Add the mean EnKF soil increment to the deterministic member #3295

ClaraDraper-NOAA · 2025-02-04T18:16:33Z

Description

Add mean EnKF soil increment to the deterministic member. Includes new regriding script and executable (in GDASApp) to perform masked bi-linear interpolation of the soil increments.

Resolves 2773

Type of change

Bug fix (fixes something broken)
[ x] New feature (adds functionality)
Maintenance (code refactor, clean-up, new CI test, etc.)

Change characteristics

Is this a breaking change (a change in existing functionality)? NO
Does this change require a documentation update? NO
Does this change require an update to any of the following submodules?
- [ YES] UFS-utils

OUTDATED:
Exercizing the new soil analysis feature requires updating UFS_UTILS to at least commit e718003

UPDATE Feb 5:
After responding to reviews, requires updating to UFS_UTILS PR 1022

How has this been tested?

Tested on hera:
C96_atm3DVar, C96C48_hybatmaerosnowDA, and the default test ran succesfully.
Confirmed new functionality works as expected.
Confirmed that the commits do not change output from cycling the DA if the the new feature is not selected.

Checklist

[ x] Any dependent changes have been merged and published
[x ] My code follows the style guidelines of this project
[ x] I have performed a self-review of my own code
[x ] I have commented my code, particularly in hard-to-understand areas
[x ] I have documented my code, including function, input, and output descriptions
[ x] My changes generate no new warnings
[ x] New and existing tests pass with my changes
This change is covered by an existing CI test or a new one has been added
[x ] Any new scripts have been added to the .github/CODEOWNERS file with owners
[x ] I have made corresponding changes to the system documentation if necessary

NOTE:

Exercizing the new feature requires some additional fix files, currently at $TMP_FIX_FILES in ush/regrid_gsiSfcIncr_to_tile.sh . These will need to be added to a fix directory, if this PR is accepted as is (note: these files could also be generated on the fly)
Exercizing the new feature requires jobs/rocoto/sfcanl.sh and sfc.sh to load the ufsda modules in place of the fv3gfs modules. My understanding is that the modules will eventually be unified, but for now I've added comments to the relevant scripts noting this.

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

…s) case

…sis.

github-advanced-security

ShellCheck found more than 20 potential problems in the proposed changes. Check the Files changed tab for more details.

CoryMartin-NOAA

first pass

env/GAEAC5.env

CoryMartin-NOAA · 2025-02-04T18:54:56Z

jobs/JGLOBAL_ATMOS_SFCANL

@@ -24,6 +24,9 @@ YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
 YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
  COMOUT_ATMOS_RESTART:COM_ATMOS_RESTART_TMPL

+RUN="enkfgdas" MEMDIR="ensstat" YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
+  COM_ATMOS_ENKF_ANALYSIS_STAT:COM_ATMOS_ANALYSIS_TMPL


COM needs to be explicit if it is COMIN or COMOUT now.

Updated to COMIN.

parm/config/gfs/config.sfcanl

CoryMartin-NOAA · 2025-02-04T18:56:38Z

scripts/exgdas_enkf_sfc.sh

@@ -225,6 +239,9 @@ if [ $DOSFCANL_ENKF = "YES" ]; then
            RUN="${GDUMP_ENS}" MEMDIR=${gmemchar} YMD=${gPDY} HH=${gcyc} declare_from_tmpl \
                COMIN_ATMOS_RESTART_MEM_PREV:COM_ATMOS_RESTART_TMPL

+            MEMDIR=${memchar} YMD=${PDY} HH=${cyc} declare_from_tmpl \
+                COM_ATMOS_ANALYSIS_MEM:COM_ATMOS_ANALYSIS_TMPL


same COM comment as before

Updated to COMIN

scripts/exgdas_enkf_sfc.sh

scripts/exglobal_atmos_sfcanl.sh

CoryMartin-NOAA · 2025-02-04T19:02:33Z

ush/regrid_gsiSfcIncr_to_tile.sh

+        memchar="mem${cmem}"
+
+        MEMDIR=${memchar} YMD=${PDY} HH=${cyc} declare_from_tmpl \
+            COM_ATMOS_ANALYSIS_MEM:COM_ATMOS_ANALYSIS_TMPL


more COM related comments in this file

aerorahul

the changes looks good. seems like some checks are failing. I tried to recommend a couple updates that might help.

ush/regrid_gsiSfcIncr_to_tile.sh

Co-authored-by: Cory Martin <[email protected]>

ClaraDraper-NOAA · 2025-02-05T01:55:03Z

Can someone please point me to the reason for the failure? I see warnings for code that I haven't changed. Am I meant to fix these?

.github/CODEOWNERS

aerorahul · 2025-02-05T13:28:01Z

parm/config/gfs/config.sfcanl

+    export DO_LNDINC=".true."
+    export DO_SOI_INC=".true."
+    export GCYCLE_INTERP_LNDINC=".false."
+    export LSOIL_INCR=2


This is a nitpicky comment - and is a case in the global-workflow in general - variables do not need to be 3 characters long e.g. DO_SOI_INC -> DO_SOIL_INC or DO_SOILINC to be (in)consistent with DO_LNDINC or something. Even INC is sometimes INCR.

This is not nitpicky at all! Or at least, it has been annoying me too. Also the mix of YES/NO, and true/false. Some of it is coming from the namelists used in submodules. I'll at least establish consistent variable names for most of the workflow, then try to clean it up over time.

I'm preparing to fix this, with a second PR to UFS_UTILS, resolving issue 1021

DavidHuber-NOAA · 2025-02-05T13:36:48Z

@ClaraDraper-NOAA If we still see errors after fixing the issue in ush/regrid_gsiSfcIncr_to_tile.sh, I can submit a PR to your branch to fix the remaining issues in scripts/exgdas_enkf_sfc.sh.

aerorahul

Did a pass through on this PR and left a few comments and suggestions. Please let me know if I can help clarify or assist.

scripts/exgdas_enkf_sfc.sh

scripts/exglobal_atmos_sfcanl.sh

ush/regrid_gsiSfcIncr_to_tile.sh

.github/CODEOWNERS

ClaraDraper-NOAA · 2025-02-05T17:09:49Z

@ClaraDraper-NOAA If we still see errors after fixing the issue in ush/regrid_gsiSfcIncr_to_tile.sh, I can submit a PR to your branch to fix the remaining issues in scripts/exgdas_enkf_sfc.sh.

I can fix exgdas_enfkf_sfs.sh, I just wasn't sure if this was even the problem since they're warnings.

TravisElless-NOAA · 2025-02-05T21:59:14Z

jobs/JGLOBAL_ATMOS_SFCANL

@@ -24,6 +24,9 @@ YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
 YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
  COMOUT_ATMOS_RESTART:COM_ATMOS_RESTART_TMPL

+RUN="enkfgdas" MEMDIR="ensstat" YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
+  COMIN_ATMOS_ENKF_ANALYSIS_STAT:COM_ATMOS_ANALYSIS_TMPL


This is looking for the current ensemble update analysis stat directory correct? Does having RUN="enkgdas" cause a failure during the gfs cycle?

I've turned off DO_GSISOILDA for the gfs runs.

ClaraDraper-NOAA · 2025-02-05T22:01:12Z

All:

I think I've addressed everything. I resolved any comments where I thought the change was obvious. Given the large number of changes, and my propensity for typos, I'm going to repeat the tests to make sure I didn't mess anything up. I'll comment again once that's done.
I've also found a bug I need to fix.
I've prepared a PR in UFS_UTILS to tidy up the variable names, as I think this is a good time to do that. I'll edit the first comment above to note that.

env/GAEAC5.env

scripts/exgdas_enkf_sfc.sh

Co-authored-by: Cory Martin <[email protected]>

CoryMartin-NOAA

last comment, otherwise I think the changes look good (have not tested).

We should turn this on in one or more of the CI tests

CoryMartin-NOAA · 2025-02-06T21:44:59Z

parm/config/gfs/config.sfcanl

+_RUN=${RUN:-"gfs"}
+_RUN=${RUN/enkf/}
+
+if [[ "${_RUN}" == "gfs" ]]; then  


Suggested change

_RUN=${RUN:-"gfs"}

_RUN=${RUN/enkf/}

if [[ "${_RUN}" == "gfs" ]]; then

if [[ "${RUN/enkf/}" == "gfs" ]]; then

There should always be a RUN I think

ClaraDraper-NOAA · 2025-02-07T01:07:35Z

last comment, otherwise I think the changes look good (have not tested).

We should turn this on in one or more of the CI tests

I've added a CI test.

ClaraDraper-NOAA · 2025-02-07T01:08:25Z

All - I have one change I need to make tomorrow (staging the orog fix files), which will require a fortran change. Otherwise, I think everything else is done. Thanks for all your input!

aerorahul · 2025-02-10T18:31:15Z

parm/config/gfs/config.esfc

+     export GCYCLE_DO_SOILINCR=".true."
+     export GCYCLE_INTERP_LANDINCR=".false."
+     export LSOIL_INCR=2
+    export REGRID_EXEC=${REGRID_EXEC:-"${HOMEgfs}/sorc/gdas.cd/build/bin/regridStates.x"}


Suggested change

export REGRID_EXEC=${REGRID_EXEC:-"${HOMEgfs}/sorc/gdas.cd/build/bin/regridStates.x"}

export REGRID_EXEC="${HOMEgfs}/sorc/gdas.cd/build/bin/regridStates.x"

No need for a pass through here since it is configured here first.

aerorahul · 2025-02-10T18:32:53Z

parm/config/gfs/config.esfc

+_RUN=${RUN:-"gfs"}
+_RUN=${RUN/enkf/}
+
+if [[ "${_RUN}" == "gfs" ]]; then  


Suggested change

_RUN=${RUN:-"gfs"}

_RUN=${RUN/enkf/}

if [[ "${_RUN}" == "gfs" ]]; then

if [[ "${RUN/enkf}" == "gfs" ]]; then

Don't really need _RUN.

aerorahul · 2025-02-10T18:33:51Z

scripts/exgdas_enkf_sfc.sh

+    export CASE_OUT=${CASE_ENS}
+    export OCNRES_OUT=${OCNRES}
+    export NMEM_REGRID=${NMEM_ENS}
+    if [ $DOIAU = "YES" ]; then


Suggested change

if [ $DOIAU = "YES" ]; then

if [[ "${DOIAU}" == "YES" ]]; then

aerorahul · 2025-02-10T18:34:28Z

scripts/exgdas_enkf_sfc.sh

+        export LFHR=6 # PDYcyc
+    fi
+
+    $REGRIDSH


Suggested change

$REGRIDSH

"${REGRIDSH}"

aerorahul · 2025-02-10T18:34:48Z

scripts/exgdas_enkf_sfc.sh

        done # ensembles

    done

 fi

-if [ $DOSFCANL_ENKF = "YES" ]; then
+if [[ $DOSFCANL_ENKF = "YES" ]]; then


Suggested change

if [[ $DOSFCANL_ENKF = "YES" ]]; then

if [[ "${DOSFCANL_ENKF}" == "YES" ]]; then

ush/regrid_gsiSfcIncr_to_tile.sh

ClaraDraper-NOAA added 16 commits December 18, 2024 23:41

Adding missing ush file

f9e9a49

Clean up calculation of forecast times required for regridding.

8120fb6

Merge branch 'develop' into feature/soilanal_det

0f150a9

Merge branch 'develop' into feature/soilanal_det

ea61f31

Added dependency on enkf for gdas_sfcanl, for GSI_SOILANAL case

1f3c8df

Tidy up timing of adding the sfc increments. Update config and xml.

0bf0a90

Fixed bug in FHR calc in regrid, added soil analysis to non-IAU (atmo…

e478210

…s) case

Added LSOIL_INC to config files. generalized regridding namelist input.

3856b1f

workaround to ease merging.

d8e945f

Merge branch 'develop' into feature/soilanal_det_clean

45c6cc1

Added back in env changes after merge.

86e0deb

Tidy up.

59e82b7

Merge branch 'develop' into feature/soilanal_det_clean

3d5b6ee

Updated UFS_UTILS to include latest update, needed for the soil analy…

b02e8af

…sis.

Updated code owners.

7ffee90

ClaraDraper-NOAA requested review from GeorgeGayno-NOAA, CoryMartin-NOAA, RussTreadon-NOAA, CatherineThomas-NOAA, WalterKolczynski-NOAA, KateFriedman-NOAA, DavidHuber-NOAA and aerorahul as code owners February 4, 2025 18:16

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ClaraDraper-NOAA and others added 2 commits February 4, 2025 15:12

Update parm/config/gfs/config.sfcanl

04e542e

Co-authored-by: Cory Martin <[email protected]>

Update scripts/exgdas_enkf_sfc.sh

fae30c6

Co-authored-by: Cory Martin <[email protected]>

more spelling

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ClaraDraper-NOAA added 4 commits February 5, 2025 17:48

Response to reviews.

4f50aae

Changes for review.

0f3b810

exgdas_enkf_upd spelling errors.

a19d56d

Cleaning up global_cycle variable names.

d726dbe

ClaraDraper-NOAA mentioned this pull request Feb 5, 2025

Cleaned up land-increment namelist and script variable names. ufs-community/UFS_UTILS#1022

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ClaraDraper-NOAA and others added 5 commits February 6, 2025 09:56

Update scripts/exgdas_enkf_sfc.sh

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Co-authored-by: Cory Martin <[email protected]>

Update scripts/exgdas_enkf_sfc.sh

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Co-authored-by: Cory Martin <[email protected]>

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Add the mean EnKF soil increment to the deterministic member #3295

Add the mean EnKF soil increment to the deterministic member #3295

ClaraDraper-NOAA commented Feb 4, 2025 •

edited

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	export REGRID_EXEC=${REGRID_EXEC:-"${HOMEgfs}/sorc/gdas.cd/build/bin/regridStates.x"}
	export REGRID_EXEC="${HOMEgfs}/sorc/gdas.cd/build/bin/regridStates.x"

	if [ $DOIAU = "YES" ]; then
	if [[ "${DOIAU}" == "YES" ]]; then

	if [[ $DOSFCANL_ENKF = "YES" ]]; then
	if [[ "${DOSFCANL_ENKF}" == "YES" ]]; then

Add the mean EnKF soil increment to the deterministic member #3295

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Add the mean EnKF soil increment to the deterministic member #3295

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ClaraDraper-NOAA commented Feb 4, 2025 • edited Loading

Description

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Change characteristics

How has this been tested?

Checklist

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ClaraDraper-NOAA commented Feb 4, 2025 •

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