Add the repair job for the reforecast

jobs/JGEFS_ATMOS_ACC

@@ -0,0 +1,28 @@
+#! /usr/bin/env bash
+#
+#
+#####################################################################
+source "${HOMEgfs}/ush/preamble.sh"
+source "${HOMEgfs}/ush/jjob_header.sh" -e "repair_replay" -c "base repair_replay"
+
+####################################
+# Specify Execution Areas
+####################################
+#
+# Construct COM variables from templates
+YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
+    COMIN_ATMOS_MASTER:COM_ATMOS_MASTER_TMPL
+    COMOUT_ATMOS_MASTER:COM_ATMOS_MASTER_TMPL
+
+export COMIN_03=${HOMEgfs}/anl
+
+########################################################
+# Execute the acc script.
+"${SCRgfs}/exgefs_atmos_repair_replay.sh"
+export err=$?; err_chk
+##############################
+# Remove the Temporary working directory
+##############################
+if [[ "${KEEPDATA}" != "YES" ]] ; then
+  rm -fr "${DATA}"
+fi

jobs/rocoto/repair_replay.sh

@@ -0,0 +1,22 @@
+#! /usr/bin/env bash
+
+source "${HOMEgfs}/ush/preamble.sh"
+
+###############################################################
+echo
+echo "=============== START TO SOURCE FV3GFS WORKFLOW MODULES ==============="
+. "${HOMEgfs}/ush/load_fv3gfs_modules.sh"
+status=$?
+[[ ${status} -ne 0 ]] && exit "${status}"
+
+export job="repair_replay"
+export jobid="${job}.$$"
+
+###############################################################
+# Execute the JJOB
+"${HOMEgfs}/jobs/JGEFS_ATMOS_ACC"
+status=$?
+[[ ${status} -ne 0 ]] && exit "${status}"
+
+
+exit 0

parm/config/gefs/config.base

@@ -133,6 +133,7 @@ export DO_OCN="NO"
 export DO_ICE="NO"
 export DO_AERO="NO"
 export DO_EXTRACTVARS="@DO_EXTRACTVARS@" # Option to process and extract a subset of products to save on disk
+export DO_REPAIR_REPLAY="@DO_REPAIR_REPLAY@" # Option to repair ave/acc/min/max variabes for f03 and f06 when one uses reply initial condition
 export AERO_FCST_RUN="" # When to run aerosol forecast: gdas, gfs, or both
 export AERO_ANL_RUN="" # When to run aerosol analysis: gdas, gfs, or both
 export WAVE_RUN="" # When to include wave suite: gdas, gfs, or both

parm/config/gefs/config.repair_replay

@@ -0,0 +1,15 @@
+#! /usr/bin/env bash                                                                                                                                                                                                                     
+
+########## config.repair_replay #########
+# repair_replay specific
+
+echo "BEGIN: config.repair_replay"
+
+
+export varlist_FLXacc03="${PARMgfs}/product/gefs_parmlist_FLXacc03.parm" # Parameter table for f03 acc/ave/min/max variables (PSL data)
+export varlist_masteracc06="${PARMgfs}/product/gefs_parmlist_masteracc06.parm" # Parameter table for f06 acc/ave/min/max variables
+export varlist_masteracc03="${PARMgfs}/product/gefs_parmlist_masteracc03.parm" # Parameter table for f06 acc/ave/min/max variables
+
+. "${EXPDIR}/config.resources" repair_replay
+
+echo "END: config.repair_replay"

parm/config/gefs/config.resources

@@ -77,6 +77,14 @@ case ${step} in
     export memory="1GB"
     ;;
 
+  "repair_replay")
+    export walltime="00:10:00"
+    export ntasks=1
+    export threads_per_task=1
+    export tasks_per_node=$(( max_tasks_per_node / threads_per_task ))
+    export memory="2GB"
+    ;;
+
   "fcst" | "efcs")
     export is_exclusive=True
 
@@ -194,6 +202,7 @@ case ${step} in
     unset NTASKS_TOT
     ;;
 
+
   "atmos_products")
     export walltime="00:15:00"
     export ntasks=24

parm/config/gefs/yaml/defaults.yaml

@@ -9,6 +9,7 @@ base:
   DO_AWIPS: "NO"
   KEEPDATA: "NO"
   DO_EXTRACTVARS: "NO"
+  DO_REPAIR_REPLAY: "NO"
   FHMAX_GFS: 120
   FHMAX_HF_GFS: 0
   FCST_BREAKPOINTS: "48"

parm/product/gefs_parmlist_FLXacc03.parm

@@ -0,0 +1,35 @@
+:WATR:surface:0-3 hour acc fcst:
+:SNOWC:surface:0-3 hour ave fcst:
+:SNOHF:surface:0-3 hour ave fcst:
+:DLWRF:surface:0-3 hour ave fcst:
+:ULWRF:surface:0-3 hour ave fcst:
+:DSWRF:surface:0-3 hour ave fcst:
+:USWRF:surface:0-3 hour ave fcst:
+:USWRF:top of atmosphere:0-3 hour ave fcst:
+:ULWRF:top of atmosphere:0-3 hour ave fcst:
+:UFLX:surface:0-3 hour ave fcst:
+:VFLX:surface:0-3 hour ave fcst:
+:SHTFL:surface:0-3 hour ave fcst:
+:LHTFL:surface:0-3 hour ave fcst:
+:PRATE:surface:0-3 hour ave fcst:
+:CPRAT:surface:0-3 hour ave fcst:
+:ALBDO:surface:0-3 hour ave fcst:
+:TCDC:entire atmosphere (considered as a single layer):0-3 hour ave fcst:
+:TCDC:boundary layer cloud layer:0-3 hour ave fcst:
+:GFLUX:surface:0-3 hour ave fcst:
+:U-GWD:surface:0-3 hour ave fcst:
+:V-GWD:surface:0-3 hour ave fcst:
+:TMP:middle cloud top level:0-3 hour ave fcst:
+:TMP:low cloud top level:0-3 hour ave fcst:
+:TMP:high cloud top level:0-3 hour ave fcst:
+:PRES:high cloud top level:0-3 hour ave fcst:
+:PRES:middle cloud top level:0-3 hour ave fcst:
+:PRES:low cloud top level:0-3 hour ave fcst:
+:PRES:high cloud bottom level:0-3 hour ave fcst:
+:PRES:middle cloud bottom level:0-3 hour ave fcst:
+:PRES:low cloud bottom level:0-3 hour ave fcst:
+:CWORK:entire atmosphere (considered as a single layer):0-3 hour ave fcst:
+:DUVB:surface:0-3 hour ave fcst:
+:CDUVB:surface:0-3 hour ave fcst:
+:TMAX:2 m above ground:0-3 hour max fcst:
+:TMIN:2 m above ground:0-3 hour min fcst:

parm/product/gefs_parmlist_masteracc03.parm

@@ -0,0 +1,42 @@
+:TSNOWP
+:DLWRF:surface
+:ULWRF:surface
+:DSWRF:surface
+:USWRF:surface
+:USWRF:top
+:ULWRF:top
+:UFLX
+:VFLX
+:SHTFL
+:LHTFL
+:PRATE
+:CPRAT
+:ALBDO
+:GFLUX
+:U-GWD
+:V-GWD
+:TCDC:entire
+:TCDC:boundary
+:HCDC:high cloud layer:182-185 min
+:LCDC:low cloud layer:182-185 min
+:MCDC:middle cloud layer:182-185 min
+:APCP
+:ACPCP
+:NCPCP
+:TMIN
+:TMAX
+:DUVB
+:CDUVB
+:CWORK
+:SNOHF
+:SNOWC
+:WATR
+:TMP:middle cloud top
+:TMP:low cloud top
+:TMP:high cloud top
+:PRES:high cloud top
+:PRES:middle cloud top
+:PRES:low cloud top
+:PRES:high cloud bottom
+:PRES:middle cloud bottom
+:PRES:low cloud bottom

parm/product/gefs_parmlist_masteracc06.parm

@@ -0,0 +1,41 @@
+:WATR
+:SNOWC
+:SNOHF
+:DLWRF:surface
+:ULWRF:surface
+:DSWRF:surface
+:USWRF:surface
+:USWRF:top
+:ULWRF:top
+:UFLX:surface
+:VFLX:surface
+:SHTFL:surface
+:LHTFL:surface
+:PRATE:surface:0
+:CPRAT:surface:0
+:ALBDO:surface
+:TCDC:entire
+:TCDC:boundary
+:HCDC:high cloud layer:0-6
+:MCDC:middle cloud layer:0-6
+:LCDC:low cloud layer:0-6
+:GFLUX:surface
+:U-GWD:surface
+:V-GWD:surface
+:APCP:surface
+:ACPCP:surface
+:NCPCP:surface
+:TMP:middle cloud top
+:TMP:low cloud top
+:TMP:high cloud top
+:PRES:high cloud top
+:PRES:middle cloud top
+:PRES:low cloud top
+:PRES:high cloud bottom
+:PRES:middle cloud bottom
+:PRES:low cloud bottom
+:CWORK
+:DUVB
+:CDUVB
+:TMAX
+:TMIN

scripts/exgefs_atmos_repair_replay.sh

@@ -0,0 +1,113 @@
+#! /usr/bin/env bash
+
+
+source "${USHgfs}/preamble.sh"
+
+cd "${DATA}" || exit 1
+
+#COMIN_03 and {COMIN_ATMOS_MASTER} are directory containing the files that we want to extract
+#Extract c00 files for f003 from PSL reanalysis data
+
+fnh=03
+echo "extracting f${fnh}"
+oufile=${DATA}/gefs.t00z.master.grb2f0${fnh}
+
+infile=${COMIN_03}/GFSPRS.GrbF03
+if [[ -f "${infile}" ]]; then #check if input file exists before extraction
+
+  ${WGRIB2} "${infile}" | grep "TSNOWP" | ${WGRIB2} -i "${infile}" -grib tmp ||true
+  ${WGRIB2} tmp -for "2:2" -append -grib  "${oufile}">/dev/null || true 
+
+  ${WGRIB2} "${infile}" | grep ":APCP:surface" | ${WGRIB2} -i "${infile}" -grib tmp ||true
+  ${WGRIB2} tmp -for "1:1" -append -grib  "${oufile}">/dev/null || true
+
+  ${WGRIB2} "${infile}" | grep ":ACPCP:surface" | ${WGRIB2} -i "${infile}" -grib tmp ||true
+  ${WGRIB2} tmp -for "1:1" -append -grib  "${oufile}">/dev/null || true
+
+  ${WGRIB2} "${infile}" | grep ":NCPCP:surface" | ${WGRIB2} -i "${infile}" -grib tmp ||true
+  ${WGRIB2} tmp -for "1:1" -append -grib  "${oufile}">/dev/null || true
+
+  ${WGRIB2} "${infile}" | grep ":HCDC:high cloud layer:0" | ${WGRIB2} -i "${infile}" -append -grib "${oufile}">/dev/null || true
+  ${WGRIB2} "${infile}" | grep ":MCDC:middle cloud layer:0" | ${WGRIB2} -i "${infile}" -append -grib "${oufile}">/dev/null || true
+  ${WGRIB2} "${infile}" | grep ":LCDC:low cloud layer:0" | ${WGRIB2} -i "${infile}" -append -grib "${oufile}">/dev/null || true
+
+  count=$(${WGRIB2} "${oufile}" | wc -l)
+  if [ ${count} -lt 7 ] ; then
+    echo "FATAL ERROR: missing input variables"
+    export err=1; err_chk
+  fi
+  rm tmp
+else
+  echo "FATAL ERROR: ${infile} does not exist"
+  export err=1; err_chk
+fi 
+
+varlist=${varlist_FLXacc03} # Parameter table for f03 acc/ave/min/max variables (PSL data)
+infile=${COMIN_03}/GFSFLX.GrbF03
+if [[ -f "${infile}" ]]; then #check if input file exists before extraction
+    ${WGRIB2} "${infile}" | grep -F -f  "${varlist}" | ${WGRIB2} -i "${infile}" -append -grib "${oufile}">/dev/null || true
+else
+  echo "FATAL ERROR: ${infile} does not exist"
+  export err=1; err_chk
+fi 
+#  done 
+
+
+#Extract individual member files for f006 master data
+fnh=006
+
+echo "extracting f${fnh}"
+infile=${COMIN_ATMOS_MASTER}/gefs.t00z.master.grb2f${fnh}
+oufile=${DATA}/gefs.t00z.master.grb2f${fnh}
+
+varlist=${varlist_masteracc06} # Parameter table for f06 acc/ave/min/max variables
+
+if [[ -f "${infile}" ]]; then #check if input file exists before extraction
+
+  ${WGRIB2} "${infile}" | grep -F -f "${varlist}" | ${WGRIB2} -i "${infile}" -append -grib  "${oufile}" || true
+  ${WGRIB2} "${infile}" | grep "TSNOWP" | ${WGRIB2} -i "${infile}" -grib tmp || true
+
+  ${WGRIB2} tmp -for "2:2" -append -grib  "${oufile}">/dev/null || true 
+  ${WGRIB2} tmp -for "1:1" -grib  TSNOWP1.dat || true
+
+else
+  echo "FATAL ERROR: ${infile} does not exist"
+  export err=1; err_chk
+fi
+
+export sorc_name=gefs_6h_ave_1mem.x
+
+"${EXECgfs}/${sorc_name}" > sorc_name.exe.out
+cat sorc_name.exe.out
+
+#output f06
+infile=${COMIN_ATMOS_MASTER}/gefs.t00z.master.grb2f006
+
+${WGRIB2} "${infile}" -match_inv | grep -v -F -f "$varlist" | ${WGRIB2} -i  "${infile}" -grib out1.grb2 || true
+${WGRIB2} out1.grb2 -not "TSNOWP" -grib out2.grb2
+
+cat out2.grb2 TSNOWP1.dat gefs.t00z.pgrb2af006 > out3.grb2
+mv "${COMIN_ATMOS_MASTER}/gefs.t00z.master.grb2f006" "${COMIN_ATMOS_MASTER}/gefs.t00z.master.grb2f006_org"
+mv out3.grb2 "${COMIN_ATMOS_MASTER}/gefs.t00z.master.grb2f006"
+
+rm -fr out1.grb2 out2.grb2 TSNOWP*.dat
+
+#output f03
+varlist=${varlist_masteracc03} # Parameter table for f03 acc/ave/min/max variables
+infile=${COMIN_ATMOS_MASTER}/gefs.t00z.master.grb2f003
+#
+${WGRIB2} "${infile}" | grep "TSNOWP" | ${WGRIB2} -i "${infile}" -grib TSNOWP2.dat || true
+${WGRIB2} TSNOWP2.dat -for "1:1" -grib  out1.grb2 >/dev/null || true
+${WGRIB2} out1.grb2 -set_ftime "0-3 hour acc fcst" -grib TSNOWP1.dat 
+
+${WGRIB2} "${infile}" -match_inv | grep -v -F -f "$varlist" | ${WGRIB2} -i  "${infile}" -grib out2.grb2 || true
+${WGRIB2} out2.grb2 -set_ftime "3 hour fcst" -grib out3.grb2
+
+cat out3.grb2 TSNOWP1.dat gefs.t00z.pgrb2af003 > gefs.t00z.master.grb2f003
+
+${NCP} "${COMIN_ATMOS_MASTER}/gefs.t00z.master.grb2f003" "${COMOUT_ATMOS_MASTER}/gefs.t00z.master.grb2f003_org"
+${NCP} gefs.t00z.master.grb2f003 "${COMOUT_ATMOS_MASTER}/gefs.t00z.master.grb2f003"
+
+rm -fr out1.grb2 out2.grb2 out3.grb2
+
+exit

sorc/link_workflow.sh

@@ -317,7 +317,7 @@ cd "${HOMEgfs}/exec" || exit 1
 for utilexe in fbwndgfs.x gaussian_sfcanl.x gfs_bufr.x supvit.x syndat_getjtbul.x \
   syndat_maksynrc.x syndat_qctropcy.x tocsbufr.x overgridid.x rdbfmsua.x \
   mkgfsawps.x enkf_chgres_recenter_nc.x tave.x vint.x ocnicepost.x webtitle.x \
-  ensadd.x ensppf.x ensstat.x wave_stat.x
+  ensadd.x ensppf.x ensstat.x wave_stat.x gefs_6h_ave_1mem.x
 do
   [[ -s "${utilexe}" ]] && rm -f "${utilexe}"
   ${LINK_OR_COPY} "${HOMEgfs}/sorc/gfs_utils.fd/install/bin/${utilexe}" .

workflow/applications/applications.py

@@ -71,6 +71,7 @@ def __init__(self, conf: Configuration) -> None:
         self.do_goes = _base.get('DO_GOES', False)
         self.do_mos = _base.get('DO_MOS', False)
         self.do_extractvars = _base.get('DO_EXTRACTVARS', False)
+        self.do_repair_replay = _base.get('DO_REPAIR_REPLAY', False)
 
         self.do_hpssarch = _base.get('HPSSARCH', False)
 

workflow/applications/gefs.py

@@ -14,11 +14,14 @@ def _get_app_configs(self):
         """
         Returns the config_files that are involved in gefs
         """
-        configs = ['stage_ic', 'fcst', 'atmos_products', 'arch']
+        configs = ['stage_ic', 'fcst', 'repair_replay', 'atmos_products', 'arch']
 
         if self.nens > 0:
             configs += ['efcs', 'atmos_ensstat']
 
+            if self.do_repair_replay:
+                configs += ['repair_replay']
+
         if self.do_wave:
             configs += ['waveinit', 'wavepostsbs', 'wavepostpnt']
             if self.do_wave_bnd:
@@ -59,6 +62,9 @@ def get_task_names(self):
         if self.nens > 0:
             tasks += ['efcs']
 
+        if self.do_repair_replay:
+            tasks += ['repair_replay']
+
         tasks += ['atmos_prod']
 
         if self.nens > 0: