Update ufs-bundle to build with head of develop of ufs-weather-model for ATM configuration by mark-a-potts · Pull Request #43 · JCSDA/ufs-bundle

mark-a-potts · 2023-12-05T19:51:21Z

Description

This PR, in combination with PRs for oops and fv3-jedi, allows the ufs-bundle to be built using the head of develop for the ufs-weather-model. Additionally, new regression tests have been added to fv3-jedi that will update the run directories needed for the UFS model and to run a sample Ensemble Forecast of the UFS.

Issue(s) addressed

Resolves #14

Dependencies

List the other PRs that this PR is dependent on:

https://github.com/JCSDA-internal/fv3-jedi/pull/1099

Impact

None.

Checklist

I have performed a self-review of my own code
I have made corresponding changes to the documentation
I have run the unit tests before creating the PR

mark-a-potts · 2023-12-05T20:02:49Z

This PR has been tested and works with UFS_APP=ATM, ATMAERO, and S2S configurations. There are no tests for ATMAERO or S2S, but both configurations build. The NG-GODAS option does not build because the soca branch required is out of date with the rest of the bundle and requires fairly significant work.

climbfuji · 2023-12-05T20:09:05Z

This PR has been tested and works with UFS_APP=ATM, ATMAERO, and S2S configurations. There are no tests for ATMAERO or S2S, but both configurations build. The NG-GODAS option does not build because the soca branch required is out of date with the rest of the bundle and requires fairly significant work.

I have an updated SOCA branch that I used for a similar effort ... I can make that work with this PR.

mark-a-potts · 2023-12-05T20:23:14Z

That would be great. I started on a merge and it looked like it was going to be a lot of work. I added a patch to handle an issue with checksum checking of restart files down in atmos_cubed_sphere. I know that there are differences in the MOM6 repo, so maybe we could add a similar patch for those and get everything working with the head of develop of the WM.

…ecasts

climbfuji · 2023-12-05T20:38:03Z

@mark-a-potts Let's fix the CI failures first. This is because of a merge last week on the JEDI side that changed the model interfaces, but nobody thought about the fv3-jedi etc branches for the UFS. Let me do this in an hour or so, ok?

mark-a-potts · 2023-12-07T19:32:48Z

I have updated this to now handle building ATM, ATMAERO, and S2S using the head of develop of the ufs-wm. NG-GODAS is still very broken, but the build with S2S will actually run the ATM regression tests without issue.

climbfuji · 2023-12-07T20:23:26Z

@mark-a-potts I resolved the merge conflict in dd72818, please take a look to see if everything looks ok

climbfuji · 2023-12-07T20:25:03Z

README.md

 ## Required thirdparty libraries

-This bundle requires the following spack-stack modules be loaded (all except `fms@2022.04` are in the `skylab-3.0.0` environment):
+This bundle requires the following spack-stack modules be loaded (all except `fms@2022.04` and `atlast@0.35.1` are in the `skylab-3.0.0` environment):


We need to update this section (and the list of modules) to something more recent

climbfuji · 2023-12-07T20:26:41Z

There is now a CI failure in the cmake step, related to fv3-jedi-data: https://github.com/JCSDA/ufs-bundle/actions/runs/7133595917/job/19426615092?pr=43

mark-a-potts · 2023-12-07T21:48:27Z

Just removed the extra fv3-jedi-data section. I think it should work now.

climbfuji · 2023-12-07T22:36:58Z

Sigh, there are so many updates to the JEDI code that it seems impossible to get a clean run! I'll hop on the instance and clear the build area, then restart the test.

mark-a-potts · 2023-12-07T23:13:11Z

The latest update to ioda seems to have broken the buid now.

climbfuji · 2023-12-07T23:18:12Z

The latest update to ioda seems to have broken the buid now.

Can you try to pull oops develop into your branch please?

mark-a-potts · 2023-12-07T23:52:15Z

Yeah, I think that was the issue. Just re-built successfully on my machine, so pushing now.

climbfuji · 2024-01-09T03:37:21Z

Last thing is to get the fv3-jedi PR merged, correct? I think you avoided the oops dependency (it's still in the PR description) for now.

mark-a-potts · 2024-01-09T14:53:34Z

Yes. The fv3-jedi PR can be done without the oops PR, and I think it would be good to do that. I will remove the mentions of oops in the PR descriptions.

…to develop

climbfuji

Please update the PR from ufs-bundle develop, revert the fv3-jedi branch name; this PR also uses temporary branches for soca and fv3-jedi-data?

climbfuji · 2024-01-31T15:22:03Z

CMakeLists.txt

-    ecbuild_bundle( PROJECT soca        GIT "https://github.com/jcsda-internal/soca.git"          BRANCH feature/ufs_dom UPDATE )  # updated from develop Dec 12 2023
-    add_dependencies(soca ufs-weather-model)
-  endif()
+  ecbuild_bundle( PROJECT fv3-jedi-data GIT "https://github.com/JCSDA-internal/fv3-jedi-data.git" BRANCH feature/ufs-EnsForecasts ) 


I still see a branch feature/ufs-EnsForecasts for fv3-jedi-data ?

climbfuji · 2024-01-31T15:22:23Z

CMakeLists.txt

-    add_dependencies(soca ufs-weather-model)
-  endif()
+  ecbuild_bundle( PROJECT fv3-jedi-data GIT "https://github.com/JCSDA-internal/fv3-jedi-data.git" BRANCH feature/ufs-EnsForecasts ) 
+  ecbuild_bundle( PROJECT fv3-jedi GIT "https://github.com/jcsda-internal/fv3-jedi.git" BRANCH feature/ufs-EnsForecasts UPDATE )  


The fv3-jedi branch feature/ufs-EnsForecasts was just merged into develop

climbfuji · 2024-01-31T15:22:39Z

CMakeLists.txt

 elseif(UFS_APP MATCHES "^(NG-GODAS)$")
-  ecbuild_bundle( PROJECT soca     GIT "https://github.com/jcsda-internal/soca.git" BRANCH feature/ufs_dom UPDATE )  # updated from develop Dec 12 2023
+# ecbuild_bundle( PROJECT soca     GIT "https://github.com/jcsda-internal/soca.git" BRANCH feature/ufs_dom UPDATE )  
+  ecbuild_bundle( PROJECT soca     GIT "https://github.com/jcsda-internal/soca.git" BRANCH feature/ufs_mark UPDATE )  


Has this been merged already?

climbfuji · 2024-01-31T15:24:31Z

There is also a conflict for README.md because my last PR replaced w3nco with w3emc.

mark-a-potts · 2024-01-31T18:17:40Z

Working on this now. The s3 bucket is currently being synched to the latest rt results, so that is delaying the testing a bit. Will update shortly.

…as+s2s

mark-a-potts · 2024-02-01T17:14:47Z

After the latest update, the ctests pass and builds now work for ATM, ATMAERO, NG-GODAS, and S2S configurations.

climbfuji

A few minor comments to reduce the amount of unnecessary changes etc, other than that this looks great!

climbfuji · 2024-02-01T17:19:19Z

.github/workflows/run_ec2_pcluster.yaml

          cd ${JEDI_ENV}
          mkdir -p build-atmaero
          cd build-atmaero
+          rm -rf *


Why is this needed?

I had to put it there to make sure the build was started fresh. I'll remove it now.

CMakeLists.txt

climbfuji · 2024-02-01T17:21:26Z

README.md

+ 21) libpng/1.6.37                    47) ectrans/1.2.0     73) py-f90nml/1.4.3              99) nemsio/2.5.4
+ 22) g2/3.4.5                         48) atlas/0.35.0      74) py-h5py/3.7.0               100) sfcio/1.4.1
+ 23) g2tmpl/1.10.2                    49) git-lfs/3.0.2     75) py-cftime/1.0.3.4           101) sigio/2.3.2
+ 24) sp/2.3.3                         50) gsibec/1.1.3      76) py-netcdf4/1.5.8            102) w3nco/2.4.1


This is reverting my recent change in README.md that replaced w3nco with w3emc

Ah, I missed that. I mostly wanted to update the fms version to 2023.02.01 which is now required by the WM. I'll get that straightened out.

Co-authored-by: Dom Heinzeller <dom.heinzeller@icloud.com>

climbfuji

Thanks for all your work on this!

climbfuji · 2024-02-01T20:37:43Z

@mark-a-potts CI tests are failing unfortunately: https://github.com/JCSDA/ufs-bundle/actions/runs/7745452671/job/21121475447?pr=43

CI tests are failing

climbfuji

Would have been nice to keep the build directories (much faster), but if it doesn't work ...

mark-a-potts added 10 commits October 20, 2023 11:26

working version with calculation of ensemble mean values

db104fe

pegged hashes for ioda, saber, ufo

f6b30cd

updated fv3-jedi-data branch

e307be2

Updated to calculate the ensemble mean of the StateSet

7ad6bc6

Updating to head of develop for ufs-wm

3119a2c

Added script to regenerate rundir for c48 case

0dd0a61

updates to handle head of develop for ufs-wm

7b6c402

different wm repos for non-ATM builds

30f7e45

updated to build s2s and aero

d55e8f7

slight changes to README

1bf0d74

added patch for checksum checking

0853610

mark-a-potts added 2 commits December 5, 2023 15:28

Merge remote-tracking branch 'origin/develop' into feature/ufs-EnsFor…

cedd860

…ecasts

cleanup

6263d82

mark-a-potts added 2 commits December 7, 2023 14:15

Updates for building ATM, ATMAERO, and S2S

2965dae

Cleaned up CMakeLists.txt a bit

0e9437e

Merge branch 'develop' into feature/ufs-EnsForecasts

dd72818

climbfuji reviewed Dec 7, 2023

View reviewed changes

removed extra jedi-data line

4004a52

mark-a-potts requested a review from frolovsa January 9, 2024 17:44

Switched patch to only appy to ng-godas after UFS-WM PR was merged in…

70bec2e

…to develop

mark-a-potts dismissed climbfuji’s stale review via 70bec2e January 12, 2024 16:31

climbfuji reviewed Jan 31, 2024

View reviewed changes

mark-a-potts and others added 6 commits January 31, 2024 15:15

Fixed patch and updated CMakeLists.txt to account for fv3-jedi pr

70608c6

Merge branch 'develop' into feature/ufs-EnsForecasts

f5849ec

Updated fms to 2023.02.01 for ufs

e39e115

tweak to remove ufs-weather-model directory in build directory

470f196

tweak to remove everything in the build directory

13c0ee7

tweak to remove everything in the build-aero directory, re-enable god…

a24ff69

…as+s2s

climbfuji reviewed Feb 1, 2024

View reviewed changes

mark-a-potts and others added 4 commits February 1, 2024 12:37

Update CMakeLists.txt

393ad39

Co-authored-by: Dom Heinzeller <dom.heinzeller@icloud.com>

Update CMakeLists.txt

3b78fac

Co-authored-by: Dom Heinzeller <dom.heinzeller@icloud.com>

Update CMakeLists.txt

36a97c2

Co-authored-by: Dom Heinzeller <dom.heinzeller@icloud.com>

Revert changes from README and get rid of rm -rf in yaml

136543d

climbfuji previously approved these changes Feb 1, 2024

View reviewed changes

This was referenced Feb 1, 2024

Update dev/emc for JEDI (SOCA) + UFS NOAA-EMC/MOM6#107

Closed

DO NOT MERGE YET - Update CMAQ submodule to CMAQv5.3.3.2_7May2022 NOAA-EMC/AQM#40

Closed

remove build directories

d322768

climbfuji approved these changes Feb 2, 2024

View reviewed changes

climbfuji merged commit 11410cc into develop Feb 2, 2024

climbfuji deleted the feature/ufs-EnsForecasts branch February 2, 2024 03:04

climbfuji mentioned this pull request Feb 2, 2024

Update ufs-bundle to use head of develop of ufs-weather-model #44

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