Feature/gsibec (#170)

* Add gsibec as a staticb option for fv3jedi_var.x (#166)

* Add missing whitespace (python coding norm) (#166)

* Add cloud liquid water and ice to gsibec control vector (#166)

* add staticb_type to 3dvar_orion.yaml (#166)

* configure hera and orion 3dvar yaml to use gsibec, add identity staticb to stage.py (#166)

* Streamline coding in stage.py (#166)

* Clean up gsibec staticb yaml (#166)

Author: RussTreadon-NOAA

build.sh

@@ -60,7 +60,7 @@ case ${BUILD_TARGET} in
     module purge
     module use $dir_root/modulefiles
     module load GDAS/$BUILD_TARGET
-    CMAKE_OPTS+=" -DMPIEXEC_EXECUTABLE=$MPIEXEC_EXEC -DMPIEXEC_NUMPROC_FLAG=$MPIEXEC_NPROC"
+    CMAKE_OPTS+=" -DMPIEXEC_EXECUTABLE=$MPIEXEC_EXEC -DMPIEXEC_NUMPROC_FLAG=$MPIEXEC_NPROC -DBUILD_GSIBEC=ON"
     module list
     set -e
     ;;

parm/atm/berror/staticb_gsibec.yaml

@@ -0,0 +1,29 @@
+covariance model: SABER
+full inverse: true
+saber blocks:
+- saber block name: gsi covariance
+  saber central block: true
+  input variables: &control_vars [eastward_wind,northward_wind,air_temperature,surface_pressure,
+                           specific_humidity,cloud_liquid_ice,cloud_liquid_water,
+                           mole_fraction_of_ozone_in_air]
+  output variables: *control_vars
+  gsi akbk: &akbk $(fv3jedi_fix_dir)/akbk.nc4
+  gsi error covariance file: &gsiberr $(fv3jedi_staticb_dir)/gsi-coeffs-gfs-global.nc4
+# gsi error covariance file: &gsiberr $(fv3jedi_staticb_dir)/global_berror.f77
+  gsi berror namelist file: &gsibnml $(fv3jedi_staticb_dir)/gfs_gsi_global.nml
+  processor layout x direction: &layout_gsib_x 3
+  processor layout y direction: &layout_gsib_y 2
+  debugging mode: false
+- saber block name: gsi interpolation to model grid
+  input variables: *control_vars
+  output variables: *control_vars
+  gsi akbk: *akbk
+  gsi error covariance file: *gsiberr
+  gsi berror namelist file: *gsibnml
+  processor layout x direction: *layout_gsib_x
+  processor layout y direction: *layout_gsib_y
+  debugging mode: false
+linear variable change:
+  linear variable change name: Control2Analysis
+  input variables: *control_vars
+  output variables: &3dvars_anal [ua,va,t,ps,sphum,ice_wat,liq_wat,o3mr]

ush/examples/run_jedi_exe/3dvar_hera.yaml

@@ -2,7 +2,7 @@ working directory: /scratch2/NCEPDEV/stmp1/Cory.R.Martin/gdas_single_test_3dvar
 GDASApp home: /scratch1/NCEPDEV/da/Cory.R.Martin/GDASApp/work/GDASApp
 GDASApp mode: variational
 executable options:
-  berror_yaml: /scratch1/NCEPDEV/da/Cory.R.Martin/GDASApp/work/GDASApp/parm/atm/berror/staticb_bump.yaml
+  berror_yaml: /scratch1/NCEPDEV/da/Cory.R.Martin/GDASApp/work/GDASApp/parm/atm/berror/staticb_gsibec.yaml
   obs_yaml_dir: /scratch1/NCEPDEV/da/Cory.R.Martin/GDASApp/work/GDASApp/parm/atm/obs/config
   yaml_template: /scratch1/NCEPDEV/da/Cory.R.Martin/GDASApp/work/GDASApp/parm/atm/variational/3dvar_dripcg.yaml
   executable: /scratch1/NCEPDEV/da/Cory.R.Martin/GDASApp/work/GDASApp/build/bin/fv3jedi_var.x
@@ -15,7 +15,8 @@ executable options:
   valid_time: 2021-12-21T06:00:00Z
   dump: gdas
   case: C96
-  case_anl: C48
+  case_anl: C96
+  staticb_type: gsibec
   dohybvar: false
   levs: 128
   interp_method: barycentric

ush/examples/run_jedi_exe/3dvar_orion.yaml

@@ -2,7 +2,7 @@ working directory: /work2/noaa/stmp/cmartin/gdas_single_test_3dvar
 GDASApp home: /work2/noaa/da/cmartin/GDASApp/work/GDASApp
 GDASApp mode: variational
 executable options:
-  berror_yaml: /work2/noaa/da/cmartin/GDASApp/work/GDASApp/parm/atm/berror/staticb_bump.yaml
+  berror_yaml: /work2/noaa/da/cmartin/GDASApp/work/GDASApp/parm/atm/berror/staticb_gsibec.yaml
   obs_yaml_dir: /work2/noaa/da/cmartin/GDASApp/work/GDASApp/parm/atm/obs/config
   yaml_template: /work2/noaa/da/cmartin/GDASApp/work/GDASApp/parm/atm/variational/3dvar_dripcg.yaml
   executable: /work2/noaa/da/cmartin/GDASApp/work/GDASApp/build/bin/fv3jedi_var.x
@@ -15,7 +15,8 @@ executable options:
   valid_time: 2021-12-21T06:00:00Z
   dump: gdas
   case: C96
-  case_anl: C48
+  case_anl: C96
+  staticb_type: gsibec
   dohybvar: false
   levs: 128
   interp_method: barycentric

ush/run_jedi_exe.py

@@ -73,6 +73,7 @@ def run_jedi_exe(yamlconfig):
         single_exec = True
         var_config = {
             'BERROR_YAML': executable_subconfig.get('berror_yaml', './'),
+            'STATICB_TYPE': executable_subconfig.get('staticb_type', 'gsibec'),
             'OBS_YAML_DIR': executable_subconfig['obs_yaml_dir'],
             'OBS_LIST': executable_subconfig['obs_list'],
             'atm': executable_subconfig.get('atm', False),

ush/ufsda/stage.py

@@ -32,9 +32,15 @@ def gdas_fix(input_fix_dir, working_dir, config):
     else:
         case_anl = config['CASE_ANL']
     layers = int(config['LEVS'])-1
-    # link static B files
-    ufsda.disk_utils.symlink(os.path.join(input_fix_dir, 'bump', case_anl),
-                             config['fv3jedi_staticb_dir'])
+
+    # figure out staticb source
+    staticb_source = config.get('STATICB_TYPE', 'gsibec')
+
+    # link staticb
+    if staticb_source in ['bump', 'gsibec']:
+        ufsda.disk_utils.symlink(os.path.join(input_fix_dir, staticb_source, case_anl),
+                                 config['fv3jedi_staticb_dir'])
+
     # link akbk file
     ufsda.disk_utils.symlink(os.path.join(input_fix_dir, 'fv3jedi',
                                           'fv3files', f"akbk{layers}.nc4"),