Create JEDI class (NOAA-EMC#2805)

This PR creates a PyGFS class called JEDI, which is to be instantiated
everytime a JEDI application is run. The AtmAnalysis and AtmEnsAnalysis
classes are no longer children of the Analysis class, but rather direct
children of the Task class. They each have a JEDI object as an
attribute, which is used to run either the variational/ensemble DA JEDI
applications or the FV3 increment converter JEDI application, depending
on which job they are created for (e.g. atmanlvar vs. atmanlfv3inc). The
intention is that a later PR will apply this framework to all analysis
task, and the PyGFS Analysis class will be removed.

parm/archive/enkf.yaml.j2

@@ -54,12 +54,14 @@ enkf:
                            "radstat.ensmean"] %}
         {% else %}
         {% if lobsdiag_forenkf %}
-        {% set da_files = ["atmens_observer.yaml",
-                           "atmens_solver.yaml",
+        {% set da_files = ["atmensanlobs.yaml",
+                           "atmensanlsol.yaml",
+                           "atmensanlfv3inc.yaml",
                            "atminc.ensmean.nc",
                            "atmensstat"] %}
         {% else %}
-        {% set da_files = ["atmens.yaml",
+        {% set da_files = ["atmensanlletkf.yaml",
+                           "atmensanlfv3inc.yaml",
                            "atminc.ensmean.nc",
                            "atmensstat"] %}
         {% endif %}

parm/archive/gdas.yaml.j2

@@ -58,7 +58,8 @@ gdas:
 
         # Analysis state
             {% if DO_JEDIATMVAR %}
-        - "{{ COMIN_ATMOS_ANALYSIS | relpath(ROTDIR) }}/{{ head }}atmvar.yaml"
+        - "{{ COMIN_ATMOS_ANALYSIS | relpath(ROTDIR) }}/{{ head }}atmanlvar.yaml"
+        - "{{ COMIN_ATMOS_ANALYSIS | relpath(ROTDIR) }}/{{ head }}atmanlfv3inc.yaml"
         - "{{ COMIN_ATMOS_ANALYSIS | relpath(ROTDIR) }}/{{ head }}atmstat"
             {% else %}
         - "{{ COMIN_ATMOS_ANALYSIS | relpath(ROTDIR) }}/{{ head }}gsistat"

parm/archive/gfsa.yaml.j2

@@ -32,7 +32,8 @@ gfsa:
 
         # State data
         {% if DO_JEDIATMVAR %}
-        - "{{ COMIN_ATMOS_ANALYSIS | relpath(ROTDIR) }}/{{ head }}atmvar.yaml"
+        - "{{ COMIN_ATMOS_ANALYSIS | relpath(ROTDIR) }}/{{ head }}atmanlvar.yaml"
+        - "{{ COMIN_ATMOS_ANALYSIS | relpath(ROTDIR) }}/{{ head }}atmanlfv3inc.yaml"
         - "{{ COMIN_ATMOS_ANALYSIS | relpath(ROTDIR) }}/{{ head }}atmstat"
         {% else %}
         - "{{ COMIN_ATMOS_ANALYSIS | relpath(ROTDIR) }}/{{ head }}gsistat"

parm/config/gfs/config.atmensanl

@@ -6,7 +6,11 @@
 echo "BEGIN: config.atmensanl"
 
 export JCB_BASE_YAML="${PARMgfs}/gdas/atm/jcb-base.yaml.j2"
-export JCB_ALGO_YAML=@JCB_ALGO_YAML@
+if [[ ${lobsdiag_forenkf} = ".false." ]] ; then
+    export JCB_ALGO_YAML=@JCB_ALGO_YAML_LETKF@
+else
+    export JCB_ALGO_YAML=@JCB_ALGO_YAML_OBS@
+fi    
 
 export INTERP_METHOD='barycentric'
 

parm/config/gfs/yaml/defaults.yaml

@@ -31,7 +31,8 @@ atmanl:
   IO_LAYOUT_Y: 1
 
 atmensanl:
-  JCB_ALGO_YAML: "${PARMgfs}/gdas/atm/jcb-prototype_lgetkf.yaml.j2"
+  JCB_ALGO_YAML_LETKF: "${PARMgfs}/gdas/atm/jcb-prototype_lgetkf.yaml.j2"
+  JCB_ALGO_YAML_OBS: "${PARMgfs}/gdas/atm/jcb-prototype_lgetkf_observer.yaml.j2"
   LAYOUT_X_ATMENSANL: 8
   LAYOUT_Y_ATMENSANL: 8
   IO_LAYOUT_X: 1

scripts/exglobal_atm_analysis_finalize.py

@@ -21,4 +21,6 @@
 
     # Instantiate the atm analysis task
     AtmAnl = AtmAnalysis(config)
+
+    # Finalize JEDI variational analysis
     AtmAnl.finalize()

scripts/exglobal_atm_analysis_fv3_increment.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
 # exglobal_atm_analysis_fv3_increment.py
 # This script creates an AtmAnalysis object
-# and runs the init_fv3_increment and fv3_increment methods
+# and runs the initialize_fv3inc and execute methods
 # which convert the JEDI increment into an FV3 increment
 import os
 
@@ -17,7 +17,9 @@
     # Take configuration from environment and cast it as python dictionary
     config = cast_strdict_as_dtypedict(os.environ)
 
-    # Instantiate the atm analysis task
-    AtmAnl = AtmAnalysis(config)
-    AtmAnl.init_fv3_increment()
-    AtmAnl.fv3_increment()
+    # Instantiate the atm analysis object
+    AtmAnl = AtmAnalysis(config, 'atmanlfv3inc')
+
+    # Initialize and execute FV3 increment converter
+    AtmAnl.initialize_jedi()
+    AtmAnl.execute(config.APRUN_ATMANLFV3INC)

scripts/exglobal_atm_analysis_initialize.py

@@ -20,5 +20,8 @@
     config = cast_strdict_as_dtypedict(os.environ)
 
     # Instantiate the atm analysis task
-    AtmAnl = AtmAnalysis(config)
-    AtmAnl.initialize()
+    AtmAnl = AtmAnalysis(config, 'atmanlvar')
+
+    # Initialize JEDI variational analysis
+    AtmAnl.initialize_jedi()
+    AtmAnl.initialize_analysis()

scripts/exglobal_atm_analysis_variational.py

@@ -18,5 +18,7 @@
     config = cast_strdict_as_dtypedict(os.environ)
 
     # Instantiate the atm analysis task
-    AtmAnl = AtmAnalysis(config)
-    AtmAnl.variational()
+    AtmAnl = AtmAnalysis(config, 'atmanlvar')
+
+    # Execute JEDI variational analysis
+    AtmAnl.execute(config.APRUN_ATMANLVAR, ['fv3jedi', 'variational'])

scripts/exglobal_atmens_analysis_finalize.py

@@ -21,4 +21,6 @@
 
     # Instantiate the atmens analysis task
     AtmEnsAnl = AtmEnsAnalysis(config)
+
+    # Finalize ensemble DA analysis
     AtmEnsAnl.finalize()

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 init_fv3_increment and fv3_increment methods
+# and runs the initialize_fv3inc and execute methods
 # which convert the JEDI increment into an FV3 increment
 import os
 
@@ -17,7 +17,9 @@
     # Take configuration from environment and cast it as python dictionary
     config = cast_strdict_as_dtypedict(os.environ)
 
-    # Instantiate the atmens analysis task
-    AtmEnsAnl = AtmEnsAnalysis(config)
-    AtmEnsAnl.init_fv3_increment()
-    AtmEnsAnl.fv3_increment()
+    # Instantiate the atmens analysis object
+    AtmEnsAnl = AtmEnsAnalysis(config, 'atmensanlfv3inc')
+
+    # Initialize and execute JEDI FV3 increment converter
+    AtmEnsAnl.initialize_jedi()
+    AtmEnsAnl.execute(config.APRUN_ATMENSANLFV3INC)

scripts/exglobal_atmens_analysis_initialize.py

@@ -20,5 +20,11 @@
     config = cast_strdict_as_dtypedict(os.environ)
 
     # Instantiate the atmens analysis task
-    AtmEnsAnl = AtmEnsAnalysis(config)
-    AtmEnsAnl.initialize()
+    if not config.lobsdiag_forenkf:
+        AtmEnsAnl = AtmEnsAnalysis(config, 'atmensanlletkf')
+    else:
+        AtmEnsAnl = AtmEnsAnalysis(config, 'atmensanlobs')
+
+    # Initialize JEDI ensemble DA analysis
+    AtmEnsAnl.initialize_jedi()
+    AtmEnsAnl.initialize_analysis()

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 letkf method
-# which executes the global atm local ensemble analysis
+# and runs the execute method which executes
+# the global atm local ensemble analysis
 import os
 
 from wxflow import Logger, cast_strdict_as_dtypedict
@@ -18,5 +18,7 @@
     config = cast_strdict_as_dtypedict(os.environ)
 
     # Instantiate the atmens analysis task
-    AtmEnsAnl = AtmEnsAnalysis(config)
-    AtmEnsAnl.letkf()
+    AtmEnsAnl = AtmEnsAnalysis(config, 'atmensanlletkf')
+
+    # Execute the JEDI ensemble DA analysis
+    AtmEnsAnl.execute(config.APRUN_ATMENSANLLETKF, ['fv3jedi', 'localensembleda'])

scripts/exglobal_atmens_analysis_obs.py

@@ -18,6 +18,7 @@
     config = cast_strdict_as_dtypedict(os.environ)
 
     # Instantiate the atmens analysis task
-    AtmEnsAnl = AtmEnsAnalysis(config)
-    AtmEnsAnl.init_observer()
-    AtmEnsAnl.observe()
+    AtmEnsAnl = AtmEnsAnalysis(config, 'atmensanlobs')
+
+    # Initialize and execute JEDI ensembler DA analysis in observer mode
+    AtmEnsAnl.execute(config.APRUN_ATMENSANLOBS, ['fv3jedi', 'localensembleda'])

scripts/exglobal_atmens_analysis_sol.py

@@ -18,6 +18,8 @@
     config = cast_strdict_as_dtypedict(os.environ)
 
     # Instantiate the atmens analysis task
-    AtmEnsAnl = AtmEnsAnalysis(config)
-    AtmEnsAnl.init_solver()
-    AtmEnsAnl.solve()
+    AtmEnsAnl = AtmEnsAnalysis(config, 'atmensanlsol')
+
+    # Initialize and execute JEDI ensemble DA analysis in solver mode
+    AtmEnsAnl.initialize_jedi()
+    AtmEnsAnl.execute(config.APRUN_ATMENSANLSOL, ['fv3jedi', 'localensembleda'])

ush/python/pygfs/jedi/__init__.py

@@ -0,0 +1 @@
+from .jedi import Jedi