Merge branch 'NOAA-EMC:develop' into feature/bugzilla_1227

.gitignore

@@ -106,6 +106,7 @@ parm/post/ice.csv
 parm/post/ocnicepost.nml.jinja2
 parm/ufs/noahmptable.tbl
 parm/ufs/model_configure.IN
+parm/ufs/model_configure_nest.IN
 parm/ufs/MOM_input_*.IN
 parm/ufs/MOM6_data_table.IN
 parm/ufs/ice_in.IN

ci/cases/pr/C96_atm3DVar.yaml

@@ -15,3 +15,6 @@ arguments:
   gfs_cyc: 1
   start: cold
   yaml: {{ HOMEgfs }}/ci/cases/yamls/gfs_defaults_ci.yaml
+
+skip_ci_on_hosts:
+  - wcoss2

ci/cases/pr/C96_atm3DVar_extended.yaml

@@ -0,0 +1,22 @@
+experiment:
+  system: gfs
+  mode: cycled
+
+arguments:
+  pslot: {{ 'pslot' | getenv }}
+  app: ATM
+  resdetatmos: 96
+  comroot: {{ 'RUNTESTS' | getenv }}/COMROOT
+  expdir: {{ 'RUNTESTS' | getenv }}/EXPDIR
+  icsdir: {{ 'ICSDIR_ROOT' | getenv }}/C96C48
+  idate: 2021122018
+  edate: 2021122118
+  nens: 0
+  gfs_cyc: 4
+  start: cold
+  yaml: {{ HOMEgfs }}/ci/cases/yamls/gfs_extended_ci.yaml
+
+skip_ci_on_hosts:
+  - hera
+  - orion
+  - hercules

ci/cases/yamls/gfs_extended_ci.yaml

@@ -0,0 +1,12 @@
+defaults:
+  !INC {{ HOMEgfs }}/parm/config/gfs/yaml/defaults.yaml
+
+base:
+  ACCOUNT: {{ 'SLURM_ACCOUNT' | getenv }}
+  DO_GOES: "YES"
+  DO_BUFRSND: "YES"
+  DO_GEMPAK: "YES"
+  DO_AWIPS: "NO"
+  DO_NPOESS: "YES"
+  DO_GENESIS_FSU: "NO"
+  FHMAX_GFS: 384

env/HERA.env

@@ -49,6 +49,10 @@ elif [[ "${step}" = "prepsnowobs" ]]; then
 
     export APRUN_CALCFIMS="${launcher} -n 1"
 
+elif [[ "${step}" = "prep_emissions" ]]; then
+
+    export APRUN="${launcher} -n 1"
+
 elif [[ "${step}" = "waveinit" ]] || [[ "${step}" = "waveprep" ]] || [[ "${step}" = "wavepostsbs" ]] || [[ "${step}" = "wavepostbndpnt" ]] || [[ "${step}" = "wavepostbndpntbll" ]] || [[ "${step}" = "wavepostpnt" ]]; then
 
     export CFP_MP="YES"

env/HERCULES.env

@@ -45,6 +45,10 @@ case ${step} in
 
     export APRUN_CALCFIMS="${launcher} -n 1"
  ;;
+ "prep_emissions")
+
+    export APRUN="${launcher} -n 1"
+ ;;
  "waveinit" | "waveprep" | "wavepostsbs" | "wavepostbndpnt" | "wavepostpnt" | "wavepostbndpntbll")
 
     export CFP_MP="YES"

env/JET.env

@@ -37,6 +37,10 @@ elif [[ "${step}" = "prepsnowobs" ]]; then
 
     export APRUN_CALCFIMS="${launcher} -n 1"
 
+elif [[ "${step}" = "prep_emissions" ]]; then
+
+    export APRUN="${launcher} -n 1"
+
 elif [[ "${step}" = "waveinit" ]] || [[ "${step}" = "waveprep" ]] || [[ "${step}" = "wavepostsbs" ]] || [[ "${step}" = "wavepostbndpnt" ]] || [[ "${step}" = "wavepostbndpntbll" ]] || [[ "${step}" = "wavepostpnt" ]]; then
 
     export CFP_MP="YES"

env/ORION.env

@@ -44,6 +44,10 @@ elif [[ "${step}" = "prepsnowobs" ]]; then
 
     export APRUN_CALCFIMS="${launcher} -n 1"
 
+elif [[ "${step}" = "prep_emissions" ]]; then
+
+    export APRUN="${launcher} -n 1"
+
 elif [[ "${step}" = "waveinit" ]] || [[ "${step}" = "waveprep" ]] || [[ "${step}" = "wavepostsbs" ]] || \
     [[ "${step}" = "wavepostbndpnt" ]] || [[ "${step}" = "wavepostpnt" ]] || [[ "${step}" == "wavepostbndpntbll" ]]; then
 

env/S4.env

@@ -37,6 +37,10 @@ elif [[ "${step}" = "prepsnowobs" ]]; then
 
     export APRUN_CALCFIMS="${launcher} -n 1"
 
+elif [[ "${step}" = "prep_emissions" ]]; then
+
+    export APRUN="${launcher} -n 1"
+
 elif [[ "${step}" = "waveinit" ]] || [[ "${step}" = "waveprep" ]] || [[ "${step}" = "wavepostsbs" ]] || [[ "${step}" = "wavepostbndpnt" ]] || [[ "${step}" = "wavepostbndpntbll" ]] || [[ "${step}" = "wavepostpnt" ]]; then
 
     export CFP_MP="YES"

env/WCOSS2.env

@@ -31,6 +31,10 @@ elif [[ "${step}" = "prepsnowobs" ]]; then
 
     export APRUN_CALCFIMS="${launcher} -n 1"
 
+elif [[ "${step}" = "prep_emissions" ]]; then
+
+    export APRUN="${launcher} -n 1"
+
 elif [[ "${step}" = "waveinit" ]] || [[ "${step}" = "waveprep" ]] || [[ "${step}" = "wavepostsbs" ]] || [[ "${step}" = "wavepostbndpnt" ]] || [[ "${step}" = "wavepostbndpntbll"  ]] || [[ "${step}" = "wavepostpnt" ]]; then
 
     export USE_CFP="YES"

gempak/ush/gfs_meta_opc_na_ver

@@ -33,8 +33,8 @@ fcsthr="f00"
 # seq won't give us any splitting problems, ignore warnings
 # shellcheck disable=SC2207,SC2312
 case ${cyc} in
-    00 | 12) IFS=$'\n' lookbacks=($(seq 6 6 84) $(seq 96 12 120)) ;;
-    06 | 18) IFS=$'\n' lookbacks=($(seq 6 6 84) $(seq 90 12 126)) ;;
+    00 | 12) lookbacks=($(IFS=$'\n' seq 6 6 84) $(IFS=$'\n' seq 96 12 120)) ;;
+    06 | 18) lookbacks=($(IFS=$'\n' seq 6 6 84) $(IFS=$'\n' seq 90 12 126)) ;;
     *)
         echo "FATAL ERROR: Invalid cycle ${cyc} passed to ${BASH_SOURCE[0]}"
         exit 100

gempak/ush/gfs_meta_opc_np_ver

@@ -33,8 +33,8 @@ fcsthr="f00"
 # seq won't give us any splitting problems, ignore warnings
 # shellcheck disable=SC2207,SC2312
 case ${cyc} in
-    00 | 12) IFS=$'\n' lookbacks=($(seq 6 6 84) $(seq 96 12 120)) ;;
-    06 | 18) IFS=$'\n' lookbacks=($(seq 6 6 84) $(seq 90 12 126)) ;;
+    00 | 12) lookbacks=($(IFS=$'\n' seq 6 6 84) $(IFS=$'\n' seq 96 12 120)) ;;
+    06 | 18) lookbacks=($(IFS=$'\n' seq 6 6 84) $(IFS=$'\n' seq 90 12 126)) ;;
     *)
         echo "FATAL ERROR: Invalid cycle ${cyc} passed to ${BASH_SOURCE[0]}"
         exit 100

gempak/ush/gfs_meta_ver.sh

@@ -32,7 +32,7 @@ MDL2="GFSHPC"
 #GENERATING THE METAFILES.
 # seq won't give us any splitting problems, ignore warnings
 # shellcheck disable=SC2207,SC2312
-IFS=$'\n' lookbacks=($(seq 6 6 180) $(seq 192 12 216))
+lookbacks=($(IFS=$'\n' seq 6 6 180) $(IFS=$'\n' seq 192 12 216))
 for lookback in "${lookbacks[@]}"; do
     init_time="$(date --utc +%Y%m%d%H -d "${PDY} ${cyc} - ${lookback} hours")"
     init_PDY=${init_time:0:8}

jobs/JGLOBAL_PREP_EMISSIONS

@@ -0,0 +1,35 @@
+#! /usr/bin/env bash
+
+source "${HOMEgfs}/ush/preamble.sh"
+source "${HOMEgfs}/ush/jjob_header.sh" -e "prep_emissions" -c "base prep_emissions"
+
+##############################################
+# Set variables used in the script
+##############################################
+# TODO: Set local variables used in this script e.g. GDATE may be needed for previous cycle
+
+##############################################
+# Begin JOB SPECIFIC work
+##############################################
+# Generate COM variables from templates
+# TODO: Add necessary COMIN, COMOUT variables for this job
+
+###############################################################
+# Run relevant script
+EXSCRIPT=${PREP_EMISSIONS_PY:-${SCRgfs}/exglobal_prep_emissions.py}
+${EXSCRIPT}
+status=$?
+(( status != 0 )) && ( echo "FATAL ERROR: Error executing ${EXSCRIPT}, ABORT!"; exit "${status}" )
+
+##############################################
+# End JOB SPECIFIC work
+##############################################
+
+##############################################
+# Final processing
+##############################################
+if [[ -e "${pgmout}" ]] ; then
+  cat "${pgmout}"
+fi
+
+exit 0

jobs/rocoto/prep_emissions.sh

@@ -0,0 +1,23 @@
+#! /usr/bin/env bash
+
+source "${HOMEgfs}/ush/preamble.sh"
+
+###############################################################
+# Source UFSDA workflow modules
+source "${HOMEgfs}/ush/load_fv3gfs_modules.sh"
+status=$?
+(( status !=  0 )) && exit "${status}"
+
+export job="prep_emissions"
+export jobid="${job}.$$"
+
+###############################################################
+# setup python path for workflow utilities and tasks
+PYTHONPATH="${PYTHONPATH:+${PYTHONPATH}:}${HOMEgfs}/ush/python"
+export PYTHONPATH
+
+###############################################################
+# Execute the JJOB
+"${HOMEgfs}/jobs/JGLOBAL_PREP_EMISSIONS"
+status=$?
+exit "${status}"

parm/config/gefs/config.base

@@ -47,9 +47,9 @@ export NOSCRUB="@NOSCRUB@"
 export BASE_GIT="@BASE_GIT@"
 
 # Toggle to turn on/off GFS downstream processing.
-export DO_BUFRSND="NO"     # BUFR sounding products
-export DO_GEMPAK="NO"      # GEMPAK products
-export DO_AWIPS="NO"       # AWIPS products
+export DO_BUFRSND="@DO_BUFRSND@"     # BUFR sounding products
+export DO_GEMPAK="@DO_GEMPAK@"       # GEMPAK products
+export DO_AWIPS="@DO_AWIPS@"         # AWIPS products
 
 # NO for retrospective parallel; YES for real-time parallel
 #  arch.sh uses REALTIME for MOS.  Need to set REALTIME=YES

parm/config/gefs/config.prep_emissions

@@ -0,0 +1,11 @@
+#! /usr/bin/env bash
+
+########## config.prep_emissions ##########
+# aerosol emissions preprocessing specific
+
+echo "BEGIN: config.prep_emissions"
+
+# Get task specific resources
+source "${EXPDIR}/config.resources" prep_emissions
+
+echo "END: config.prep_emissions"

parm/config/gefs/config.resources

@@ -69,6 +69,14 @@ case ${step} in
     export memory_waveinit="2GB"
     ;;
 
+  "prep_emissions")
+    export wtime_prep_emissions="00:10:00"
+    export npe_prep_emissions=1
+    export nth_prep_emissions=1
+    export npe_node_prep_emissions=$(( npe_node_max / nth_prep_emissions ))
+    export memory_prep_emissions="1GB"
+    ;;
+
   "fcst" | "efcs")
     export is_exclusive=True
 

parm/config/gefs/yaml/defaults.yaml

@@ -4,6 +4,9 @@ base:
   DO_JEDIOCNVAR: "NO"
   DO_JEDISNOWDA: "NO"
   DO_MERGENSST: "NO"
+  DO_BUFRSND: "NO"
+  DO_GEMPAK: "NO"
+  DO_AWIPS: "NO"
   KEEPDATA: "NO" 
   FHMAX_GFS: 120
   USE_OCN_PERTURB_FILES: "false"

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.base

@@ -65,18 +65,18 @@ export NOSCRUB="@NOSCRUB@"
 export BASE_GIT="@BASE_GIT@"
 
 # Toggle to turn on/off GFS downstream processing.
-export DO_GOES="@DO_GOES@" # GOES products
-export DO_BUFRSND="NO"     # BUFR sounding products
-export DO_GEMPAK="NO"      # GEMPAK products
-export DO_AWIPS="NO"       # AWIPS products
-export DO_NPOESS="NO"      # NPOESS products
-export DO_TRACKER="YES"    # Hurricane track verification
-export DO_GENESIS="YES"    # Cyclone genesis verification
-export DO_GENESIS_FSU="NO" # Cyclone genesis verification (FSU)
-export DO_VERFOZN="YES"    # Ozone data assimilation monitoring
-export DO_VERFRAD="YES"    # Radiance data assimilation monitoring
-export DO_VMINMON="YES"    # GSI minimization monitoring
-export DO_MOS="NO"         # GFS Model Output Statistics - Only supported on WCOSS2
+export DO_GOES="@DO_GOES@"               # GOES products
+export DO_BUFRSND="@DO_BUFRSND@"         # BUFR sounding products
+export DO_GEMPAK="@DO_GEMPAK@"           # GEMPAK products
+export DO_AWIPS="@DO_AWIPS@"             # AWIPS products
+export DO_NPOESS="@DO_NPOESS@"           # NPOESS products
+export DO_TRACKER="@DO_TRACKER@"         # Hurricane track verification
+export DO_GENESIS="@DO_GENESIS@"         # Cyclone genesis verification
+export DO_GENESIS_FSU="@DO_GENESIS_FSU@" # Cyclone genesis verification (FSU)
+export DO_VERFOZN="YES"                  # Ozone data assimilation monitoring
+export DO_VERFRAD="YES"                  # Radiance data assimilation monitoring
+export DO_VMINMON="YES"                  # GSI minimization monitoring
+export DO_MOS="NO"                       # GFS Model Output Statistics - Only supported on WCOSS2
 
 # NO for retrospective parallel; YES for real-time parallel
 #  arch.sh uses REALTIME for MOS.  Need to set REALTIME=YES

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

parm/config/gfs/yaml/defaults.yaml

@@ -6,6 +6,13 @@ base:
   DO_JEDISNOWDA: "NO"
   DO_MERGENSST: "NO"
   DO_GOES: "NO"
+  DO_BUFRSND: "NO"
+  DO_GEMPAK: "NO"
+  DO_AWIPS: "NO"
+  DO_NPOESS: "NO"
+  DO_TRACKER: "YES"
+  DO_GENESIS: "YES"
+  DO_GENESIS_FSU: "NO"
   FHMAX_GFS: 120
   DO_VRFY_OCEANDA: "NO"
   GSI_SOILANAL: "NO"

scripts/exgfs_atmos_grib2_special_npoess.sh

@@ -153,7 +153,8 @@ for (( fhr=SHOUR; fhr <= FHOUR; fhr = fhr + FHINC )); do
    # existence of the restart files
    ###############################
    export pgm="postcheck"
-   grib_file="${COM_ATMOS_MASTER}/${RUN}.t${cyc}z.goesmasterf${fhr3}.grb2"
+   # grib_file="${COM_ATMOS_MASTER}/${RUN}.t${cyc}z.goesmasterf${fhr3}.grb2"
+   grib_file="${COM_ATMOS_MASTER}/${RUN}.t${cyc}z.special.grb2f${fhr3}"
    if ! wait_for_file "${grib_file}" "${SLEEP_INT}" "${SLEEP_LOOP_MAX}"; then
       echo "FATAL ERROR: GOES master grib file ${grib_file} not available after max sleep time"
       export err=9

scripts/exglobal_prep_emissions.py

@@ -0,0 +1,25 @@
+#!/usr/bin/env python3
+# exglobal_prep_emissions.py
+# This script creates a emissions object
+# which perform the pre-processing for aerosol emissions
+import os
+
+from wxflow import Logger, cast_strdict_as_dtypedict
+from pygfs import AerosolEmissions
+
+
+# Initialize root logger
+logger = Logger(level=os.environ.get("LOGGING_LEVEL", "DEBUG"), colored_log=True)
+
+
+if __name__ == '__main__':
+
+    # Take configuration from environment and cast it as python dictionary
+    config = cast_strdict_as_dtypedict(os.environ)
+
+    # Instantiate the emissions pre-processing task
+    emissions = AerosolEmissions(config)
+    emissions.initialize()
+    emissions.configure()
+    emissions.execute(emissions.task_config.DATA, emissions.task_config.APRUN)
+    emissions.finalize()