update RDASApp submodules to match mpasjedi-v3.0.1 (#194)

List of submodule changes. issue #193 ``` ioda c7b8760f -> d49ed17e ufo 92ccfb2a -> 94d50d64 oops 35820130 -> d77217323 vader e3457cba -> 6d56a1eb5 mpas 3ecd59e2 -> 41e9a3fb8 # repo URL also changed mpas-jedi a1c60997 -> b9d596d7c #fv3-jedi d3c800b8 -> c99519638 #fv3-jedi-lm a6e97d76 -> 30ef7a390 ``` --------- Co-authored-by: guoqing.ge <Guoqing.Ge@noaa.gov>
NOAA-EMC · Oct 22, 2024 · 6967dd5 · 6967dd5
1 parent dffa109
commit 6967dd5
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diff --git a/.gitmodules b/.gitmodules
@@ -65,7 +65,7 @@
 	ignore = all
 [submodule "sorc/mpas"]
 	path = sorc/mpas
-	url = https://github.com/jcsda-internal/MPAS-Model
+	url = https://github.com/MPAS-Dev/MPAS-Model
 	branch = release-stable 
 	ignore = all
 [submodule "sorc/mpas-jedi"]

diff --git a/bundle/mpas-jedi-data/testinput_tier_1/obs b/bundle/mpas-jedi-data/testinput_tier_1/obs
@@ -0,0 +1 @@
+../../../fix/jcsda/mpas-jedi-data/testinput_tier_1/obs
diff --git a/fix/crtm b/fix/crtm
diff --git a/fix/crtm/2.3.0 b/fix/crtm/2.3.0
@@ -0,0 +1 @@
+../.agent/crtm/2.3.0
diff --git a/fix/crtm/2.4.0 b/fix/crtm/2.4.0
@@ -0,0 +1 @@
+../.agent/crtm/2.4.0
diff --git a/fix/crtm/2.4.1_skylab_4.0 b/fix/crtm/2.4.1_skylab_4.0
@@ -0,0 +1 @@
+../.agent/crtm/2.4.1_skylab_4.0
diff --git a/fix/crtm/fix_REL-3.1.1.2 b/fix/crtm/fix_REL-3.1.1.2
@@ -0,0 +1 @@
+../.agent/crtm/fix_REL-3.1.1.2
diff --git a/fix/expr_data/mpas_2024052700/bkg b/fix/expr_data/mpas_2024052700/bkg
@@ -1 +1 @@
-../../.agent/expr_data/mpas_2024052700/bkg
+../../.agent/expr_data/mpas_2024052700_mpasout/bkg
diff --git a/fix/expr_data/mpas_2024052700/ens b/fix/expr_data/mpas_2024052700/ens
@@ -1 +1 @@
-../../.agent/expr_data/mpas_2024052700/ens
+../../.agent/expr_data/mpas_2024052700_mpasout/ens
diff --git a/fix/expr_data/mpas_2024052700/invariant.nc b/fix/expr_data/mpas_2024052700/invariant.nc
@@ -0,0 +1 @@
+../../.agent/expr_data/mpas_2024052700_mpasout/invariant.nc
diff --git a/fix/expr_data/mpas_2024052700/obs b/fix/expr_data/mpas_2024052700/obs
@@ -1 +1 @@
-../../.agent/expr_data/mpas_2024052700/obs
+../../.agent/expr_data/mpas_2024052700_mpasout/obs
diff --git a/fix/jcsda/fv3-jedi-data b/fix/jcsda/fv3-jedi-data
@@ -1 +1 @@
-../.agent/jcsda/fv3-jedi-data
+../.agent/jcsda/fv3-jedi-data_2085be5_20241008
diff --git a/fix/jcsda/ioda-data b/fix/jcsda/ioda-data
@@ -1 +1 @@
-../.agent/jcsda/ioda-data
+../.agent/jcsda/ioda-data_20241011
diff --git a/fix/physics/VEGPARM.TBL b/fix/physics/VEGPARM.TBL
@@ -1 +1 @@
-../.agent/physics/VEGPARM.TBL
+../.agent/physics/VEGPARM.TBL.20241011
diff --git a/rrfs-test/scripts/link_mpasjedi_expr.sh b/rrfs-test/scripts/link_mpasjedi_expr.sh
@@ -48,10 +48,10 @@ cp ${RDASApp}/rrfs-test/ush/mpasjedi_spread.py .
 
 mkdir -p data
 cd data
-mkdir -p bumploc bkg obs obs_ctest ens
+mkdir -p bumploc obs obs_ctest ens
 ln -snf ${RDASApp}/fix/bumploc/${BUMPLOC} bumploc/${BUMPLOC}
-ln -snf ${RDASApp}/fix/expr_data/${exprname}/bkg/restart.2024-05-27_00.00.00.nc .
-ln -snf ${RDASApp}/fix/expr_data/${exprname}/bkg/restart.2024-05-27_00.00.00.nc static.nc
+ln -snf ${RDASApp}/fix/expr_data/${exprname}/bkg/mpasout.2024-05-27_00.00.00.nc .
+ln -snf ${RDASApp}/fix/expr_data/${exprname}/invariant.nc invariant.nc
 ln -snf ${RDASApp}/fix/expr_data/${exprname}/obs/* obs/
 ln -snf ${RDASApp}/fix/expr_data/${exprname}/obs_ctest/* obs_ctest/
 ln -snf ${RDASApp}/fix/expr_data/${exprname}/ens/* ens/

diff --git a/rrfs-test/scripts/setup_experiment.sh b/rrfs-test/scripts/setup_experiment.sh
@@ -98,8 +98,8 @@ elif [[ $DYCORE == "MPAS" ]]; then
   mkdir -p data; cd data
   mkdir -p bumploc bkg obs ens
   ln -snf ${YOUR_PATH_TO_RDASAPP}/fix/bumploc/* bumploc/.
-  ln -snf ${YOUR_PATH_TO_RDASAPP}/fix/expr_data/${TEST_DATA}/bkg/restart.2024-05-27_00.00.00.nc .
-  ln -snf ${YOUR_PATH_TO_RDASAPP}/fix/expr_data/${TEST_DATA}/bkg/restart.2024-05-27_00.00.00.nc static.nc
+  ln -snf ${YOUR_PATH_TO_RDASAPP}/fix/expr_data/${TEST_DATA}/bkg/mpasout.2024-05-27_00.00.00.nc .
+  ln -snf ${YOUR_PATH_TO_RDASAPP}/fix/expr_data/${TEST_DATA}/invariant.nc invariant.nc
   ln -snf ${YOUR_PATH_TO_RDASAPP}/fix/expr_data/${TEST_DATA}/obs/* obs/
   ln -snf ${YOUR_PATH_TO_RDASAPP}/fix/expr_data/${TEST_DATA}/ens/* ens/
   cp -p $YOUR_PATH_TO_RDASAPP/rrfs-test/scripts/templates/run_bump_template.sh run_bump.sh

diff --git a/rrfs-test/testinput/rrfs_mpasjedi_2024052700_Ens3Dvar.yaml b/rrfs-test/testinput/rrfs_mpasjedi_2024052700_Ens3Dvar.yaml
@@ -45,7 +45,7 @@ cost function:
   analysis variables: *incvars
   background:
     state variables: [spechum,surface_pressure,temperature,uReconstructMeridional,uReconstructZonal,theta,rho,u,qv,pressure,landmask,xice,snowc,skintemp,ivgtyp,isltyp,snowh,vegfra,u10,v10,lai,smois,tslb,pressure_p,qc,qi,qg,qr,qs,cldfrac]
-    filename: data/restart.2024-05-27_00.00.00.nc
+    filename: data/mpasout.2024-05-27_00.00.00.nc
     date: *analysisDate
   background error:
     covariance model: ensemble
@@ -66,10 +66,10 @@ cost function:
     members from template:
       template:
         <<: *memberConfig
-        filename: ./data/ens/mem%iMember%/restart.2024-05-27_00.00.00.nc
+        filename: ./data/ens/mem%iMember%/mpasout.2024-05-27_00.00.00.nc
       pattern: "%iMember%"
       start: 1
-      zero padding: 2
+      zero padding: 3
       nmembers: 30
 
   observations:

diff --git a/rrfs-test/testinput/rrfs_mpasjedi_2024052700_bumploc.yaml b/rrfs-test/testinput/rrfs_mpasjedi_2024052700_bumploc.yaml
@@ -8,7 +8,7 @@ geometry:
   bump vunit: "modellevel" # modellevel, height
 background:
   state variables: &vars [spechum,surface_pressure,temperature,uReconstructMeridional,uReconstructZonal]
-  filename: "./data/restart.2024-05-27_00.00.00.nc"
+  filename: "./data/mpasout.2024-05-27_00.00.00.nc"
   date: *validDate
 
 background error:

diff --git a/rrfs-test/testinput/rrfs_mpasjedi_2024052700_getkf_observer.yaml b/rrfs-test/testinput/rrfs_mpasjedi_2024052700_getkf_observer.yaml
@@ -16,10 +16,10 @@ background:
     members from template:
       template:
         <<: *memberConfig
-        filename: ./data/ens/mem%iMember%/restart.2024-05-27_00.00.00.nc
+        filename: ./data/ens/mem%iMember%/mpasout.2024-05-27_00.00.00.nc
       pattern: "%iMember%"
       start: 1
-      zero padding: 2
+      zero padding: 3
       nmembers: 30
 
 observations:

diff --git a/rrfs-test/testinput/rrfs_mpasjedi_2024052700_getkf_solver.yaml b/rrfs-test/testinput/rrfs_mpasjedi_2024052700_getkf_solver.yaml
@@ -16,10 +16,10 @@ background:
     members from template:
       template:
         <<: *memberConfig
-        filename: ./data/ens/mem%iMember%/restart.2024-05-27_00.00.00.nc
+        filename: ./data/ens/mem%iMember%/mpasout.2024-05-27_00.00.00.nc
       pattern: "%iMember%"
       start: 1
-      zero padding: 2
+      zero padding: 3
       nmembers: 30
 
 observations:

diff --git a/rrfs-test/testinput/streams.atmosphere b/rrfs-test/testinput/streams.atmosphere
@@ -1,15 +1,15 @@
 <streams>
-<immutable_stream name="static"
+<immutable_stream name="invariant"
                   type="input"
                   precision="single"
-                  filename_template="data/static.nc"
+                  filename_template="data/invariant.nc"
                   io_type="pnetcdf,cdf5"
                   input_interval="initial_only" />
 
 <immutable_stream name="input"
                   type="input"
                   precision="single"
-                  filename_template="data/restart.2024-05-27_00.00.00.nc"
+                  filename_template="data/mpasout.2024-05-27_00.00.00.nc"
                   io_type="pnetcdf,cdf5"
                   input_interval="initial_only" />
 

diff --git a/rrfs-test/testinput_expr/rrfs_mpasjedi_2024052700_Ens3Dvar.yaml b/rrfs-test/testinput_expr/rrfs_mpasjedi_2024052700_Ens3Dvar.yaml
@@ -1,41 +1,3 @@
-
-# application-agnostic anchors that specify observation errors
-# applicable to Variational, HofX3D
-
-# reusable latitude bands for all observation types
-_conventional obs localizations: &heightAndHorizObsLoc
-  _blank: null
-
-_nonconventional obs localizations: &horizObsLoc
-  _blank: null
-
-_obs space: &ObsSpace
-  obs perturbations seed: 1
-  io pool:
-    max pool size: 10
-  distribution:
-    name: RoundRobin
-
-_obs error diagonal: &ObsErrorDiagonal
-  covariance model: diagonal
-  # Note: the same 'obs perturbations seed' must be used for all members for the 'zero-mean perturbations' option to work
-  zero-mean perturbations: true
-  member: 1
-  number of members: 1
-
-_get values: &GetValues
-  nnearest: 3
-
-_multi iteration filter: &multiIterationFilter
-  apply at iterations: 0,1,2,3,4,5
-# ObsAnchors and ObsErrorAnchors are automatically prepended above this line
-_iteration: &iterationConfig
-  geometry:
-    nml_file: ./namelist.atmosphere
-    streams_file: ./streams.atmosphere
-    deallocate non-da fields: true
-    interpolation type: unstructured
-  gradient norm reduction: 1e-3
 _member: &memberConfig
   date: &analysisDate '2024-05-27T00:00:00Z'
   state variables: &incvars [spechum,surface_pressure,temperature,uReconstructMeridional,uReconstructZonal]
@@ -48,11 +10,23 @@ variational:
   minimizer:
     algorithm: DRPCG
   iterations:
-  - <<: *iterationConfig
+  - geometry:
+      nml_file: ./namelist.atmosphere
+      streams_file: ./streams.atmosphere
+      deallocate non-da fields: true
+      interpolation type: unstructured
+    gradient norm reduction: 1e-3
     diagnostics:
       departures: ombg
     ninner: 50
-  - <<: *iterationConfig
+  - geometry:
+      nml_file: ./namelist.atmosphere
+      streams_file: ./streams.atmosphere
+      deallocate non-da fields: true
+      interpolation type: unstructured
+    gradient norm reduction: 1e-3
+    diagnostics:
+      departures: ombg
     ninner: 50
 final:
   diagnostics:
@@ -68,11 +42,11 @@ cost function:
     streams_file: ./streams.atmosphere
     deallocate non-da fields: true
     interpolation type: unstructured
-  analysis variables: *incvars 
+  analysis variables: *incvars
   background:
     state variables: [spechum,surface_pressure,temperature,uReconstructMeridional,uReconstructZonal,theta,rho,u,qv,pressure,landmask,xice,snowc,skintemp,ivgtyp,isltyp,snowh,vegfra,u10,v10,lai,smois,tslb,pressure_p,qc,qi,qg,qr,qs,cldfrac]
-    filename: data/restart.2024-05-27_00.00.00.nc
-    date: *analysisDate 
+    filename: data/mpasout.2024-05-27_00.00.00.nc
+    date: *analysisDate
   background error:
     covariance model: ensemble
     localization:
@@ -92,10 +66,10 @@ cost function:
     members from template:
       template:
         <<: *memberConfig
-        filename: ./data/ens/mem%iMember%/restart.2024-05-27_00.00.00.nc
-      pattern: %iMember%
+        filename: ./data/ens/mem%iMember%/mpasout.2024-05-27_00.00.00.nc
+      pattern: "%iMember%"
       start: 1
-      zero padding: 2 
+      zero padding: 3
       nmembers: 30
   observations:
      observers:

diff --git a/rrfs-test/testinput_expr/rrfs_mpasjedi_2024052700_bumploc.yaml b/rrfs-test/testinput_expr/rrfs_mpasjedi_2024052700_bumploc.yaml
@@ -8,7 +8,7 @@ geometry:
   bump vunit: "modellevel" # modellevel, height
 background:
   state variables: &vars [spechum,surface_pressure,temperature,uReconstructMeridional,uReconstructZonal]
-  filename: "./data/restart.2024-05-27_00.00.00.nc"
+  filename: "./data/mpasout.2024-05-27_00.00.00.nc"
   date: *validDate
 
 background error:

diff --git a/rrfs-test/testinput_expr/rrfs_mpasjedi_2024052700_getkf.yaml b/rrfs-test/testinput_expr/rrfs_mpasjedi_2024052700_getkf.yaml
@@ -16,10 +16,10 @@ background:
     members from template:
       template:
         <<: *memberConfig
-        filename: ./data/ens/mem%iMember%/restart.2024-05-27_00.00.00.nc
-      pattern: %iMember%
+        filename: ./data/ens/mem%iMember%/mpasout.2024-05-27_00.00.00.nc
+      pattern: "%iMember%"
       start: 1
-      zero padding: 2
+      zero padding: 3
       nmembers: 30
 
 observations:

diff --git a/rrfs-test/testinput_expr/rrfs_mpasjedi_2024052700_getkf_observer.yaml b/rrfs-test/testinput_expr/rrfs_mpasjedi_2024052700_getkf_observer.yaml
@@ -16,10 +16,10 @@ background:
     members from template:
       template:
         <<: *memberConfig
-        filename: ./data/ens/mem%iMember%/restart.2024-05-27_00.00.00.nc
-      pattern: %iMember%
+        filename: ./data/ens/mem%iMember%/mpasout.2024-05-27_00.00.00.nc
+      pattern: "%iMember%"
       start: 1
-      zero padding: 2
+      zero padding: 3
       nmembers: 30
 
 observations:

diff --git a/rrfs-test/testinput_expr/rrfs_mpasjedi_2024052700_getkf_solver.yaml b/rrfs-test/testinput_expr/rrfs_mpasjedi_2024052700_getkf_solver.yaml
@@ -16,10 +16,10 @@ background:
     members from template:
       template:
         <<: *memberConfig
-        filename: ./data/ens/mem%iMember%/restart.2024-05-27_00.00.00.nc
-      pattern: %iMember%
+        filename: ./data/ens/mem%iMember%/mpasout.2024-05-27_00.00.00.nc
+      pattern: "%iMember%"
       start: 1
-      zero padding: 2
+      zero padding: 3
       nmembers: 30
 
 observations:

diff --git a/rrfs-test/testinput_expr/rrfs_mpasjedi_2024052700_letkf.yaml b/rrfs-test/testinput_expr/rrfs_mpasjedi_2024052700_letkf.yaml
@@ -16,10 +16,10 @@ background:
     members from template:
       template:
         <<: *memberConfig
-        filename: ./data/ens/mem%iMember%/restart.2024-05-27_00.00.00.nc
-      pattern: %iMember%
+        filename: ./data/ens/mem%iMember%/mpasout.2024-05-27_00.00.00.nc
+      pattern: "%iMember%"
       start: 1
-      zero padding: 2
+      zero padding: 3
       nmembers: 30
 
 observations:

diff --git a/rrfs-test/testinput_expr/streams.atmosphere b/rrfs-test/testinput_expr/streams.atmosphere
@@ -1,15 +1,15 @@
 <streams>
-<immutable_stream name="static"
+<immutable_stream name="invariant"
                   type="input"
                   precision="single"
-                  filename_template="data/static.nc"
+                  filename_template="data/invariant.nc"
                   io_type="pnetcdf,cdf5"
                   input_interval="initial_only" />
 
 <immutable_stream name="input"
                   type="input"
                   precision="single"
-                  filename_template="data/restart.2024-05-27_00.00.00.nc"
+                  filename_template="data/mpasout.2024-05-27_00.00.00.nc"
                   io_type="pnetcdf,cdf5"
                   input_interval="initial_only" />