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Update gcycle to be able to read re-gridded GSI increment land files.#1010

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GeorgeGayno-NOAA merged 14 commits into
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ClaraDraper-NOAA:feature/gcycle_fv3incr
Feb 4, 2025
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Update gcycle to be able to read re-gridded GSI increment land files.#1010
GeorgeGayno-NOAA merged 14 commits into
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ClaraDraper-NOAA:feature/gcycle_fv3incr

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@ClaraDraper-NOAA
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@ClaraDraper-NOAA ClaraDraper-NOAA commented Dec 16, 2024

DESCRIPTION OF CHANGES:

Generalized the reading in of land increments to be:

  1. soil increment OR snow increment file
  2. on the GSI output grid to be regridded within global_cycle OR on the native model grid

Native model grid files may come from JEDI, or be from GSI and been regridded using a separate program. The read routine will detect which.

Also, changed the number of soil levels to be updated from 3 to 2. This will change the test output for all tests adding soil increments.

TESTS CONDUCTED:

If there are changes to the build or source code, the tests below must be conducted. Contact a repository manager if you need assistance.

  • Compile branch on all Tier 1 machines using Intel (Orion, Jet, Hera, Hercules and WCOSS2). Done using 4d6403f.
  • Compile branch on Hera using GNU. Done using 4d6403f. The global_cycle code had no warnings.
  • Compile branch in 'Debug' mode on WCOSS2. Done on Dogwood using 4d6403f. No warnings.
  • Run unit tests locally on any Tier 1 machine. Done on Hera using GNU and 4d6403f. All tests passed.
  • Run global_cycle consistency tests locally on all Tier 1 machines. Done using 4d6403f. The new test ran to completion with no errors. The other tests all passed as expected.

Describe any additional tests performed.

  • Created the Doxygen without warnings using 07ac8bd.

DEPENDENCIES:

None.

DOCUMENTATION:

N/A

ISSUE:

Fixes #1008

@ClaraDraper-NOAA
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@GeorgeGayno-NOAA Submitting this as a draft for now, while I do the tests. I'm not sure which are the unit tests and which are the consistency tests?

I'm currently running rt.sh, with all the tests commented out except global_cycle.
I expect it to be zero-diff without the lsoil_incr change in global_cycle.sh, so am checking that, then will change the lsoil_incr.
I'll check it compiles with gnu on hera.
What other test should I do? ( note: I don't have access to any machines other than hera and gaeia)

@GeorgeGayno-NOAA GeorgeGayno-NOAA self-requested a review December 16, 2024 17:48
@GeorgeGayno-NOAA
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@GeorgeGayno-NOAA Submitting this as a draft for now, while I do the tests. I'm not sure which are the unit tests and which are the consistency tests?

I'm currently running rt.sh, with all the tests commented out except global_cycle. I expect it to be zero-diff without the lsoil_incr change in global_cycle.sh, so am checking that, then will change the lsoil_incr. I'll check it compiles with gnu on hera. What other test should I do? ( note: I don't have access to any machines other than hera and gaeia)

The regression tests are in ./reg_tests/global_cycle. To run just the global_cycle test, you can invoke ./driver.hera.sh from the command line with no arguments. You don't need to bother with the ./rt.sh script.

The unit tests may be run by some slight modifications to the ./build_all.sh script:

 # The unit test data download is part of the build system. Not all machines can
 # access the EMC ftp site, so turn off the build (-DBUILD_TESTING=OFF) of the units tests accordingly.
 # Those with access to the EMC ftp site are: Orion and Hera.
-CMAKE_FLAGS+=" -DBUILD_TESTING=${BUILD_TESTING:-OFF}"
+CMAKE_FLAGS+=" -DBUILD_TESTING=${BUILD_TESTING:-ON}"

You may also need to update ./cmake/mpiexec.hera for an ACCOUNT you have access to.

@ClaraDraper-NOAA
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All 5 consistency checks passed on hera.
Compiled with gnu on hera.

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@GeorgeGayno-NOAA How do I confirm that the ctests passed. The first pass through, they didn't and I fixed it. build_all.sh compiled, but I can't find a report of the test results.

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@GeorgeGayno-NOAA How do I confirm that the ctests passed. The first pass through, they didn't and I fixed it. build_all.sh compiled, but I can't find a report of the test results.

When I test your branch on Hera, I see one unit test failing:

      Start 26: global_cycle-ftst_read_increments
26/38 Test #26: global_cycle-ftst_read_increments ...........***Failed    3.74 sec

The test results will be in ./build/Testing/Temporary/LastTest.log. The test fails because of a missing file:

 FATAL ERROR: OPENING FILE: ./fnbgsi.001: No such file or directory
 STOP.

I can take a look.

@ClaraDraper-NOAA
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@GeorgeGayno-NOAA Is that from standard out? I think I'm not actually running the tests. Let me follow up on that.

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@GeorgeGayno-NOAA Is that from standard out? I think I'm not actually running the tests. Let me follow up on that.

That is the output from the build_all.sh script after setting BUILD_TESTING=ON and uncommenting 'ctest' at the bottom.

@ClaraDraper-NOAA
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@GeorgeGayno-NOAA Is that from standard out? I think I'm not actually running the tests. Let me follow up on that.

That is the output from the build_all.sh script after setting BUILD_TESTING=ON and uncommenting 'ctest' at the bottom.

Just came here to say I found the ctest line! I'm running it now. I'll sort out the failing test.

@ClaraDraper-NOAA
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I fixed it. The reg_tests and ctests pass on hera, and gnu compilation works on hera. Converting from a draft. Yuan Xue and Tseganeh Gichamo would be good reviewers.

@ClaraDraper-NOAA ClaraDraper-NOAA marked this pull request as ready for review December 18, 2024 15:05
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Do we need another regression test for a GSI case on the native grid?

ClaraDraper-NOAA added a commit to ClaraDraper-NOAA/global-workflow that referenced this pull request Dec 18, 2024
i) write out the ensemble mean reanalysis, and apply it to the deterministic member.
ii) replace UFS_UTILS regridding of Gaussian soil analysis to model grid with an external ESMF-based program (with appropriate land masking)

Requires:
sorc/gsi_enkf.fd develop after Tue Nov 12. Latest works.
sorc/gdas.cd/sorc/da-utils PR: NOAA-EMC/DA-utils#5
sorc/ufs_utils.fd from PR: ufs-community/UFS_UTILS#1010
Comment thread sorc/global_cycle.fd/cycle.f90 Outdated
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Overall, looks good to me. Thanks!

@GeorgeGayno-NOAA
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@ClaraDraper-NOAA - make sure you have merged the latest updates from 'develop'.

@GeorgeGayno-NOAA GeorgeGayno-NOAA requested a review from tsga January 13, 2025 16:16
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Looks good to me.
@ClaraDraper-NOAA I am guessing the "gaussian_to_fv3_interp" function will soon be replaced by the ESMF re-gridding code you just wrote?

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Do we need another regression test for a GSI case on the native grid?

To expand on my comment, there are two regression tests for applying land increments: C192.jedi_lndincsoilnoahmp.sh and C192.gsi_lndincsoilnoahmp.sh. The latter uses GSI data that needs to be re-gridded to the tiles. Should a test using tiled GSI data (no re-gridding necessary) be added? If you have a test case using tiled GSI data, I would be happy to convert it into a test.

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Is logical do_lndinc really needed? Are do_soi_inc and do_sno_inc sufficient?

@ClaraDraper-NOAA
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@ClaraDraper-NOAA - make sure you have merged the latest updates from 'develop'.

done.

@GeorgeGayno-NOAA
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Do we need another regression test for a GSI case on the native grid?

To expand on my comment, there are two regression tests for applying land increments: C192.jedi_lndincsoilnoahmp.sh and C192.gsi_lndincsoilnoahmp.sh. The latter uses GSI data that needs to be re-gridded to the tiles. Should a test using tiled GSI data (no re-gridding necessary) be added? If you have a test case using tiled GSI data, I would be happy to convert it into a test.

The read routine is slightly different for a re-gridded GSI file than for the two test cases that are already there. If you'd like me to prepare a new test, I can.

Yes. Please do.

@ClaraDraper-NOAA
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Looks good to me. @ClaraDraper-NOAA I am guessing the "gaussian_to_fv3_interp" function will soon be replaced by the ESMF re-gridding code you just wrote?

This PR effectively adds the option to do either. However, the ESMF regridding is more appropriate - so perhaps in the future we can just delete the gaussian_to_fv3_interp as you suggest.

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Do we need another regression test for a GSI case on the native grid?

To expand on my comment, there are two regression tests for applying land increments: C192.jedi_lndincsoilnoahmp.sh and C192.gsi_lndincsoilnoahmp.sh. The latter uses GSI data that needs to be re-gridded to the tiles. Should a test using tiled GSI data (no re-gridding necessary) be added? If you have a test case using tiled GSI data, I would be happy to convert it into a test.

The read routine is slightly different for a re-gridded GSI file than for the two test cases that are already there. If you'd like me to prepare a new test, I can.

Yes. Please do.

I just added a new test, and have checked it passes on hera. I added the new test to the drivers for the other machines, except s4 which looks a bit different to the others.

The additional files that you need to add to the COMIN are:
/scratch2/BMC/gsienkf/Clara.Draper/gerrit-hera/PRprep/NEWTEST_UFS_UTILS/UFS_UTILS_COMIN/soil_xainc*

Examples of the baseline files are here:
/scratch2/BMC/gsienkf/Clara.Draper/gerrit-hera/PRprep/NEWTEST_UFS_UTILS/NEW_BASELINE_FILES/c192.gsitile_lndincsoilnoahmp

@ClaraDraper-NOAA
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Is logical do_lndinc really needed? Are do_soi_inc and do_sno_inc sufficient?

@GeorgeGayno-NOAA Yes, do_lndinc is redundant, since it can be turned on by the do_*_inc options. However, my preference would be to keep it (together with the DO_SFCCYCLE and DONST) to make it clear which actions (adding land increments, updating land model parameters, and/or updating NST) cycle if being called for. It's up to you though - if you'd like me to remove it, let me know. We could either completely remove it, or remove it from the namelists, and set it internally.

@ClaraDraper-NOAA
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@GeorgeGayno-NOAA I think I've addressed everything, let me know if there's anything else I can do.

@GeorgeGayno-NOAA
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Is logical do_lndinc really needed? Are do_soi_inc and do_sno_inc sufficient?

@GeorgeGayno-NOAA Yes, do_lndinc is redundant, since it can be turned on by the do_*_inc options. However, my preference would be to keep it (together with the DO_SFCCYCLE and DONST) to make it clear which actions (adding land increments, updating land model parameters, and/or updating NST) cycle if being called for. It's up to you though - if you'd like me to remove it, let me know. We could either completely remove it, or remove it from the namelists, and set it internally.

Ok. We can keep it. But I would update the script and code prologs, so the general user knows how to set each variable. For example, I am guessing if 'do_soi_inc' is set to true, then 'do_lndinc' must also be set to true.

Comment thread ush/global_cycle.sh Outdated
# DO_SOI_INC_GSI Call routine to update soil states with gsi(gaussian) increment files
# DO_SNO_INC_JEDI Call routine to update snow states with jedi increment files
# DO_SOI_INC_JEDI Call routine to update soil states with jedi increment files
# DO_SOI_INC Call routine to update soil states
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I would add more detail on how to set each logical.

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I've updated the comments, and added some logic into the global_driver.sh to set DO_LNDINC to true if either of DO_SNO_INC or DO_SOI_INC it true.

@GeorgeGayno-NOAA
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Do we need another regression test for a GSI case on the native grid?

To expand on my comment, there are two regression tests for applying land increments: C192.jedi_lndincsoilnoahmp.sh and C192.gsi_lndincsoilnoahmp.sh. The latter uses GSI data that needs to be re-gridded to the tiles. Should a test using tiled GSI data (no re-gridding necessary) be added? If you have a test case using tiled GSI data, I would be happy to convert it into a test.

The read routine is slightly different for a re-gridded GSI file than for the two test cases that are already there. If you'd like me to prepare a new test, I can.

Yes. Please do.

I just added a new test, and have checked it passes on hera. I added the new test to the drivers for the other machines, except s4 which looks a bit different to the others.

The additional files that you need to add to the COMIN are: /scratch2/BMC/gsienkf/Clara.Draper/gerrit-hera/PRprep/NEWTEST_UFS_UTILS/UFS_UTILS_COMIN/soil_xainc*

Examples of the baseline files are here: /scratch2/BMC/gsienkf/Clara.Draper/gerrit-hera/PRprep/NEWTEST_UFS_UTILS/NEW_BASELINE_FILES/c192.gsitile_lndincsoilnoahmp

Great. I will host these files in the official location on each machine.

@GeorgeGayno-NOAA
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Do we need another regression test for a GSI case on the native grid?

To expand on my comment, there are two regression tests for applying land increments: C192.jedi_lndincsoilnoahmp.sh and C192.gsi_lndincsoilnoahmp.sh. The latter uses GSI data that needs to be re-gridded to the tiles. Should a test using tiled GSI data (no re-gridding necessary) be added? If you have a test case using tiled GSI data, I would be happy to convert it into a test.

The read routine is slightly different for a re-gridded GSI file than for the two test cases that are already there. If you'd like me to prepare a new test, I can.

Yes. Please do.

I just added a new test, and have checked it passes on hera. I added the new test to the drivers for the other machines, except s4 which looks a bit different to the others.

Don't worry about s4. That is not an officially supported machine. Only WCOSS2, Jet, Hera, Hercules and Orion are supported.

The additional files that you need to add to the COMIN are: /scratch2/BMC/gsienkf/Clara.Draper/gerrit-hera/PRprep/NEWTEST_UFS_UTILS/UFS_UTILS_COMIN/soil_xainc*

Examples of the baseline files are here: /scratch2/BMC/gsienkf/Clara.Draper/gerrit-hera/PRprep/NEWTEST_UFS_UTILS/NEW_BASELINE_FILES/c192.gsitile_lndincsoilnoahmp

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I placed the new baseline files on Hera:

[role.ufsutils@hfe11 c192.gsitile_lndincsoilnoahmp]$ pwd
/scratch1/NCEPDEV/nems/role.ufsutils/ufs_utils/reg_tests/global_cycle/baseline_data/c192.gsitile_lndincsoilnoahmp
[role.ufsutils@hfe11 c192.gsitile_lndincsoilnoahmp]$ ls -l
total 223104
-r--r--r-- 1 role.ufsutils nems 38073028 Jan 27 16:08 20190730.000000.sfcanl_data.tile1.nc
-r--r--r-- 1 role.ufsutils nems 38073028 Jan 27 16:08 20190730.000000.sfcanl_data.tile2.nc
-r--r--r-- 1 role.ufsutils nems 38073028 Jan 27 16:08 20190730.000000.sfcanl_data.tile3.nc
-r--r--r-- 1 role.ufsutils nems 38073028 Jan 27 16:08 20190730.000000.sfcanl_data.tile4.nc
-r--r--r-- 1 role.ufsutils nems 38073028 Jan 27 16:08 20190730.000000.sfcanl_data.tile5.nc
-r--r--r-- 1 role.ufsutils nems 38073028 Jan 27 16:08 20190730.000000.sfcanl_data.tile6.nc

and the new input files here:

/scratch1/NCEPDEV/nems/role.ufsutils/ufs_utils/reg_tests/global_cycle/input_data_noahmp
[role.ufsutils@hfe11 input_data_noahmp]$ ls -l soil_xainc.*
-rw-r--r-- 1 role.ufsutils nems 1187094 Jan 27 15:59 soil_xainc.gsi.tile1.nc.pr1010
-rw-r--r-- 1 role.ufsutils nems 1187094 Jan 27 15:59 soil_xainc.gsi.tile2.nc.pr1010
-rw-r--r-- 1 role.ufsutils nems 1187094 Jan 27 15:59 soil_xainc.gsi.tile3.nc.pr1010
-rw-r--r-- 1 role.ufsutils nems 1187094 Jan 27 15:59 soil_xainc.gsi.tile4.nc.pr1010
-rw-r--r-- 1 role.ufsutils nems 1187094 Jan 27 15:59 soil_xainc.gsi.tile5.nc.pr1010
-rw-r--r-- 1 role.ufsutils nems 1187094 Jan 27 15:59 soil_xainc.gsi.tile6.nc.pr1010
lrwxrwxrwx 1 role.ufsutils nems      30 Jan 27 16:03 soil_xainc.tile1.nc -> soil_xainc.gsi.tile1.nc.pr1010
lrwxrwxrwx 1 role.ufsutils nems      30 Jan 27 16:03 soil_xainc.tile2.nc -> soil_xainc.gsi.tile2.nc.pr1010
lrwxrwxrwx 1 role.ufsutils nems      30 Jan 27 16:03 soil_xainc.tile3.nc -> soil_xainc.gsi.tile3.nc.pr1010
lrwxrwxrwx 1 role.ufsutils nems      30 Jan 27 16:04 soil_xainc.tile4.nc -> soil_xainc.gsi.tile4.nc.pr1010
lrwxrwxrwx 1 role.ufsutils nems      30 Jan 27 16:04 soil_xainc.tile5.nc -> soil_xainc.gsi.tile5.nc.pr1010
lrwxrwxrwx 1 role.ufsutils nems      30 Jan 27 16:04 soil_xainc.tile6.nc -> soil_xainc.gsi.tile6.nc.pr1010

I will push the data to the other machines after we verify everything is working.

@ClaraDraper-NOAA
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@GeorgeGayno-NOAA Apologies for the poor PR behaviour. I just pushed a minor change to a variable name in the scripts (INTERP_LNDINC to GCYCLE_INTERP_LNDINC), since this makes the function clearer in global_workflow. The tests pass on hera with this change.

Comment thread reg_tests/global_cycle/C192.gsitile_lndincsoilnoahmp.sh
Comment thread reg_tests/global_cycle/C192.gsitile_lndincsoilnoahmp.sh
@GeorgeGayno-NOAA
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I found a bug in C192.gsi_lndincsoilnoahmp.sh that is not related to this issue. But I would like to fix it:

/scratch1/NCEPDEV/da/George.Gayno/ufs_utils.git/UFS_UTILS.clara/reg_tests/global_cycle $ git diff C192.gsi_lndincsoilnoahmp.sh
--- a/reg_tests/global_cycle/C192.gsi_lndincsoilnoahmp.sh
+++ b/reg_tests/global_cycle/C192.gsi_lndincsoilnoahmp.sh
@@ -88,7 +88,7 @@ if [ $test_failed -ne 0 ]; then
   echo "<<< C192 GSI based LANDINC SOIL-NOAHMP CYCLE TEST FAILED. >>>"
   echo "**********************************************"
   if [ "$UPDATE_BASELINE" = "TRUE" ]; then
-    $HOMEgfs/reg_tests/update_baseline.sh $HOMEreg "c192.lndincsoilnoahmp" $commit_num
+    $HOMEgfs/reg_tests/update_baseline.sh $HOMEreg "c192.gsi_lndincsoilnoahmp" $commit_num
   fi
 else
   echo

Comment thread ush/global_cycle_driver.sh
@ClaraDraper-NOAA
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I found a bug in C192.gsi_lndincsoilnoahmp.sh that is not related to this issue. But I would like to fix it:

/scratch1/NCEPDEV/da/George.Gayno/ufs_utils.git/UFS_UTILS.clara/reg_tests/global_cycle $ git diff C192.gsi_lndincsoilnoahmp.sh
--- a/reg_tests/global_cycle/C192.gsi_lndincsoilnoahmp.sh
+++ b/reg_tests/global_cycle/C192.gsi_lndincsoilnoahmp.sh
@@ -88,7 +88,7 @@ if [ $test_failed -ne 0 ]; then
   echo "<<< C192 GSI based LANDINC SOIL-NOAHMP CYCLE TEST FAILED. >>>"
   echo "**********************************************"
   if [ "$UPDATE_BASELINE" = "TRUE" ]; then
-    $HOMEgfs/reg_tests/update_baseline.sh $HOMEreg "c192.lndincsoilnoahmp" $commit_num
+    $HOMEgfs/reg_tests/update_baseline.sh $HOMEreg "c192.gsi_lndincsoilnoahmp" $commit_num
   fi
 else
   echo

I fixed this.

@ClaraDraper-NOAA
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@GeorgeGayno-NOAA I've addressed everything.

@GeorgeGayno-NOAA
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The C192.gsitile_lndincsoilnoahmp.sh test is failing. It is looking for a layer 2 slc_inc record.

readingslc2_inc

 FATAL ERROR: READING slc*_inc ID: NetCDF: Variable not found

The input files are here: /scratch1/NCEPDEV/nems/role.ufsutils/ufs_utils/reg_tests/global_cycle/input_data_noahmp/soil_xainc.??? These files have 3 layers of soilt_inc, but only 1 layer of slc_incr. The test sets LSOIL_INCR=3 Did I baseline the wrong input files?

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The C192.gsitile_lndincsoilnoahmp.sh test is failing. It is looking for a layer 2 slc_inc record.

readingslc2_inc

 FATAL ERROR: READING slc*_inc ID: NetCDF: Variable not found

The input files are here: /scratch1/NCEPDEV/nems/role.ufsutils/ufs_utils/reg_tests/global_cycle/input_data_noahmp/soil_xainc.??? These files have 3 layers of soilt_inc, but only 1 layer of slc_incr. The test sets LSOIL_INCR=3 Did I baseline the wrong input files?

I updated to files to fix this. The new ones are here:

/scratch2/BMC/gsienkf/Clara.Draper/gerrit-hera/PRprep/NEWTEST_UFS_UTILS/UFS_UTILS_COMIN $ ncdump -c soil_xainc.006
netcdf soil_xainc {
dimensions:
xaxis_1 = 192 ;
yaxis_1 = 192 ;
variables:
double soilt1_inc(yaxis_1, xaxis_1) ;
double soilt2_inc(yaxis_1, xaxis_1) ;
double soilt3_inc(yaxis_1, xaxis_1) ;
double slc1_inc(yaxis_1, xaxis_1) ;
double slc2_inc(yaxis_1, xaxis_1) ;
double slc3_inc(yaxis_1, xaxis_1) ;
data:
}

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@ClaraDraper-NOAA - 'develop' was updated on Friday. Please merge these changes to your branch. They should not conflict with your PR.

@ClaraDraper-NOAA
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@ClaraDraper-NOAA - 'develop' was updated on Friday. Please merge these changes to your branch. They should not conflict with your PR.

done.

@GeorgeGayno-NOAA GeorgeGayno-NOAA merged commit e718003 into ufs-community:develop Feb 4, 2025
@ClaraDraper-NOAA ClaraDraper-NOAA deleted the feature/gcycle_fv3incr branch February 5, 2025 19:56
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Add reading of externally re-gridded gsi land increment files

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