Add the repair job for the reforecast

jobs/JGEFS_ATMOS_ACC

@@ -0,0 +1,95 @@
+#! /usr/bin/env bash
+#
+#
+#####################################################################
+# 8/14/2024, Hong Guan Scripts to repair F0306 for GEFSv13 reforecasts
+#################################################################### 
+source "${HOMEgfs}/ush/preamble.sh"
+source "${HOMEgfs}/ush/jjob_header.sh" -e "repairf0306" -c "base repairf0306"
+
+####################################
+# obtain unique process id (pid) and make temp directory
+####################################
+
+export pid=$$
+export date=${CDATE}
+yyyymmdd=`echo $date | cut -c1-8`
+echo `date` $0 `date -u` begin
+
+####################################
+# File To Log Msgs
+####################################
+export jlogfile=${jlogfile:-$COMROOT/logs/jlogfiles/jlogfile.${job}.${pid}}
+echo $jlogfile
+
+####################################
+# Determine Job Output Name on System
+####################################
+export outid="LL$job"
+export jobid="${outid}.o${pid}"
+export pgmout="OUTPUT.${pid}"
+export pgmerr=errfile
+echo $outid,$jobid,$pgmout,$pgmerr
+
+####################################
+####################################
+# Specify Execution Areas
+####################################
+export HOMEgefs=${HOMEgfs}
+export EXECacc=${EXECacc:-$HOMEgefs/exec}
+export SORCacc=${SORCacc:-$HOMEgefs/sorc/gefs_postacc.fd}
+export SCRIPTSens_acc=$HOMEgefs/scripts
+export FIXens_acc=${FIXacc:-$HOMEgefs/fix}
+
+export PARMgefs=$HOMEgefs/rocoto/parm
+echo $PARMgefs
+
+# Construct COM variables from templates
+#YMD=${PDY} HH=${cyc} declare_from_tmpl -rx COM_ATMOS_ANALYSIS COM_ATMOS_HISTORY COM_ATMOS_MASTER
+ YMD=${PDY} HH=${cyc} declare_from_tmpl -rx COM_ATMOS_MASTER
+
+
+##############################
+# Run setpdy and initialize PDY variables
+##############################
+#
+#export COMIN_master=${COMIN_master:-$COMROOT/$PSLOT/gefs.$PDY/00/mem001/model_data/atmos/master}
+export COMIN_master=${COMIN_master:-$COM_ATMOS_MASTER}
+export COMIN_00and03=$HOMEgefs/anl
+
+####################################
+# Create member list
+####################################
+
+#export homesyndir=$HOMEacc
+
+echo
+env | sort
+echo
+
+########################################################
+# Execute the acc script.
+export cmodel=ens
+export ymdh=${date}
+
+#msg="Begin job for $job"
+#postmsg "$jlogfile" "$msg"
+
+echo ${ymdh}
+$SCRIPTSens_acc/gefs_atmos_f0306.sh   ${ymdh} ${DATA} > fv3gefsrf_0306acc.${cmodel}.${ymdh}.out
+
+################################
+msg="JOB COMPLETED NORMALLY"
+#postmsg "$jlogfile" "$msg"
+
+exit
+
+##############################
+# Remove the Temporary working directory
+##############################
+if [[ $KEEPDATA != "YES" ]]; then
+	cd $DATAROOT
+	rm -rf $DATA
+fi
+
+echo `date` $job completed

jobs/rocoto/repairf0306.sh

@@ -0,0 +1,23 @@
+#! /usr/bin/env bash
+
+source "${HOMEgfs}/ush/preamble.sh"
+
+###############################################################
+echo
+echo "=============== START TO SOURCE FV3GFS WORKFLOW MODULES ==============="
+. ${HOMEgfs}/ush/load_ufswm_modules.sh
+status=$?
+[[ ${status} -ne 0 ]] && exit ${status}
+
+export job="repairf0306"
+export jobid="${job}.$$"
+
+###############################################################
+echo
+echo "=============== START TO RUN EXTRACTVARS ==============="
+# Execute the JJOB
+${HOMEgfs}/jobs/JGEFS_ATMOS_ACC
+status=$?
+[[ ${status} -ne 0 ]] && exit ${status}
+
+exit 0

parm/config/gefs/config.repairf0306

@@ -0,0 +1,11 @@
+#! /usr/bin/env bash                                                                                                                                                                                                                     
+
+########## config.repairf0306 #########
+# repairf0306 specific
+
+echo "BEGIN: config.repairf0306"
+
+
+. "${EXPDIR}/config.resources" repairf0306
+
+echo "END: config.repairf0306"

parm/config/gefs/config.resources

@@ -77,6 +77,14 @@ case ${step} in
     export memory="1GB"
     ;;
 
+  "repairf0306")
+    export wtime_repairf0306="00:10:00"
+    export npe_repairf0306=1
+    export nth_repairf0306=1
+    export npe_node_repairf0306=$(( npe_node_max / nth_repairf0306 ))
+    export memory_repairf0306="2GB"
+    ;;
+
   "fcst" | "efcs")
     export is_exclusive=True
 
@@ -186,14 +194,15 @@ case ${step} in
         declare -x "walltime"="06:00:00"
         ;;
       *)
-        echo "FATAL ERROR: Resources not defined for job ${step} at resolution ${CASE}"
+        echo "FATAL ERROR: Resources not defined for job ${job} at resolution ${CASE}"
         exit 4
         ;;
     esac
 
     unset NTASKS_TOT
     ;;
 
+
   "atmos_products")
     export walltime="00:15:00"
     export ntasks=24

scripts/gefs_atmos_f0306.sh

@@ -0,0 +1,191 @@
+#!/bin/ksh
+
+set -xa
+cdate=$1
+DATA=$2
+
+foutmax=6 #last lead hour to extract 
+cd $DATA
+
+ddate=`echo $cdate | cut -c1-8`
+YYYY=`echo $cdate | cut -c1-4`
+MONTH=`echo $cdate | cut -c5-6`
+DAY=`echo $cdate | cut -c7-8`
+
+# COMIN_00and03 and COMIN_master are directory containing the files that we want to extract
+#Extract c00 files for f003 from PSL reanalysis data
+
+    for fnh in 03; do
+      echo "extracting f${fnh}"
+      oufile=$DATA/gefs.t00z.master.grb2f0${fnh}
+
+      infile=$COMIN_00and03/GFSPRS.GrbF03
+      if [ -f $infile ]; then #check if input file exists before extraction
+
+      $WGRIB2 $infile | grep "TSNOWP" | $WGRIB2 -i $infile -grib tmp
+      $WGRIB2 tmp -for "2:2" -append -grib  $oufile>/dev/null
+
+      $WGRIB2 $infile | grep ":APCP:surface" | $WGRIB2 -i $infile -grib tmp
+      $WGRIB2 tmp -for "1:1" -append -grib  $oufile>/dev/null
+
+      $WGRIB2 $infile | grep ":ACPCP:surface" | $WGRIB2 -i $infile -grib tmp
+      $WGRIB2 tmp -for "1:1" -append -grib  $oufile>/dev/null
+
+      $WGRIB2 $infile | grep ":NCPCP:surface" | $WGRIB2 -i $infile -grib tmp
+      $WGRIB2 tmp -for "1:1" -append -grib  $oufile>/dev/null
+
+      $WGRIB2 $infile | grep ":HCDC:high cloud layer:0" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+      $WGRIB2 $infile | grep ":MCDC:middle cloud layer:0" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+      $WGRIB2 $infile | grep ":LCDC:low cloud layer:0" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+      rm tmp
+   else
+    echo "$infile does not exist"
+   fi 
+
+      infile=$COMIN_00and03/GFSFLX.GrbF03
+      if [ -f $infile ]; then #check if input file exists before extraction
+        $WGRIB2 $infile | grep "WATR" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+        $WGRIB2 $infile | grep "SNOWC" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+        $WGRIB2 $infile | grep "SNOHF" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+        $WGRIB2 $infile | grep ":DLWRF:surface:0" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+        $WGRIB2 $infile | grep ":ULWRF:surface:0" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+        $WGRIB2 $infile | grep ":DSWRF:surface:0" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+        $WGRIB2 $infile | grep ":USWRF:surface:0" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+        $WGRIB2 $infile | grep ":USWRF:top" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+        $WGRIB2 $infile | grep ":ULWRF:top" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+        $WGRIB2 $infile | grep ":UFLX:surface" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+        $WGRIB2 $infile | grep ":VFLX:surface" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+        $WGRIB2 $infile | grep ":SHTFL:surface:0" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+        $WGRIB2 $infile | grep ":LHTFL:surface:0" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+        $WGRIB2 $infile | grep ":PRATE:surface:0" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+        $WGRIB2 $infile | grep ":CPRAT:surface:0" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+        $WGRIB2 $infile | grep ":ALBDO:surface" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+        $WGRIB2 $infile | grep ":TCDC:entire" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+        $WGRIB2 $infile | grep ":TCDC:boundary" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+        $WGRIB2 $infile | grep ":GFLUX:surface:0" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+        $WGRIB2 $infile | grep ":U-GWD:surface" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+        $WGRIB2 $infile | grep ":V-GWD:surface" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+        $WGRIB2 $infile | grep "TMP:middle cloud top" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+        $WGRIB2 $infile | grep "TMP:low cloud top" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+        $WGRIB2 $infile | grep "TMP:high cloud top" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+        $WGRIB2 $infile | grep "PRES:high cloud top" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+        $WGRIB2 $infile | grep "PRES:middle cloud top" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+        $WGRIB2 $infile | grep "PRES:low cloud top" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+        $WGRIB2 $infile | grep "PRES:high cloud bottom" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+        $WGRIB2 $infile | grep "PRES:middle cloud bottom" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+        $WGRIB2 $infile | grep "PRES:low cloud bottom" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+        $WGRIB2 $infile | grep "CWORK" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+        $WGRIB2 $infile | grep "DUVB" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+        $WGRIB2 $infile | grep "CDUVB" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+        $WGRIB2 $infile | grep "TMAX" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+        $WGRIB2 $infile | grep "TMIN" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+      else
+        echo "$infile does not exist"
+      fi 
+  done #fnh
+
+  #Extract individual member files for f006 master data
+  fnh=006
+
+   echo "extracting f${fnh}"
+    infile=$COMIN_master/gefs.t00z.master.grb2f${fnh}
+    oufile=$DATA/gefs.t00z.master.grb2f${fnh}
+
+   if [ -f $infile ]; then #check if input file exists before extraction
+#    rm -f $outfile/gefs.t00z.master.grb2f${fnh}  #remove outfile if it already exists before extraction
+    $WGRIB2 $infile | grep "TSNOWP" | $WGRIB2 -i $infile -grib tmp
+    $WGRIB2 tmp -for "2:2" -append -grib  $oufile>/dev/null
+    $WGRIB2 $infile | grep "WATR" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+    $WGRIB2 $infile | grep "SNOWC" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+    $WGRIB2 $infile | grep "SNOHF" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+    $WGRIB2 $infile | grep ":DLWRF:surface" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+    $WGRIB2 $infile | grep ":ULWRF:surface" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+    $WGRIB2 $infile | grep ":DSWRF:surface" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+    $WGRIB2 $infile | grep ":USWRF:surface" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+    $WGRIB2 $infile | grep ":USWRF:top" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+    $WGRIB2 $infile | grep ":ULWRF:top" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+    $WGRIB2 $infile | grep ":UFLX:surface" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+    $WGRIB2 $infile | grep ":VFLX:surface" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+    $WGRIB2 $infile | grep ":SHTFL:surface" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+    $WGRIB2 $infile | grep ":LHTFL:surface" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+    $WGRIB2 $infile | grep ":PRATE:surface:0" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+    $WGRIB2 $infile | grep ":CPRAT:surface:0" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+    $WGRIB2 $infile | grep ":ALBDO:surface" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+    $WGRIB2 $infile | grep ":TCDC:entire" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+    $WGRIB2 $infile | grep ":TCDC:boundary" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+    $WGRIB2 $infile | grep ":HCDC:high cloud layer:0-6" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+    $WGRIB2 $infile | grep ":MCDC:middle cloud layer:0-6" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+    $WGRIB2 $infile | grep ":LCDC:low cloud layer:0-6" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+    $WGRIB2 $infile | grep ":GFLUX:surface" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+    $WGRIB2 $infile | grep ":U-GWD:surface" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+    $WGRIB2 $infile | grep ":V-GWD:surface" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+    $WGRIB2 $infile | grep ":APCP:surface" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+    $WGRIB2 $infile | grep ":ACPCP:surface" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+    $WGRIB2 $infile | grep ":NCPCP:surface" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+    $WGRIB2 $infile | grep "TMP:middle cloud top" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+    $WGRIB2 $infile | grep "TMP:low cloud top" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+    $WGRIB2 $infile | grep "TMP:high cloud top" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+    $WGRIB2 $infile | grep "PRES:high cloud top" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+    $WGRIB2 $infile | grep "PRES:middle cloud top" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+    $WGRIB2 $infile | grep "PRES:low cloud top" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+    $WGRIB2 $infile | grep "PRES:high cloud bottom" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+    $WGRIB2 $infile | grep "PRES:middle cloud bottom" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+    $WGRIB2 $infile | grep "PRES:low cloud bottom" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+    $WGRIB2 $infile | grep "CWORK" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+    $WGRIB2 $infile | grep "DUVB" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+    $WGRIB2 $infile | grep "CDUVB" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+    $WGRIB2 $infile | grep "TMAX" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+    $WGRIB2 $infile | grep "TMIN" | $WGRIB2 -i $infile -append -grib $oufile>/dev/null
+
+   else
+    echo "$infile does not exist"
+   fi
+
+ export exec_dir=$EXECacc
+ export sorc_dir=$SORCacc
+ export sorc_name=gefs_6h_ave_1mem
+
+#   cd $DATA
+
+   $exec_dir/$sorc_name >sorc_name.exe.out
+   cat sorc_name.exe.out
+
+#output f06
+   infile=$COMIN_master/gefs.t00z.master.grb2f006
+
+    $WGRIB2 $infile | grep "TSNOWP" | $WGRIB2 -i $infile -grib TSNOWP2.dat
+    $WGRIB2  TSNOWP2.dat -for "1:1" -append -grib  TSNOWP1.dat >/dev/null
+
+   $WGRIB2 $infile -not "(ULWRF|USWRF)" -not "(TSNOWP|DLWRF|DSWRF|UFLX|VFLX|SHTFL|LHTFL|PRATE|CPRAT|ALBDO|GFLUX|U-GWD|V-GWD)" -not "TCDC:(entire|boundary)" -not "HCDC:high cloud layer:0-6" -not "LCDC:low cloud layer:0-6" -not "MCDC:middle cloud layer:0-6" -not "(APCP|ACPCP|NCPCP)" -not "(TMIN|TMAX|DUVB|CDUVB|CWORK|SNOHF|SNOWC|WATR)" -not "(TMP:middle cloud top|TMP:low cloud top|TMP:high cloud top)" -not "(PRES:high cloud top|PRES:middle cloud top|PRES:low cloud top|PRES:high cloud bottom|PRES:middle cloud bottom|PRES:low cloud bottom)" -grib out1.grb2
+
+   cat out1.grb2 gefs.t00z.pgrb2af006 TSNOWP1.dat > out2.grb
+
+   mv $COMIN_master/gefs.t00z.master.grb2f006 $COMIN_master/gefs.t00z.master.grb2f006_org
+   mv $COMIN_master/gefs.t00z.master.grb2if006 $COMIN_master/gefs.t00z.master.grb2if006_org
+
+   mv out2.grb $COMIN_master/gefs.t00z.master.grb2f006
+   $GRB2INDEX $COMIN_master/gefs.t00z.master.grb2f006  $COMIN_master/gefs.t00z.master.grb2if006
+
+   rm -fr out1.grb2 out2.grb TSNOWP*.dat
+
+#output f03
+   infile=$COMIN_master/gefs.t00z.master.grb2f003
+#
+    $WGRIB2 $infile | grep "TSNOWP" | $WGRIB2 -i $infile -grib TSNOWP2.dat
+    $WGRIB2  TSNOWP2.dat -for "1:1" -grib  out.grb >/dev/null
+    $WGRIB2   out.grb -set_ftime "0-3 hour acc fcst" -grib TSNOWP1.dat 
+
+   $WGRIB2 $infile -not "(TSNOWP|ULWRF|USWRF)" -not "(DLWRF|DSWRF|UFLX|VFLX|SHTFL|LHTFL|PRATE|CPRAT|ALBDO|GFLUX|U-GWD|V-GWD)" -not "TCDC:(entire|boundary)" -not "HCDC:high cloud layer:182-185 min" -not "LCDC:low cloud layer:182-185 min" -not "MCDC:middle cloud layer:182-185 min" -not "(APCP|ACPCP|NCPCP)" -not "(TMIN|TMAX|DUVB|CDUVB|CWORK|SNOHF|SNOWC|WATR)" -not "(TMP:middle cloud top|TMP:low cloud top|TMP:high cloud top)" -not "(PRES:high cloud top|PRES:middle cloud top|PRES:low cloud top|PRES:high cloud bottom|PRES:middle cloud bottom|PRES:low cloud bottom)" -grib out1.grb
+
+   $WGRIB2   out1.grb -set_ftime "3 hour fcst" -grib out2.grb
+   cat out2.grb gefs.t00z.pgrb2af003 TSNOWP1.dat > out3.grb
+
+   mv $COMIN_master/gefs.t00z.master.grb2f003 $COMIN_master/gefs.t00z.master.grb2f003_org
+   mv $COMIN_master/gefs.t00z.master.grb2if003 $COMIN_master/gefs.t00z.master.grb2if003_org
+
+   mv out3.grb $COMIN_master/gefs.t00z.master.grb2f003
+   $GRB2INDEX $COMIN_master/gefs.t00z.master.grb2f003  $COMIN_master/gefs.t00z.master.grb2if003
+
+   rm -fr out.grb out1.grb out2.grb
+
+   exit

workflow/applications/gefs.py

@@ -14,7 +14,7 @@ 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', 'repairf0306', 'atmos_products', 'arch']
 
         if self.nens > 0:
             configs += ['efcs', 'atmos_ensstat']
@@ -59,6 +59,8 @@ def get_task_names(self):
         if self.nens > 0:
             tasks += ['efcs']
 
+        tasks += ['repairf0306']
+
         tasks += ['atmos_prod']
 
         if self.nens > 0:
@@ -76,9 +78,14 @@ def get_task_names(self):
                 tasks += ['wavepostbndpnt', 'wavepostbndpntbll']
             tasks += ['wavepostpnt']
 
+<<<<<<< HEAD
+
+        return {f"{self._base['CDUMP']}": tasks}
+=======
         if self.do_extractvars:
             tasks += ['extractvars']
 
         tasks += ['arch']
 
         return {f"{self._base['RUN']}": tasks}
+>>>>>>> EMC/develop