SS paths from version variables. commit 3330cd7 Author: David Huber <david.huber@noaa.gov> Date: Tue Feb 20 09:06:19 2024 -0600 Removed MET/METplus 'not available' comments commit fdc638c Author: David Huber <david.huber@noaa.gov> Date: Tue Feb 20 08:35:15 2024 -0600 Move SS module path to version files. commit d7d28a6 Author: David Huber <david.huber@noaa.gov> Date: Tue Feb 20 07:53:15 2024 -0600 Update comment about METplus support. commit a812f88 Author: David Huber <david.huber@noaa.gov> Date: Tue Feb 20 07:45:45 2024 -0600 Update verif-global to latest WCOSS2 support. commit d81f07f Author: David Huber <david.huber@noaa.gov> Date: Tue Feb 20 07:41:38 2024 -0600 Clean up build_upp.sh. -Corrected whitespace (tabs instead of spaces) -Removed debug print statement -Alphebetized flags commit ae7eb19 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Fri Feb 16 16:15:40 2024 -0500 Fix whitespace in build_upp.sh. Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> commit 48b34d0 Author: David Huber <david.huber@dlogin05.dogwood.wcoss2.ncep.noaa.gov> Date: Fri Feb 16 20:56:55 2024 +0000 Added verif-global support back to WCOSS2. commit 4529e8c Author: henrywinterbottom-wxdev <henry.winterbottom.wxdev@gmail.com> Date: Fri Feb 16 11:12:01 2024 -0700 Bug fix. commit 8e4f94d Author: henrywinterbottom-wxdev <henry.winterbottom.wxdev@gmail.com> Date: Fri Feb 16 11:04:41 2024 -0700 Updates requested by reviewer Rahul Mahajan. commit 4624ce2 Author: henrywinterbottom-wxdev <henry.winterbottom.wxdev@gmail.com> Date: Fri Feb 16 10:52:11 2024 -0700 Updates requested by reviewer; testing -- DO NOT REVIEW. commit ed25bbd Author: henrywinterbottom-wxdev <henry.winterbottom.wxdev@gmail.com> Date: Fri Feb 16 09:33:59 2024 -0700 Linter corrections. commit 6a0b7bf Merge: f9fb64e 2415b7b Author: David Huber <david.huber@noaa.gov> Date: Fri Feb 16 09:50:22 2024 -0600 Merge branch 'ss160' of github.com:DavidHuber-NOAA/global-workflow into ss160 commit f9fb64e Merge: 777d97d a23b7f2 Author: David Huber <david.huber@noaa.gov> Date: Fri Feb 16 09:49:42 2024 -0600 Merge remote-tracking branch 'emc/develop' into ss160 commit 7ca45db Merge: 73bc76b a23b7f2 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Fri Feb 16 07:46:35 2024 -0700 Merge branch 'NOAA-EMC:develop' into feature/gfsv17_issue_2125 commit eb2ed53 Merge: 9929277 a23b7f2 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Fri Feb 16 07:46:24 2024 -0700 Merge branch 'NOAA-EMC:develop' into feature/gwdev_issue_2129 commit a23b7f2 Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com> Date: Fri Feb 16 09:37:58 2024 -0500 Add JEDI 3DEnVar atmosphere only CI test stub (NOAA-EMC#2309) commit cf83885 Author: Jessica Meixner <jessica.meixner@noaa.gov> Date: Fri Feb 16 01:55:02 2024 -0500 Add unstructured grid for HR3/GFS (NOAA-EMC#2230) This adds the capability to use unstructured grids in the global workflow, which will be used in HR3. There are new fix files for a low-resolution 100km grid and a grid closer to our targeted GFSv17 grid which has the resolution combined from the older multi_1 and GFSv16 grids. The fix file update is here: NOAA-EMC#2229 Note: This now means that GFS tests need a new build option: `./build_all.sh -w` So that PDLIB=ON is turned on for compiling relevant UFS and WW3 codes. Resolves NOAA-EMC#1547 commit 9929277 Merge: eb8791c 094e3b8 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Thu Feb 15 15:05:50 2024 -0700 Merge branch 'NOAA-EMC:develop' into feature/gwdev_issue_2129 commit 094e3b8 Author: Cory Martin <cory.r.martin@noaa.gov> Date: Thu Feb 15 14:43:55 2024 -0500 Move IMS remapping files from COM_OBS to FIXgdas (NOAA-EMC#2322) * Add in IMS obs fix directory and update submodule for gdas commit d465ea0 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Thu Feb 15 19:25:02 2024 +0000 Set HOMEgfs for module_setup in CI driver (NOAA-EMC#2321) Hotfixes to CI Bash system from updates with sourcing `detect_machine.sh` in `ush/module-setup.sh` using **HOMEgfs**. commit 2415b7b Author: David Huber <david.huber@noaa.gov> Date: Thu Feb 15 19:21:17 2024 +0000 Load default rocoto on Jet. commit eb8791c Merge: 60d5ee6 638684e Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Thu Feb 15 11:56:40 2024 -0700 Merge branch 'NOAA-EMC:develop' into feature/gwdev_issue_2129 commit 777d97d Author: David Huber <david.huber@noaa.gov> Date: Thu Feb 15 12:34:59 2024 -0600 Fixed Orion cdo version. commit ef07235 Author: DavidHuber <david.huber@noaa.gov> Date: Thu Feb 15 16:29:32 2024 +0000 Revert UFS hash. commit 0ce8c0d Author: DavidHuber <david.huber@noaa.gov> Date: Thu Feb 15 14:55:48 2024 +0000 Fix git version in Hera's gwsetup module. commit 3080a34 Author: DavidHuber <david.huber@noaa.gov> Date: Wed Feb 14 20:52:34 2024 +0000 Fixed xarray version for SS/1.6.0. commit 49392dd Author: DavidHuber <david.huber@noaa.gov> Date: Wed Feb 14 20:29:41 2024 +0000 Updated GSI-Utils hash to head of develop. commit c3553f0 Merge: 4568653 638684e Author: DavidHuber <david.huber@noaa.gov> Date: Wed Feb 14 20:28:14 2024 +0000 Merge remote-tracking branch 'origin/develop' into ss160 commit 4568653 Author: David Huber <david.huber@noaa.gov> Date: Wed Feb 14 14:22:13 2024 -0600 Reupgrade Hercules to SS/1.6.0 commit 638684e Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed Feb 14 14:55:21 2024 -0500 Remove `finddate.sh` from system (NOAA-EMC#2308) * Retire finddate.sh usage from system * Update gfs-utils hash to 7a84c88 - New hash includes removal of finddate.sh Refs NOAA-EMC#2279 commit 2b160f8 Author: DavidHuber <david.huber@noaa.gov> Date: Wed Feb 14 18:31:28 2024 +0000 Reenable METplus jobs on Hercules. commit 8f59002 Author: DavidHuber <david.huber@noaa.gov> Date: Wed Feb 14 18:30:23 2024 +0000 Update GSI hashes. commit 73bc76b Author: henrywinterbottom-wxdev <henry.winterbottom.wxdev@gmail.com> Date: Wed Feb 14 09:27:37 2024 -0700 Updates based on user request. commit e4bc674 Author: henrywinterbottom-wxdev <henry.winterbottom.wxdev@gmail.com> Date: Wed Feb 14 08:03:45 2024 -0700 Corrected based on reviewer review. commit 60d5ee6 Merge: 40f2cf6 1aaef05 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Tue Feb 13 18:08:33 2024 -0700 Merge branch 'NOAA-EMC:develop' into feature/gwdev_issue_2129 commit 0330411 Merge: 929b903 1aaef05 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Tue Feb 13 17:58:12 2024 -0700 Merge branch 'NOAA-EMC:develop' into feature/gfsv17_issue_2125 commit 1aaef05 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Tue Feb 13 18:15:59 2024 -0500 Jenkins Pipeline updates for Canceling Jobs (NOAA-EMC#2307) Tuning updates for Jenkins Pipeline : - Added short circuit for all parallel runs of cases on error of any - Fixed canceling of all scheduled jobs on first case error - Added feature to save error log files to Jenkins Archive facility on fail commit 6404892 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Feb 13 14:57:37 2024 -0500 Ocean/ice product generation for GFS and GEFS (NOAA-EMC#2286) This PR does several things: 1. the model output for ocean and ice in the `COM/` directory are now named per EE2 convention for coupled model. E.g `gfs.ocean.t12z.6hr_avg.f120.nc` and `gfs.ocean.t12z.daily.f120.nc` 2. The products are generated using the `ocnicepost.fd` utility developed by @DeniseWorthen in https://github.com/NOAA-EMC/gfs-utils and converted to grib2 using example scripts provided by @GwenChen-NOAA using `wgrib2`. 3. NetCDF products on the native grid are also generated by subsetting variables from the raw model output. This is done with `xarray`. 4. updates the hash of https://github.com/NOAA-EMC/gfs-utils to include fixes in `ocnicepost.fd` 5. removes NCL related scripting that was previously used for ocean/ice interpolation and `reg2grb2` used for converting to grib2. 6. updates archive scripts to accommodate updated file names 7. removes intermediate ocean processed files such as 2D/3D/xsect data- sets 8. separate jobs are added for ocean and ice product generation. 9. removes intermediate restarts for the mediator and only saves the medi- ator restart at the end of the forecast in `COM`. 10. Increases memory for offline UPP when run at C768. The program segfaults with an OOM when memory is self allocated based on PEs by the scheduler on Hera. 11. Enables ocean/ice ensemble product generation for GEFS 12. Some minor clean-ups Fixes NOAA-EMC#935 Fixes NOAA-EMC#1317 Fixes NOAA-EMC#1864 commit 40f2cf6 Author: henrywinterbottom-wxdev <henry.winterbottom.wxdev@gmail.com> Date: Tue Feb 13 10:18:53 2024 -0700 Implemented ush/detect_machine.sh for host determination and removed redundant checks for expected file paths. commit 929b903 Merge: 2d08d01 3f99f70 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Tue Feb 13 08:31:06 2024 -0700 Merge branch 'NOAA-EMC:develop' into feature/gfsv17_issue_2125 commit 3f99f70 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Tue Feb 13 00:57:18 2024 -0500 Add wave post jobs to GEFS (NOAA-EMC#2292) Adds the wave post jobs for gridded and points to GEFS. Boundary point jobs are added even though the current GEFS buoy file does not contain any (tested by manually subbing in the GFS buoy file). Resolves NOAA-EMC#827 commit 842adf3 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Mon Feb 12 12:50:08 2024 -0500 Added additional test cases to the pr list in Jenkins (NOAA-EMC#2306) C48mx500_3DVarAOWCDA, C96C48_hybatmDA, and C96_atmsnowDA Co-authored-by: terrance.mcguinness <terrance.mcguinness@noaa.gov> commit bb4ca65 Author: CatherineThomas-NOAA <59020064+CatherineThomas-NOAA@users.noreply.github.com> Date: Mon Feb 12 14:50:41 2024 +0000 Redo v16.3 config.base changes for DA increments (NOAA-EMC#2304) Include the additional hydrometeors to the INCREMENTS_TO_ZERO and INCVARS_ZERO_STRAT variables in config.base that were modified in v16.3. Resolves: NOAA-EMC#2303 commit 061992b Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Sat Feb 10 01:33:36 2024 -0500 Fix Jenkins success reporting (NOAA-EMC#2302) Moving the post section back outside of main Run Experiments stage. This allows the system to correctly report the **Success** status until after all tests pass. _Had originally moved them in attempts to solve "Not an SCM GitHub Job" issue and cause the reporting to misbehave._ Also ran through Jenkins linter and updated some messaging that was incorrectly reporting system build type. commit 28ccf78 Merge: b972f66 54daa31 Author: David Huber <david.huber@noaa.gov> Date: Fri Feb 9 14:00:43 2024 -0600 Merge remote-tracking branch 'emc/develop' into ss160 commit b972f66 Author: David Huber <david.huber@noaa.gov> Date: Fri Feb 9 10:47:00 2024 -0600 Fix SS versions for CI modules. commit 4b01d8e Author: David Huber <david.huber@noaa.gov> Date: Fri Feb 9 10:44:30 2024 -0600 Revert Hercules modules to SS/1.5.1. commit 54daa31 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Thu Feb 8 15:48:38 2024 -0500 Jenkins Declartive Pipeline for CI with gfs/gefs multibuilds (NOAA-EMC#2246) Adding top level Jenkins file for CI tests running on Jenkins Controller: - Declarative Multi-branch Pipeline (has enhanced restart capabilities on a per section bases) - Starts Pipeline from Label PR same as BASH system (for now) - Progress and restarts can me managed with CAC Login at [EPIC OAR Jenkins](https://jenkins.epic.oarcloud.noaa.gov) - Has logic for multi **gfs/gefs** system builds (arguments based on a configuration file `ci/casts/yamls/build.yaml`) - Any number of **systems** may be added by manual adding an ele- ment to the matrix in the Jenkinsfile - _It may be possible to dynamic add matrix values with a specialty plug-in_ - Currently only runs on **Orion** and **Hera** using `mterry` account Resolves NOAA-EMC#2119 Resolves NOAA-EMC#2118 commit 43429e2 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Thu Feb 8 15:30:28 2024 -0500 Enable AO WCDA test (NOAA-EMC#1963) This PR: - adds GSI + SOCA C48 5-deg ocean 3DVar test (courtesy @guillaumevernieres) - adds a toggle to optionally disable ocnanalvrfy job. commit 2d08d01 Merge: 4745d4a f563528 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Thu Feb 8 07:24:54 2024 -0700 Merge branch 'NOAA-EMC:develop' into feature/gfsv17_issue_2125 commit f563528 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Wed Feb 7 15:09:12 2024 -0500 Update JGLOBAL_FORECAST for octal error (NOAA-EMC#2295) Add "10#" to ENSMEM value > 0 check to handle octal errors. commit 4745d4a Author: henrywinterbottom-wxdev <henry.winterbottom.wxdev@gmail.com> Date: Wed Feb 7 08:45:49 2024 -0700 Removed jlogfile references. commit 5894ca2 Author: henrywinterbottom-wxdev <henry.winterbottom.wxdev@gmail.com> Date: Wed Feb 7 08:32:16 2024 -0700 Removed dummy variable passed to perl scripts. commit dae884a Author: henrywinterbottom-wxdev <henry.winterbottom.wxdev@gmail.com> Date: Wed Feb 7 08:29:49 2024 -0700 Removed jlogfile and postmsg references within gempak scripts. commit 801058f Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Wed Feb 7 00:41:59 2024 -0700 Consolidate `npe_node_max` (NOAA-EMC#2289) - The environment variable `npe_node_max` is removed from all files beneath `global-workflow/env`; - The environment variable `npe_node_max` is removed from `parm/config/gefs/config.ufs` and `parm/config/gfs/config.ufs`; - The environment variable `npe_node_max` is maintained only within `parm/config/gefs/config.resources` and `parm/config/gfs/config.resources`. Resolves NOAA-EMC#2133 commit b0325e0 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Wed Feb 7 00:40:20 2024 -0700 Removes files module loading file no longer used by the GW (NOAA-EMC#2281) Removes `module-setup.csh.inc` and `module-setup.sh.inc`. The module `ush/module-setup.sh` is updated such that it now sources `ush/detect_machine.sh` to determine which supported platform the global-workflow is being execute on. Resolves NOAA-EMC#2130 commit 1ccc989 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Mon Feb 5 14:16:07 2024 -0500 Remove EnKF forecast groups (NOAA-EMC#2280) Removes the grouping of EnKF forecasts so each job only runs one forecast. Member and MEMDIR are now set at the workflow manager (rocoto) level. This change makes much of the system simpler (especially dependencies) and allows the elimination of the separate efcs scripts. Metatask names of updated jobs have been updated to make them a little less opaque by using the same name name as its constituent tasks (e.g. the forecast metatask is named `enkgdasfcst`, not `enkfgdasefcs`). Metatasks that weren't updated retain the same names as before for now. Resolves NOAA-EMC#2254 commit 9f3383f Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Mon Feb 5 12:15:13 2024 -0700 Updated detect_machine.sh using that from UFS WM. (NOAA-EMC#2252) Updates `ush/detect_machine.sh` to match the UFS weather-model `tests/detect_machine.sh` prepared by @BrianCurtis-NOAA Resolves NOAA-EMC#2228 commit 7d68b0b Author: CatherineThomas-NOAA <59020064+CatherineThomas-NOAA@users.noreply.github.com> Date: Sun Feb 4 22:02:41 2024 +0000 Update global_cycle for fractional grid (NOAA-EMC#2262) The hash for ufs_utils is updated to include the changes for fractional grid support within global_cycle. This commit also removes the hack to skip global_cycle in cycling mode with v17 physics. Resolves: NOAA-EMC#1775 Refs: ufs-community/UFS_UTILS#815 Refs: ufs-community/UFS_UTILS#891 commit ed592a6 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Sat Feb 3 02:55:14 2024 -0500 Retire cycle-specific FHMAX_GFS variables (NOAA-EMC#2278) This PR retires the `FHMAX_GFS_${cyc}` variables that allowed users to specify different gfs forecast lengths for each cycle. This function is no longer supported in global-workflow. The `FHMAX_GFS_*` variables will be removed and will no longer be checked to set the final `FHMAX_GFS` variable. The same forecast length will be set for every cycle. This PR also includes a small fix to add new post parm files into the `.gitignore` file. This was intended to be included in a different PR but that PR is on hold for further testing so it is being included here to get it into `develop` sooner. Resolves NOAA-EMC#2218 commit 977e2d6 Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com> Date: Fri Feb 2 07:49:09 2024 -0700 New GDASApp hash. (NOAA-EMC#2285) commit b5f2bd9 Merge: 4d66742 0400e1f Author: David Huber <david.huber@noaa.gov> Date: Tue Jan 30 13:55:00 2024 -0600 Merge branch 'ss160' of github.com:DavidHuber-NOAA/global-workflow into ss160 commit 0400e1f Author: David Huber <david.huber@noaa.gov> Date: Tue Jan 30 09:57:11 2024 -0600 Fix gfs_utils Orion spack-stack env path. commit 6bbe823 Author: DWesl <22566757+DWesl@users.noreply.github.com> Date: Mon Jan 29 21:15:30 2024 -0500 Use seq to generate the list of times, instead of a bash for-loop (NOAA-EMC#2264) I'm running a year-long forecast, which means I get a large portion of the log file dedicated to these loops. `seq ${START} ${STEP} ${STOP}` will generate a sequence going from START to STOP by STEP, including STOP if relevant. That seems to be the purpose of these loops. It will by default separate the list with newlines, but `seq -s ' ' ${START} ${STEP} ${STOP}` will separate them with spaces instead, more closely mimicing the previous behavior. I would like this to be two lines in the log, rather than a few hundred, and this may also be faster, though probably more for reasons of fewer writes to disk than because bash isn't designed for arithmetic. commit d5bee38 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Mon Jan 29 14:35:02 2024 -0500 Correct typos in GFS config.resources (NOAA-EMC#2267) This PR corrects some typos in `parm/config/gfs/config.resources` that were introduced in PR NOAA-EMC#2216. The esfc job was failing in tests on WCOSS2 due to insufficient memory. This lead to discovering the other typos. The esfc job completes without error after its memory is set back to `80GB` from the incorrect `8GB`. Resolves NOAA-EMC#2266 commit 81557be Author: David Huber <david.huber@noaa.gov> Date: Mon Jan 29 12:13:31 2024 -0600 Update monitor hash to noaa-emc with SS/1.6.0 support. commit 2238dd6 Author: DavidHuber <david.huber@noaa.gov> Date: Mon Jan 29 13:21:30 2024 +0000 Update Orion, Hercules, S4 modulefiles. commit 6ffd94f Author: DavidHuber <david.huber@noaa.gov> Date: Fri Jan 26 16:01:23 2024 +0000 Update GDAS hash to include SS/1.6.0 support. commit be11f85 Merge: 56b9680 04e0772 Author: DavidHuber <david.huber@noaa.gov> Date: Fri Jan 26 15:34:24 2024 +0000 Merge branch 'ss160' of github.com:DavidHuber-NOAA/global-workflow into ss160 commit 8ff3448 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Fri Jan 26 10:12:18 2024 -0500 Add a yaml for snow DA testing. (NOAA-EMC#2199) - adds a new test yaml C96_atmsnowDA.yaml for 3DVar atmosphere with GSI and Land (Snow) DA with JEDI - moves a few yamls from platforms/ to yamls/ - adds ability to overwrite a previously created experiment as an addition to user input. --------- Co-authored-by: Cory Martin <cory.r.martin@noaa.gov> commit 04e0772 Author: David Huber <david.huber@noaa.gov> Date: Fri Jan 26 07:16:25 2024 -0600 Update ufs_utils hash for spack-stack/1.6.0 support. commit 3d44ff3 Author: Barry Baker <bbakernoaa@users.noreply.github.com> Date: Thu Jan 25 14:33:27 2024 -0500 GOCART ExtData biogenic climatology fix (NOAA-EMC#2253) Updates the ExtData for biogenic emissions to be climatology rather than for current time. Fixes an issue which will crash by default for other years. commit 66f58b8 Author: Guillaume Vernieres <guillaume.vernieres@noaa.gov> Date: Thu Jan 25 13:16:41 2024 -0500 Added missing container case in gfs/config.resources (NOAA-EMC#2258) fixes NOAA-EMC#2257 commit 553b4f2 Author: WenMeng-NOAA <48260754+WenMeng-NOAA@users.noreply.github.com> Date: Thu Jan 25 13:00:45 2024 -0500 Fix post parm links (NOAA-EMC#2243) Change symbolic links under parm/post with the latest version of develop branch from UPP repository and enable MERRA2 aerosol fields. Resolves NOAA-EMC#2259 commit 4d66742 Merge: 6c05803 afa09e3 Author: David Huber <david.huber@noaa.gov> Date: Thu Jan 25 07:49:08 2024 -0600 Merge branch 'ss160' of github.com:DavidHuber-NOAA/global-workflow into ss160 commit 6c05803 Author: David Huber <david.huber@noaa.gov> Date: Thu Jan 25 07:48:42 2024 -0600 Fix wgrib2/gfs_utils on Hercules. commit ee6f536 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Thu Jan 25 07:43:13 2024 -0500 Update GFS version to v16.3.13 in index.rst (NOAA-EMC#2256) GFSv16.3.13 WAFS update was implemented Refs NOAA-EMC#2013 commit 2445d44 Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com> Date: Thu Jan 25 06:17:11 2024 -0500 Simplify and extend load_ufsda_modules to Hercules (NOAA-EMC#2245) GDASApp jobs do not run on Hercules because `ush/load_ufsda_modules.sh` does not include logic to load the appropriate GDASApp modules on Hercules. This PR extends `load_ufsda_modules.sh` functionality to Hercules, thereby enabling GDASApp jobs to run on Hercules. Resolves NOAA-EMC#2244 commit 56b9680 Author: DavidHuber <david.huber@noaa.gov> Date: Wed Jan 24 19:47:34 2024 +0000 Update hashes (revert WCOSS2 modules). commit afa09e3 Author: DavidHuber <david.huber@noaa.gov> Date: Wed Jan 24 18:59:40 2024 +0000 New (cleaner history) gdas hash. commit a9eaec2 Author: DavidHuber <david.huber@noaa.gov> Date: Wed Jan 24 18:52:27 2024 +0000 Update gdasapp to include ss/1.6.0 support. commit 5ef8eb2 Merge: 4c46354 e400068 Author: DavidHuber <david.huber@noaa.gov> Date: Wed Jan 24 17:08:54 2024 +0000 Merge branch 'ss160' of github.com:DavidHuber-NOAA/global-workflow into ss160 commit 4c46354 Author: DavidHuber <david.huber@noaa.gov> Date: Wed Jan 24 17:05:12 2024 +0000 Reenable verif-global support commit f775755 Author: DavidHuber <david.huber@noaa.gov> Date: Wed Jan 24 16:59:10 2024 +0000 Assign fcsthrs for awips_g2 job. commit e400068 Author: David Huber <david.huber@noaa.gov> Date: Mon Jan 22 15:01:07 2024 -0600 More gsi-addon path fixes. commit f663d47 Author: David Huber <david.huber@noaa.gov> Date: Mon Jan 22 14:41:59 2024 -0600 Fix gsi-addon paths for hercules, orion, and S4. commit e304bbe Author: DavidHuber <david.huber@noaa.gov> Date: Mon Jan 22 18:59:34 2024 +0000 Better optimize build jobs (more ufs jobs). commit ccc6e2d Author: DavidHuber <david.huber@noaa.gov> Date: Mon Jan 22 18:56:18 2024 +0000 Reenable verif-global. NOAA-EMC#2195 commit 3ef3411 Merge: 4365f63 f4d187f Author: DavidHuber <david.huber@noaa.gov> Date: Mon Jan 22 18:39:10 2024 +0000 Merge remote-tracking branch 'origin/develop' into ss160 commit 4365f63 Author: DavidHuber <david.huber@noaa.gov> Date: Mon Jan 22 18:37:25 2024 +0000 Corrected the SS env. name in the version files. NOAA-EMC#2195 commit f4d187f Author: AndrewEichmann-NOAA <58948505+AndrewEichmann-NOAA@users.noreply.github.com> Date: Mon Jan 22 12:28:28 2024 -0500 Converts obsproc to obsprep in prepoceanobs config file (NOAA-EMC#2236) Converts obsproc to obsprep in prepoceanobs config file as a compliment to mutually depended GDASApp PR NOAA-EMC/GDASApp#858 The motivations are explained in refs NOAA-EMC/GDASApp#857 commit 9a09d30 Author: DavidHuber <david.huber@noaa.gov> Date: Fri Jan 19 21:23:50 2024 +0000 Corrected gsi-addon-dev spelling. commit 21ff645 Author: DavidHuber <david.huber@noaa.gov> Date: Fri Jan 19 21:11:34 2024 +0000 Update modulefiles, submodules to spack-stack 1.6.0. NOAA-EMC#2195 commit d4c55d1 Author: Kate Friedman <kate.friedman@noaa.gov> Date: Fri Jan 19 15:43:37 2024 -0500 Update typing hint for WCOSS version of python (NOAA-EMC#2238) The typing hint `typing.List` was deprecated with python 3.9 in favor of using the primitive `list[str]`, but the functional version of python on WCOSS2 is <3.9, causing `setup_xml.py` to fail there. This replaces `list[str]` as a typing hint with the deprecated form until the supported version on WCOSS2 is >=3.9. commit 4919287 Author: Barry Baker <bbakernoaa@users.noreply.github.com> Date: Thu Jan 18 22:31:27 2024 -0500 GOCART Emission updates for GEFSv13 and GDAS (NOAA-EMC#2201) This PR addresses several things needed for more recent simulations using GOCART2G as well as preparing for the GEFSv13 30 year run. The main updates are: - Update CEDS to use monthly emission files instead of daily. This will drastically reduce the number of files needed. No science change - Update biogenic MEGAN inputs to use a climatology rather than the offline biogenic previously used. This is needed to deal with simulations where the current dataset is not available. - Update volcanic SO4 emissions to use degassing emissions only. This is to support the need for more recent simulations where data is not available. commit 13d25cf Author: Kate Friedman <kate.friedman@noaa.gov> Date: Thu Jan 18 22:29:43 2024 -0500 Add `POSTAMBLE_CMD` into preamble postamble (NOAA-EMC#2235) This PR adds the ability to run a command at the end of jobs via the preamble's postamble function. A new command can be set via `POSTAMBLE_CMD` and will be invoked at the end of jobs. Users can add the command to the top of an env file to have every job run it or it can be placed within a job if-block in the env file to run for just that job. Resolves NOAA-EMC#1145 commit 7759163 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Thu Jan 18 01:13:49 2024 -0500 Add option to create WGNE atmosphere products (NOAA-EMC#2233) Adds option to create WGNE products for the atmosphere. Resolves NOAA-EMC#1951 Resolves NOAA-EMC#2226 commit d95ed85 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Wed Jan 17 18:04:56 2024 -0500 Use ufs.configure, model_configure, MOM_input, data_table, and ice_in templates from UFS-weather-model (NOAA-EMC#2051) This PR: - links `ufs.configure.*.IN`, `model_configure.IN`, `MOM_input_${OCNRES}.in`, `MOM6_data_table.IN`, and `ice_in.IN` from ufs-weather-model into the global-workflow `parm/ufs` directory - prepares local variables for use in the templates in the respective functions for FV3, MOM6, and CICE6 - uses `atparse.bash` to render these templates into fully formed namelists - Work was performed by @DeniseWorthen in the ufs-weather-model to templatize several variables that are hard-wired in the ufs-weather-model for CICE. See ufs-community/ufs-weather-model/NOAA-EMC#2010 commit 44a66dd Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com> Date: Wed Jan 17 13:52:09 2024 -0500 Update gdas.cd hash to use gsibec tag 1.1.3 (NOAA-EMC#2231) (NOAA-EMC#2234) commit 9046d97 Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Wed Jan 17 10:19:18 2024 -0500 Add basic atmos products for GEFS and refactor resources (NOAA-EMC#2216) * Add basic atmos products for GEFS Adds basic atmosphere products for GEFS members (no mean or spread). To facilitate the addition of GEFS parameter lists, the existing GFS lists are renamed. They are also relocated to `parm/products/` direc tory instead of `parm/post/`. GEFS v12 uses different parameter lists for different resolutions, but for this implementation, the 0p25 lists are used for all resolutions. However, to hedge against the final con- figuration, all of the GEFS parameter lists have been added to parm. Implementation of different parameter lists for each resolution will take additional refactoring of the atmos_products job, as it currently assumes all resolutions use the same lists. The new GEFS rocoto task is implented as two loops of metatasks (made possible by PR NOAA-EMC#2189). The member is set at the rocoto level, so the setting in `config.base` had to be updated to accept a pass-through. The generation of a forecast hour list is moved up to its own function in `rocoto.tasks`, separate from the post groups which are not used. This can be used as a model for future metatasks (or refactoring of old ones). `rocoto_viewer.py` does function with the nested metatasks, though only one level of folding is available and the metatask name is that of the lower metatask (though it encompasses the entire outer metatask). Additionally, the GEFS `config.resources` had diverged from the GFS version, which included not having a section for the atm products job. This led to the refactoring of the GFS `config.resources`, including switching to using a `case` statement instead of sequential `elif`. This refactored script was then copied over to GEFS, replacing the old one, with all jobs not currently implemented for GEFS removed (except wave post, whose inclusion is immenent). New blocks can be copied over from GFS as they are added. Resolves NOAA-EMC#823 commit fbba174 Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com> Date: Tue Jan 16 14:05:48 2024 -0500 Update GDASApp (gdas.cd) hash (NOAA-EMC#2225) GDASApp now uses gitsubmodules commit dddd837 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Tue Jan 16 12:17:19 2024 -0500 Fix ocean resolution for the S2SWA test (NOAA-EMC#2223) commit 83edaf1 Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Tue Jan 16 11:07:02 2024 -0500 Apply fixes to archiving jobs (NOAA-EMC#2221) Add checks for potentially missing log/data files and update log names for archiving. Missing sflux index files are also added to the products script. Resolves NOAA-EMC#2076 commit c590476 Author: Rahul Mahajan <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 (NOAA-EMC#2219) commit c041968 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 (NOAA-EMC#2214) Two series of updates: 1) Update setup scripts to now allow users to provide ocean resolution 2) Housekeeping to retire the `COMROT` variable, replacing it with other variables as needed, and reduce the `ROTDIR` variable usage. Both updates change options for the workflow setup API. Refs NOAA-EMC#2061 commit 997f978 Author: AndrewEichmann-NOAA <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 (NOAA-EMC#2215) Enables use of ocean obs prep task in WCDA cycling and removes R2D2 from same. Runs task gdasprepoceanobs before gdasocnanalprep -- obtains ocean data nc4 files from DMPDIR, processes them into IODA format and copies them to COM_OBS. Replaces the current R2D2 processing. commit 12a5bb1 Merge: 4cb5802 6492c2d Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Fri Jan 12 09:26:27 2024 -0500 Merge pull request NOAA-EMC#2217 from DavidHuber-NOAA/update/versions Update and clean up version and module files commit 6492c2d Author: David Huber <david.huber@noaa.gov> Date: Thu Jan 11 11:49:08 2024 -0600 Update orion module/version files for met/metplus NOAA-EMC#2123 commit 94c9937 Author: DavidHuber <david.huber@noaa.gov> Date: Thu Jan 11 17:42:53 2024 +0000 Comment met/metplus out from Hera modulefile. NOAA-EMC#2123 commit 8c32f8b Merge: a65e4c6 4cb5802 Author: David Huber <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 a65e4c6 Author: David Huber <david.huber@noaa.gov> Date: Thu Jan 11 11:34:19 2024 -0600 Initial update of version/module files NOAA-EMC#2123 commit 4cb5802 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 (NOAA-EMC#2212) Fix OpenMP over-allocation of resources running MPMD tasks Co-authored-by: Innocent Souopgui <isouopgui@redlineperf.com> commit b056b53 Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net> Date: Mon Jan 8 17:28:05 2024 -0500 Add Hercules as valid machine in CI scripts (NOAA-EMC#2207) Few updates to CI scripts to include names for hercules that where missed the first time. commit 6574d29 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Mon Jan 8 17:25:47 2024 -0500 Fix invalid GH action and restart file name (NOAA-EMC#2210) Resolves a typo that leads to an invalid workflow yaml and fixes the restart filename in restart detection. Resolves NOAA-EMC#2205 commit 69605ea Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Mon Jan 8 17:00:28 2024 -0500 Stop attempting to comment link to RTD for non-PRs (NOAA-EMC#2209) Adds a check so comments with a link to documentation are only generated for PRs. commit 4e160a8 Author: Rahul Mahajan <aerorahul@users.noreply.github.com> Date: Mon Jan 8 13:10:15 2024 -0500 Enable UPP for GOES processing (NOAA-EMC#2203) Wnables the creation of special master grib2 files from UPP for GOES processing commit c15875b Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com> Date: Mon Jan 8 09:56:06 2024 -0500 Port cycling to Hercules (NOAA-EMC#2196) Adds cycled support for Hercules (excluding gsi-monitor). Partially resolves NOAA-EMC#1588 GSI monitoring is disabled on Hercules due to missing Perl modules. That will be enabled in a later PR. commit ef6827d Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Mon Jan 8 09:43:12 2024 -0500 Refactor rocoto task XML creation (NOAA-EMC#2189) Refactors the rocoto task generation to be recursive. This will allow nested metatasks to loop over multiple variables, which is needed for GEFS product generation. As part of this refactor, there is no longer separate arguments to designate metatasks. Instead, task dicts can include a nested 'task_dict' as well as a 'var_dict' containing the variables to loop over. The nested task dict can then either have another layer, or be the innermost task. To accommodate the new recursive nature, some defaults that were previously defined in create_wf_task() had to be pushed down into the function that creates the innermost task. Also, former keywords have been absorbed by the task dict. Refs NOAA-EMC#823 Refs NOAA-EMC#827 commit 2b81cfa Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov> Date: Mon Jan 8 09:41:03 2024 -0500 Update fix versions (NOAA-EMC#2198) Updates fix versions for a few components: - Update cice and mom6 versions to support C96/1p00 marine - Update wave to change betamax setting for glo_025 waves Resolves NOAA-EMC#2004 Resolves NOAA-EMC#2107
kayeekayee
added a commit
to kayeekayee/global-workflow
that referenced
this issue
Apr 11, 2024
Squashed commit of the following:
commit c54fe98c4fe8d811907366d4ba6ff16347bf174c
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Tue Apr 2 15:58:49 2024 -0400
Move bash utility functions out of preamble (#2447)
The preamble was accumulating a bunch of utility functions. These
functions are now moved to a separate file that is sourced by the
preamble. The only functions remaining in the preamble are those related
to script control and logging (`set_trace()`, `set_strict()`,
`postamble()`).
Resolves #2346
commit 4a39c8afc0555a8f2d621efb55589b9b309a416c
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Tue Apr 2 18:00:21 2024 +0000
Reenable the minimization monitor on Hera (#2446)
This allows the minimization monitor to run on Hera Rocky 8.
A missing perl module was added (List/MoreUtils.pm), but had to be
installed under the perl/5.38.0 installation, thus that module needs to
be loaded.
Resolves #2439
commit 0eaa53771b5e8d476d3b5feabd3181c8dc48629a
Author: Travis Elless <113720457+TravisElless-NOAA@users.noreply.github.com>
Date: Tue Apr 2 00:31:14 2024 -0400
Fix rotating member bugs (#2443)
When PR #2427 introduced the rotating subset of member guess states for
the early-cycle EnKF, the rotating member calculation function was
omitted from the DOSFCANL_ENKF if block in the enkf surface script. This
PR adds this feature to this section. This PR also removes hard coded
values that were included in this function and are replaced with a
variable equal to the number of late cycle members.
Resolves #2441
commit 39ba9d720c38ac85239a1eb1696c78df82396644
Author: CatherineThomas-NOAA <59020064+CatherineThomas-NOAA@users.noreply.github.com>
Date: Mon Apr 1 17:48:42 2024 -0400
Remove the reset of upper layer humidity (#2449)
# Description
The parameter "nudge_qv" resets the upper layer humidity to HALOE
climatology when cold starting. This parameter has been set to ".true."
but is no longer needed using v16+ ICs and will now be set to ".false."
by default.
Resolves: #2448
commit 7f6bf216566e92bbe072ebe4b64d26cc60fb53f1
Author: Jiarui Dong <Jiarui.Dong@noaa.gov>
Date: Mon Apr 1 13:08:33 2024 -0400
Archive the snow DA analysis into HPSS (#2414)
This PR adds the capabilities to archive the snow analysis output into
HPSS. Changes are made to archive the snow stats, letkfoi yaml file and
snow analysis into HPSS.
commit c1b11a2559e618f61866498b5dad503ba74d8332
Author: Neil Barton <103681022+NeilBarton-NOAA@users.noreply.github.com>
Date: Mon Apr 1 13:05:57 2024 -0400
Add GEFS ENS Atmos options (#2392)
This PR adds the FV3 atmos perturbation options when running GEFS. This
is needed for GEFS reforecasts and GEFS operational forecasts.
This PR continues to address the below issues
#1720
#1921
Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com>
Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Co-authored-by: Bing Fu <48262811+bingfu-NOAA@users.noreply.github.com>
commit 834ce31348a627e14d448cdbe33d4ec0dabe99e4
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Fri Mar 29 13:17:08 2024 -0400
Refactor gempak jobs for new COM and style (#2374)
Updates the gempak jobs to fit the new COM structure while also
refactoring them some to improve the style. Despite these technical
changes, the overall structure is left unchanged for most scripts,
though some have been rewritten to make the needed changes easier. Some
of these scripts had already been updated some in the original COM
refactor and thus needed fewer updates.
Style updates includes converting all gempak scripts to bash, making
them shellcheck compliant, and removing trailing whitespace. Further
refactoring to improve maintainability will be needed in the future (see
#2341, #2342, #2343, #2348).
The GFS gif scripts were identical except the forecast hour, so they are
collapsed down into two: one for f000 and one for other forecast hours.
The gempak executables have short path limits. To get around this
without having the gempak module recompiled, target directories (mostly
relevant for the gempak meta jobs) are symlinked into the working
directory to drasticly reduce the path lengths.
Part of this update includes replacing existing MPMD calls with the new
standard `ush/run_mpmd.sh` script.
A new function, `wait_for_file()`, is introduced to standardize waiting
for a file to be available.
Gempak forecast hours are often hard-coded within scripts. In addition
to issues with maintainability, this causes problems for shorter
forecasts, such as we typically run for testing purposes. For now, we
simply check the values against the forecast length and reduce if
necessary. Future work (#2348) will be needed to remove these hard-coded
values with variables set in the config file (or just use update gempak
products to match standard output time variables).
One-degree gempak files have been updated to include `1p00` in the
filename.
Several gempak job dependencies are corrected.
Fake gempak data for external models is being staged on tier-1 machines
to allow testing.
**Output has not been verified.** Future PRs will likely be needed to
bring full functionality online.
Resolves #2158
Resolves #2152
Resolves #2151
Resolves #2249
Resolves #2247
Refs #2157
Refs #2348
commit 20635b0639656769842218d544ec7ce2436337c5
Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
Date: Fri Mar 29 08:15:29 2024 +0000
Turn GEFS CI test on for Hera (#2442)
Re-enabling gefs case to test gefs system builds in Jenkins on Hera.
Co-authored-by: TerrenceMcGuinness-NOAA <terry.mcguinness@noaa.gov>
Co-authored-by: terrance.mcguinness <terrance.mcguinness@noaa.gov>
Co-authored-by: Walter.Kolczynski <Walter.Kolczynski@noaa.gov>
commit ba6a9d5fa6a079b1e3fdd424a493252bbf499c5d
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Thu Mar 28 17:34:22 2024 -0400
Modify APP based on RUN (#2413)
There is a need to change which coupled components are on depending on
the current `RUN`. To facilitate this, the `APP` is modified prior to
the setting of the `DO_<component>` variables based on `RUN`, turning
off components as desired.
This new system also replaces the `DO_<component>_ENKF` switches that
were formerly used to turn components off for the ensemble.
Also expands allows apps for cycled to include S2SWA.
Resolves #2318
commit 3ff7a92c25564ddf984cb09cb5667ae8fafe01a0
Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
Date: Thu Mar 28 17:48:00 2024 +0000
Fix post log arg check and don't create build semaphore (#2440)
Two Hot Fixes to Jenkins latest updates:
1. Logic fixed in checking for mutually exclusive use of gists and repo
for publishing error files
2. Removed creation of build success file semaphore forcing complete
rebuild as the default behavior for rerun/restarts
Co-authored-by: TerrenceMcGuinness-NOAA <terry.mcguinness@noaa.gov>
Co-authored-by: terrance.mcguinness <terrance.mcguinness@noaa.gov>
commit d6be3b5c3a1b8fd025a303b40e0660e2914906a7
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date: Wed Mar 27 20:56:18 2024 -0600
Update global-workflow and subcomponents to Hera/Rocky 8 partition (#2421)
This PR addresses issue #2329. The following is accomplished:
- All submodule RDHPCS Hera stacks are updated to be compatible with the
Rocky-8 distro spack-stack;
- The global-workflow version files `versions/build.hera.ver` and
`versions/run.hera.ver` are updated for Rocky-8;
- All submodule hashes have been updated to be compliant with the
Rocky-8 distro spack-stack (see the reference PRs below);
- Update to `parm/config/config.base` is made for not yet compliant
packages;
- Relevant updates are made to `modulefiles/module_base.hera.lua` and
`modulefiles/module_gwsetup.lua`.
Resolves #2329
Refs: [#958](https://github.com/NOAA-EMC/GDASApp/issues/958)
[#49](https://github.com/NOAA-EMC/gfs-utils/issues/49)
[#124](https://github.com/NOAA-EMC/GSI-Monitor/issues/124)
[#31](https://github.com/NOAA-EMC/GSI-utils/issues/31)
[#2167](https://github.com/ufs-community/ufs-weather-model/issues/2167)
[#2143](https://github.com/ufs-community/ufs-weather-model/issues/2143)
[#913](https://github.com/ufs-community/UFS_UTILS/issues/913)
Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com>
Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
commit 47302153f13f6b23539be841b78ed78664599c08
Author: Travis Elless <113720457+TravisElless-NOAA@users.noreply.github.com>
Date: Wed Mar 27 21:14:57 2024 -0400
Add a rotating subset of members for early-cycle enkf (#2427)
The early-cycle EnKF needs the ability to run with fewer members than
the late-cycle due to operational resource constraints. Because of this
requirement, the introduction of a rotating subset of member first-guess
states used by the early-cycle ensemble is also needed in order to
preserve the rotating member initial condition functionality currently
used by the GEFS.
Co-authored-by: Travis J Elless <telless@Orion-login-1.HPC.MsState.Edu>
Co-authored-by: travis elless <travis.j.elless@dlogin07.dogwood.wcoss2.ncep.noaa.gov>
commit 94c282ef6fdcd47076e932bcadb5bdd55236aa05
Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
Date: Wed Mar 27 20:28:15 2024 +0000
Uploading error logs to GitHub from Jenkins CI Runs (#2429)
This PR enhances the user experience within GitHub for when errors occur
during build and running of CI cases from within the PR messages. This
is done by uploading the error logs to GitHub Gists and then publishing
the links to them along with the full paths of the logs on disk.
This PR adds the python Class **GitHubPR** in
`${HOMEgfs}/ci/scripts/utils/githubpr.py` by inhearting the GitHub Class
from **pyGitHub**. We use this module to introduce a helper python
utility that can publish a list of log files into a GitHub Gist and/or
the designated branch **error_logs** in the **emcbot** repo
**ci-global-workflows** for storing error log files for review from any
git configured terminal. This upload feature will also create
persistence of errors over time.
Also the `build_all.sh -k` script has been updated to support a "quick
kill" feature (thanks David) that stops the parallel builds whenever one
fails and creates an error_log file that has the paths to the error
files that are also uploaded and published in the PR messages in GitHub.
Co-authored-by: TerrenceMcGuinness-NOAA <terry.mcguinness@noaa.gov>
Co-authored-by: terrance.mcguinness <terrance.mcguinness@noaa.gov>
Co-authored-by: DavidHuber <david.huber@noaa.gov>
Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
commit 6c5065e2e83a45b14505e7575aa4500482ef7452
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Wed Mar 27 03:39:16 2024 -0400
Add option to use traditional threading in the UFS (#2384)
# Description
This PR:
- adds the option of running the ufs-weather-model with traditional
threading in addition to ESMF-managed threading. See new toggle
`USE_ESMF_THREADING=YES|NO` set in `config.fcst`
- does not change the current default of using ESMF-managed threading.
Traditional threading use might need a little more fine tuning for the
job-card specification. This will be achieved when the UFSWM RT
completely switches over to traditional threading
- updates the hash of the ufs-weather-model to the PR
https://github.com/ufs-community/ufs-weather-model/pull/2172
Resolves #2277
In addition to the above stated objectives, this PR also addresses open
issues. In particular, this PR:
- adds a newline at the end of `diag_table_aod`. Fixes #2407
@zhanglikate
- reserves more memory on WCOSS2 for offline UPP when running at C768.
Fixes #2408 @WenMeng-NOAA
Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
commit bc1c46dfd7393c5164abcdc2dfa76a9c4bc834b8
Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com>
Date: Tue Mar 26 22:27:30 2024 -0400
Correct GDASApp paths (#2435)
The changes in this PR
- account for changes in GDASApp directory structure
- generalize how the path to the GDASApp python ioda library is
specified
Resolves #2434
commit f0b912be6f2cf2fac590272253f19cb082fbf5f2
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Mon Mar 25 21:46:32 2024 +0000
Fix *earc jobs where the number of members isn't a multiple of 10 (#2424)
This limits the earc search for ensemble members to the maximum number
of members, which prevents attempting to send non-existent members to
HPSS if the number of ensemble members is not a multiple of 10.
Resolves #2390s
commit daeb0c855017f8ffd6f06870744b825b276097f3
Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
Date: Fri Mar 22 17:40:04 2024 +0000
hotfix to update full path to error logs on CI case fail (#2425)
This hotfix PR prepends the full path to the error logs on disk to be
communitated correctly to the GitHub message to the PR that is being
processed when there is a failure in from a case.
commit 50f75526549245f2b5d984cdb44e402852e086ec
Author: YaliMao-NOAA <53870326+YaliMao-NOAA@users.noreply.github.com>
Date: Thu Mar 21 16:58:25 2024 +0000
Add WAFS jobs, scripts and ush to GFS v17 workflow repository (#2412)
# Description
This PR adds WAFS jobs, scripts and ush to GFS v17 workflow repository
---------
Co-authored-by: yali mao <yali.mao@clogin04.cactus.wcoss2.ncep.noaa.gov>
Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com>
Co-authored-by: yali mao <yali.mao@clogin09.cactus.wcoss2.ncep.noaa.gov>
commit 03ba78ae3df589211d2776254c6e8584ecdc226f
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Thu Mar 21 13:33:50 2024 +0000
Hotfix: send the correct number of build jobs for the UFS (#2423)
This fixes a bug in build_ufs.sh that was causing the UFS to always
build with 8 jobs (except on the cloud).
commit 4d1bf5266f00b35778ea47896f438e3ef612628d
Author: Kate Friedman <kate.friedman@noaa.gov>
Date: Wed Mar 20 14:00:31 2024 -0400
Updates to RTD documentation (#2418)
Updates to the RTD documentation include:
- Textual updates
- Better definition of GDA subfolder structure
- Added note about GDAur having been discontinued
- Adjust copyright and author information
- Fix Git version table and update its contents
- Add "Table of Contents" header before table of contents on front page
- Add AWS ICs path to init page
- Add link to UFS_UTILS gdas_init RTD documentation
- Add note about bash to `gw_setup.sh` section and added a warning block
Refs #2395
commit afe874ee8b28942e459796cd1005ec598458a5b7
Author: Neil Barton <103681022+NeilBarton-NOAA@users.noreply.github.com>
Date: Tue Mar 19 14:35:02 2024 -0400
Add GEFS Ocean Perturbation Options (#2385)
This PR adds the MOM6 ocean perturbation options when running GEFS. This
is needed for GEFS reforecasts and GEFS operational forecasts.
This PR continues to address the below issues
https://github.com/NOAA-EMC/global-workflow/issues/1720
https://github.com/NOAA-EMC/global-workflow/issues/1921
Fixes #2403
commit fa855baa851b0cb635edd1b9ae1bfed5112d41e5
Author: Clara Draper <33430543+ClaraDraper-NOAA@users.noreply.github.com>
Date: Mon Mar 18 12:49:14 2024 -0600
Add initial GSI-based soil analysis capability (#2263)
First set of changes for adding the new soil analysis, from the
assimilation of screen-level T and q. The changes here enable the
screen-level observations to be assimilated in the Hybrid (Var and EnKF)
update, and the soil temperature and soil moisture updates to be made in
the EnKF only. The functionality is turned on by setting GSI_SOILANAL to
YES in config.base.
Resolves #1479
commit e9700d84b521907ee23e1584712f80e25e60f08e
Author: Jessica Meixner <jessica.meixner@noaa.gov>
Date: Mon Mar 18 09:32:13 2024 -0400
re-enable ci/cases/pr/C48mx500_3DVarAOWCDA.yaml (#2405)
Updates to re-enable C48mx500_3DVarAOWCDA CI test after it was disabled
in https://github.com/NOAA-EMC/global-workflow/pull/2371
Fixes github.com/NOAA-EMC/global-workflow/issues/2404
commit 3ccffeee120340ab580fc9d96b552970c9f42a8f
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Mon Mar 18 09:30:35 2024 -0400
Parse jediyaml only once (#2387)
`JEDIYAML` was being parsed 3 times; once in `get_obs_dict`, second in
`get_bias_dict` and a third time in `initialize` for the specific
component analysis task.
This PR:
- eliminates the duplications and constructs the `jedi_config`
dictionary just once. The dictionary is written out before calling the
executable.
- updates hash to gdasapp
- updates configs for snow, aerosol, atmvar and atmens JEDI-DA to
include `JEDI_FIX_YAML` and `CRTM_FIX_YAML` . This allows greater
flexibility and control over the contents of these fix data sets to be
copied into the run directory.
- Combines snowDA and aerosolDA into a single test
Co-authored-by: Cory Martin <cory.r.martin@noaa.gov>
Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
commit a5f24951c5bef142747c6f6cc6abd474f0b53ac2
Author: CatherineThomas-NOAA <59020064+CatherineThomas-NOAA@users.noreply.github.com>
Date: Fri Mar 15 14:47:54 2024 -0400
Fix ensemble archive groups to include all members (#2402)
The number of groups used in the ensemble archive step (earc) needs to
include a task for the ensemble stat files such as the mean and the
spread, resulting in `n_groups+1` tasks for `earc`.
Resolves: #2390
commit 056cfdca9e7fd7426a315fcbffc38d8ee2891212
Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
Date: Fri Mar 15 18:30:23 2024 +0000
GitHub message error paths (#2401)
Add feature to message paths to error logs of failed experiments to
GitHub Messaging the PR from Jenkins.
commit d897ee4936d62160811d936248c8555187f81b65
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Thu Mar 14 12:37:49 2024 -0400
Missed a comma from the hotfix this AM (#2399)
This PR is a hotfix to the hotfix from earlier this AM. A comma was
missing.
commit 906540acacf1b2ce4c0489d0d9d4913f53a4e8ad
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Thu Mar 14 10:40:03 2024 -0400
Fix KeyError issue in ocean/ice postprocessing job. (#2398)
The jjob for ocean and ice pp, only defines the component specific
history and grib directory. This causes an error in the exscript trying
to pull keys for both ocean and ice. Fix this. Surprised this has not
caused failures before today
Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
commit c27f243ce24c60261718f15628f6ab30d7b09f7b
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Wed Mar 13 13:31:57 2024 -0400
Remove documentation about generating ICs using global-workflow (#2397)
Removes instructions on generating ics using global-workflow and
directs the user to use ufs-utils.
commit 0edbdc197441582f9c402da0f3a7f144b88960c7
Author: DavidNew-NOAA <134300700+DavidNew-NOAA@users.noreply.github.com>
Date: Tue Mar 12 16:30:45 2024 -0400
Changed config.atmanl to allow non-hybrid background error yamls (#2394)
# Description
Makes change so that if DOHYBVAR equals "NO", then the JEDI background
error yaml is set to staticb_${STATICB_TYPE}.yaml.j2 rather than
hybvar_${STATICB_TYPE}.yaml.j2. This allows GDAS to run without hybvar,
which may be necessary for development purposes.
This is all accomplished by a simple switch in config.atmanl.
commit ccb1f528489e740bb2adc4958146552323dd8709
Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com>
Date: Tue Mar 12 10:45:39 2024 -0400
Add JEDI atmosphere only CI (#2357)
The PR contains a minimal set of changes to enable JEDI atmospheric DA
CI testing. Prototype JEDI atmospheric cycling has begun. The JEDI
atmosphere DA CI case provides an automated way to see if future PRs
impact JEDI atmospheric cycling.
Resolves #2294
Dependency: GDASApp PR
[#937](https://github.com/NOAA-EMC/GDASApp/pull/937)
commit b96f5ebbb1968bd539336652b87a2faa8ce68fd4
Author: Kate Friedman <kate.friedman@noaa.gov>
Date: Tue Mar 12 07:58:40 2024 -0400
Add switch to control `debug=true` on WCOSS2 for development testing (#2388)
Adds a switch (`DEBUG_POSTSCRIPT`) to control whether
`debug=true` is set when submitting development rocoto jobs to PBS
schedulers (currently just WCOSS2).
There isn't an equivalent flag to set for SLURM on the RDHPCS.
Have added this new switch to documentation.
Refs #619
commit 02d650500353663d0b193ef14003897daa5dd86c
Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
Date: Mon Mar 11 21:51:16 2024 +0000
Rewrote pr_list_database.py to use wxflow's SQLiteDB Class (#2376)
This PR updates the `pr_list_database.py` code to use **wxflow**
SQLiteDB Class
- Improved code's readability
- Uses better code style matching project's software culture
- Better docstring standards
Co-authored-by: tmcguinness <terry.mcguinness@noaa.gov>
Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com>
Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
commit a3374607d01fbdabbec0660afb82b5eb3677b4af
Author: AndrewEichmann-NOAA <58948505+AndrewEichmann-NOAA@users.noreply.github.com>
Date: Fri Mar 8 16:08:42 2024 -0500
Return ocnanalrun npes resource setting back to previous value (#2386)
Variable `npes` in `ocnanalrun` entry of `config.resources` was
erroneously changed in
https://github.com/NOAA-EMC/global-workflow/pull/2299 and this PR
changes it back.
Resolves https://github.com/NOAA-EMC/GDASApp/issues/962
commit d7e9bde84aebe922039589bd2bcd65832c1074eb
Author: BoCui-NOAA <53531984+BoCui-NOAA@users.noreply.github.com>
Date: Thu Mar 7 16:14:28 2024 -0500
Add new BUFR table file parm/product/bufr_ij9km.txt for GFSv17 C1152 (#2383)
This PR will add a new table file parm/product/bufr_ij9km.txt, and
modify ush/gfs_bufr.sh to choose the different bufr table files based on
the GFSv17 run resolution, i.e. use file bufr_ij9km.txt for C1152 or
bufr_ij13km.txt, for C768.
Resolves #2382
commit 4a525bef3bbed2ea60a71f71b3740c82df125c36
Author: AndrewEichmann-NOAA <58948505+AndrewEichmann-NOAA@users.noreply.github.com>
Date: Thu Mar 7 16:12:31 2024 -0500
Add global-workflow infrastructure for ocean analysis recentering task (#2299)
Adds jjob, rocoto script, config file, and basic `config.resources`
entry for ocean analysis recentering task
This PR is a dependency for further work on the associated issue within
global-workflow and GDASApp
Refs https://github.com/NOAA-EMC/GDASApp/issues/912
commit f83d17a937006add55241ed453e42f4fcbae50aa
Author: Kate Friedman <kate.friedman@noaa.gov>
Date: Thu Mar 7 09:29:14 2024 -0500
Clean out non-gfs top level variables (#2366)
Clean out non-gfs top level variables that are duplicates or no longer needed.
Also standardize how we set these variables in scripts.
Refs #2332
commit c7b306e052497aef0022cd53550a168d2c5b6e5b
Author: Guillaume Vernieres <guillaume.vernieres@noaa.gov>
Date: Wed Mar 6 16:16:08 2024 -0500
Forgotten templated DO_VRFY_OCEANDA (#2379)
# Description
This PR adds the possibility to use the switch for the ocean and sea-ice
DA verify task from the yaml configuration.
- fixes
[GDASApp/issues/954](https://github.com/NOAA-EMC/GDASApp/issues/954)
commit ba6a4fdf6e245b57530f2b20e6f0ccf567115720
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Tue Mar 5 19:09:48 2024 +0000
Add Hercules support for the GSI monitor (#2373)
# Description
This updates the GSI monitor hash and updates the modulefiles to add
support for the monitor on Hercules.
commit 732a874a2c6793296f136afb23545fab9869b181
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Mon Mar 4 16:04:26 2024 -0500
Reformat snowDA templates to jinja2 (#2371)
# Description
This PR:
- replaces use of non-jinja2 templates in the yaml templates.
Specifically `$( )` in favor of pure jinja2.
- uses jinja2's built-in capability to include templates within
templates, thereby allowing to assemble a completely rendered template
before passing it to for e.g. yaml loader.
- requires updates to `wxflow` and `gdasapp`
- Changes in `wxflow` in `parse_j2yaml` are **not** backwards compatible
Additionally, this PR:
- renames `config.base.emc.dyn` to `config.base`. Resolves #2347
commit d1fa41106e991556606b0f62a15bf45f469f4f79
Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
Date: Sat Mar 2 04:54:26 2024 +0000
Reduce Jenkins messaging to GitHub (#2370)
This PR updates the Jenkins Pipeline code with safeguards against the
errors caused when Jenkins fails to authenticate with GitHub to message
or update a label. This was achieved simply by:
- Reducing the number out messages sent to the GitHub PR
- Putting try blocks around most of the update label calls
Co-authored-by: tmcguinness <terry.mcguinness@noaa.gov>
commit 52fa3cb32d8b50e47f391b82ea8901435fc88aff
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date: Fri Mar 1 12:36:27 2024 -0700
Adding debug option for all build scripts (#2326)
This PR addresses issue #300 that allows building in `debug` mode.
Co-authored-by: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com>
commit 91738cbf871d8cdce46912e2c11e304d567a2aae
Author: DWesl <22566757+DWesl@users.noreply.github.com>
Date: Fri Mar 1 13:46:42 2024 -0500
Sort list of coupler restart files for restart time determination (#2360)
The loop in the following conditional seems to assume the list is
sorted, so make that explicit in the array construction.
commit 23c25527ad2a62275cd9105bd103b8520a28e573
Author: Neil Barton <103681022+NeilBarton-NOAA@users.noreply.github.com>
Date: Fri Mar 1 13:45:39 2024 -0500
Update stage IC to handle ocean perturbations (#2364)
This PR adds the option to stage ocean perturbation files for ensemble
forecasts. These perturbation files are used in GEFS forecasts.
A new variable is introduced in config.base to use the ocean
perturbation files.
This PR does not include using these perturbation files. A future PR
will address this.
commit 8efe05f475b81e7cf6376745d5f1ce31987cb4eb
Author: Jessica Meixner <jessica.meixner@noaa.gov>
Date: Fri Mar 1 07:41:56 2024 -0500
Turn on C48mx500_3DVarAOWCDA test on hera (#2363)
This PR activates the C48mx500_3DVarAOWCDA test on hera. This required
an update of the gdas app.
commit 5166593945e9ecc04dfa3409752576c08797d09f
Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
Date: Thu Feb 29 20:14:41 2024 +0000
Move Jenkinsfile into ci subdirectory (#2355)
Just moves the Jenkinsfile into the ci directory
Co-authored-by: tmcguinness <terry.mcguinness@noaa.gov>
commit b7af315bb9dea77b37c6d030b71060b87bedf33e
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Wed Feb 28 22:20:58 2024 +0000
Fix rocoto forecast hour determination for GEFS (#2351)
The function that generates the list of forecast hours for rocoto was
trying to use variables that are not defined for GEFS, causing workflow
generation to fail. The function is updated to not try to load these
variables before loading the ones actually used for GFS/ GEFS.
Also turns GEFS CI test back on and adds an entry to stage C192 ICs
(note: these have not been placed in the centralized location.)
commit d3a49271b6c3816a9feeb7f6fb474797bacf1d7e
Author: Cory Martin <cory.r.martin@noaa.gov>
Date: Wed Feb 28 09:38:49 2024 -0500
Rename the land DA jobs to snow DA to better reflect what they are doing (#2330)
This PR renames all of the land DA jobs to snow DA to better reflect
that this is a JEDI-based snow analysis capability and not a more
generic land surface analysis.
commit 2693810d6ea9d9b20090777ff3a98e3d072c76d7
Author: Jessica Meixner <jessica.meixner@noaa.gov>
Date: Tue Feb 27 01:25:51 2024 -0500
Update ufs-waether-model hash (#2338)
Routine update of ufs-weather-model hash.
Other small updates:
* removes comment referencing closed issue.
* Updates the CICE diag frequency to once per day as recommend here:
https://github.com/NOAA-EMC/global-workflow/issues/1810#issuecomment-1686278925
* Updated amount of time for C384 gdas forecast as it was running out of
time
* Removed unused variable wave_sys_ver
commit 9608852784871ebf03d92b53bde891b6dcab8684
Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com>
Date: Mon Feb 26 14:10:01 2024 -0500
Update JEDI ATM to use .nc for obs and generalize x,y layout (#2336)
# Description
The changes in this PR are twofold
1. replace `.nc4` suffix for JEDI ATM observation related files with
`.nc`
2. use templated variables to specify `{layout_x, layout_y}` for JEDI
ATM variational and local ensemble apps
The first change conforms with the Unidata recommendation that netCDF
files end with the suffix `.nc`. The second change replaces hardwired
JEDI ATM var and ens `{layout_x, layout_y}` in `config.resources` with a
more flexible approach.
Resolves #2335
commit c5c84660f10f0ef9ce939231b2f7fda498b39a29
Author: Kate Friedman <kate.friedman@noaa.gov>
Date: Mon Feb 26 10:18:50 2024 -0500
Remove FIX* variables for fix subfolders (#2337)
Remove `FIX*` variables for fix subfolders and replace them with the remaining `FIXgfs` variable and the subfolder name (e.g. `${FIXam}` -> `${FIXgfs}/am`).
The UFS_UTILS and GDASApp repos were similarly updated. This PR includes a new UFS_UTILS hash.
The updated GDASAPP hash was already committed within the spack-stack/1.6.0 PR #2239.
Resolves #2184
commit 950c38a093c6a4e2b67e18c76390280d8bfbaef7
Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
Date: Fri Feb 23 21:15:46 2024 +0000
Fix several Jenkins issues (#2334)
Jenkins Updates Resolving final kinks:
- Removed all `git` shell commands and now exclusively use Software Control
Manger (**scm**) plugin.
- Add feature for skipping hosts per configuration specified in case yaml files.
- Solved and tested false positive builds and experiments.
- Tested archiving of task error log on case fail
- First case fail quits pipeline and cancels all pending scheduled jobs
- Duel build per yaml configuration arguments supported
- All designated case files in PR directory pass on intended host (fully tested
on Hera)
Remaining updates:
- Fist build fail short circuit when building sub-modules and archiving build
error log.
- Re-build/no-build built in logic for Replay and Rerunning previously failed
experiments.
commit c67393a203285792b852da0d83fd10fa47155669
Merge: 6f9afff07 79d305e8c
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Fri Feb 23 14:18:15 2024 +0000
Merge pull request #2239 from DavidHuber-NOAA/ss160
Update to spack-stack 1.6.0
Includes all submodules except the UFS, which will be updated at a later time.
commit 79d305e8cbc339208ea6fe0475ddc56af94a285b
Author: David Huber <david.huber@noaa.gov>
Date: Thu Feb 22 14:53:57 2024 -0600
Disable snow DA tests
commit 0459203e97211b041520b39e93a188951396ba33
Author: David Huber <david.huber@noaa.gov>
Date: Thu Feb 22 12:55:51 2024 -0600
Update GDASApp hash to current develop
commit 5c96eb2272fe6117f9e4a4c0c790db58e4870d46
Author: David Huber <david.huber@noaa.gov>
Date: Thu Feb 22 12:37:47 2024 -0600
Update GDAS hash to allow modified snow DA analysis
commit 79144f2403a33d08140577cc3e8a61d6c4924403
Merge: abbb0b8a7 6f9afff07
Author: DavidHuber <david.huber@noaa.gov>
Date: Thu Feb 22 15:14:39 2024 +0000
Merge remote-tracking branch 'origin/develop' into ss160
commit abbb0b8a76b39d34433802fd4e3d7973fb9f0a39
Merge: 4ad837ea1 4529e8cf3
Author: DavidHuber <david.huber@noaa.gov>
Date: Thu Feb 22 15:11:03 2024 +0000
Merge remote-tracking branch 'henry/feature/gwdev_issue_2129' into ss160
commit 4ad837ea157b98d2bd173cb696c4d30d142e5540
Merge: 516b2a270 7ca45db8f
Author: DavidHuber <david.huber@noaa.gov>
Date: Thu Feb 22 15:10:24 2024 +0000
Merge remote-tracking branch 'henry/feature/gfsv17_issue_2125' into ss160
commit 516b2a270234bdab5714ef2705c83dd3835b134d
Author: DavidHuber <david.huber@noaa.gov>
Date: Thu Feb 22 14:19:16 2024 +0000
Updated GDAS to include rocoto/1.3.6 on Hera.
commit 6f9afff073dd589096f992a3448fb7f0e62c9804
Author: Jessica Meixner <jessica.meixner@noaa.gov>
Date: Wed Feb 21 13:09:44 2024 -0500
Add some flexibility for ocean/ice output (#2327)
This adds functionality to have ocean/ice output frequency be separate from the atm model. One time was created because there's an assumption in the post that these are the same. This could be further modified to remove this assumption.
Refs #1629
commit f6d3015ab9f9fd23ce0081baa2edbc5d9f5f3e16
Author: David Huber <david.huber@noaa.gov>
Date: Tue Feb 20 09:53:08 2024 -0600
Update GDASApp hash to include SS/1.6.0 support.
commit 0bf340bce2f865c582e5305f0c5984cd3affe74e
Author: David Huber <david.huber@noaa.gov>
Date: Tue Feb 20 09:07:32 2024 -0600
Construct SS paths from version variables.
commit 3330cd7310bde8090b68720c225656074676d6b2
Author: David Huber <david.huber@noaa.gov>
Date: Tue Feb 20 09:06:19 2024 -0600
Removed MET/METplus 'not available' comments
commit fdc638ca1616b347912caec77e5abc2d3e6f18af
Author: David Huber <david.huber@noaa.gov>
Date: Tue Feb 20 08:35:15 2024 -0600
Move SS module path to version files.
commit d7d28a6b65b84c8d821abd2c13d0c068bd5ad6d8
Author: David Huber <david.huber@noaa.gov>
Date: Tue Feb 20 07:53:15 2024 -0600
Update comment about METplus support.
commit a812f88af3fc043d57494840e81a7527723858e4
Author: David Huber <david.huber@noaa.gov>
Date: Tue Feb 20 07:45:45 2024 -0600
Update verif-global to latest WCOSS2 support.
commit d81f07fbf53666a37ab01bd463152e10252869ae
Author: David Huber <david.huber@noaa.gov>
Date: Tue Feb 20 07:41:38 2024 -0600
Clean up build_upp.sh.
-Corrected whitespace (tabs instead of spaces)
-Removed debug print statement
-Alphebetized flags
commit ae7eb194cbe2213e564807dd7bc03a28d493eff2
Author: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Fri Feb 16 16:15:40 2024 -0500
Fix whitespace in build_upp.sh.
Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com>
commit 48b34d0f388a398bb91f7c3b1e5f8338f4beb7b9
Author: David Huber <david.huber@dlogin05.dogwood.wcoss2.ncep.noaa.gov>
Date: Fri Feb 16 20:56:55 2024 +0000
Added verif-global support back to WCOSS2.
commit 4529e8cf3736ffbacf615a27e99f4d1beec391aa
Author: henrywinterbottom-wxdev <henry.winterbottom.wxdev@gmail.com>
Date: Fri Feb 16 11:12:01 2024 -0700
Bug fix.
commit 8e4f94d13d32849b2862a9d59aa070f4103c61ae
Author: henrywinterbottom-wxdev <henry.winterbottom.wxdev@gmail.com>
Date: Fri Feb 16 11:04:41 2024 -0700
Updates requested by reviewer Rahul Mahajan.
commit 4624ce21c99ab303afa10c1dd8ddcce7b6f715ca
Author: henrywinterbottom-wxdev <henry.winterbottom.wxdev@gmail.com>
Date: Fri Feb 16 10:52:11 2024 -0700
Updates requested by reviewer; testing -- DO NOT REVIEW.
commit ed25bbd0b26a893d32ce4a10b368dec2bb722424
Author: henrywinterbottom-wxdev <henry.winterbottom.wxdev@gmail.com>
Date: Fri Feb 16 09:33:59 2024 -0700
Linter corrections.
commit 6a0b7bf214815c13eec98a93bd3abe9978de04e4
Merge: f9fb64ef8 2415b7b4f
Author: David Huber <david.huber@noaa.gov>
Date: Fri Feb 16 09:50:22 2024 -0600
Merge branch 'ss160' of github.com:DavidHuber-NOAA/global-workflow into ss160
commit f9fb64ef802b683d7b369f8e8268d423ab581481
Merge: 777d97d3a a23b7f2fd
Author: David Huber <david.huber@noaa.gov>
Date: Fri Feb 16 09:49:42 2024 -0600
Merge remote-tracking branch 'emc/develop' into ss160
commit 7ca45db8fa32c84ef117ff2938a650822c81a786
Merge: 73bc76bfd a23b7f2fd
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date: Fri Feb 16 07:46:35 2024 -0700
Merge branch 'NOAA-EMC:develop' into feature/gfsv17_issue_2125
commit eb2ed53857eb3387735488a1ce5d701ff680e3db
Merge: 9929277dc a23b7f2fd
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date: Fri Feb 16 07:46:24 2024 -0700
Merge branch 'NOAA-EMC:develop' into feature/gwdev_issue_2129
commit a23b7f2fdca5be700d257e28052a0104f2173a0f
Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com>
Date: Fri Feb 16 09:37:58 2024 -0500
Add JEDI 3DEnVar atmosphere only CI test stub (#2309)
commit cf83885548bb3a6740c033f42479ce2ad283a4a9
Author: Jessica Meixner <jessica.meixner@noaa.gov>
Date: Fri Feb 16 01:55:02 2024 -0500
Add unstructured grid for HR3/GFS (#2230)
This adds the capability to use unstructured grids in the global workflow,
which will be used in HR3. There are new fix files for a low-resolution
100km grid and a grid closer to our targeted GFSv17 grid which has the
resolution combined from the older multi_1 and GFSv16 grids.
The fix file update is here: NOAA-EMC/global-workflow#2229
Note: This now means that GFS tests need a new build option:
`./build_all.sh -w` So that PDLIB=ON is turned on for compiling relevant
UFS and WW3 codes.
Resolves NOAA-EMC/global-workflow#1547
commit 9929277dc7d0ad90f5366faf4b5f2278969a0aa2
Merge: eb8791ccb 094e3b86d
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date: Thu Feb 15 15:05:50 2024 -0700
Merge branch 'NOAA-EMC:develop' into feature/gwdev_issue_2129
commit 094e3b86da44f1d3fc1d99f68f6fdfcd36deb09f
Author: Cory Martin <cory.r.martin@noaa.gov>
Date: Thu Feb 15 14:43:55 2024 -0500
Move IMS remapping files from COM_OBS to FIXgdas (#2322)
* Add in IMS obs fix directory and update submodule for gdas
commit d465ea06e8b2a8f3a5eb1120647c1e2ce5197d66
Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
Date: Thu Feb 15 19:25:02 2024 +0000
Set HOMEgfs for module_setup in CI driver (#2321)
Hotfixes to CI Bash system from updates with sourcing
`detect_machine.sh` in `ush/module-setup.sh` using **HOMEgfs**.
commit 2415b7b4f3e6c376aca27707510001141cc9dd92
Author: David Huber <david.huber@noaa.gov>
Date: Thu Feb 15 19:21:17 2024 +0000
Load default rocoto on Jet.
commit eb8791ccbe684828dc529d0e553551969274fc22
Merge: 60d5ee64b 638684e0b
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date: Thu Feb 15 11:56:40 2024 -0700
Merge branch 'NOAA-EMC:develop' into feature/gwdev_issue_2129
commit 777d97d3a1c9f5ec5e8af3ca40a41224ec7099a1
Author: David Huber <david.huber@noaa.gov>
Date: Thu Feb 15 12:34:59 2024 -0600
Fixed Orion cdo version.
commit ef0723503c72f295de93521c7102c43e75c47417
Author: DavidHuber <david.huber@noaa.gov>
Date: Thu Feb 15 16:29:32 2024 +0000
Revert UFS hash.
commit 0ce8c0dbc13227884fef1c637e93616a28c68d34
Author: DavidHuber <david.huber@noaa.gov>
Date: Thu Feb 15 14:55:48 2024 +0000
Fix git version in Hera's gwsetup module.
commit 3080a34253e8e24105bf2be72b6a872b1c072935
Author: DavidHuber <david.huber@noaa.gov>
Date: Wed Feb 14 20:52:34 2024 +0000
Fixed xarray version for SS/1.6.0.
commit 49392dd47ff84b6586052aeae6879d7d8050b746
Author: DavidHuber <david.huber@noaa.gov>
Date: Wed Feb 14 20:29:41 2024 +0000
Updated GSI-Utils hash to head of develop.
commit c3553f0d8e6a05c6234e7c14a179983aa44fd6f3
Merge: 4568653a6 638684e0b
Author: DavidHuber <david.huber@noaa.gov>
Date: Wed Feb 14 20:28:14 2024 +0000
Merge remote-tracking branch 'origin/develop' into ss160
commit 4568653a67aa37c902379db628fb10f69fe7190f
Author: David Huber <david.huber@noaa.gov>
Date: Wed Feb 14 14:22:13 2024 -0600
Reupgrade Hercules to SS/1.6.0
commit 638684e0bfcd06700cc8695f09824891a0a1eee1
Author: Kate Friedman <kate.friedman@noaa.gov>
Date: Wed Feb 14 14:55:21 2024 -0500
Remove `finddate.sh` from system (#2308)
* Retire finddate.sh usage from system
* Update gfs-utils hash to 7a84c88 - New hash includes removal of finddate.sh
Refs #2279
commit 2b160f8470bed16c513ca4a5665e2b6d4448c50e
Author: DavidHuber <david.huber@noaa.gov>
Date: Wed Feb 14 18:31:28 2024 +0000
Reenable METplus jobs on Hercules.
commit 8f5900265a31e894060bbe9c89b262f4df0b1760
Author: DavidHuber <david.huber@noaa.gov>
Date: Wed Feb 14 18:30:23 2024 +0000
Update GSI hashes.
commit 73bc76bfd47f2cff54df55e15d9ed8969683367d
Author: henrywinterbottom-wxdev <henry.winterbottom.wxdev@gmail.com>
Date: Wed Feb 14 09:27:37 2024 -0700
Updates based on user request.
commit e4bc674cf3b2df10e0b0dfd50a8ecb0f4f7825d8
Author: henrywinterbottom-wxdev <henry.winterbottom.wxdev@gmail.com>
Date: Wed Feb 14 08:03:45 2024 -0700
Corrected based on reviewer review.
commit 60d5ee64bda7a16c1f2dc20c8badcd7c8fc4e592
Merge: 40f2cf6cd 1aaef05d3
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date: Tue Feb 13 18:08:33 2024 -0700
Merge branch 'NOAA-EMC:develop' into feature/gwdev_issue_2129
commit 03304112347a673b7a0fcc404703bb10960bc47a
Merge: 929b90330 1aaef05d3
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date: Tue Feb 13 17:58:12 2024 -0700
Merge branch 'NOAA-EMC:develop' into feature/gfsv17_issue_2125
commit 1aaef05d317cd1eec548ef2b9842679c531cef8b
Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
Date: Tue Feb 13 18:15:59 2024 -0500
Jenkins Pipeline updates for Canceling Jobs (#2307)
Tuning updates for Jenkins Pipeline :
- Added short circuit for all parallel runs of cases on error of any
- Fixed canceling of all scheduled jobs on first case error
- Added feature to save error log files to Jenkins Archive facility on fail
commit 64048926627f8c9edb087de286095e3b93a214c2
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Tue Feb 13 14:57:37 2024 -0500
Ocean/ice product generation for GFS and GEFS (#2286)
This PR does several things:
1. the model output for ocean and ice in the `COM/` directory are now
named per EE2 convention for coupled model.
E.g `gfs.ocean.t12z.6hr_avg.f120.nc` and `gfs.ocean.t12z.daily.f120.nc`
2. The products are generated using the `ocnicepost.fd` utility developed
by @DeniseWorthen in https://github.com/NOAA-EMC/gfs-utils and
converted to grib2 using example scripts provided by @GwenChen-NOAA
using `wgrib2`.
3. NetCDF products on the native grid are also generated by subsetting
variables from the raw model output. This is done with `xarray`.
4. updates the hash of https://github.com/NOAA-EMC/gfs-utils to include
fixes in `ocnicepost.fd`
5. removes NCL related scripting that was previously used for ocean/ice
interpolation and `reg2grb2` used for converting to grib2.
6. updates archive scripts to accommodate updated file names
7. removes intermediate ocean processed files such as 2D/3D/xsect data-
sets
8. separate jobs are added for ocean and ice product generation.
9. removes intermediate restarts for the mediator and only saves the medi-
ator restart at the end of the forecast in `COM`.
10. Increases memory for offline UPP when run at C768. The program
segfaults with an OOM when memory is self allocated based on PEs by
the scheduler on Hera.
11. Enables ocean/ice ensemble product generation for GEFS
12. Some minor clean-ups
Fixes #935
Fixes #1317
Fixes #1864
commit 40f2cf6cd70ac94e01babc96982f37ae1b0c7e79
Author: henrywinterbottom-wxdev <henry.winterbottom.wxdev@gmail.com>
Date: Tue Feb 13 10:18:53 2024 -0700
Implemented ush/detect_machine.sh for host determination and removed redundant checks for expected file paths.
commit 929b90330c7eb345011c2c850915e0004ca26b11
Merge: 2d08d015a 3f99f700c
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date: Tue Feb 13 08:31:06 2024 -0700
Merge branch 'NOAA-EMC:develop' into feature/gfsv17_issue_2125
commit 3f99f700c987526c8eb754b3f4c7b698b3e9b1dc
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Tue Feb 13 00:57:18 2024 -0500
Add wave post jobs to GEFS (#2292)
Adds the wave post jobs for gridded and points to GEFS. Boundary
point jobs are added even though the current GEFS buoy file does
not contain any (tested by manually subbing in the GFS buoy file).
Resolves #827
commit 842adf38087aec9f1c0bca9567e4b11d494e14c7
Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
Date: Mon Feb 12 12:50:08 2024 -0500
Added additional test cases to the pr list in Jenkins (#2306)
C48mx500_3DVarAOWCDA, C96C48_hybatmDA, and C96_atmsnowDA
Co-authored-by: terrance.mcguinness <terrance.mcguinness@noaa.gov>
commit bb4ca65fe5524f76e40b97346339f1dda6680ce1
Author: CatherineThomas-NOAA <59020064+CatherineThomas-NOAA@users.noreply.github.com>
Date: Mon Feb 12 14:50:41 2024 +0000
Redo v16.3 config.base changes for DA increments (#2304)
Include the additional hydrometeors to the
INCREMENTS_TO_ZERO and INCVARS_ZERO_STRAT
variables in config.base that were modified
in v16.3.
Resolves: #2303
commit 061992bb6160554430cf688adf6184f01b732098
Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
Date: Sat Feb 10 01:33:36 2024 -0500
Fix Jenkins success reporting (#2302)
Moving the post section back outside of main Run Experiments
stage. This allows the system to correctly report the **Success**
status until after all tests pass.
_Had originally moved them in attempts to solve "Not an SCM
GitHub Job" issue and cause the reporting to misbehave._
Also ran through Jenkins linter and updated some messaging
that was incorrectly reporting system build type.
commit 28ccf78073a20ba1e4d3b379d164109b54ff6708
Merge: b972f66fc 54daa31ce
Author: David Huber <david.huber@noaa.gov>
Date: Fri Feb 9 14:00:43 2024 -0600
Merge remote-tracking branch 'emc/develop' into ss160
commit b972f66fc924790c48f38d395e7141fa78ef9d90
Author: David Huber <david.huber@noaa.gov>
Date: Fri Feb 9 10:47:00 2024 -0600
Fix SS versions for CI modules.
commit 4b01d8eeca26c3b3d843a4b1e7b1618f281de68f
Author: David Huber <david.huber@noaa.gov>
Date: Fri Feb 9 10:44:30 2024 -0600
Revert Hercules modules to SS/1.5.1.
commit 54daa31ce0a3c23d4d74def5e54436a39a899ed4
Author: TerrenceMcGuinness-NOAA <terrence.mcguinness@cox.net>
Date: Thu Feb 8 15:48:38 2024 -0500
Jenkins Declartive Pipeline for CI with gfs/gefs multibuilds (#2246)
Adding top level Jenkins file for CI tests running on Jenkins Controller:
- Declarative Multi-branch Pipeline (has enhanced restart capabilities
on a per section bases)
- Starts Pipeline from Label PR same as BASH system (for now)
- Progress and restarts can me managed with CAC Login at [EPIC OAR
Jenkins](https://jenkins.epic.oarcloud.noaa.gov)
- Has logic for multi **gfs/gefs** system builds (arguments based on a
configuration file `ci/casts/yamls/build.yaml`)
- Any number of **systems** may be added by manual adding an ele-
ment to the matrix in the Jenkinsfile
- _It may be possible to dynamic add matrix values with a specialty
plug-in_
- Currently only runs on **Orion** and **Hera** using `mterry` account
Resolves #2119
Resolves #2118
commit 43429e23c12c1f2050b3a3f356abdec98dc73ea0
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Thu Feb 8 15:30:28 2024 -0500
Enable AO WCDA test (#1963)
This PR:
- adds GSI + SOCA C48 5-deg ocean 3DVar test (courtesy @guillaumevernieres)
- adds a toggle to optionally disable ocnanalvrfy job.
commit 2d08d015afb9c850577efd9754add16b10c45ae6
Merge: 4745d4a06 f56352874
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date: Thu Feb 8 07:24:54 2024 -0700
Merge branch 'NOAA-EMC:develop' into feature/gfsv17_issue_2125
commit f56352874d6dc133a4f1181f77c8f91ca38a6416
Author: Kate Friedman <kate.friedman@noaa.gov>
Date: Wed Feb 7 15:09:12 2024 -0500
Update JGLOBAL_FORECAST for octal error (#2295)
Add "10#" to ENSMEM value > 0 check to handle octal errors.
commit 4745d4a06148cc6c702c647e12ede4875e3a5862
Author: henrywinterbottom-wxdev <henry.winterbottom.wxdev@gmail.com>
Date: Wed Feb 7 08:45:49 2024 -0700
Removed jlogfile references.
commit 5894ca2bf11e8ab7910c69781a9fbe51352a7e8c
Author: henrywinterbottom-wxdev <henry.winterbottom.wxdev@gmail.com>
Date: Wed Feb 7 08:32:16 2024 -0700
Removed dummy variable passed to perl scripts.
commit dae884a7c48b4a30c1844685c3d0ef50c9b78344
Author: henrywinterbottom-wxdev <henry.winterbottom.wxdev@gmail.com>
Date: Wed Feb 7 08:29:49 2024 -0700
Removed jlogfile and postmsg references within gempak scripts.
commit 801058ffb0cbbfe101fd5b686aed79c5bf7538c1
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date: Wed Feb 7 00:41:59 2024 -0700
Consolidate `npe_node_max` (#2289)
- The environment variable `npe_node_max` is removed from all
files beneath `global-workflow/env`;
- The environment variable `npe_node_max` is removed from
`parm/config/gefs/config.ufs` and `parm/config/gfs/config.ufs`;
- The environment variable `npe_node_max` is maintained only
within `parm/config/gefs/config.resources` and
`parm/config/gfs/config.resources`.
Resolves #2133
commit b0325e0157598702cbba6c3cc09af0120881e2b4
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date: Wed Feb 7 00:40:20 2024 -0700
Removes files module loading file no longer used by the GW (#2281)
Removes `module-setup.csh.inc` and `module-setup.sh.inc`.
The module `ush/module-setup.sh` is updated such that it now sources
`ush/detect_machine.sh` to determine which supported platform the
global-workflow is being execute on.
Resolves #2130
commit 1ccc9896b361f2aaef8e6e7592a06ae4cfb7c491
Author: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Mon Feb 5 14:16:07 2024 -0500
Remove EnKF forecast groups (#2280)
Removes the grouping of EnKF forecasts so each job only runs
one forecast. Member and MEMDIR are now set at the workflow
manager (rocoto) level. This change makes much of the system
simpler (especially dependencies) and allows the elimination of
the separate efcs scripts.
Metatask names of updated jobs have been updated to make
them a little less opaque by using the same name name as its
constituent tasks (e.g. the forecast metatask is named
`enkgdasfcst`, not `enkfgdasefcs`). Metatasks that weren't
updated retain the same names as before for now.
Resolves #2254
commit 9f3383fd8d8322428a40b94764a172a16872995e
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date: Mon Feb 5 12:15:13 2024 -0700
Updated detect_machine.sh using that from UFS WM. (#2252)
Updates `ush/detect_machine.sh` to match the UFS weather-model
`tests/detect_machine.sh` prepared by @BrianCurtis-NOAA
Resolves #2228
commit 7d68b0b164f0ffcd56867ae4fdab67905d9589eb
Author: CatherineThomas-NOAA <59020064+CatherineThomas-NOAA@users.noreply.github.com>
Date: Sun Feb 4 22:02:41 2024 +0000
Update global_cycle for fractional grid (#2262)
The hash for ufs_utils is updated to include the changes for
fractional grid support within global_cycle. This commit also
removes the hack to skip global_cycle in cycling mode with
v17 physics.
Resolves: #1775
Refs: ufs-community/UFS_UTILS#815
Refs: ufs-community/UFS_UTILS#891
commit ed592a6ecfabc0d0b64a6e276531b7bc5ae3b8ea
Author: Kate Friedman <kate.friedman@noaa.gov>
Date: Sat Feb 3 02:55:14 2024 -0500
Retire cycle-specific FHMAX_GFS variables (#2278)
This PR retires the `FHMAX_GFS_${cyc}` variables that allowed users to specify
different gfs forecast lengths for each cycle. This function is no longer supported
in global-workflow. The `FHMAX_GFS_*` variables will be removed and will no
longer be checked to set the final `FHMAX_GFS` variable. The same forecast
length will be set for every cycle.
This PR also includes a small fix to add new post parm files into the `.gitignore`
file. This was intended to be included in a different PR but that PR is on hold for
further testing so it is being included here to get it into `develop` sooner.
Resolves #2218
commit 977e2d67b268477321aa26fc56073dd373e4f979
Author: Henry R. Winterbottom <49202169+HenryWinterbottom-NOAA@users.noreply.github.com>
Date: Fri Feb 2 07:49:09 2024 -0700
New GDASApp hash. (#2285)
commit b5f2bd9ec5632c4be43004604eed0e130dfe1735
Merge: 4d667421d 0400e1f35
Author: David Huber <david.huber@noaa.gov>
Date: Tue Jan 30 13:55:00 2024 -0600
Merge branch 'ss160' of github.com:DavidHuber-NOAA/global-workflow into ss160
commit 0400e1f3558be8e34c1298d32e14999c9dd46f8c
Author: David Huber <david.huber@noaa.gov>
Date: Tue Jan 30 09:57:11 2024 -0600
Fix gfs_utils Orion spack-stack env path.
commit 6bbe823e729291db326d108765d3a92a99552a58
Author: DWesl <22566757+DWesl@users.noreply.github.com>
Date: Mon Jan 29 21:15:30 2024 -0500
Use seq to generate the list of times, instead of a bash for-loop (#2264)
I'm running a year-long forecast, which means I get a large portion of the log file dedicated to these loops.
`seq ${START} ${STEP} ${STOP}` will generate a sequence going from START to STOP by STEP, including STOP if relevant. That seems to be the purpose of these loops. It will by default separate the list with newlines, but `seq -s ' ' ${START} ${STEP} ${STOP}` will separate them with spaces instead, more closely mimicing the previous behavior.
I would like this to be two lines in the log, rather than a few hundred, and this may also be faster, though probably more for reasons of fewer writes to disk than because bash isn't designed for arithmetic.
commit d5bee38979cde547861261d1cd150f3a61601d4b
Author: Kate Friedman <kate.friedman@noaa.gov>
Date: Mon Jan 29 14:35:02 2024 -0500
Correct typos in GFS config.resources (#2267)
This PR corrects some typos in `parm/config/gfs/config.resources` that were
introduced in PR #2216. The esfc job was failing in tests on WCOSS2 due to
insufficient memory. This lead to discovering the other typos. The esfc job
completes without error after its memory is set back to `80GB` from the
incorrect `8GB`.
Resolves #2266
commit 81557beca9eecd878e7b25b3822e30a4276f4a16
Author: David Huber <david.huber@noaa.gov>
Date: Mon Jan 29 12:13:31 2024 -0600
Update monitor hash to noaa-emc with SS/1.6.0 support.
commit 2238dd6ac0094ba2ff5e1027e964ef29ad33352c
Author: DavidHuber <david.huber@noaa.gov>
Date: Mon Jan 29 13:21:30 2024 +0000
Update Orion, Hercules, S4 modulefiles.
commit 6ffd94fd95f54ceb940f0c9201774ad73fbb055b
Author: DavidHuber <david.huber@noaa.gov>
Date: Fri Jan 26 16:01:23 2024 +0000
Update GDAS hash to include SS/1.6.0 support.
commit be11f85f28cf832e5fbb390fdd387f1bdecb5f82
Merge: 56b968080 04e0772d9
Author: DavidHuber <david.huber@noaa.gov>
Date: Fri Jan 26 15:34:24 2024 +0000
Merge branch 'ss160' of github.com:DavidHuber-NOAA/global-workflow into ss160
commit 8ff344844e28c3b2d03a0356f88b14635f318c12
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Fri Jan 26 10:12:18 2024 -0500
Add a yaml for snow DA testing. (#2199)
- adds a new test yaml C96_atmsnowDA.yaml for 3DVar atmosphere with GSI and Land (Snow) DA with JEDI
- moves a few yamls from platforms/ to yamls/
- adds ability to overwrite a previously created experiment as an addition to user input.
---------
Co-authored-by: Cory Martin <cory.r.martin@noaa.gov>
commit 04e0772d9d3e77ac5a24ce4570d48cb41424a08b
Author: David Huber <david.huber@noaa.gov>
Date: Fri Jan 26 07:16:25 2024 -0600
Update ufs_utils hash for spack-stack/1.6.0 support.
commit 3d44ff38c5c3324c22fc104fe3259b4ac864c6d6
Author: Barry Baker <bbakernoaa@users.noreply.github.com>
Date: Thu Jan 25 14:33:27 2024 -0500
GOCART ExtData biogenic climatology fix (#2253)
Updates the ExtData for biogenic emissions to be climatology rather than
for current time. Fixes an issue which will crash by default for other years.
commit 66f58b8ab1a9524d6be95271f27a06c2f32e5f78
Author: Guillaume Vernieres <guillaume.vernieres@noaa.gov>
Date: Thu Jan 25 13:16:41 2024 -0500
Added missing container case in gfs/config.resources (#2258)
fixes #2257
commit 553b4f2e74ef610115436b75f7f6df100babd8dd
Author: WenMeng-NOAA <48260754+WenMeng-NOAA@users.noreply.github.com>
Date: Thu Jan 25 13:00:45 2024 -0500
Fix post parm links (#2243)
Change symbolic links under parm/post with the latest version of develop branch from UPP repository and enable MERRA2 aerosol fields.
Resolves #2259
commit 4d667421d5eefea2347ea1dd8097e39e167d7201
Merge: 6c058039e afa09e356
Author: David Huber <david.huber@noaa.gov>
Date: Thu Jan 25 07:49:08 2024 -0600
Merge branch 'ss160' of github.com:DavidHuber-NOAA/global-workflow into ss160
commit 6c058039e209c67ea477d37d2d6f76b7a2fa68ac
Author: David Huber <david.huber@noaa.gov>
Date: Thu Jan 25 07:48:42 2024 -0600
Fix wgrib2/gfs_utils on Hercules.
commit ee6f536ea0228c60f5a8bec4037cd6f7ea63b816
Author: Kate Friedman <kate.friedman@noaa.gov>
Date: Thu Jan 25 07:43:13 2024 -0500
Update GFS version to v16.3.13 in index.rst (#2256)
GFSv16.3.13 WAFS update was implemented
Refs #2013
commit 2445d44d0d66f35512080b0bd5867501660793bb
Author: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com>
Date: Thu Jan 25 06:17:11 2024 -0500
Simplify and extend load_ufsda_modules to Hercules (#2245)
GDASApp jobs do not run on Hercules because `ush/load_ufsda_modules.sh` does
not include logic to load the appropriate GDASApp modules on Hercules. This PR
extends `load_ufsda_modules.sh` functionality to Hercules, thereby enabling
GDASApp jobs to run on Hercules.
Resolves #2244
commit 56b9680803f109720f6439276a0e5783a9c49352
Author: DavidHuber <david.huber@noaa.gov>
Date: Wed Jan 24 19:47:34 2024 +0000
Update hashes (revert WCOSS2 modules).
commit afa09e356503f1befc162df9a79dc9ce7414dc22
Author: DavidHuber <david.huber@noaa.gov>
Date: Wed Jan 24 18:59:40 2024 +0000
New (cleaner history) gdas hash.
commit a9eaec23d5103ea766342ff81d77df8e0f6d9a58
Author: DavidHuber <david.huber@noaa.gov>
Date: Wed Jan 24 18:52:27 2024 +0000
Update gdasapp to include ss/1.6.0 support.
commit 5ef8eb24eeaeaff9c9a03767d929f2114fd4840f
Merge: 4c463548b e400068a2
Author: DavidHuber <david.huber@noaa.gov>
Date: Wed Jan 24 17:08:54 2024 +0000
Merge branch 'ss160' of github.com:DavidHuber-NOAA/global-workflow into ss160
commit 4c463548b0c38f36c13c01716fa0b1e91544e440
Author: DavidHuber <david.huber@noaa.gov>
Date: Wed Jan 24 17:05:12 2024 +0000
Reenable verif-global support
commit f775755df5f1579edfafbce9a7b47034907d023f
Author: DavidHuber <david.huber@noaa.gov>
Date: Wed Jan 24 16:59:10 2024 +0000
Assign fcsthrs for awips_g2 job.
commit e400068a2951e5fa3b130369861b4a60ece01491
Author: David Huber <david.huber@noaa.gov>
Date: Mon Jan 22 15:01:07 2024 -0600
More gsi-addon path fixes.
commit f663d4786f226f8164d348d403e8d105cc3d801b
Author: David Huber <david.huber@noaa.gov>
Date: Mon Jan 22 14:41:59 2024 -0600
Fix gsi-addon paths for hercules, orion, and S4.
commit e304bbeb364067e411fb50801796d000b44d9147
Author: DavidHuber <david.huber@noaa.gov>
Date: Mon Jan 22 18:59:34 2024 +0000
Better optimize build jobs (more ufs jobs).
commit ccc6e2d445d4c2e2f44fb907c7bc972b1e69f6ff
Author: DavidHuber <david.huber@noaa.gov>
Date: Mon Jan 22 18:56:18 2024 +0000
Reenable verif-global. #2195
commit 3ef3411f856b0c5a9cf51686f3a51a2252596690
Merge: 4365f63e5 f4d187f4e
Author: DavidHuber <david.huber@noaa.gov>
Date: Mon Jan 22 18:39:10 2024 +0000
Merge remote-tracking branch 'origin/develop' into ss160
commit 4365f63e54e2ddb9b88e768a6e88a92504b5d482
Author: DavidHuber <david.huber@noaa.gov>
Date: Mon Jan 22 18:37:25 2024 +0000
Corrected the SS env. name in the version files. #2195
commit f4d187f4e45fe89583d18987d68a883490827104
Author: AndrewEichmann-NOAA <58948505+AndrewEichmann-NOAA@users.noreply.github.com>
Date: Mon Jan 22 12:28:28 2024 -0500
Converts obsproc to obsprep in prepoceanobs config file (#2236)
Converts obsproc to obsprep in prepoceanobs config file as a compliment to mutually depended GDASApp PR NOAA-EMC/GDASApp#858
The motivations are explained in refs NOAA-EMC/GDASApp#857
commit 9a09d3082208ad206cf6e7103a53bfb7c4946f4a
Author: DavidHuber <david.huber@noaa.gov>
Date: Fri Jan 19 21:23:50 2024 +0000
Corrected gsi-addon-dev spelling.
commit 21ff6458aac9372b26cc223f6a114953a137067e
Author: DavidHuber <david.huber@noaa.gov>
Date: Fri Jan 19 21:11:34 2024 +0000
Update modulefiles, submodules to spack-stack 1.6.0. #2195
commit d4c55d1011f8b0385d25b62ac04710837ed8413e
Author: Kate Friedman <kate.friedman@noaa.gov>
Date: Fri Jan 19 15:43:37 2024 -0500
Update typing hint for WCOSS version of python (#2238)
The typing hint `typing.List` was deprecated with python 3.9 in favor
of using the primitive `list[str]`, but the functional version of python
on WCOSS2 is <3.9, causing `setup_xml.py` to fail there. This replaces
`list[str]` as a typing hint with the deprecated form until the supported
version on WCOSS2 is >=3.9.
commit 491928712ae1dabac62750450c9cad8f538c2a3e
Author: Barry Baker <bbakernoaa@users.noreply.github.com>
Date: Thu Jan 18 22:31:27 2024 -0500
GOCART Emission updates for GEFSv13 and GDAS (#2201)
This PR addresses several things needed for more recent simulations using
GOCART2G as well as preparing for the GEFSv13 30 year run. The main
updates are:
- Update CEDS to use monthly emission files instead of daily. This will
drastically reduce the number of files needed. No science change
- Update biogenic MEGAN inputs to use a climatology rather than the
offline biogenic previously used. This is needed to deal with simulations
where the current dataset is not available.
- Update volcanic SO4 emissions to use degassing emissions only. This is
to support the need for more recent simulations where data is not available.
commit 13d25cfc3614de978bfd4b7f273d1f13cb820878
Author: Kate Friedman <kate.friedman@noaa.gov>
Date: Thu Jan 18 22:29:43 2024 -0500
Add `POSTAMBLE_CMD` into preamble postamble (#2235)
This PR adds the ability to run a command at the end of jobs via the
preamble's postamble function. A new command can be set via
`POSTAMBLE_CMD` and will be invoked at the end of jobs. Users can
add the command to the top of an env file to have every job run it or
it can be placed within a job if-block in the env file to run for just that
job.
Resolves #1145
commit 7759163c668eb6ccc11dc1ecd39c0dc5d433cdc1
Author: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Thu Jan 18 01:13:49 2024 -0500
Add option to…
kayeekayee
pushed a commit
to kayeekayee/global-workflow
that referenced
this issue
May 30, 2024
…pp-physics (NOAA-EMC#300) - renames the ccpp-framework and ccpp-physics branches from master to main in .gitmodules - updates the submodule pointer for ccpp-physics for several small changes described in NCAR/ccpp-physics#658 - updates the submodule pointer for ccpp-framework for a small update described in NCAR/ccpp-framework#372 - add missing Intel DEBUG flags specific to CCPP
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This is a tracking issue to monitor the progress of updating makefiles from packages used by global-workflow. This issue should link to the corresponding GitHub issues in the offending packages to ensure all are addressing this issue.
Jen Yang 2021-03-12 06:46:05 UTC
Scanned the makefiles in gfs.v16.0 source code package, and found the following makefiles missing debug or clean target. Please update the makefiles to add the debug or clean target. This can be addressed in the next major upgrade.
Missing debug target:
Missing clean target:
Refs: Bugzilla #1218
The text was updated successfully, but these errors were encountered: