Single Executable for main GDAS JEDI applications (NOAA-EMC#2565)

Changes that accompany GDAS PR (NOAA-EMC/GDASApp/pull/1075) that allows
building of a single gdas executable, which should be more compliant
with NCO requirements.

Addresses NOAA-EMC/GDASApp#1085

parm/config/gfs/config.aeroanl

@@ -18,7 +18,7 @@ export JEDI_FIX_YAML="${PARMgfs}/gdas/aero_jedi_fix.yaml.j2"
 export io_layout_x=@IO_LAYOUT_X@
 export io_layout_y=@IO_LAYOUT_Y@
 
-export JEDIEXE="${EXECgfs}/fv3jedi_var.x"
+export JEDIEXE="${EXECgfs}/gdas.x"
 
 if [[ "${DOIAU}" == "YES" ]]; then
   export aero_bkg_times="3,6,9"

parm/config/gfs/config.atmanl

@@ -28,6 +28,6 @@ export layout_y_atmanl=@LAYOUT_Y_ATMANL@
 export io_layout_x=@IO_LAYOUT_X@
 export io_layout_y=@IO_LAYOUT_Y@
 
-export JEDIEXE=${EXECgfs}/fv3jedi_var.x
+export JEDIEXE=${EXECgfs}/gdas.x
 
 echo "END: config.atmanl"

parm/config/gfs/config.atmensanl

@@ -18,6 +18,6 @@ export layout_y_atmensanl=@LAYOUT_Y_ATMENSANL@
 export io_layout_x=@IO_LAYOUT_X@
 export io_layout_y=@IO_LAYOUT_Y@
 
-export JEDIEXE=${EXECgfs}/fv3jedi_letkf.x
+export JEDIEXE=${EXECgfs}/gdas.x
 
 echo "END: config.atmensanl"

parm/config/gfs/config.snowanl

@@ -11,7 +11,7 @@ source "${EXPDIR}/config.resources" snowanl
 export OBS_LIST="${PARMgfs}/gdas/snow/obs/lists/gdas_snow.yaml.j2"
 
 # Name of the JEDI executable and its yaml template
-export JEDIEXE="${EXECgfs}/fv3jedi_letkf.x"
+export JEDIEXE="${EXECgfs}/gdas.x"
 export JEDIYAML="${PARMgfs}/gdas/snow/letkfoi/letkfoi.yaml.j2"
 
 # Ensemble member properties

sorc/link_workflow.sh

@@ -333,33 +333,16 @@ fi
 
 # GDASApp
 if [[ -d "${HOMEgfs}/sorc/gdas.cd/build" ]]; then
-  declare -a JEDI_EXE=("fv3jedi_addincrement.x" \
-                       "fv3jedi_diffstates.x" \
-                       "fv3jedi_ensvariance.x" \
-                       "fv3jedi_hofx.x" \
-                       "fv3jedi_var.x" \
-                       "fv3jedi_convertincrement.x" \
-                       "fv3jedi_dirac.x" \
-                       "fv3jedi_error_covariance_training.x" \
-                       "fv3jedi_letkf.x" \
-                       "fv3jedi_convertstate.x" \
-                       "fv3jedi_eda.x" \
-                       "fv3jedi_forecast.x" \
+  declare -a JEDI_EXE=("gdas.x" \
+                       "gdas_soca_gridgen.x" \
+                       "gdas_soca_error_covariance_toolbox.x" \
+                       "gdas_soca_setcorscales.x" \
                        "fv3jedi_plot_field.x" \
-                       "fv3jedi_data_checker.py" \
-                       "fv3jedi_enshofx.x" \
-                       "fv3jedi_hofx_nomodel.x" \
-                       "fv3jedi_testdata_downloader.py" \
                        "fv3jedi_fv3inc.x" \
                        "gdas_ens_handler.x" \
                        "gdas_incr_handler.x" \
                        "gdas_obsprovider2ioda.x" \
                        "gdas_socahybridweights.x" \
-                       "soca_convertincrement.x" \
-                       "soca_error_covariance_training.x" \
-                       "soca_setcorscales.x" \
-                       "soca_gridgen.x" \
-                       "soca_var.x" \
                        "bufr2ioda.x" \
                        "calcfIMS.exe" \
                        "apply_incr.exe" )

ush/python/pygfs/task/aero_analysis.py

@@ -109,8 +109,10 @@ def execute(self: Analysis) -> None:
         chdir(self.task_config.DATA)
 
         exec_cmd = Executable(self.task_config.APRUN_AEROANL)
-        exec_name = os.path.join(self.task_config.DATA, 'fv3jedi_var.x')
+        exec_name = os.path.join(self.task_config.DATA, 'gdas.x')
         exec_cmd.add_default_arg(exec_name)
+        exec_cmd.add_default_arg('fv3jedi')
+        exec_cmd.add_default_arg('variational')
         exec_cmd.add_default_arg(self.task_config.jedi_yaml)
 
         try:

ush/python/pygfs/task/analysis.py

@@ -292,46 +292,6 @@ def get_fv3ens_dict(config: Dict[str, Any]) -> Dict[str, Any]:
         }
         return ens_dict
 
-    @staticmethod
-    @logit(logger)
-    def execute_jediexe(workdir: Union[str, os.PathLike], aprun_cmd: str, jedi_exec: str, jedi_yaml: str) -> None:
-        """
-        Run a JEDI executable
-
-        Parameters
-        ----------
-        workdir : str | os.PathLike
-            Working directory where to run containing the necessary files and executable
-        aprun_cmd : str
-            Launcher command e.g. mpirun -np <ntasks> or srun, etc.
-        jedi_exec : str
-            Name of the JEDI executable e.g. fv3jedi_var.x
-        jedi_yaml : str | os.PathLike
-            Name of the yaml file to feed the JEDI executable e.g. fv3jedi_var.yaml
-
-        Raises
-        ------
-        OSError
-            Failure due to OS issues
-        WorkflowException
-            All other exceptions
-        """
-
-        os.chdir(workdir)
-
-        exec_cmd = Executable(aprun_cmd)
-        exec_cmd.add_default_arg([os.path.join(workdir, jedi_exec), jedi_yaml])
-
-        logger.info(f"Executing {exec_cmd}")
-        try:
-            exec_cmd()
-        except OSError:
-            logger.exception(f"FATAL ERROR: Failed to execute {exec_cmd}")
-            raise OSError(f"{exec_cmd}")
-        except Exception:
-            logger.exception(f"FATAL ERROR: Error occured during execution of {exec_cmd}")
-            raise WorkflowException(f"{exec_cmd}")
-
     @staticmethod
     @logit(logger)
     def tgz_diags(statfile: str, diagdir: str) -> None:

ush/python/pygfs/task/atm_analysis.py

@@ -118,8 +118,10 @@ def variational(self: Analysis) -> None:
         chdir(self.task_config.DATA)
 
         exec_cmd = Executable(self.task_config.APRUN_ATMANLVAR)
-        exec_name = os.path.join(self.task_config.DATA, 'fv3jedi_var.x')
+        exec_name = os.path.join(self.task_config.DATA, 'gdas.x')
         exec_cmd.add_default_arg(exec_name)
+        exec_cmd.add_default_arg('fv3jedi')
+        exec_cmd.add_default_arg('variational')
         exec_cmd.add_default_arg(self.task_config.jedi_yaml)
 
         try:
@@ -144,10 +146,17 @@ def init_fv3_increment(self: Analysis) -> None:
     @logit(logger)
     def fv3_increment(self: Analysis) -> None:
         # Run executable
-        self.execute_jediexe(self.runtime_config.DATA,
-                             self.task_config.APRUN_ATMANLFV3INC,
-                             self.task_config.jedi_exe,
-                             self.task_config.jedi_yaml)
+        exec_cmd = Executable(self.task_config.APRUN_ATMANLFV3INC)
+        exec_cmd.add_default_arg(self.task_config.jedi_exe)
+        exec_cmd.add_default_arg(self.task_config.jedi_yaml)
+
+        try:
+            logger.debug(f"Executing {exec_cmd}")
+            exec_cmd()
+        except OSError:
+            raise OSError(f"Failed to execute {exec_cmd}")
+        except Exception:
+            raise WorkflowException(f"An error occured during execution of {exec_cmd}")
 
     @logit(logger)
     def finalize(self: Analysis) -> None:

ush/python/pygfs/task/atmens_analysis.py

@@ -148,8 +148,10 @@ def execute(self: Analysis) -> None:
         chdir(self.task_config.DATA)
 
         exec_cmd = Executable(self.task_config.APRUN_ATMENSANL)
-        exec_name = os.path.join(self.task_config.DATA, 'fv3jedi_letkf.x')
+        exec_name = os.path.join(self.task_config.DATA, 'gdas.x')
         exec_cmd.add_default_arg(exec_name)
+        exec_cmd.add_default_arg('fv3jedi')
+        exec_cmd.add_default_arg('localensembleda')
         exec_cmd.add_default_arg(self.task_config.jedi_yaml)
 
         try:

ush/python/pygfs/task/snow_analysis.py

@@ -310,10 +310,20 @@ def execute(self) -> None:
                              AttrDict({key: localconf[key] for key in ['DATA', 'ntiles', 'current_cycle']}))
 
         logger.info("Running JEDI LETKF")
-        self.execute_jediexe(localconf.DATA,
-                             localconf.APRUN_SNOWANL,
-                             os.path.basename(localconf.JEDIEXE),
-                             localconf.jedi_yaml)
+        exec_cmd = Executable(localconf.APRUN_SNOWANL)
+        exec_name = os.path.join(localconf.DATA, 'gdas.x')
+        exec_cmd.add_default_arg(exec_name)
+        exec_cmd.add_default_arg('fv3jedi')
+        exec_cmd.add_default_arg('localensembleda')
+        exec_cmd.add_default_arg(localconf.jedi_yaml)
+
+        try:
+            logger.debug(f"Executing {exec_cmd}")
+            exec_cmd()
+        except OSError:
+            raise OSError(f"Failed to execute {exec_cmd}")
+        except Exception:
+            raise WorkflowException(f"An error occured during execution of {exec_cmd}")
 
         logger.info("Creating analysis from backgrounds and increments")
         self.add_increments(localconf)