Make necessary bugfixes to get aerosol cycling going (#1349)

Makes a number of bugfixes that were overlooked in #1106 that now allow for 3DVar aerosol DA cycling on Hera/Orion.

Also updates the GDASApp hash to the most recent commit in develop.

Externals.cfg

@@ -50,7 +50,7 @@ protocol = git
 required = False
 
 [GDASApp]
-hash = f7c23af
+hash = a00b5da
 local_path = sorc/gdas.cd
 repo_url = https://github.com/NOAA-EMC/GDASApp.git
 protocol = git

parm/parm_gdas/aeroanl_inc_vars.yaml

@@ -1 +1 @@
-['dust1', 'dust2', 'dust3', 'dust4', 'dust5', 'seas1', 'seas2', 'seas3', 'seas4', 'so4', 'oc1', 'oc2', 'bc1', 'bc2']
+incvars: ['dust1', 'dust2', 'dust3', 'dust4', 'dust5', 'seas1', 'seas2', 'seas3', 'seas4', 'so4', 'oc1', 'oc2', 'bc1', 'bc2']

sorc/checkout.sh

@@ -165,7 +165,7 @@ if [[ ${checkout_gsi} == "YES" ]]; then
 fi
 
 if [[ ${checkout_gdas} == "YES" ]]; then
-  checkout "gdas.cd" "https://github.com/NOAA-EMC/GDASApp.git" "f7c23af"; errs=$((errs + $?))
+  checkout "gdas.cd" "https://github.com/NOAA-EMC/GDASApp.git" "a00b5da"; errs=$((errs + $?))
 fi
 
 if [[ ${checkout_gsi} == "YES" || ${checkout_gdas} == "YES" ]]; then

ush/load_ufsda_modules.sh

@@ -53,6 +53,14 @@ elif [[ -d /scratch1 ]] ; then
   module load prod_util
 elif [[ -d /work ]] ; then
   # We are on MSU Orion
+  # prod_util stuff, find a better solution later...
+  #module use /apps/contrib/NCEP/hpc-stack/libs/hpc-stack/modulefiles/compiler/intel/2022.1.2/
+  #module load prod_util
+  export UTILROOT=/work2/noaa/da/python/opt/intel-2022.1.2/prod_util/1.2.2
+  export MDATE=/work2/noaa/da/python/opt/intel-2022.1.2/prod_util/1.2.2/bin/mdate
+  export NDATE=/work2/noaa/da/python/opt/intel-2022.1.2/prod_util/1.2.2/bin/ndate
+  export NHOUR=/work2/noaa/da/python/opt/intel-2022.1.2/prod_util/1.2.2/bin/nhour
+  export FSYNC=/work2/noaa/da/python/opt/intel-2022.1.2/prod_util/1.2.2/bin/fsync_file
   module load "${MODS}/orion"
   if [[ "${DEBUG_WORKFLOW:-NO}" == "YES" ]] ; then
      module list
@@ -62,9 +70,6 @@ elif [[ -d /work ]] ; then
   ncdump=$( which ncdump )
   NETCDF=$( echo "${ncdump}" | cut -d " " -f 3 )
   export NETCDF
-  # prod_util stuff, find a better solution later...
-  module use /apps/contrib/NCEP/hpc-stack/libs/hpc-stack/modulefiles/compiler/intel/2022.1.2/
-  module load prod_util
 elif [[ -d /glade ]] ; then
   # We are on NCAR Yellowstone
   echo WARNING: UFSDA NOT SUPPORTED ON THIS PLATFORM

ush/python/pygfs/task/aero_analysis.py

@@ -13,6 +13,7 @@
 from pygw.timetools import to_isotime, to_fv3time, to_timedelta
 from pygw.fsutils import rm_p
 from pygw.template import Template, TemplateConstants
+from pygw.timetools import to_fv3time
 from pygw.yaml_file import YAMLFile
 from pygw.logger import logit
 from pygfs.task.analysis import Analysis
@@ -84,8 +85,8 @@ def initialize(self: Analysis) -> None:
 
         # stage berror files
         # copy BUMP files, otherwise it will assume ID matrix
-        if self.task_config.get('STATICB_TYPE', 'bump_aero') in ['bump_aero']:
-            FileHandler(AerosolAnalysis.get_berror_dict(self.task_config)).sync()
+        if self.task_config.get('STATICB_TYPE', 'identity') in ['bump']:
+            FileHandler(self.get_berror_dict(self.task_config)).sync()
 
         # stage backgrounds
         FileHandler(self.get_bkg_dict(AttrDict(self.task_config, **self.task_config))).sync()
@@ -148,8 +149,8 @@ def finalize(self: Analysis) -> None:
         src = os.path.join(self.task_config['DATA'], f"{self.task_config['CDUMP']}.t{self.runtime_config['cyc']:02d}z.aerovar.yaml")
         dest = os.path.join(self.task_config['COMOUTaero'], f"{self.task_config['CDUMP']}.t{self.runtime_config['cyc']:02d}z.aerovar.yaml")
         yaml_copy = {
-            'mkdir': self.task_config['COMOUTaero'],
-            'copy': [src, dest]
+            'mkdir': [self.task_config['COMOUTaero']],
+            'copy': [[src, dest]]
         }
         FileHandler(yaml_copy).sync()
 
@@ -192,7 +193,7 @@ def _add_fms_cube_sphere_increments(self: Analysis) -> None:
         fms_bkg_file_template = os.path.join(self.task_config.comin_ges_atm, 'RESTART', f'{self.task_config.cdate_fv3}.fv_tracer.res.tileX.nc')
         # get list of increment vars
         incvars_list_path = os.path.join(self.task_config['HOMEgfs'], 'parm', 'parm_gdas', 'aeroanl_inc_vars.yaml')
-        incvars = YAMLFile(path=incvars_list_path)
+        incvars = YAMLFile(path=incvars_list_path)['incvars']
         super().add_fv3_increments(fms_inc_file_template, fms_bkg_file_template, incvars)
 
     @logit(logger)
@@ -254,10 +255,10 @@ def get_berror_dict(self, config: Dict[str, Any]) -> Dict[str, List[str]]:
         berror_dict: Dict
             a dictionary containing the list of background error files to copy for FileHandler
         """
-        super.get_berror_dict(config)
+        super().get_berror_dict(config)
         # aerosol static-B needs nicas, cor_rh, cor_rv and stddev files.
         b_dir = config['BERROR_DATA_DIR']
-        b_datestr = config['BERROR_DATE']
+        b_datestr = to_fv3time(config['BERROR_DATE'])
         berror_list = []
 
         for ftype in ['cor_rh', 'cor_rv', 'stddev']:

ush/python/pygfs/task/analysis.py

@@ -22,7 +22,8 @@ class Analysis(Task):
     """
 
     def __init__(self, config: Dict[str, Any]) -> None:
-        super().__init__(config, ntiles=6)
+        super().__init__(config)
+        self.config.ntiles = 6
 
     def initialize(self) -> None:
         super().initialize()
@@ -85,7 +86,7 @@ def add_fv3_increments(self, inc_file_tmpl: str, bkg_file_tmpl: str, incvars: Li
                     rstfile.variables[vname][:] = anl[:]
                     try:
                         rstfile.variables[vname].delncattr('checksum')  # remove the checksum so fv3 does not complain
-                    except AttributeError:
+                    except (AttributeError, RuntimeError):
                         pass  # checksum is missing, move on
 
     @logit(logger)

workflow/rocoto/workflow_tasks.py

@@ -463,8 +463,7 @@ def aeroanlinit(self):
         data = f'&ROTDIR;/gdas.@Y@m@d/@H/atmos/gdas.t@Hz.atmf009.nc'
         dep_dict = {'type': 'data', 'data': data, 'offset': '-06:00:00'}
         deps.append(rocoto.add_dependency(dep_dict))
-        data = f'{dmpdir}/{self.cdump}{dump_suffix}.@Y@m@d/@H/atmos/{self.cdump}.t@Hz.updated.status.tm00.bufr_d'
-        dep_dict = {'type': 'data', 'data': data}
+        dep_dict = {'type': 'task', 'name': f'{self.cdump}prep'}
         deps.append(rocoto.add_dependency(dep_dict))
         dependencies = rocoto.create_dependency(dep_condition='and', dep=deps)