Merge pull request #4 from CoryMartin-NOAA/feature/diffusion_exe

Add steps to compute diffusion parameters

parm/config/gfs/config.aeroanl

@@ -20,6 +20,7 @@ export io_layout_y=@IO_LAYOUT_Y@
 
 export JEDIEXE="${EXECgfs}/gdas.x"
 export BMATEXE="${EXECgfs}/gdasapp_chem_diagb.x"
+export DIFFUSIONEXE="${EXECgfs}/gdas_fv3jedi_error_covariance_toolbox.x"
 
 if [[ "${DOIAU}" == "YES" ]]; then
   export aero_bkg_times="3,6,9"

parm/config/gfs/config.aeroanlgenb

@@ -10,8 +10,9 @@ source "${EXPDIR}/config.resources" aeroanlgenb
 
 export BMATYAML="${PARMgfs}/gdas/aero/berror/aero_diagb.yaml.j2"
 export DIFFUSIONYAML="${PARMgfs}/gdas/aero/berror/aero_diffusionparm.yaml.j2"
-export iterations=10
-export fixed value=1.0
+export aero_diffusion_iter=10
+export aero_diffusion_horiz_len=2500e3
+export aero_diffusion_fixed_val=1.0
 
 
 echo "END: config.aeroanlgenb"

parm/ufs/gocart/ExtData.other

@@ -17,12 +17,12 @@ DU_UTHRES         '1'  Y E           -           none none uthres      ExtData/n
 
 #====== Sulfate Sources =================================================
 # Anthropogenic (BF & FF) emissions -- allowed to input as two layers
-SU_ANTHROL1 NA  N Y %y4-%m2-%d2t12:00:00 none none SO2      ExtData/nexus/CEDS/v2019/monthly/%y4/CEDS_2019_monthly.%y4%m2.nc
-SU_ANTHROL2 NA  N Y %y4-%m2-%d2t12:00:00 none none SO2_elev ExtData/nexus/CEDS/v2019/monthly/%y4/CEDS_2019_monthly.%y4%m2.nc
+SU_ANTHROL1 NA  Y Y %y4-%m2-%d2t12:00:00 none none SO2      ExtData/nexus/CEDS/v2019/monthly/%y4/CEDS_2019_monthly.%y4%m2.nc
+SU_ANTHROL2 NA  Y Y %y4-%m2-%d2t12:00:00 none none SO2_elev ExtData/nexus/CEDS/v2019/monthly/%y4/CEDS_2019_monthly.%y4%m2.nc
 
 # Ship emissions
-SU_SHIPSO2 NA  N Y %y4-%m2-%d2t12:00:00 none none SO2_ship  ExtData/nexus/CEDS/v2019/monthly/%y4/CEDS_2019_monthly.%y4%m2.nc
-SU_SHIPSO4 NA  N Y %y4-%m2-%d2t12:00:00 none none SO4_ship  ExtData/nexus/CEDS/v2019/monthly/%y4/CEDS_2019_monthly.%y4%m2.nc
+SU_SHIPSO2 NA  Y Y %y4-%m2-%d2t12:00:00 none none SO2_ship  ExtData/nexus/CEDS/v2019/monthly/%y4/CEDS_2019_monthly.%y4%m2.nc
+SU_SHIPSO4 NA  Y Y %y4-%m2-%d2t12:00:00 none none SO4_ship  ExtData/nexus/CEDS/v2019/monthly/%y4/CEDS_2019_monthly.%y4%m2.nc
 
 # Aircraft fuel consumption
 SU_AIRCRAFT NA  Y Y %y4-%m2-%d2t12:00:00 none none none /dev/null
@@ -63,11 +63,11 @@ OC_MTPO     NA  Y Y %y4-%m2-%d2t12:00:00 none none mtpo     ExtData/nexus/MEGAN_
 OC_BIOFUEL NA  Y Y %y4-%m2-%d2t12:00:00 none none biofuel /dev/null
 
 # Anthropogenic (BF & FF) emissions -- allowed to input as two layers
-OC_ANTEOC1 NA  N Y %y4-%m2-%d2t12:00:00 none none OC       ExtData/nexus/CEDS/v2019/monthly/%y4/CEDS_2019_monthly.%y4%m2.nc
-OC_ANTEOC2 NA  N Y %y4-%m2-%d2t12:00:00 none none OC_elev  ExtData/nexus/CEDS/v2019/monthly/%y4/CEDS_2019_monthly.%y4%m2.nc
+OC_ANTEOC1 NA  Y Y %y4-%m2-%d2t12:00:00 none none OC       ExtData/nexus/CEDS/v2019/monthly/%y4/CEDS_2019_monthly.%y4%m2.nc
+OC_ANTEOC2 NA  Y Y %y4-%m2-%d2t12:00:00 none none OC_elev  ExtData/nexus/CEDS/v2019/monthly/%y4/CEDS_2019_monthly.%y4%m2.nc
 
 # EDGAR based ship emissions
-OC_SHIP    NA  N Y %y4-%m2-%d2t12:00:00 none none OC_ship  ExtData/nexus/CEDS/v2019/monthly/%y4/CEDS_2019_monthly.%y4%m2.nc
+OC_SHIP    NA  Y Y %y4-%m2-%d2t12:00:00 none none OC_ship  ExtData/nexus/CEDS/v2019/monthly/%y4/CEDS_2019_monthly.%y4%m2.nc
 
 # Aircraft fuel consumption
 OC_AIRCRAFT NA  N Y %y4-%m2-%d2t12:00:00 none none oc_aviation /dev/null
@@ -88,11 +88,11 @@ pSOA_ANTHRO_VOC NA Y Y %y4-%m2-%d2t12:00:00 none none biofuel /dev/null
 BC_BIOFUEL NA  Y Y %y4-%m2-%d2t12:00:00 none none biofuel /dev/null
 
 # Anthropogenic (BF & FF) emissions -- allowed to input as two layers
-BC_ANTEBC1 NA  N Y %y4-%m2-%d2t12:00:00 none none BC       ExtData/nexus/CEDS/v2019/monthly/%y4/CEDS_2019_monthly.%y4%m2.nc
-BC_ANTEBC2 NA  N Y %y4-%m2-%d2t12:00:00 none none BC_elev  ExtData/nexus/CEDS/v2019/monthly/%y4/CEDS_2019_monthly.%y4%m2.nc
+BC_ANTEBC1 NA  Y Y %y4-%m2-%d2t12:00:00 none none BC       ExtData/nexus/CEDS/v2019/monthly/%y4/CEDS_2019_monthly.%y4%m2.nc
+BC_ANTEBC2 NA  Y Y %y4-%m2-%d2t12:00:00 none none BC_elev  ExtData/nexus/CEDS/v2019/monthly/%y4/CEDS_2019_monthly.%y4%m2.nc
 
 # EDGAR based ship emissions
-BC_SHIP NA  N Y %y4-%m2-%d2t12:00:00 none none BC_ship     ExtData/nexus/CEDS/v2019/monthly/%y4/CEDS_2019_monthly.%y4%m2.nc
+BC_SHIP NA  Y Y %y4-%m2-%d2t12:00:00 none none BC_ship     ExtData/nexus/CEDS/v2019/monthly/%y4/CEDS_2019_monthly.%y4%m2.nc
 
 # Aircraft fuel consumption
 BC_AIRCRAFT NA  N Y %y4-%m2-%d2t12:00:00 none none bc_aviation /dev/null

scripts/exglobal_aero_analysis_generate_bmatrix.py

@@ -18,8 +18,9 @@
     # Take configuration from environment and cast it as python dictionary
     config = cast_strdict_as_dtypedict(os.environ)
 
-    # Instantiate the aerosol variance tasks
+    # Instantiate the aerosol variance and diffusion correlation tasks
     AeroB = AerosolBMatrix(config)
     AeroB.initialize()
     AeroB.computeVariance()
+    AeroB.computeDiffusion()
     AeroB.finalize()

sorc/link_workflow.sh

@@ -359,6 +359,7 @@ if [[ -d "${HOMEgfs}/sorc/gdas.cd/build" ]]; then
   declare -a JEDI_EXE=("gdas.x" \
                        "gdas_soca_gridgen.x" \
                        "gdas_soca_error_covariance_toolbox.x" \
+                       "gdas_fv3jedi_error_covariance_toolbox.x" \
                        "gdas_soca_setcorscales.x" \
                        "fv3jedi_plot_field.x" \
                        "gdasapp_chem_diagb.x" \

ush/python/pygfs/task/aero_analysis.py

@@ -86,6 +86,8 @@ def initialize(self: Analysis) -> None:
         # copy BUMP files, otherwise it will assume ID matrix
         if self.task_config.get('STATICB_TYPE', 'identity') in ['bump']:
             FileHandler(self.get_berror_dict(self.task_config)).sync()
+        if self.task_config.get('STATICB_TYPE', 'identity') in ['diffusion']:
+            FileHandler(self.get_berror_dict(self.task_config)).sync()
 
         # stage backgrounds
         FileHandler(self.get_bkg_dict(AttrDict(self.task_config, **self.task_config))).sync()
@@ -286,7 +288,6 @@ def get_berror_dict(self, config: Dict[str, Any]) -> Dict[str, List[str]]:
             a dictionary containing the list of background error files to copy for FileHandler
         """
         # aerosol static-B needs nicas, cor_rh, cor_rv and stddev files.
-        b_dir = config.BERROR_DATA_DIR
         b_datestr = to_fv3time(config.BERROR_DATE)
         analysis_dir = config.COM_CHEM_ANALYSIS
         cycle_datestr = to_fv3time(config.current_cycle)
@@ -305,17 +306,16 @@ def get_berror_dict(self, config: Dict[str, Any]) -> Dict[str, List[str]]:
                     os.path.join(analysis_dir, tracer), os.path.join(config.DATA, 'berror', tracer)
                 ])
 
-        # the remaining B matrix files are fixed and come from a fix directory
-        radius = 'cor_aero_universe_radius'
+        # the diffusion correlation files are computed every cycle and are available in COM
+        diff_hz = 'diffusion_hz.nc'
+        diff_vt = 'diffusion_vt.nc'
         berror_list.append([
-            os.path.join(b_dir, radius), os.path.join(config.DATA, 'berror', radius)
+            os.path.join(config.COM_CHEM_ANALYSIS, diff_hz), os.path.join(config.DATA, 'berror', diff_hz)
         ])
-        nproc = config.ntiles * config.layout_x * config.layout_y
-        for nn in range(1, nproc + 1):
-            berror_list.append([
-                os.path.join(b_dir, f'nicas_aero_nicas_local_{nproc:06}-{nn:06}.nc'),
-                os.path.join(config.DATA, 'berror', f'nicas_aero_nicas_local_{nproc:06}-{nn:06}.nc')
-            ])
+        berror_list.append([
+            os.path.join(config.COM_CHEM_ANALYSIS, diff_vt), os.path.join(config.DATA, 'berror', diff_vt)
+        ])
+
         berror_dict = {
             'mkdir': [os.path.join(config.DATA, 'berror')],
             'copy': berror_list,

ush/python/pygfs/task/aero_bmatrix.py

@@ -61,20 +61,26 @@ def initialize(self: BMatrix) -> None:
         FileHandler(self.get_bkg_dict(AttrDict(self.task_config, **self.task_config))).sync()
 
         # generate diagb YAML file
-        logger.debug(f"Generate bmat YAML file: {self.task_config.bmat_yaml}")
+        logger.info(f"Generate bmat YAML file: {self.task_config.bmat_yaml}")
         save_as_yaml(self.task_config.bmat_config, self.task_config.bmat_yaml)
         logger.info(f"Wrote bmat YAML to: {self.task_config.bmat_yaml}")
 
         # generate diffusion parameters YAML file
-        logger.debug(f"Generate diffusion YAML file: {self.task_config.diffusion_yaml}")
+        logger.info(f"Generate diffusion YAML file: {self.task_config.diffusion_yaml}")
         save_as_yaml(self.task_config.diffusion_config, self.task_config.diffusion_yaml)
         logger.info(f"Wrote diffusion YAML to: {self.task_config.diffusion_yaml}")
 
         # create output directory
         FileHandler({'mkdir': [os.path.join(self.task_config['DATA'], 'stddev')]}).sync()
 
+        # create diffusion output directory
+        FileHandler({'mkdir': [os.path.join(self.task_config['DATA'], 'diffusion')]}).sync()
+
         # link executable to run directory
+        logger.info(f'before link_bmatexe')
         self.link_bmatexe()
+        logger.info(f'before link_diffusion_exe')
+        self.link_diffusion_exe()
 
     @logit(logger)
     def computeVariance(self) -> None:
@@ -96,6 +102,26 @@ def computeVariance(self) -> None:
 
         pass
 
+    @logit(logger)
+    def computeDiffusion(self) -> None:
+
+        chdir(self.task_config.DATA)
+
+        exec_cmd_diffusion = Executable(self.task_config.APRUN_AEROGENB)
+        exec_name_diffusion = os.path.join(self.task_config.DATA, 'gdas_fv3jedi_error_covariance_toolbox.x')
+        exec_cmd_diffusion.add_default_arg(exec_name_diffusion)
+        exec_cmd_diffusion.add_default_arg(self.task_config.diffusion_yaml)
+
+        try:
+            logger.debug(f"Executing {exec_cmd_diffusion}")
+            exec_cmd_diffusion()
+        except OSError:
+            raise OSError(f"Failed to execute {exec_cmd_diffusion}")
+        except Exception:
+            raise WorkflowException(f"An error occured during execution of {exec_cmd_diffusion}")
+
+        pass
+
     @logit(logger)
     def finalize(self) -> None:
         super().finalize()
@@ -106,8 +132,7 @@ def finalize(self) -> None:
         dest_diffusion = os.path.join(self.task_config.COM_CHEM_ANALYSIS, f"{self.task_config['CDUMP']}.t{self.runtime_config['cyc']:02d}z.chem_diffusion.yaml")
         yaml_copy = {
             'mkdir': [self.task_config.COM_CHEM_ANALYSIS],
-            'copy': [[src, dest]],
-            'copy': [[src_diffusion, dest_diffusion]]
+            'copy': [[src, dest], [src_diffusion, dest_diffusion]]
         }
         FileHandler(yaml_copy).sync()
 
@@ -129,6 +154,16 @@ def finalize(self) -> None:
 
         FileHandler({'copy': stddevlist}).sync()
 
+        # Diffusion files
+        diff_hz = 'diffusion_hz.nc'
+        diff_vt = 'diffusion_vt.nc'
+        src_hz = os.path.join(self.task_config.DATA, 'diffusion', diff_hz)
+        dest_hz = os.path.join(self.task_config.COM_CHEM_ANALYSIS, diff_hz)
+        src_vt = os.path.join(self.task_config.DATA, 'diffusion', diff_vt)
+        dest_vt = os.path.join(self.task_config.COM_CHEM_ANALYSIS, diff_vt)
+        difflist = [[src_hz, dest_hz], [src_vt, dest_vt]]
+        FileHandler({'copy': difflist}).sync()
+
     @logit(logger)
     def link_bmatexe(self) -> None:
         """
@@ -155,6 +190,34 @@ def link_bmatexe(self) -> None:
 
         return
 
+    @logit(logger)
+    def link_diffusion_exe(self) -> None:
+        """
+
+        This method links a JEDI (fv3jedi_error_covariance_toolbox.x)
+        executable to the run directory
+
+        Parameters
+        ----------
+        Task: GDAS task
+
+        Returns
+        ----------
+        None
+        """
+
+        exe_src_diffusion = self.task_config.DIFFUSIONEXE
+
+        # TODO: linking is not permitted per EE2.  Needs work in JEDI to be able to copy the exec.
+        logger.info(f"Link executable {exe_src_diffusion} to DATA/")
+        logger.warn("Linking is not permitted per EE2.")
+        exe_dest_diffusion = os.path.join(self.task_config.DATA, os.path.basename(exe_src_diffusion))
+        if os.path.exists(exe_dest_diffusion):
+            rm_p(exe_dest_diffusion)
+        os.symlink(exe_src_diffusion, exe_dest_diffusion)
+
+        return
+
     @logit(logger)
     def get_bkg_dict(self, task_config: Dict[str, Any]) -> Dict[str, List[str]]:
         """Compile a dictionary of model background files to copy

workflow/applications/gfs_cycled.py

@@ -152,9 +152,6 @@ def get_task_names(self):
 
         gdas_gfs_common_tasks_before_fcst += ['sfcanl', 'analcalc']
 
-        if self.do_aero:
-            gdas_gfs_common_tasks_before_fcst += ['aeroanlgenb', 'aeroanlinit', 'aeroanlvar', 'aeroanlfinal']
-
         if self.do_jedisnowda:
             gdas_gfs_common_tasks_before_fcst += ['prepsnowobs', 'snowanl']
 
@@ -182,7 +179,7 @@ def get_task_names(self):
             gdas_tasks += wave_prep_tasks
 
         if self.do_aero and 'gdas' in self.aero_anl_cdumps:
-            gdas_tasks += ['aeroanlinit', 'aeroanlvar', 'aeroanlfinal']
+            gdas_tasks += ['aeroanlgenb', 'aeroanlinit', 'aeroanlvar', 'aeroanlfinal']
             if self.do_prep_obs_aero:
                 gdas_tasks += ['prepobsaero']
 
@@ -221,7 +218,7 @@ def get_task_names(self):
             gfs_tasks += wave_prep_tasks
 
         if self.do_aero and 'gfs' in self.aero_anl_cdumps:
-            gfs_tasks += ['aeroanlinit', 'aeroanlvar', 'aeroanlfinal']
+            gfs_tasks += ['aeroanlgenb', 'aeroanlinit', 'aeroanlvar', 'aeroanlfinal']
             if self.do_prep_obs_aero:
                 gfs_tasks += ['prepobsaero']