Move the variational scripts to the g-w (#1282)

This PR needs to be merged before - [NOAA-EMC/global-workflow#2920 It depends on - [NOAA-EMC/jcb-gdas#26 and will require an update to the `jcb-gdas` submodules. It will break the GDASApp marine CI until the `g-w` pr is merged.
NOAA-EMC · Sep 18, 2024 · 55e895f · 55e895f
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diff --git a/parm/jcb-gdas b/parm/jcb-gdas
diff --git a/parm/soca/berror/soca_diagb.yaml.j2 b/parm/soca/berror/soca_diagb.yaml.j2
@@ -12,7 +12,7 @@ background:
   read_from_file: 1
 
 background error:
-  datadir: ./diagb/
+  datadir: ./staticb/
   date: '{{ MARINE_WINDOW_MIDDLE | to_isotime }}'
   exp: bkgerr_stddev
   type: incr

diff --git a/parm/soca/berror/soca_ensb.yaml.j2 b/parm/soca/berror/soca_ensb.yaml.j2
@@ -34,44 +34,44 @@ steric height:
   - linear variable change name: BalanceSOCA  # Only the steric balance is applied
 
 ensemble mean output:
-  datadir: ./diagb/
+  datadir: ./staticb/
   date: '{{ MARINE_WINDOW_BEGIN | to_isotime }}'
   exp: ens_mean
   type: incr
 
 ssh output:
   unbalanced:
-    datadir: ./diagb/
+    datadir: ./staticb/
     date: '{{ MARINE_WINDOW_BEGIN | to_isotime }}'
     exp: ssh_unbal_stddev
     type: incr
 
   steric:
-    datadir: ./diagb/
+    datadir: ./staticb/
     date: '{{ MARINE_WINDOW_BEGIN | to_isotime }}'
     exp: ssh_steric_stddev
     type: incr
 
   total:
-    datadir: ./diagb/
+    datadir: ./staticb/
     date: '{{ MARINE_WINDOW_BEGIN | to_isotime }}'
     exp: ssh_total_stddev
     type: incr
 
   explained variance:
-    datadir: ./diagb/
+    datadir: ./staticb/
     date: '{{ MARINE_WINDOW_BEGIN | to_isotime }}'
     exp: steric_explained_variance
     type: incr
 
   recentering error:
-    datadir: ./diagb/
+    datadir: ./staticb/
     date: '{{ MARINE_WINDOW_BEGIN | to_isotime }}'
     exp: ssh_recentering_error
     type: incr
 
 background error output:
-  datadir: ./diagb/
+  datadir: ./staticb/
   date: '{{ MARINE_WINDOW_BEGIN | to_isotime }}'
   exp: bkgerr_stddev
   type: incr
@@ -90,7 +90,7 @@ trajectory:
 
 output increment:
   # TODO: Revert this when fms can take more than 128 charactres file names
-  datadir: '{{ ENSPERT_RELPATH }}/ens/'
+  datadir: '{{ ENSPERT_RELPATH }}/enspert/'
   date: '{{ MARINE_WINDOW_BEGIN | to_isotime }}'
   exp: trash
   type: incr

diff --git a/parm/soca/berror/soca_parameters_diffusion_hz.yaml.j2 b/parm/soca/berror/soca_parameters_diffusion_hz.yaml.j2
@@ -27,11 +27,11 @@ background error:
             filename: ocn.cor_rh.incr.0001-01-01T00:00:00Z.nc
             variable name: ave_ssh
         write:
-          filename: hz_ocean.nc
+          filename: ./staticb/hz_ocean.nc
 
       - name: ice
         horizontal:
           as gaussian: true
           fixed value: 50000.0
         write:
-          filename: hz_ice.nc
+          filename: ./staticb/hz_ice.nc
diff --git a/parm/soca/berror/soca_parameters_diffusion_vt.yaml.j2 b/parm/soca/berror/soca_parameters_diffusion_vt.yaml.j2
@@ -29,4 +29,4 @@ background error:
             filename: vt_scales.nc
             variable name: vt
         write:
-          filename: vt_ocean.nc
+          filename: ./staticb/vt_ocean.nc
diff --git a/parm/soca/berror/soca_vtscales.yaml.j2 b/parm/soca/berror/soca_vtscales.yaml.j2
@@ -1,6 +1,6 @@
 gridspec_filename: soca_gridspec.nc
 restart_filename: ./INPUT/MOM.res.nc
-mld_filename: './diagb/ocn.bkgerr_stddev.incr.{{ MARINE_WINDOW_END | to_isotime }}.nc'
+mld_filename: './staticb/ocn.bkgerr_stddev.incr.{{ MARINE_WINDOW_END | to_isotime }}.nc'
 output_filename: ./vt_scales.nc
 output_variable_vt: vt
 output_variable_hz: hz

diff --git a/parm/soca/fms/input.nml.j2 b/parm/soca/fms/input.nml.j2
@@ -0,0 +1,28 @@
+ &MOM_input_nml
+        output_directory = './',
+        input_filename = 'r'
+        restart_input_dir = 'INPUT/',
+        restart_output_dir = 'RESTART/',
+        parameter_filename = 'MOM_input' /
+
+ &diag_manager_nml
+ /
+
+ &ocean_solo_nml
+            months = 0
+            days   = 1
+            date_init = {{ date_init }},
+            hours = 0
+            minutes = 0
+            seconds = 0
+            calendar = 'NOLEAP' /
+
+ &fms_io_nml
+      max_files_w=100
+      checksum_required=.false.
+/
+
+ &fms_nml
+       clock_grain='MODULE'
+       domains_stack_size = {{ domain_stack_size }}
+       clock_flags='SYNC' /
diff --git a/parm/soca/marine-jcb-base.yaml b/parm/soca/marine-jcb-base.yaml
@@ -17,8 +17,8 @@ final_increment_file: marine_final_increment
 
 # Assimilation standard things (not prepended with model choice)
 # ----------------------------
-window_begin: '{{ATM_WINDOW_BEGIN}}'
-window_length: '{{ATM_WINDOW_LENGTH}}'
+window_begin: '{{MARINE_WINDOW_BEGIN}}'
+window_length: '{{MARINE_WINDOW_LENGTH}}'
 bound_to_include: begin
 minimizer: RPCG
 final_diagnostics_departures: oman
@@ -29,24 +29,24 @@ analysis_variables: [cicen, hicen, hsnon, socn, tocn, uocn, vocn, ssh]
 
 # Model things
 # ------------
-marine_window_begin: '{{ATM_WINDOW_BEGIN}}'
-marine_window_middle: '{{ATM_WINDOW_MIDDLE}}'
+marine_window_begin: '{{MARINE_WINDOW_BEGIN}}'
+marine_window_middle: '{{MARINE_WINDOW_MIDDLE}}'
 
 # Geometry
 marine_soca_files_path: .
 
-# Background
+# Initial conditions
 marine_background_path: ./INPUT/
-marine_background_time: '{{ATM_WINDOW_BEGIN}}'
+marine_background_time: '{{MARINE_WINDOW_BEGIN_ISO}}'
 
 # Pseudo model
 marine_forecast_timestep: PT3H
-marine_pseudo_model_states: !INC ${BKG_LIST}
+marine_pseudo_model_states: !INC 'bkg_list.yaml'
 
 # Background error model
 background_error_file: '{{berror_model}}'
 marine_number_ensemble_members: '{{nmem_ens}}'
-marine_stddev_time: '{{ATM_WINDOW_MIDDLE}}'
+marine_stddev_time: '{{MARINE_WINDOW_MIDDLE}}'
 
 # Observations
 observations: all_observations

diff --git a/parm/soca/obs/config/adt_rads_all.yaml b/parm/soca/obs/config/adt_rads_all.yaml
@@ -3,11 +3,11 @@ obs space:
   obsdatain:
     engine:
       type: H5File
-      obsfile: !ENV ${DATA}/obs/${OPREFIX}adt_rads_all.${PDY}${cyc}.nc4
+      obsfile: ${DATA}/obs/${OPREFIX}adt_rads_all.${PDY}${cyc}.nc4
   obsdataout:
     engine:
       type: H5File
-      obsfile: !ENV ${DATA}/diags/adt_rads_all.${PDY}${cyc}.nc4
+      obsfile: ${DATA}/diags/adt_rads_all.${PDY}${cyc}.nc4
   simulated variables: [absoluteDynamicTopography]
   io pool:
     max pool size: 1

diff --git a/parm/soca/obs/config/icec_amsr2_north.yaml b/parm/soca/obs/config/icec_amsr2_north.yaml
@@ -3,11 +3,11 @@ obs space:
   obsdatain:
     engine:
       type: H5File
-      obsfile: !ENV ${DATA}/obs/${OPREFIX}icec_amsr2_north.${PDY}${cyc}.nc4
+      obsfile: ${DATA}/obs/${OPREFIX}icec_amsr2_north.${PDY}${cyc}.nc4
   obsdataout:
     engine:
       type: H5File
-      obsfile: !ENV ${DATA}/diags/icec_amsr2_north.${PDY}${cyc}.nc4
+      obsfile: ${DATA}/diags/icec_amsr2_north.${PDY}${cyc}.nc4
   simulated variables: [seaIceFraction]
   io pool:
     max pool size: 1

diff --git a/parm/soca/obs/config/icec_amsr2_south.yaml b/parm/soca/obs/config/icec_amsr2_south.yaml
@@ -3,11 +3,11 @@ obs space:
   obsdatain:
     engine:
       type: H5File
-      obsfile: !ENV ${DATA}/obs/${OPREFIX}icec_amsr2_south.${PDY}${cyc}.nc4
+      obsfile: ${DATA}/obs/${OPREFIX}icec_amsr2_south.${PDY}${cyc}.nc4
   obsdataout:
     engine:
       type: H5File
-      obsfile: !ENV ${DATA}/diags/icec_amsr2_south.${PDY}${cyc}.nc4
+      obsfile: ${DATA}/diags/icec_amsr2_south.${PDY}${cyc}.nc4
   simulated variables: [seaIceFraction]
   io pool:
     max pool size: 1

diff --git a/parm/soca/obs/config/insitu_profile_argo.yaml b/parm/soca/obs/config/insitu_profile_argo.yaml
@@ -3,7 +3,7 @@ obs space:
   obsdatain:
     engine:
       type: H5File
-      obsfile: !ENV ${DATA}/obs/${OPREFIX}insitu_profile_argo.${PDY}${cyc}.nc4
+      obsfile: ${DATA}/obs/${OPREFIX}insitu_profile_argo.${PDY}${cyc}.nc4
     obsgrouping:
       group variables: [latitude, longitude, dateTime]
       sort variable: depth
@@ -12,7 +12,7 @@ obs space:
   obsdataout:
     engine:
       type: H5File
-      obsfile: !ENV ${DATA}/diags/insitu_profile_argo.${PDY}${cyc}.nc4
+      obsfile: ${DATA}/diags/insitu_profile_argo.${PDY}${cyc}.nc4
   simulated variables: [waterTemperature, salinity]
   observed variables: [waterTemperature, salinity]
 #  derived variables: [waterPressure]

diff --git a/parm/soca/obs/config/insitu_profile_bathy.yaml b/parm/soca/obs/config/insitu_profile_bathy.yaml
@@ -3,11 +3,11 @@ obs space:
   obsdatain:
     engine:
       type: H5File
-      obsfile: !ENV ${DATA}/obs/${OPREFIX}insitu_profile_bathy.${PDY}${cyc}.nc4
+      obsfile: ${DATA}/obs/${OPREFIX}insitu_profile_bathy.${PDY}${cyc}.nc4
   obsdataout:
     engine:
       type: H5File
-      obsfile: !ENV ${DATA}/diags/insitu_profile_bathy.${PDY}${cyc}.nc4
+      obsfile: ${DATA}/diags/insitu_profile_bathy.${PDY}${cyc}.nc4
   simulated variables: [waterTemperature]
   io pool:
     max pool size: 1

diff --git a/parm/soca/obs/config/insitu_profile_dbuoy.yaml b/parm/soca/obs/config/insitu_profile_dbuoy.yaml
@@ -3,11 +3,11 @@ obs space:
   obsdatain:
     engine:
       type: H5File
-      obsfile: !ENV ${DATA}/obs/${OPREFIX}insitu_profile_dbuoy.${PDY}${cyc}.nc4
+      obsfile: ${DATA}/obs/${OPREFIX}insitu_profile_dbuoy.${PDY}${cyc}.nc4
   obsdataout:
     engine:
       type: H5File
-      obsfile: !ENV ${DATA}/diags/insitu_profile_dbuoy.${PDY}${cyc}.nc4
+      obsfile: ${DATA}/diags/insitu_profile_dbuoy.${PDY}${cyc}.nc4
   simulated variables: [waterTemperature]
   observed variables: [waterTemperature]
   io pool:

diff --git a/parm/soca/obs/config/insitu_profile_dbuoyb.yaml b/parm/soca/obs/config/insitu_profile_dbuoyb.yaml
@@ -3,11 +3,11 @@ obs space:
   obsdatain:
     engine:
       type: H5File
-      obsfile: !ENV ${DATA}/obs/${OPREFIX}insitu_profile_dbuoyb.${PDY}${cyc}.nc4
+      obsfile: ${DATA}/obs/${OPREFIX}insitu_profile_dbuoyb.${PDY}${cyc}.nc4
   obsdataout:
     engine:
       type: H5File
-      obsfile: !ENV ${DATA}/diags/insitu_profile_dbuoyb.${PDY}${cyc}.nc4
+      obsfile: ${DATA}/diags/insitu_profile_dbuoyb.${PDY}${cyc}.nc4
   simulated variables: [waterTemperature]
   observed variables: [waterTemperature]
   io pool:

diff --git a/parm/soca/obs/config/insitu_profile_glider.yaml b/parm/soca/obs/config/insitu_profile_glider.yaml
@@ -3,11 +3,11 @@ obs space:
   obsdatain:
     engine:
       type: H5File
-      obsfile: !ENV ${DATA}/obs/${OPREFIX}insitu_profile_glider.${PDY}${cyc}.nc4
+      obsfile: ${DATA}/obs/${OPREFIX}insitu_profile_glider.${PDY}${cyc}.nc4
   obsdataout:
     engine:
       type: H5File
-      obsfile: !ENV ${DATA}/diags/insitu_profile_glider.${PDY}${cyc}.nc4
+      obsfile: ${DATA}/diags/insitu_profile_glider.${PDY}${cyc}.nc4
   simulated variables: [waterTemperature]
   observed variables: [waterTemperature]
   io pool:

diff --git a/parm/soca/obs/config/insitu_profile_marinemammal.yaml b/parm/soca/obs/config/insitu_profile_marinemammal.yaml
@@ -3,11 +3,11 @@ obs space:
   obsdatain:
     engine:
       type: H5File
-      obsfile: !ENV ${DATA}/obs/${OPREFIX}insitu_profile_marinemammal.${PDY}${cyc}.nc4
+      obsfile: ${DATA}/obs/${OPREFIX}insitu_profile_marinemammal.${PDY}${cyc}.nc4
   obsdataout:
     engine:
       type: H5File
-      obsfile: !ENV ${DATA}/diags/insitu_profile_marinemammal.${PDY}${cyc}.nc4
+      obsfile: ${DATA}/diags/insitu_profile_marinemammal.${PDY}${cyc}.nc4
   simulated variables: [waterTemperature]
   observed variables: [waterTemperature]
   io pool:

diff --git a/parm/soca/obs/config/insitu_profile_mbuoy.yaml b/parm/soca/obs/config/insitu_profile_mbuoy.yaml
@@ -3,11 +3,11 @@ obs space:
   obsdatain:
     engine:
       type: H5File
-      obsfile: !ENV ${DATA}/obs/${OPREFIX}insitu_profile_mbuoy.${PDY}${cyc}.nc4
+      obsfile: ${DATA}/obs/${OPREFIX}insitu_profile_mbuoy.${PDY}${cyc}.nc4
   obsdataout:
     engine:
       type: H5File
-      obsfile: !ENV ${DATA}/diags/insitu_profile_mbuoy.${PDY}${cyc}.nc4
+      obsfile: ${DATA}/diags/insitu_profile_mbuoy.${PDY}${cyc}.nc4
   simulated variables: [waterTemperature]
   observed variables: [waterTemperature]
   io pool:

diff --git a/parm/soca/obs/config/insitu_profile_mbuoyb.yaml b/parm/soca/obs/config/insitu_profile_mbuoyb.yaml
@@ -3,11 +3,11 @@ obs space:
   obsdatain:
     engine:
       type: H5File
-      obsfile: !ENV ${DATA}/obs/${OPREFIX}insitu_profile_mbuoyb.${PDY}${cyc}.nc4
+      obsfile: ${DATA}/obs/${OPREFIX}insitu_profile_mbuoyb.${PDY}${cyc}.nc4
   obsdataout:
     engine:
       type: H5File
-      obsfile: !ENV ${DATA}/diags/insitu_profile_mbuoyb.${PDY}${cyc}.nc4
+      obsfile: ${DATA}/diags/insitu_profile_mbuoyb.${PDY}${cyc}.nc4
   simulated variables: [waterTemperature]
   observed variables: [waterTemperature]
   io pool:

diff --git a/parm/soca/obs/config/insitu_profile_tesac.yaml b/parm/soca/obs/config/insitu_profile_tesac.yaml
@@ -3,11 +3,11 @@ obs space:
   obsdatain:
     engine:
       type: H5File
-      obsfile: !ENV ${DATA}/obs/${OPREFIX}insitu_profile_tesac.${PDY}${cyc}.nc4
+      obsfile: ${DATA}/obs/${OPREFIX}insitu_profile_tesac.${PDY}${cyc}.nc4
   obsdataout:
     engine:
       type: H5File
-      obsfile: !ENV ${DATA}/diags/insitu_profile_tesac.${PDY}${cyc}.nc4
+      obsfile: ${DATA}/diags/insitu_profile_tesac.${PDY}${cyc}.nc4
   simulated variables: [waterTemperature]
   observed variables: [waterTemperature]
   io pool:

diff --git a/parm/soca/obs/config/insitu_profile_tesac_salinity.yaml b/parm/soca/obs/config/insitu_profile_tesac_salinity.yaml
@@ -3,11 +3,11 @@ obs space:
   obsdatain:
     engine:
       type: H5File
-      obsfile: !ENV ${DATA}/obs/${OPREFIX}insitu_profile_tesac.${PDY}${cyc}.nc4
+      obsfile: ${DATA}/obs/${OPREFIX}insitu_profile_tesac.${PDY}${cyc}.nc4
   obsdataout:
     engine:
       type: H5File
-      obsfile: !ENV ${DATA}/diags/insitu_profile_tesac_salinity.${PDY}${cyc}.nc4
+      obsfile: ${DATA}/diags/insitu_profile_tesac_salinity.${PDY}${cyc}.nc4
   simulated variables: [salinity]
   observed variables: [salinity]
   io pool:

diff --git a/parm/soca/obs/config/insitu_profile_xbtctd.yaml b/parm/soca/obs/config/insitu_profile_xbtctd.yaml
@@ -3,11 +3,11 @@ obs space:
   obsdatain:
     engine:
       type: H5File
-      obsfile: !ENV ${DATA}/obs/${OPREFIX}insitu_profile_xbtctd.${PDY}${cyc}.nc4
+      obsfile: ${DATA}/obs/${OPREFIX}insitu_profile_xbtctd.${PDY}${cyc}.nc4
   obsdataout:
     engine:
       type: H5File
-      obsfile: !ENV ${DATA}/diags/insitu_profile_xbtctd.${PDY}${cyc}.nc4
+      obsfile: ${DATA}/diags/insitu_profile_xbtctd.${PDY}${cyc}.nc4
   simulated variables: [waterTemperature]
   observed variables: [waterTemperature]
   io pool:

diff --git a/parm/soca/obs/config/insitu_surface_altkob.yaml b/parm/soca/obs/config/insitu_surface_altkob.yaml
@@ -3,11 +3,11 @@ obs space:
   obsdatain:
     engine:
       type: H5File
-      obsfile: !ENV ${DATA}/obs/${OPREFIX}insitu_surface_altkob.${PDY}${cyc}.nc4
+      obsfile: ${DATA}/obs/${OPREFIX}insitu_surface_altkob.${PDY}${cyc}.nc4
   obsdataout:
     engine:
       type: H5File
-      obsfile: !ENV ${DATA}/diags/insitu_surface_altkob.${PDY}${cyc}.nc4
+      obsfile: ${DATA}/diags/insitu_surface_altkob.${PDY}${cyc}.nc4
   simulated variables: [seaSurfaceTemperature]
   io pool:
     max pool size: 1

diff --git a/parm/soca/obs/config/insitu_surface_trkob.yaml b/parm/soca/obs/config/insitu_surface_trkob.yaml
@@ -3,11 +3,11 @@ obs space:
   obsdatain:
     engine:
       type: H5File
-      obsfile: !ENV ${DATA}/obs/${OPREFIX}insitu_surface_trkob.${PDY}${cyc}.nc4
+      obsfile: ${DATA}/obs/${OPREFIX}insitu_surface_trkob.${PDY}${cyc}.nc4
   obsdataout:
     engine:
       type: H5File
-      obsfile: !ENV ${DATA}/diags/insitu_surface_trkob.${PDY}${cyc}.nc4
+      obsfile: ${DATA}/diags/insitu_surface_trkob.${PDY}${cyc}.nc4
   simulated variables: [seaSurfaceTemperature]
   io pool:
     max pool size: 1