Auto GitFlow - develop → MAPL-v3 - this updates the yaml to be in syn w/ the upcoming fv3-jedi PR 1335

components.yaml

@@ -92,7 +92,7 @@ GEOSana_GridComp:
 mksi:
    local: ./src/Components/@GEOSana_GridComp/GEOSaana_GridComp/GSI_GridComp/@mksi
    remote: ../GEOS_mksi.git
-   tag: v5.42.6
+   tag: v5.42.7
    develop: develop
 
 GEOSgcm_GridComp:
@@ -251,7 +251,7 @@ umwm:
 GEOSgcm_App:
   local: ./src/Applications/@GEOSgcm_App
   remote: ../GEOSgcm_App.git
-  tag: v2.3.8.4
+  tag: v2.3.8.5
   develop: develop
 
 Ocean-LETKF:

src/Applications/GEOSdas_App/jedi/etc/CMakeLists.txt

@@ -12,6 +12,7 @@ set (ALLETC
    jedi_acquire_ebkg.j
    jedi_acquire_ioda.j
    jedi_acquire_vbc.j
+   jedi_diffstates.j
    jedi_run_var.j
    mkiau.rc.tenv
    obsop_name_map.yaml

src/Applications/GEOSdas_App/jedi/etc/JEDIanaConfig.csh

@@ -1,3 +1,6 @@
+# SLURM specials
+setenv GEOSJEDI_QOS @GEOSJEDI_QOS
+setenv GEOSJEDI_PARTITION  @GEOSJEDI_PARTITION
 
 # Top options
 setenv JEDI_SET    1           # bring bkg/obs/ens
@@ -34,7 +37,7 @@ setenv JEDI_ADDINC_MPIRUN "mpirun -np 12"
 setenv JEDI_CNVANA_MPIRUN "mpirun -np 12"
 setenv JEDI_CNVENS_MPIRUN "mpirun -np 12"
 setenv JEDI_CNVINC_MPIRUN "mpirun -np 12"
-setenv JEDI_GETINC_MPIRUN "mpirun -np 48"
+setenv JEDI_GETINC_MPIRUN "mpirun -np @JEDI_DIF_NTASKS"
 setenv JEDI_NCPUS @JEDI_VAR_NCPUS
 setenv JEDI_FV3VAR_MPIRUN "mpirun -perhost @JEDI_VAR_PERHOST -np $JEDI_NCPUS"
 

src/Applications/GEOSdas_App/jedi/etc/convertana_geos.yaml

@@ -6,28 +6,99 @@ input geometry:
   npx: @JEDI_BKG_HRES
   npy: @JEDI_BKG_HRES
   npz: @JEDI_BKG_VRES
-  field metadata override: fv3-jedi/fieldmetadata/geos.yaml
 output geometry:
   akbk: fv3-jedi/fv3files/akbk@JEDI_BKG_VRES.nc4
 # interpolation method: bump
   npx: @JEDI_BKG_HRES_OUT
   npy: @JEDI_BKG_HRES_OUT
   npz: @JEDI_BKG_VRES
-  field metadata override: fv3-jedi/fieldmetadata/geos.yaml
 states:
 - input:
     datetime: $ISO_STATES_DATE
     filetype: cube sphere history
     provider: geos
     filename: &mybkg $JEDI_CUBED_BKG
     datapath: ./
-    state variables: [ua,va,t,delp,ps,q,qi,ql,qr,qs,o3ppmv,phis,
-                  qls,qcn,cfcn,frocean,frland,varflt,ustar,bstar,
-                  zpbl,cm,ct,cq,kcbl,tsm,khl,khu,frlake,frseaice,
-                  sheleg,ts,soilt,soilm,u10m,v10m,co2]
+    state variables: 
+    - eastward_wind
+    - northward_wind
+    - air_temperature
+    - air_pressure_thickness
+    - air_pressure_at_surface
+    - water_vapor_mixing_ratio_wrt_moist_air
+    - cloud_liquid_ice
+    - cloud_liquid_water
+    - rain_water
+    - snow_water
+    - mole_fraction_of_ozone_in_air
+    - geopotential_height_times_gravity_at_surface
+    - initial_mass_fraction_of_large_scale_cloud_condensate
+    - initial_mass_fraction_of_convective_cloud_condensate
+    - convective_cloud_area_fraction
+    - fraction_of_ocean
+    - fraction_of_land
+    - isotropic_variance_of_filtered_topography
+    - surface_velocity_scale
+    - surface_buoyancy_scale
+    - planetary_boundary_layer_height
+    - surface_exchange_coefficient_for_momentum
+    - surface_exchange_coefficient_for_heat
+    - surface_exchange_coefficient_for_moisture
+    - KCBL_before_moist
+    - surface_temp_before_moist
+    - lower_index_where_Kh_greater_than_2
+    - upper_index_where_Kh_greater_than_2
+    - fraction_of_lake
+    - fraction_of_ice
+    - vtype
+    - stype
+    - vfrac
+    - sheleg
+    - skin_temperature_at_surface
+    - soilt
+    - soilm
+    - eastward_wind_at_surface
+    - northward_wind_at_surface
+    - sea_surface_temperature
+    field io names: &field_io_names
+      eastward_wind: ua
+      northward_wind: va
+      air_temperature: t
+      air_pressure_thickness: delp
+      water_vapor_mixing_ratio_wrt_moist_air: q
+      cloud_liquid_ice: qi
+      cloud_liquid_water: ql
+      rain_water: qr
+      snow_water: qs
+      mole_fraction_of_ozone_in_air: o3ppmv
+      geopotential_height_times_gravity_at_surface: phis
+      initial_mass_fraction_of_large_scale_cloud_condensate: qls
+      initial_mass_fraction_of_convective_cloud_condensate: qcn
+      convective_cloud_area_fraction: cfcn
+      fraction_of_ocean: frocean
+      fraction_of_land: frland
+      isotropic_variance_of_filtered_topography: varflt
+      surface_velocity_scale: ustar
+      surface_buoyancy_scale: bstar
+      planetary_boundary_layer_height: zpbl
+      surface_exchange_coefficient_for_momentum: cm
+      surface_exchange_coefficient_for_heat: ct
+      surface_exchange_coefficient_for_moisture: cq
+      KCBL_before_moist: kcbl
+      surface_temp_before_moist: tsm
+      lower_index_where_Kh_greater_than_2: khl
+      upper_index_where_Kh_greater_than_2: khu
+      fraction_of_lake: frlake
+      fraction_of_ice: frseaice
+      skin_temperature_at_surface: ts
+      eastward_wind_at_surface: u10m
+      northward_wind_at_surface: v10m
+      air_pressure_at_surface: ps
+      sea_surface_temperature: ts_found
 #vtype, stype,vfrac,
   output:
     filetype: cube sphere history
     provider: geos
     datapath: ./$OUTDIR
     filename: *mybkg
+    field io names: *field_io_names

src/Applications/GEOSdas_App/jedi/etc/convertinc_geos.yaml

@@ -7,25 +7,46 @@ input geometry:
   npx: $JEDI_BKG_HRES
   npy: $JEDI_BKG_HRES
   npz: @JEDI_BKG_VRES
-  field metadata override: ./fieldmetadata/geos.yaml
 output geometry:
   layout: [2,1]
   akbk: ./fv3files/akbk@JEDI_BKG_VRES.nc4
   npx: $JEDI_BKG_HRES
   npy: $JEDI_BKG_HRES
   npz: @JEDI_BKG_VRES
-  field metadata override: ./fieldmetadata/geos.yaml
 
 linear variable change:
   variable change name: Model2GeoVaLs
-  input variables: &inputvars [ua,va,t,ps,q,o3ppmv,ts]
-  output variables: [ua,va,t,ps,q,o3ppmv,ts]
+  input variables: &myvars
+  - eastward_wind
+  - northward_wind
+  - air_temperature
+  - water_vapor_mixing_ratio_wrt_moist_air
+  - cloud_liquid_ice
+  - cloud_liquid_water
+  - rain_water
+  - snow_water
+  - mole_fraction_of_ozone_in_air
+  - air_pressure_at_surface
+  - skin_temperature_at_surface
+  field io names: &field_io_names
+    eastward_wind: ua
+    northward_wind: va
+    air_temperature: t
+    water_vapor_mixing_ratio_wrt_moist_air: q
+    cloud_liquid_ice: qi
+    cloud_liquid_water: ql
+    rain_water: qr
+    snow_water: qs
+    mole_fraction_of_ozone_in_air: o3ppmv
+    air_pressure_at_surface: ps
+    skin_temperature_at_surface: ts
+  output variables: *myvars
 increments:
 - date: "$JEDI_ISO_DATE_ANA"
-  input variables: *inputvars
+  input variables: *myvars
   trajectory:
     datetime: "$JEDI_ISO_DATE_ANA"
-    state variables: *inputvars
+    state variables: *myvars
     filetype: cube sphere history
     provider: geos
     datapath: ./bkg

src/Applications/GEOSdas_App/jedi/etc/diffstates_geos.yaml

@@ -6,61 +6,61 @@ state geometry:
   npx: @JEDI_BKG_HRES
   npy: @JEDI_BKG_HRES
   npz: @JEDI_BKG_VRES
-  field metadata override: fv3-jedi/fieldmetadata/geos.yaml
   layout:
-  - 4
-  - 2
+  - @JEDI_DIF_XLAYOUT
+  - @JEDI_DIF_YLAYOUT
 increment geometry:
   akbk: fv3-jedi/fv3files/akbk@JEDI_BKG_VRES.nc4
   npx: @JEDI_BKG_HRES
   npy: @JEDI_BKG_HRES
   npz: @JEDI_BKG_VRES
-  field metadata override: fv3-jedi/fieldmetadata/geos.yaml
   layout:
-  - 4
-  - 2
+  - @JEDI_DIF_XLAYOUT
+  - @JEDI_DIF_YLAYOUT
 state1:
   datetime: $ISO_STATES_DATE
   filetype: cube sphere history
   provider: geos
   datapath: ./ana
   filename: $JEDI_CUBED_ANA
-  state variables:
-  - ua
-  - va
-  - t
-  - q
-  - qi
-  - ql
-  - qr
-  - qs
-  - o3ppmv
-  - ps
-  - phis
-  - ts
+  state variables: &statevars
+  - eastward_wind
+  - northward_wind
+  - air_temperature
+  - water_vapor_mixing_ratio_wrt_moist_air
+  - cloud_liquid_ice
+  - cloud_liquid_water
+  - rain_water
+  - snow_water
+  - mole_fraction_of_ozone_in_air
+  - geopotential_height_times_gravity_at_surface
+  - air_pressure_at_surface
+  - skin_temperature_at_surface
+  field io names: &field_io_names
+    eastward_wind: ua
+    northward_wind: va
+    air_temperature: t
+    water_vapor_mixing_ratio_wrt_moist_air: q
+    cloud_liquid_ice: qi
+    cloud_liquid_water: ql
+    rain_water: qr
+    snow_water: qs
+    mole_fraction_of_ozone_in_air: o3ppmv
+    geopotential_height_times_gravity_at_surface: phis
+    air_pressure_at_surface: ps
+    skin_temperature_at_surface: ts
 # - delp
 state2:
   datetime: $ISO_STATES_DATE
   filetype: cube sphere history
   provider: geos
   datapath: ./bkg
   filename: $JEDI_CUBED_BKG
-  state variables:
-  - ua
-  - va
-  - t
-  - q
-  - qi
-  - ql
-  - qr
-  - qs
-  - o3ppmv
-  - ps
-  - phis
-  - ts
-# - delp
+  state variables: *statevars
+  field io names: *field_io_names
 output:
   filetype: auxgrid
   gridtype: latlon
   datapath: ./inc
   filename: $EXPID.jedi_inc1.eta.
+  field io names: *field_io_names