Unify obs and test configurations between FV3-JEDI and MPAS-JEDI (#255)

## Description
The goal of this PR is to unify the obs and configuration between
FV3-JEDI and MPAS-JEDI.

fix/bumploc/conus12km-401km11levels

@@ -1 +1 @@
-../.agent/bumploc/conus12km-401km11levels_20240912
+../.agent/bumploc/conus12km-401km11levels_20241212_mpi160

fix/expr_data/fv3_2024052700/Data/bkg

@@ -0,0 +1 @@
+../../../.agent/expr_data/fv3_2024052700/Data/bkg

fix/expr_data/fv3_2024052700/Data/crtm

@@ -0,0 +1 @@
+../../../.agent/crtm/2.4.0

fix/expr_data/fv3_2024052700/Data/fieldmetadata

@@ -0,0 +1 @@
+../../../.agent/expr_data/fv3_2024052700/Data/fieldmetadata

fix/expr_data/fv3_2024052700/Data/geovals

@@ -0,0 +1 @@
+../../../.agent/expr_data/fv3_2024052700/Data/geovals

fix/expr_data/fv3_2024052700/Data/inputs

@@ -0,0 +1 @@
+../../../.agent/expr_data/fv3_2024052700/Data/inputs

fix/expr_data/fv3_2024052700/Data/obs

@@ -0,0 +1 @@
+../../../.agent/expr_data/obs_2024052700

fix/expr_data/mpas_2024052700/obs

@@ -1 +1 @@
-../../.agent/expr_data/mpas_2024052700_mpasout/obs
+../../.agent/expr_data/obs_2024052700

fix/graphinfo/conus12km_mpas.graph.info

@@ -0,0 +1 @@
+../.agent/graphinfo/conus12km_mpas.graph.info

fix/graphinfo/conus12km_mpas.graph.info.part.160

@@ -0,0 +1 @@
+../.agent/graphinfo/conus12km_mpas.graph.info.part.160

rrfs-test/CMakeLists.txt

@@ -31,15 +31,17 @@ set (src_yaml "${CMAKE_SOURCE_DIR}/rrfs-test/testinput")
 if(FV3_DYCORE)
 
       message(STATUS "MACHINE_ID is " ${MACHINE_ID})
-      set(RESTORE_MPI_ARGS ${MPI_ARGS})
-      if("${MACHINE_ID}" STREQUAL "orion" OR "${MACHINE_ID}" STREQUAL "hercules")
-         message(STATUS "Because MACHINE_ID is orion, adding exclusive MPI option" )
-         set(MPI_ARGS "${MPI_ARGS} --exclusive")
-      endif()   
-      set(MPI_ARGS "${MPI_ARGS} --time=00:30:00")
 
       get_all_keys(rrfs_fv3jedi_tests caselist)
       foreach(case ${caselist})
+
+         set(RESTORE_MPI_ARGS ${MPI_ARGS})
+         if("${MACHINE_ID}" STREQUAL "orion" OR "${MACHINE_ID}" STREQUAL "hercules")
+            message(STATUS "Because MACHINE_ID is orion, adding exclusive MPI option" )
+            set(MPI_ARGS "${MPI_ARGS} --exclusive")
+         endif()   
+         set(MPI_ARGS "${MPI_ARGS} --time=00:30:00")
+
          get_from_dictionary(rrfs_fv3jedi_tests case exe)
          set(casedir "${CMAKE_CURRENT_BINARY_DIR}/rundir-${case}")
          set(src_casedir "${rrfs-test_data_local}/rrfs-data_fv3jedi_2024052700")
@@ -67,24 +69,25 @@ if(FV3_DYCORE)
                         ARGS     ${target_test}.yaml
                         COMMAND  ${exe} )
 	 endif()
+         set(MPI_ARGS ${RESTORE_MPI_ARGS})
       endforeach()
-      set(MPI_ARGS ${RESTORE_MPI_ARGS})
 
 endif()
 
 if(MPAS_DYCORE)
 
       message(STATUS "MACHINE_ID is " ${MACHINE_ID})
-      set(RESTORE_MPI_ARGS ${MPI_ARGS})
-      if("${MACHINE_ID}" STREQUAL "orion" OR "${MACHINE_ID}" STREQUAL "hercules")
-         message(STATUS "Because MACHINE_ID is orion, adding exclusive MPI option" )
-         set(MPI_ARGS "${MPI_ARGS} --exclusive")
-      endif()   
-      set(MPI_ARGS "${MPI_ARGS} --ntasks-per-node=4")
-      set(MPI_ARGS "${MPI_ARGS} --time=00:30:00")
 
       get_all_keys(rrfs_mpasjedi_tests caselist)
       foreach(case ${caselist})
+
+         set(RESTORE_MPI_ARGS ${MPI_ARGS})
+         if("${MACHINE_ID}" STREQUAL "orion" OR "${MACHINE_ID}" STREQUAL "hercules")
+            message(STATUS "Because MACHINE_ID is orion, adding exclusive MPI option" )
+            set(MPI_ARGS "${MPI_ARGS} --exclusive")
+         endif()   
+         set(MPI_ARGS "${MPI_ARGS} --time=00:30:00")
+
 	 get_from_dictionary(rrfs_mpasjedi_tests case exe)
          set(casedir "${CMAKE_CURRENT_BINARY_DIR}/rundir-${case}")
          set(src_casedir "${rrfs-test_data_local}/rrfs-data_mpasjedi_2024052700")
@@ -105,21 +108,22 @@ if(MPAS_DYCORE)
 	 file(COPY ${src_yaml}/${case}.yaml DESTINATION ${casedir})
          set(target_test ${case})
 	 if ("${target_test}" STREQUAL "rrfs_mpasjedi_2024052700_getkf_solver")
+           set(MPI_ARGS "${MPI_ARGS} --ntasks-per-node=8")
            ecbuild_add_test( TARGET ${target_test}
-                        MPI      120
+                        MPI      160
 			WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/rundir-${target_test}
                         ARGS     ${target_test}.yaml
 			TEST_DEPENDS "rrfs_mpasjedi_2024052700_getkf_observer"
                         COMMAND  ${exe} )
 	 else()
            ecbuild_add_test( TARGET ${target_test}
-                        MPI      120
+                        MPI      160
 			WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/rundir-${target_test}
                         ARGS     ${target_test}.yaml
                         COMMAND  ${exe} )
 	 endif()
+         set(MPI_ARGS ${RESTORE_MPI_ARGS})
       endforeach()
-      set(MPI_ARGS ${RESTORE_MPI_ARGS})
 
       ########################
       ### Bufr2ioda ctests ###
@@ -131,10 +135,13 @@ if(MPAS_DYCORE)
       set(src_casedir "${rrfs-test_data_local}/rrfs-data_mpasjedi_2024052700")
       if (NOT EXISTS "${casedir}")
          file(MAKE_DIRECTORY ${casedir})
+         file(MAKE_DIRECTORY ${casedir}/bufr)
       endif()
       file(CREATE_LINK ${src_casedir}/data ${casedir}/data SYMBOLIC)
-      configure_file(${src_casedir}/data/obs/bufr/rap.t00z.prepbufr.tm00 ${casedir}/prepbufr COPYONLY)
-      file(COPY ${src_yaml}/${case}.yaml DESTINATION ${casedir})
+      set (src_yaml "${CMAKE_SOURCE_DIR}/rrfs-test/IODA/yaml")
+      configure_file(${src_casedir}/data/obs/bufr/rap.t00z.prepbufr.tm00 ${casedir}/bufr/prepbufr COPYONLY)
+      configure_file(${src_yaml}/prepbufr_msonet.yaml ${casedir}/${case}.yaml COPYONLY)
+      execute_process(COMMAND sed -i "s/@REFERENCETIME@/2024-05-27T00:00:00Z/g" ${casedir}/${case}.yaml)
       set(MPI_ARGS "--time=00:05:00 --mem=64G")
       set(IODA_CONV_COMP_TOL "5.0e-4")
       ecbuild_add_test( TARGET  ${case}
@@ -145,8 +152,8 @@ if(MPAS_DYCORE)
            		ARGS    ${CMAKE_SOURCE_DIR}/rrfs-test/ush/iodaconv_comp_rrfs.sh
                                 netcdf
                                 "${CMAKE_BINARY_DIR}/bin/bufr2ioda.x ${case}.yaml"
-                                data/obs/ioda_mesonet.nc
-                                ioda_mesonet.nc 
+                                data/obs/ioda_msonet.nc
+                                ioda_msonet.nc 
 			        ${IODA_CONV_COMP_TOL}
                         DEPENDS bufr2ioda.x )
 

rrfs-test/IODA/offline_domain_check_satrad.py

@@ -187,6 +187,8 @@ def shrink_boundary(points, centroid, factor=0.01):
 if 'grid_lat' in grid_ds.variables and 'grid_lon' in grid_ds.variables:  # FV3 grid
     grid_lat = grid_ds.variables['grid_lat'][:, :]
     grid_lon = grid_ds.variables['grid_lon'][:, :]
+    grid_lat = grid_lat.flatten()
+    grid_lon = grid_lon.flatten()
     dycore = "FV3"
 elif 'latCell' in grid_ds.variables and 'lonCell' in grid_ds.variables:  # MPAS grid
     grid_lat = np.degrees(grid_ds.variables['latCell'][:])  # Convert radians to degrees
@@ -296,7 +298,11 @@ def shrink_boundary(points, centroid, factor=0.01):
                 g.createVariable(var, vartype, dimensions, fill_value=fill)
             except:
                 g.createVariable(var, 'str', dimensions, fill_value=fill)
-            g.variables[var][:] = invar[:][inside_indices]
+            # If variable has only dimensions of channel then we do not need to process it 
+            if g.variables[var].dimensions[0] == 'Channel': 
+                g.variables[var][:] = invar[:][:]
+            else: 
+                g.variables[var][:] = invar[:][inside_indices]
             # Copy attributes for this variable
             for attr in invar.ncattrs():
                 if '_FillValue' in attr: continue

rrfs-test/gsi_fix/anavinfo

@@ -0,0 +1,79 @@
+met_guess::
+!var     level    crtm_use    desc              orig_name
+  ps        1      -1         surface_pressure     ps
+  z         1      -1         geopotential_height  phis
+  u        65       2         zonal_wind           u
+  v        65       2         meridional_wind      v
+  w        65      -1         vertical velocity    w
+  tv       65       2         virtual_temperature  tv
+  q        65       2         specific_humidity    sphu
+  oz       65       2         ozone                ozone
+  delp     65      -1         fv3 del pressure     delp
+  t2m       1      -1         2-m_T                t2m
+  q2m       1      -1         2-m_Q                q2m
+!  ql       65      10         cloud_condensate     QCLOUD
+!  qr       65      10         rain                 QRAIN
+!  qs       65      10         snow                 QSNOW
+!  qi       65      10         ice                  QICE
+!  qg       65      10         graupel              QGRAUP
+!  dbz      65      10         reflectivity         REFL_10CM
+::
+
+state_derivatives::
+!var  level  src
+ ps   1      met_guess
+ u    65     met_guess
+ v    65     met_guess
+ tv   65     met_guess
+ q    65     met_guess
+ oz   65     met_guess
+ prse 66     met_guess
+::
+
+state_tendencies::
+!var  levels  source
+ u    65      met_guess
+ v    65      met_guess
+ tv   65      met_guess
+ q    65      met_guess
+ oz   65      met_guess
+ prse 66      met_guess
+::
+
+state_vector::  
+!var     level  itracer source     funcof
+ u        65      0     met_guess    u
+ v        65      0     met_guess    v
+ w        65      0     met_guess    w
+ tv       65      0     met_guess    tv
+ tsen     65      0     met_guess    tv,q
+ q        65      1     met_guess    q
+! oz       65      1     met_guess    oz
+ prse     66      0     met_guess    prse
+ ps        1      0     met_guess    prse
+ sst       1      0     met_guess    sst
+! qr       65      1     met_guess    qr
+! ql       65      1     met_guess    qc
+! qs       65      1     met_guess    qs
+! qi       65      1     met_guess    qi
+! qg       65      1     met_guess    qg
+! dbz      65      1     met_guess    dbz
+::
+
+control_vector::
+!var     level  itracer as/tsfc_sdv  an_amp0   source  funcof
+ sf       65      0       0.90        -1.0     state    u,v
+ vp       65      0       0.90        -1.0     state    u,v
+ ps        1      0       1.00        -1.0     state    prse
+ t        65      0       1.40        -1.0     state    tv
+ q        65      1       0.80        -1.0     state    q
+ sst       1      0       1.00        -1.0     state    sst
+ stl       1      0       1.00        -1.0     motley   sst
+ sti       1      0       1.00        -1.0     motley   sst
+! qr       65      1       1.0        -1.0     state    qr
+! qs       65      1       1.0        -1.0     state    qs
+! qi       65      1       1.0        -1.0     state    qi
+! qg       65      1       1.0        -1.0     state    qg
+! ql       65      1       1.0        -1.0     state    qc
+! dbz      65      1       1.00        -1.0     state    dbz
+::