JCB-based obs+bias staging, Jedi class updates, and marine B-matrix refactoring

parm/config/gfs/config.atmanl

@@ -6,7 +6,8 @@
 echo "BEGIN: config.atmanl"
 
 export JCB_BASE_YAML="${PARMgfs}/gdas/atm/jcb-base.yaml.j2"
-export JCB_ALGO_YAML=@JCB_ALGO_YAML@
+export JCB_ALGO_YAML_VAR=@JCB_ALGO_YAML_VAR@
+export JCB_ALGO_FV3INC="fv3jedi_fv3inc_variational"
 
 export STATICB_TYPE=@STATICB_TYPE@
 export LOCALIZATION_TYPE="bump"
@@ -33,6 +34,7 @@ export layout_y_atmanl=@LAYOUT_Y_ATMANL@
 export io_layout_x=@IO_LAYOUT_X@
 export io_layout_y=@IO_LAYOUT_Y@
 
-export JEDIEXE=${EXECgfs}/gdas.x
+export JEDIEXE_VAR="${EXECgfs}/gdas.x"
+export JEDIEXE_FV3INC="${EXECgfs}/fv3jedi_fv3inc.x"
 
 echo "END: config.atmanl"

parm/config/gfs/config.atmanlfv3inc

@@ -8,7 +8,4 @@ echo "BEGIN: config.atmanlfv3inc"
 # Get task specific resources
 . "${EXPDIR}/config.resources" atmanlfv3inc
 
-export JCB_ALGO=fv3jedi_fv3inc_variational
-export JEDIEXE=${EXECgfs}/fv3jedi_fv3inc.x
-
 echo "END: config.atmanlfv3inc"

parm/config/gfs/config.atmensanl

@@ -6,11 +6,11 @@
 echo "BEGIN: config.atmensanl"
 
 export JCB_BASE_YAML="${PARMgfs}/gdas/atm/jcb-base.yaml.j2"
-if [[ ${lobsdiag_forenkf} = ".false." ]] ; then
-    export JCB_ALGO_YAML=@JCB_ALGO_YAML_LETKF@
-else
-    export JCB_ALGO_YAML=@JCB_ALGO_YAML_OBS@
-fi    
+
+export JCB_ALGO_YAML_LETKF=@JCB_ALGO_YAML_LETKF@
+export JCB_ALGO_YAML_OBS=@JCB_ALGO_YAML_OBS@
+export JCB_ALGO_YAML_SOL=@JCB_ALGO_YAML_SOL@
+export JCB_ALGO_FV3INC="fv3jedi_fv3inc_lgetkf"
 
 export INTERP_METHOD='barycentric'
 
@@ -24,6 +24,7 @@ export layout_y_atmensanl=@LAYOUT_Y_ATMENSANL@
 export io_layout_x=@IO_LAYOUT_X@
 export io_layout_y=@IO_LAYOUT_Y@
 
-export JEDIEXE=${EXECgfs}/gdas.x
+export JEDIEXE_LETKF=${EXECgfs}/gdas.x
+export JEDIEXE_FV3INC=${EXECgfs}/fv3jedi_fv3inc.x
 
 echo "END: config.atmensanl"

parm/config/gfs/config.atmensanlfv3inc

@@ -8,7 +8,4 @@ echo "BEGIN: config.atmensanlfv3inc"
 # Get task specific resources
 . "${EXPDIR}/config.resources" atmensanlfv3inc
 
-export JCB_ALGO=fv3jedi_fv3inc_lgetkf
-export JEDIEXE=${EXECgfs}/fv3jedi_fv3inc.x
-
 echo "END: config.atmensanlfv3inc"

parm/config/gfs/config.atmensanlobs

@@ -8,6 +8,4 @@ echo "BEGIN: config.atmensanlobs"
 # Get task specific resources
 . "${EXPDIR}/config.resources" atmensanlobs
 
-export JCB_ALGO_YAML=@JCB_ALGO_YAML@
-
 echo "END: config.atmensanlobs"

parm/config/gfs/config.atmensanlsol

@@ -8,6 +8,4 @@ echo "BEGIN: config.atmensanlsol"
 # Get task specific resources
 . "${EXPDIR}/config.resources" atmensanlsol
 
-export JCB_ALGO_YAML=@JCB_ALGO_YAML@
-
 echo "END: config.atmensanlsol"

parm/config/gfs/config.marineanl

@@ -17,4 +17,23 @@ export MARINE_ENSDA_STAGE_BKG_YAML_TMPL="${PARMgfs}/gdas/soca/ensda/stage_ens_me
 export MARINE_DET_STAGE_BKG_YAML_TMPL="${PARMgfs}/gdas/soca/soca_det_bkg_stage.yaml.j2"
 export MARINE_JCB_GDAS_ALGO="${PARMgfs}/gdas/jcb-gdas/algorithm/marine"
 
+export JCB_BASE_YAML="${PARMgfs}/gdas/soca/marine-jcb-base.yaml"
+
+export JCB_ALGO_GRIDGEN="soca_gridgen"
+export JCB_ALGO_DIAGB="soca_diagb"
+export JCB_ALGO_SETCORSCALES="soca_setcorscales"
+export JCB_ALGO_PARAMETERS_DIFFUSION_HZ="soca_parameters_diffusion_hz"
+export JCB_ALGO_VTSCALES="soca_vtscales"
+export JCB_ALGO_PARAMETERS_DIFFUSION_VT="soca_parameters_diffusion_vt"
+export JCB_ALGO_ENSB="soca_ensb"
+export JCB_ALGO_ENSWEIGHTS="soca_ensweights"
+
+export JEDIEXE_GRIDGEN="${EXECgfs}/gdas_soca_gridgen.x"
+export JEDIEXE_DIAGB="${EXECgfs}/gdas_soca_diagb.x"
+export JEDIEXE_SETCORSCALES="${EXECgfs}/gdas_soca_setcorscales.x"
+export JEDIEXE_PARAMETERS_DIFFUSION_HZ="${EXECgfs}/gdas_soca_error_covariance_toolbox.x"
+export JEDIEXE_PARAMETERS_DIFFUSION_VT="${EXECgfs}/gdas_soca_error_covariance_toolbox.x"
+export JEDIEXE_ENSB="${EXECgfs}/gdas_ens_handler.x"
+export JEDIEXE_ENSWEIGHTS="${EXECgfs}/gdas_socahybridweights.x"
+
 echo "END: config.marineanl"

parm/config/gfs/config.marinebmat

@@ -8,12 +8,4 @@ echo "BEGIN: config.marinebmat"
 # Get task specific resources
 . "${EXPDIR}/config.resources" marinebmat
 
-export BERROR_DIAGB_YAML="${PARMgfs}/gdas/soca/berror/soca_diagb.yaml.j2"
-export BERROR_VTSCALES_YAML="${PARMgfs}/gdas/soca/berror/soca_vtscales.yaml.j2"
-export BERROR_DIFFV_YAML="${PARMgfs}/gdas/soca/berror/soca_parameters_diffusion_vt.yaml.j2"
-export BERROR_HZSCALES_YAML="${PARMgfs}/gdas/soca/berror/soca_setcorscales.yaml"
-export BERROR_DIFFH_YAML="${PARMgfs}/gdas/soca/berror/soca_parameters_diffusion_hz.yaml.j2"
-export BERROR_ENS_RECENTER_YAML="${PARMgfs}/gdas/soca/berror/soca_ensb.yaml.j2"
-export BERROR_HYB_WEIGHTS_YAML="${PARMgfs}/gdas/soca/berror/soca_ensweights.yaml.j2"
-
 echo "END: config.marinebmat"

parm/config/gfs/yaml/defaults.yaml

@@ -23,7 +23,7 @@ base:
   FHMAX_ENKF_GFS: 12
 
 atmanl:
-  JCB_ALGO_YAML: "${PARMgfs}/gdas/atm/jcb-prototype_3dvar.yaml.j2"
+  JCB_ALGO_YAML_VAR: "${PARMgfs}/gdas/atm/jcb-prototype_3dvar.yaml.j2"
   STATICB_TYPE: "gsibec"
   LAYOUT_X_ATMANL: 8
   LAYOUT_Y_ATMANL: 8
@@ -33,16 +33,11 @@ atmanl:
 atmensanl:
   JCB_ALGO_YAML_LETKF: "${PARMgfs}/gdas/atm/jcb-prototype_lgetkf.yaml.j2"
   JCB_ALGO_YAML_OBS: "${PARMgfs}/gdas/atm/jcb-prototype_lgetkf_observer.yaml.j2"
+  JCB_ALGO_YAML_SOL: "${PARMgfs}/gdas/atm/jcb-prototype_lgetkf_solver.yaml.j2"
   LAYOUT_X_ATMENSANL: 8
   LAYOUT_Y_ATMENSANL: 8
   IO_LAYOUT_X: 1
   IO_LAYOUT_Y: 1
-
-atmensanlobs:
-  JCB_ALGO_YAML: "${PARMgfs}/gdas/atm/jcb-prototype_lgetkf_observer.yaml.j2"
-
-atmensanlsol:
-  JCB_ALGO_YAML: "${PARMgfs}/gdas/atm/jcb-prototype_lgetkf_solver.yaml.j2"
 
 aeroanl:
   IO_LAYOUT_X: 1

scripts/exglobal_atm_analysis_fv3_increment.py

@@ -1,8 +1,8 @@
 #!/usr/bin/env python3
 # exglobal_atm_analysis_fv3_increment.py
 # This script creates an AtmAnalysis object
-# and runs the initialize_fv3inc and execute methods
-# which convert the JEDI increment into an FV3 increment
+# and runs the execute method of its Jedi
+# object attribute
 import os
 
 from wxflow import Logger, cast_strdict_as_dtypedict
@@ -18,8 +18,7 @@
     config = cast_strdict_as_dtypedict(os.environ)
 
     # Instantiate the atm analysis object
-    AtmAnl = AtmAnalysis(config, 'atmanlfv3inc')
+    AtmAnl = AtmAnalysis(config)
 
     # Initialize and execute FV3 increment converter
-    AtmAnl.initialize_jedi()
-    AtmAnl.execute(config.APRUN_ATMANLFV3INC)
+    AtmAnl.jedi['atmanlfv3inc'].execute(config.APRUN_ATMANLFV3INC)

scripts/exglobal_atm_analysis_initialize.py

@@ -2,8 +2,8 @@
 # exglobal_atm_analysis_initialize.py
 # This script creates an AtmAnalysis class
 # and runs the initialize method
-# which create and stage the runtime directory
-# and create the YAML configuration
+# which creates and stages the runtime directory
+# and creates the YAML configuration
 # for a global atm variational analysis
 import os
 
@@ -20,8 +20,7 @@
     config = cast_strdict_as_dtypedict(os.environ)
 
     # Instantiate the atm analysis task
-    AtmAnl = AtmAnalysis(config, 'atmanlvar')
+    AtmAnl = AtmAnalysis(config)
 
     # Initialize JEDI variational analysis
-    AtmAnl.initialize_jedi()
-    AtmAnl.initialize_analysis()
+    AtmAnl.initialize()

scripts/exglobal_atm_analysis_variational.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
 # exglobal_atm_analysis_variational.py
 # This script creates an AtmAnalysis object
-# and runs the execute method
+# and runs the execute method of its Jedi object attribute
 # which executes the global atm variational analysis
 import os
 
@@ -18,7 +18,7 @@
     config = cast_strdict_as_dtypedict(os.environ)
 
     # Instantiate the atm analysis task
-    AtmAnl = AtmAnalysis(config, 'atmanlvar')
+    AtmAnl = AtmAnalysis(config)
 
     # Execute JEDI variational analysis
-    AtmAnl.execute(config.APRUN_ATMANLVAR, ['fv3jedi', 'variational'])
+    AtmAnl.jedi['atmanlvar'].execute(config.APRUN_ATMANLVAR)

scripts/exglobal_atmens_analysis_fv3_increment.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
 # exglobal_atmens_analysis_fv3_increment.py
 # This script creates an AtmEnsAnalysis object
-# and runs the initialize_fv3inc and execute methods
+# and runs the execute method of its Jedi object attribute
 # which convert the JEDI increment into an FV3 increment
 import os
 
@@ -18,8 +18,7 @@
     config = cast_strdict_as_dtypedict(os.environ)
 
     # Instantiate the atmens analysis object
-    AtmEnsAnl = AtmEnsAnalysis(config, 'atmensanlfv3inc')
+    AtmEnsAnl = AtmEnsAnalysis(config)
 
     # Initialize and execute JEDI FV3 increment converter
-    AtmEnsAnl.initialize_jedi()
-    AtmEnsAnl.execute(config.APRUN_ATMENSANLFV3INC)
+    AtmEnsAnl.jedi['atmensanlfv3inc'].execute(config.APRUN_ATMENSANLFV3INC)

scripts/exglobal_atmens_analysis_initialize.py

@@ -2,8 +2,8 @@
 # exglobal_atmens_analysis_initialize.py
 # This script creates an AtmEnsAnalysis class
 # and runs the initialize method
-# which create and stage the runtime directory
-# and create the YAML configuration
+# which creates and stages the runtime directory
+# and creates the YAML configuration
 # for a global atm local ensemble analysis
 import os
 
@@ -20,11 +20,7 @@
     config = cast_strdict_as_dtypedict(os.environ)
 
     # Instantiate the atmens analysis task
-    if not config.lobsdiag_forenkf:
-        AtmEnsAnl = AtmEnsAnalysis(config, 'atmensanlletkf')
-    else:
-        AtmEnsAnl = AtmEnsAnalysis(config, 'atmensanlobs')
+    AtmEnsAnl = AtmEnsAnalysis(config)
 
     # Initialize JEDI ensemble DA analysis
-    AtmEnsAnl.initialize_jedi()
-    AtmEnsAnl.initialize_analysis()
+    AtmEnsAnl.initialize()

scripts/exglobal_atmens_analysis_letkf.py

@@ -1,8 +1,8 @@
 #!/usr/bin/env python3
 # exglobal_atmens_analysis_letkf.py
 # This script creates an AtmEnsAnalysis object
-# and runs the execute method which executes
-# the global atm local ensemble analysis
+# and runs the execute method of its Jedi object attribute
+# which executes the global atm local ensemble analysis
 import os
 
 from wxflow import Logger, cast_strdict_as_dtypedict
@@ -18,7 +18,12 @@
     config = cast_strdict_as_dtypedict(os.environ)
 
     # Instantiate the atmens analysis task
-    AtmEnsAnl = AtmEnsAnalysis(config, 'atmensanlletkf')
+    AtmEnsAnl = AtmEnsAnalysis(config)
+
+    # Initalize JEDI ensemble DA application
+    # Note: This is normally done in AtmEnsAnl.initialize(), but that method now
+    #       initializes the split observer-solver. This case is just for testing.
+    AtmEnsAnl.jedi['atmensanlletkf'].initialize(AtmEnsAnl.task_config)
 
     # Execute the JEDI ensemble DA analysis
-    AtmEnsAnl.execute(config.APRUN_ATMENSANLLETKF, ['fv3jedi', 'localensembleda'])
+    AtmEnsAnl.jedi['atmensanlletkf'].execute(config.APRUN_ATMENSANLLETKF)

scripts/exglobal_atmens_analysis_obs.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
 # exglobal_atmens_analysis_obs.py
 # This script creates an AtmEnsAnalysis object
-# and runs the execute method
+# and runs the execute method of its Jedi object attribute
 # which executes the global atm local ensemble analysis in observer mode
 import os
 
@@ -18,7 +18,7 @@
     config = cast_strdict_as_dtypedict(os.environ)
 
     # Instantiate the atmens analysis task
-    AtmEnsAnl = AtmEnsAnalysis(config, 'atmensanlobs')
+    AtmEnsAnl = AtmEnsAnalysis(config)
 
     # Initialize and execute JEDI ensembler DA analysis in observer mode
-    AtmEnsAnl.execute(config.APRUN_ATMENSANLOBS, ['fv3jedi', 'localensembleda'])
+    AtmEnsAnl.jedi['atmensanlobs'].execute(config.APRUN_ATMENSANLOBS)

scripts/exglobal_atmens_analysis_sol.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
 # exglobal_atmens_analysis_sol.py
 # This script creates an AtmEnsAnalysis object
-# and runs the execute method
+# and runs the execute method of its Jedi object attribute
 # which executes the global atm local ensemble analysis in solver mode
 import os
 
@@ -18,8 +18,7 @@
     config = cast_strdict_as_dtypedict(os.environ)
 
     # Instantiate the atmens analysis task
-    AtmEnsAnl = AtmEnsAnalysis(config, 'atmensanlsol')
+    AtmEnsAnl = AtmEnsAnalysis(config)
 
     # Initialize and execute JEDI ensemble DA analysis in solver mode
-    AtmEnsAnl.initialize_jedi()
-    AtmEnsAnl.execute(config.APRUN_ATMENSANLSOL, ['fv3jedi', 'localensembleda'])
+    AtmEnsAnl.jedi['atmensanlsol'].execute(config.APRUN_ATMENSANLSOL)

scripts/exglobal_marinebmat.py

@@ -20,5 +20,5 @@
     # Create an instance of the MarineBMat task
     marineBMat = MarineBMat(config)
     marineBMat.initialize()
-    marineBMat.execute()
+    marineBMat.execute(config.APRUN_MARINEBMAT)
     marineBMat.finalize()