Sync RDASApp submodules with upstream repositories #217

SamuelDegelia-NOAA · 2024-11-04T21:35:18Z

This PR syncs the RDASApp submodules with their respective upstream repositories. Each submodule is updated to the head of their develop branches. Here are the updated hashes for each submodule:

fv3-jedi:        d3c800b -> 2c72009
fv3-jedi-lm:     a6e97d7 -> 3254bb8
ioda:            d49ed17 -> eaacb84
iodaconv:        b540ace -> 1bce7ab
mpas-jedi:       b9d596d -> 0edc6b9
oops:            d772173 -> b2e6d27
saber:           bba6f7e -> ac8d8aa
ufo:             94d50d6 -> 7c9d9a3
vader:           6d56a1e -> aedb250

The ufo-data and ioda-data staged data are also updated under the role accounts and their links are updated in RDASApp. The mpas-jedi-data and fv3-jedi-data directories are already up to date. Here are the new hashes (the directories are now also labeled in RDAS_DATA):

ufo-data: b45d99e
ioda-data: 25afc2c

Note that CRTM, MPAS, and gsibec submodules are not updated since we have those set as tagged versions.

Following some variable name updates in UFO, some of the yaml files were also updated. Also, fv3-jedi now expects pressure variables named DELP instead of delp, so the fv3-jedi case data for rrfs-test has also been updated. Thanks to @delippi for making those variable changes.

Finally, the EnVar test in rrfs-test failed with a small reference mismatch error, so the test reference data there has also been updated.

The ufo, mpas-jedi, fv3-jedi, and rrfs-test ctests were run as part of this update. I will update the PR with results from these tests momentarily.

EDIT: Updated instructions for syncing submodules with upstream repositories can be found here.

…mixing_ratio_wrt_moist_air" for fv3jedi

…lia-NOAA/RDASApp into feature/sync_upstream

SamuelDegelia-NOAA · 2024-11-04T21:36:10Z

Results from UFO ctests

99% tests passed, 4 tests failed out of 511

Label Time Summary:
GEOS                  = 239.06 sec*proc (3 tests)
HofX                  = 710.66 sec*proc (10 tests)
QC                    = 1205.69 sec*proc (16 tests)
UV                    = 159.29 sec*proc (2 tests)
actions               =  15.83 sec*proc (4 tests)
aircraft              = 216.35 sec*proc (3 tests)
compo                 = 152.88 sec*proc (2 tests)
crtm                  = 620.77 sec*proc (54 tests)
errors                = 1309.44 sec*proc (8 tests)
executable            = 3193.51 sec*proc (52 tests)
filters               = 10660.14 sec*proc (193 tests)
fov                   =  27.01 sec*proc (3 tests)
gnssro                =  74.25 sec*proc (1 test)
instrument            = 2069.23 sec*proc (28 tests)
metoffice             =  77.36 sec*proc (2 tests)
mpi                   = 15888.14 sec*proc (475 tests)
obsfunctions          = 568.40 sec*proc (87 tests)
operators             = 872.21 sec*proc (150 tests)
ozone                 =   0.77 sec*proc (2 tests)
pibal                 =  75.89 sec*proc (1 test)
predictors            = 132.33 sec*proc (27 tests)
profile               = 194.51 sec*proc (41 tests)
radarVAD              = 161.01 sec*proc (2 tests)
rass                  = 159.91 sec*proc (2 tests)
satwinds              = 268.74 sec*proc (3 tests)
scatwinds             = 234.16 sec*proc (3 tests)
script                = 12756.23 sec*proc (459 tests)
sfcLand               = 238.35 sec*proc (3 tests)
sfcMarine             = 239.63 sec*proc (3 tests)
sonde                 = 247.28 sec*proc (3 tests)
ufo                   = 15949.74 sec*proc (511 tests)
unit_tests            = 457.32 sec*proc (95 tests)
utils                 =   8.87 sec*proc (2 tests)
variablenamemap       =   2.84 sec*proc (1 test)
variabletransforms    = 103.47 sec*proc (24 tests)

Total Test time (real) = 15968.22 sec

The following tests FAILED:
        146 - ufo_test_tier1_test_ufo_qc_variableassignment (Failed)
        166 - ufo_test_tier1_test_ufo_tropics_qc_filters (Failed)
        494 - ufo_test_tier1_test_ufo_variabletransforms_rhumidity (Failed)
        497 - ufo_test_tier1_test_ufo_variabletransforms_shumidity (Failed)
Errors while running CTest
Output from these tests are in: /scratch1/BMC/zrtrr/Samuel.Degelia/RDASApp_updatesub/RDASApp/build/ufo/Testing/Temporary/LastTest.log
Use "--rerun-failed --output-on-failure" to re-run the failed cases verbosely.

For these four failures, test 146 already failed before this update due to a floating point reference error. Test 166 fails due to a CRTM error (likely due to our CRTM version lagging behind that used for the ufo repo).

Tests 494 and 497 fail due to a UFO update from a few days ago that expects an error but that did not occur in my testing. So because that error did not occur, it considers the ctest failed. Overall I do not think this is a concern.

SamuelDegelia-NOAA · 2024-11-04T21:36:40Z

Results from fv3-jedi ctests

94% tests passed, 7 tests failed out of 127

Label Time Summary:
fv3-jedi    = 971.16 sec*proc (126 tests)
fv3jedi     = 975.27 sec*proc (127 tests)
mpi         = 962.61 sec*proc (115 tests)
script      = 975.27 sec*proc (127 tests)

Total Test time (real) = 976.05 sec

The following tests FAILED:
         70 - fv3jedi_test_tier1_hofx_nomodel_abi_radii (Failed)
         88 - fv3jedi_test_tier1_hyb-3dvar (Failed)
         91 - fv3jedi_test_tier1_3dvar_lam_cmaq (Failed)
         96 - fv3jedi_test_tier1_hyb-fgat_fv3lm (Failed)
         98 - fv3jedi_test_tier1_4denvar (Failed)
         99 - fv3jedi_test_tier1_4denvar_seq (Failed)
        111 - fv3jedi_test_tier1_diffstates_lam_cmaq (Failed)
Errors while running CTest
Output from these tests are in: /scratch1/BMC/zrtrr/Samuel.Degelia/RDASApp_ufobugfix/RDASApp/build/fv3-jedi/Testing/Temporary/LastTest.log
Use "--rerun-failed --output-on-failure" to re-run the failed cases verbosely.

We expect these tests to fail as documented in the Wiki page here and thus these are not a concern.

SamuelDegelia-NOAA · 2024-11-04T21:37:04Z

Results from mpas-jedi ctests

The following tests FAILED:
         37 - test_mpasjedi_3denvar_amsua_allsky (Failed)
         38 - test_mpasjedi_3denvar_amsua_bc (Failed)
         40 - test_mpasjedi_3dfgat (Failed)
         43 - test_mpasjedi_4denvar_VarBC (Failed)
         44 - test_mpasjedi_4denvar_VarBC_nonpar (Failed)
         47 - test_mpasjedi_4dfgat (Failed)
         54 - test_mpasjedi_lgetkf_height_vloc (Failed)

Again, we expect these tests to fail as documented in the Wiki page here and thus these are not a concern.

guoqing-noaa · 2024-11-04T21:42:56Z

@SamuelDegelia-NOAA Thanks for the PR. We really need this.

@Junjun-NOAA Does this PR meet your need on the new SABER codes?

SamuelDegelia-NOAA · 2024-11-04T22:04:20Z

Results from rrfs-test ctests:

(eva) [Samuel.Degelia@hfe07 rrfs-test]$ ctest -j7
Test project /scratch1/BMC/zrtrr/Samuel.Degelia/RDASApp_updatesub/RDASApp/build/rrfs-test
    Start 4: rrfs_mpasjedi_2024052700_getkf_observer
    Start 3: rrfs_mpasjedi_2024052700_Ens3Dvar
    Start 6: rrfs_mpasjedi_2024052700_bumploc
    Start 1: rrfs_fv3jedi_hyb_2022052619
    Start 2: rrfs_fv3jedi_letkf_2022052619
    Start 7: rrfs_bufr2ioda_msonet
1/7 Test #7: rrfs_bufr2ioda_msonet .....................   Passed   28.78 sec
2/7 Test #2: rrfs_fv3jedi_letkf_2022052619 .............   Passed   52.06 sec
3/7 Test #1: rrfs_fv3jedi_hyb_2022052619 ...............   Passed  124.14 sec
4/7 Test #6: rrfs_mpasjedi_2024052700_bumploc ..........   Passed  178.97 sec
5/7 Test #4: rrfs_mpasjedi_2024052700_getkf_observer ...   Passed  551.88 sec
    Start 5: rrfs_mpasjedi_2024052700_getkf_solver
6/7 Test #3: rrfs_mpasjedi_2024052700_Ens3Dvar .........   Passed  578.95 sec
7/7 Test #5: rrfs_mpasjedi_2024052700_getkf_solver .....   Passed  1370.04 sec

100% tests passed, 0 tests failed out of 7

Label Time Summary:
mpi            = 2884.83 sec*proc (7 tests)
rdas-bundle    = 2884.83 sec*proc (7 tests)
script         = 2884.83 sec*proc (7 tests)

Total Test time (real) = 1922.68 sec

Junjun-NOAA · 2024-11-04T23:02:04Z

@SamuelDegelia-NOAA Thanks for the PR. We really need this.

@Junjun-NOAA Does this PR meet your need on the new SABER codes?

@guoqing-noaa Yes, this PR has exactly the same SABER codes as I am using. Thanks @SamuelDegelia-NOAA for this PR.

delippi · 2024-11-05T15:26:54Z

@SamuelDegelia-NOAA, thanks for putting this together. Make sure to update the instructions on the wiki and it would be nice if you could link it to your initial comment on this PR as well.

I have a hunch as to why some of the ufo ctests fail. I have a couple of PRs I'm working on in ufo and fv3-jedi that might fix that as well as some other issues. But as you say, that isn't an issue for now.

SamuelDegelia-NOAA · 2024-11-05T15:28:39Z

@SamuelDegelia-NOAA, thanks for putting this together. Make sure to update the instructions on the wiki and it would be nice if you could link it to your initial comment on this PR as well.

I have a hunch as to why some of the ufo ctests fail. I have a couple of PRs I'm working on in ufo and fv3-jedi that might fix that as well as some other issues. But as you say, that isn't an issue for now.

Definitely will do - working up updating those instructions now.

SamuelDegelia-NOAA · 2024-11-05T15:38:03Z

Note: I have not synced RDAS_DATA between Hera and Orion/Jet yet. I was planning to do that this morning but forgot about the maintenance. So we should wait until I can sync those data tomorrow before running any CI tests.

rrfsbot · 2024-11-06T15:52:38Z

PASSED on jet

started build_and_test on jet at UTC time: Wed Nov 6 14:46:24 UTC 2024
finished at UTC time: Wed Nov 6 15:52:37 UTC 2024

Test project /lfs5/BMC/wrfruc/rrfsbot/PRs_RDASApp/217/build/rrfs-test
    Start 4: rrfs_mpasjedi_2024052700_getkf_observer
    Start 1: rrfs_fv3jedi_hyb_2022052619
    Start 2: rrfs_fv3jedi_letkf_2022052619
    Start 3: rrfs_mpasjedi_2024052700_Ens3Dvar
    Start 6: rrfs_mpasjedi_2024052700_bumploc
    Start 7: rrfs_bufr2ioda_msonet
1/7 Test #2: rrfs_fv3jedi_letkf_2022052619 .............   Passed   64.67 sec
2/7 Test #7: rrfs_bufr2ioda_msonet .....................   Passed   88.44 sec
3/7 Test #1: rrfs_fv3jedi_hyb_2022052619 ...............   Passed  136.21 sec
4/7 Test #6: rrfs_mpasjedi_2024052700_bumploc ..........   Passed  203.65 sec
5/7 Test #4: rrfs_mpasjedi_2024052700_getkf_observer ...   Passed  441.59 sec
    Start 5: rrfs_mpasjedi_2024052700_getkf_solver
6/7 Test #3: rrfs_mpasjedi_2024052700_Ens3Dvar .........   Passed  619.26 sec
7/7 Test #5: rrfs_mpasjedi_2024052700_getkf_solver .....   Passed  1632.88 sec

100% tests passed, 0 tests failed out of 7

Label Time Summary:
mpi            = 3186.69 sec*proc (7 tests)
rdas-bundle    = 3186.69 sec*proc (7 tests)
script         = 3186.69 sec*proc (7 tests)

Total Test time (real) = 2074.49 sec

workdir: /lfs5/BMC/wrfruc/rrfsbot/PRs_RDASApp/217

ShunLiu-NOAA · 2024-11-06T17:00:12Z

@hu5970 and @delippi Thanks for reviewing this PR. I think we can merge this PR now.

delippi · 2024-11-06T17:06:31Z

@hu5970 and @delippi Thanks for reviewing this PR. I think we can merge this PR now.

I think so. @SamuelDegelia-NOAA do we need to wait for any tests on other machines or any staging of data on any machine?

SamuelDegelia-NOAA · 2024-11-06T17:18:49Z

All the data is staged now, but I would like to run the rrfs tests on Orion/Hercules before merging. I have not done any testing there yet. It looks like the CI tests aren't running there, so I'll manually build and do some tests.

guoqing-noaa · 2024-11-06T17:20:54Z

FYI, the test on Hercules did not start because there is a leftover from a previous CI test which stopped in the mid-stage due to the HPC maintenance.

rrfsbot · 2024-11-06T17:22:28Z

PASSED on hera

started build_and_test on hera at UTC time: Wed Nov 6 16:18:38 UTC 2024
finished at UTC time: Wed Nov 6 17:22:27 UTC 2024

Test project /scratch1/NCEPDEV/fv3-cam/rrfsbot/PRs_RDASApp/217/build/rrfs-test
    Start 4: rrfs_mpasjedi_2024052700_getkf_observer
    Start 1: rrfs_fv3jedi_hyb_2022052619
    Start 2: rrfs_fv3jedi_letkf_2022052619
    Start 3: rrfs_mpasjedi_2024052700_Ens3Dvar
    Start 6: rrfs_mpasjedi_2024052700_bumploc
    Start 7: rrfs_bufr2ioda_msonet
1/7 Test #7: rrfs_bufr2ioda_msonet .....................   Passed   32.31 sec
2/7 Test #2: rrfs_fv3jedi_letkf_2022052619 .............   Passed   44.39 sec
3/7 Test #1: rrfs_fv3jedi_hyb_2022052619 ...............   Passed  112.59 sec
4/7 Test #6: rrfs_mpasjedi_2024052700_bumploc ..........   Passed  122.46 sec
5/7 Test #4: rrfs_mpasjedi_2024052700_getkf_observer ...   Passed  358.82 sec
    Start 5: rrfs_mpasjedi_2024052700_getkf_solver
6/7 Test #3: rrfs_mpasjedi_2024052700_Ens3Dvar .........   Passed  443.53 sec
7/7 Test #5: rrfs_mpasjedi_2024052700_getkf_solver .....   Passed  1373.28 sec

100% tests passed, 0 tests failed out of 7

Label Time Summary:
mpi            = 2487.39 sec*proc (7 tests)
rdas-bundle    = 2487.39 sec*proc (7 tests)
script         = 2487.39 sec*proc (7 tests)

Total Test time (real) = 1732.13 sec

workdir: /scratch1/NCEPDEV/fv3-cam/rrfsbot/PRs_RDASApp/217

SamuelDegelia-NOAA · 2024-11-06T17:41:59Z

FYI, the test on Hercules did not start because there is a leftover from a previous CI test which stopped in the mid-stage due to the HPC maintenance.

Ah I see, thanks for the explanation and for restarting the tests @guoqing-noaa!

rrfsbot · 2024-11-06T18:35:35Z

PASSED on hercules

started build_and_test on hercules at UTC time: Wed Nov 6 17:31:00 UTC 2024
finished at UTC time: Wed Nov 6 18:35:34 UTC 2024

Test project /work/noaa/wrfruc/rrfsbot/PRs_RDASApp/217/build/rrfs-test
    Start 4: rrfs_mpasjedi_2024052700_getkf_observer
    Start 1: rrfs_fv3jedi_hyb_2022052619
    Start 2: rrfs_fv3jedi_letkf_2022052619
    Start 3: rrfs_mpasjedi_2024052700_Ens3Dvar
    Start 6: rrfs_mpasjedi_2024052700_bumploc
    Start 7: rrfs_bufr2ioda_msonet
1/7 Test #7: rrfs_bufr2ioda_msonet .....................   Passed   28.32 sec
2/7 Test #2: rrfs_fv3jedi_letkf_2022052619 .............   Passed   45.05 sec
3/7 Test #1: rrfs_fv3jedi_hyb_2022052619 ...............   Passed  124.86 sec
4/7 Test #6: rrfs_mpasjedi_2024052700_bumploc ..........   Passed  138.63 sec
5/7 Test #4: rrfs_mpasjedi_2024052700_getkf_observer ...   Passed  650.42 sec
    Start 5: rrfs_mpasjedi_2024052700_getkf_solver
6/7 Test #3: rrfs_mpasjedi_2024052700_Ens3Dvar .........   Passed  1284.21 sec
7/7 Test #5: rrfs_mpasjedi_2024052700_getkf_solver .....   Passed  1293.49 sec

100% tests passed, 0 tests failed out of 7

Label Time Summary:
mpi            = 3564.99 sec*proc (7 tests)
rdas-bundle    = 3564.99 sec*proc (7 tests)
script         = 3564.99 sec*proc (7 tests)

Total Test time (real) = 1943.92 sec

workdir: /work/noaa/wrfruc/rrfsbot/PRs_RDASApp/217

SamuelDegelia-NOAA · 2024-11-06T18:41:10Z

I think this PR is good to merge now that the Hercules/Orion test passed. Thanks all for reviewing.

SamuelDegelia-NOAA and others added 8 commits October 31, 2024 19:35

Update submodules

d483457

Replace "specific_humidity" with "specific_humidity" to "water_vapor_…

28798c2

…mixing_ratio_wrt_moist_air" for fv3jedi

Updated staged ioda-data and ufo-data

3773473

Change surface_geopotential_height to geopotential_height_at_surface

cbf585c

Updated link to fv3jedi staged data that replaces 'delp' with 'DELP'

10a498d

Merge branch 'NOAA-EMC:develop' into feature/sync_upstream

63949c9

Update test reference for Ens3Dvar test

c416b86

Merge branch 'feature/sync_upstream' of https://github.com/SamuelDege…

ea74bcd

…lia-NOAA/RDASApp into feature/sync_upstream

SamuelDegelia-NOAA mentioned this pull request Nov 4, 2024

Update OOPS and use reduce obs space filter action for pre-filters #209

Closed

SamuelDegelia-NOAA requested review from hu5970, ShunLiu-NOAA, delippi, guoqing-noaa, hongli-wang, HaidaoLin-NOAA and Junjun-NOAA November 4, 2024 21:40

ShunLiu-NOAA approved these changes Nov 5, 2024

View reviewed changes

Merge branch 'develop' into feature/sync_upstream

0a2aa83

delippi approved these changes Nov 5, 2024

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SamuelDegelia-NOAA added test_hercules test_jet labels Nov 6, 2024

rrfsbot added Passed_jet and removed test_jet running_jet labels Nov 6, 2024

SamuelDegelia-NOAA added the test_hera label Nov 6, 2024

rrfsbot added running_hera and removed test_hera labels Nov 6, 2024

hu5970 approved these changes Nov 6, 2024

View reviewed changes

rrfsbot added running_hercules and removed test_hercules labels Nov 6, 2024

rrfsbot added Passed_hera and removed running_hera labels Nov 6, 2024

guoqing-noaa added test_hercules and removed running_hercules labels Nov 6, 2024

rrfsbot added running_hercules and removed test_hercules labels Nov 6, 2024

rrfsbot added Passed_hercules and removed running_hercules labels Nov 6, 2024

guoqing-noaa approved these changes Nov 6, 2024

View reviewed changes

ShunLiu-NOAA merged commit daae9af into NOAA-EMC:develop Nov 7, 2024
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SamuelDegelia-NOAA deleted the feature/sync_upstream branch November 14, 2024 16:37

Junjun-NOAA mentioned this pull request Nov 17, 2024

Generate a regional static BE by interpolating BJ's global BE #113

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Sync RDASApp submodules with upstream repositories #217

Sync RDASApp submodules with upstream repositories #217

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Sync RDASApp submodules with upstream repositories #217

Sync RDASApp submodules with upstream repositories #217

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