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Update JEDI hashes in sorc #1123

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merged 24 commits into from
Jun 5, 2024
Merged

Update JEDI hashes in sorc #1123

merged 24 commits into from
Jun 5, 2024

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RussTreadon-NOAA
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This PR updates the hashes for select JEDI repositories in the GDASApp sorc directory. Updating the submodule hashes necessitates corresponding changes elsewhere in GDASApp. These additional changes include

  • soca updates (see GDASApp issue #1093)
  • update names for select radiance bias correction terms
  • correcting the path to satbias2ioda.x in test/atm/test_convert_gsi_satbias.sh

Resolves #1117

@RussTreadon-NOAA RussTreadon-NOAA mentioned this pull request May 22, 2024
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@RussTreadon-NOAA
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NOTE This PR is opened in draft mode since full functionality of the changes in this PR depends on other PRs

  • OOPS PR #2645. Once this PR is merged, the change to .gitmodules in the PR will be reverted
  • jcb-gdas PR #8
  • GSI-utils PR #43 & g-w PR #2592

Additionally the amsua_n19 bias correction files in GDASAPP_TESTDATA need to be updated to the new bias correction term naming convention. Once this is done in the authoritative GDASAPP_TESTDATA the changes to modulefiles/GDAS/orion.intel.lua will be reverted.

@CoryMartin-NOAA
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Now that generic diffusion is in JEDI/SABER, @andytangborn will need the latest versions of OOPS and SABER in GDASApp soon to coincide with some workflow changes. Is the OOPS bugfix created by Bo essential to include in this PR (meaning does it affect our current configuration)?

@RussTreadon-NOAA
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@CoryMartin-NOAA , OOPS PR #2645 is required for the JEDI ATM lgetkf to run as it currently does. Without PR #2645, lgetkf writes increments for all variables in the input state. This causes problems for downstream applications.

@RussTreadon-NOAA
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@CoryMartin-NOAA : This PR can be changed to Ready for review along with jcb-gdas PR #8 with the caveat that not all existing GDASApp functionality will be available.

@CoryMartin-NOAA
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Thanks @RussTreadon-NOAA I think we can wait a few more days to see if that gets merged in

@RussTreadon-NOAA RussTreadon-NOAA mentioned this pull request May 30, 2024
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@RussTreadon-NOAA RussTreadon-NOAA mentioned this pull request May 31, 2024
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@CoryMartin-NOAA
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@RussTreadon-NOAA @guillaumevernieres are you both okay if we just start the process of updating to develop now, with the understanding we'll need to do it again soon for the GETKF changes? @andytangborn would like to move forward with testing of diffusion for the aerosols and that depends on recent OOPS and SABER changes. If so, I can work towards updating the submodules again, and test.

@emcbot emcbot added the hera-GW-RT-Running Automated testing with global-workflow running on Hera label Jun 5, 2024
@RussTreadon-NOAA
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I'm kicking off the automated testing but I am also going to compile myself.

Doing likewise on Orion.

@emcbot emcbot added orion-GW-RT-Running Automated testing with global-workflow running on Orion and removed orion-GW-RT Queue for automated testing with global-workflow on Orion labels Jun 5, 2024
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emcbot commented Jun 5, 2024

Automated Global-Workflow GDASApp Testing Results:
Machine: orion

Start: Wed Jun  5 11:08:54 CDT 2024 on Orion-login-1.HPC.MsState.Edu
---------------------------------------------------
Build:                                 *SUCCESS*
Build: Completed at Wed Jun  5 11:59:07 CDT 2024
---------------------------------------------------
Tests:                                  *Failed*
Tests: Failed at Wed Jun  5 12:33:39 CDT 2024
Tests: 83% tests passed, 8 tests failed out of 47
	1775 - test_gdasapp_atm_jjob_var_init (Failed)
	1776 - test_gdasapp_atm_jjob_var_run (Failed)
	1777 - test_gdasapp_atm_jjob_var_inc (Failed)
	1778 - test_gdasapp_atm_jjob_var_final (Failed)
	1779 - test_gdasapp_atm_jjob_ens_init (Failed)
	1780 - test_gdasapp_atm_jjob_ens_run (Failed)
	1781 - test_gdasapp_atm_jjob_ens_inc (Failed)
	1782 - test_gdasapp_atm_jjob_ens_final (Failed)
Tests: see output at /work2/noaa/stmp/cmartin/CI/GDASApp/workflow/PR/1123/global-workflow/sorc/gdas.cd/build/log.ctest

@emcbot emcbot added orion-GW-RT-Failed Automated testing with global-workflow failed on Orion and removed orion-GW-RT-Running Automated testing with global-workflow running on Orion labels Jun 5, 2024
@CoryMartin-NOAA
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Looks like a JCB issue on Orion CI, due to an old JCB still in the global-workflow that it checked out. I expect the same issue on Hera.

@CoryMartin-NOAA
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After fixing JCB issues, I now get "lapseRate does not exist in ufo::PredictorFactory". @RussTreadon-NOAA is it working for you or did you get the same error?

@RussTreadon-NOAA
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Yes, automated CI using g-w develop will fail due to g-w using an older snapshot of jcb. I updated sorc/jcb in my working copy on Orion (look in /work2/noaa/da/rtreadon/git/global-workflow/update_gdasapp).

47 out of 47 GDASApp ctests pass from my build. g-w C96C48_ufs_hybatmDA CI has run through the var and lgetkf apps ... provided sorc/jcb is updated.

@CoryMartin-NOAA
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Hmm, I wonder why mine is not working. It seems like it has an old UFO hash for some reason. Let me double check this after my meeting.

@CoryMartin-NOAA
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Ok @guillaumevernieres FYI we can no longer trust the automated CI as for whatever reason it is not updating submodules properly... not intended to hold up this PR (to the contrary) but something we need to sort out ASAP

@CoryMartin-NOAA
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Ok, I know what the problem is, the CI does not work on forks, and since this is a branch on Russ's fork, it did not even check out the changes properly.

@RussTreadon-NOAA
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Ok, I know what the problem is, the CI does not work on forks, and since this is a branch on Russ's fork, it did not even check out the changes properly.

Oops, my bad. Sorry.

@RussTreadon-NOAA
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g-w C96C48_ufs_hybatmDA CI has completed the gdas and enkfgdas cycles. The gfs fcst and downstream jobs remain. DA jobs successfully ran to completion.

@CoryMartin-NOAA
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no problem @RussTreadon-NOAA you've uncovered a flaw in our CI!

I was able to compile your branch manually, that plus your testing, I think is sufficient to get this PR in as it is long overdue.

CoryMartin-NOAA
CoryMartin-NOAA approved these changes Jun 5, 2024
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Approved pending successful completion of the forecast jobs in @RussTreadon-NOAA 's test

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emcbot commented Jun 5, 2024

Automated Global-Workflow GDASApp Testing Results:
Machine: hera

Start: Wed Jun  5 16:14:48 UTC 2024 on hfe01
---------------------------------------------------
Build:                                 *SUCCESS*
Build: Completed at Wed Jun  5 17:03:53 UTC 2024
---------------------------------------------------
Tests:                                  *Failed*
Tests: Failed at Wed Jun  5 19:03:29 UTC 2024
Tests: 79% tests passed, 10 tests failed out of 47
	1774 - test_gdasapp_atm_jjob_var_init (Failed)
	1775 - test_gdasapp_atm_jjob_var_run (Failed)
	1776 - test_gdasapp_atm_jjob_var_inc (Failed)
	1777 - test_gdasapp_atm_jjob_var_final (Failed)
	1778 - test_gdasapp_atm_jjob_ens_init (Failed)
	1779 - test_gdasapp_atm_jjob_ens_run (Failed)
	1780 - test_gdasapp_atm_jjob_ens_inc (Failed)
	1781 - test_gdasapp_atm_jjob_ens_final (Failed)
Tests: see output at /scratch1/NCEPDEV/da/Cory.R.Martin/CI/GDASApp/workflow/PR/1123/global-workflow/sorc/gdas.cd/build/log.ctest

@emcbot emcbot added hera-GW-RT-Failed Automated testing with global-workflow failed on Hera and removed hera-GW-RT-Running Automated testing with global-workflow running on Hera labels Jun 5, 2024
@RussTreadon-NOAA
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g-w C96C48_ufs_hybatmDA CI completed on Orion. All jobs passed

Orion-login-4:/work2/noaa/stmp/rtreadon/EXPDIR/prsub$ rocotostat -d prsub.db -w prsub.xml -c all -s
   CYCLE         STATE           ACTIVATED              DEACTIVATED
202402231800        Done    Jun 05 2024 17:21:32    Jun 05 2024 17:40:28
202402240000        Done    Jun 05 2024 17:21:32    Jun 05 2024 19:40:33

@CoryMartin-NOAA
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Thanks @RussTreadon-NOAA are we ready to merge this in?

@RussTreadon-NOAA
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@CoryMartin-NOAA , yes, let's merge this PR into develop. Other developers want the JEDI repo updates, right?

@RussTreadon-NOAA RussTreadon-NOAA self-assigned this Jun 5, 2024
@CoryMartin-NOAA
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Yes, @andytangborn in particular. Thanks @RussTreadon-NOAA I'll merge!

@CoryMartin-NOAA CoryMartin-NOAA merged commit 825f19c into NOAA-EMC:develop Jun 5, 2024
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danholdaway added a commit that referenced this pull request Jun 6, 2024
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Merge branch 'develop' into feature/rename_atm
6c7c58a 
* develop:
  Update JEDI hashes in sorc (#1123)
guillaumevernieres
guillaumevernieres reviewed Jun 13, 2024
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utils/soca/gdas_soca_diagb.h
@@ -300,12 +300,12 @@ namespace gdasapp {
}

// Update the layer thickness halo
nodeColumns.haloExchange(xbFs["hocn"]);
xbFs["hocn"].haloExchange();
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Turns out this is using the wrong function space ...

@guillaumevernieres guillaumevernieres mentioned this pull request Jun 13, 2024
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@RussTreadon-NOAA RussTreadon-NOAA deleted the feature/submodules branch June 13, 2024 17:46
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Update hashes for JEDI submodules
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@RussTreadon-NOAA @CoryMartin-NOAA @guillaumevernieres @emcbot