Merge pull request #120 from XianwuXue-NOAA/feature/v13_atmos_fcst

Make atmos_fcst job work using GFSv17 and new COM structure

jobs/JGEFS_ATMOS_PREP

@@ -65,13 +65,13 @@ export COMPONENT="atmos"
 #############################
 # Source relevant config files
 #############################
-configs="gefs gefs_atmos_prep"
-config_path=$PARMgefs/parm_gefs
+configs="base prep"
+config_path=${PARMgefs}/config
 for config in $configs; do
-  . ${config_path}/${config}.parm
+  . ${config_path}/config.${config}
   export err=$?
   if [[ $err != 0 ]]; then
-    echo "FATAL ERROR in $(basename $BASH_SOURCE): Error while loading parm file ${config_path}/${config}.parm"
+    echo "FATAL ERROR in $(basename $BASH_SOURCE): Error while loading parm file ${config_path}/config.${config}"
     exit ${err}
   fi
 done

jobs/JGEFS_FORECAST

@@ -1,18 +1,11 @@
-#!/bin/ksh
+#! /usr/bin/env bash
 
-echo "$(date -u) begin ${.sh.file}"
-
-set -xa
-if [[ ${STRICT:-NO} == "YES" ]]; then
-	# Turn on strict bash error checking
-	set -eu
-fi
-export PS4='$SECONDS + $(basename ${.sh.file})[$LINENO] '
+source "${HOMEgefs:-${HOMEgfs}}/ush/preamble.sh"
 
 ####################################
 # Determine Job Output Name on System
 ####################################
-export jobid=${jobid:-"$job.$PBS_JOBID"}
+export jobid=${jobid:-"${job}.${PBS_JOBID}"}
 export pgmout="OUTPUT.${PBS_JOBID}"
 export pgmerr=errfile
 
@@ -23,12 +16,6 @@ export DATA=${DATA:-${DATAROOT}/${jobid}}
 mkdir -p $DATA
 cd $DATA
 
-######################################
-# Set up compute resources
-######################################
-export total_tasks=${total_tasks:-320}
-export APRUN=${gefsmpexec:-"mpiexec -n $total_tasks"}
-
 ####################################
 # Specify NET and RUN Name and model
 ####################################
@@ -55,8 +42,8 @@ setpdy.sh
 source PDY
 
 if [ ${FORECAST_SEGMENT} = lr ]; then
-    export cyc=00
-    export cycle=t${cyc}z
+  export cyc=00
+  export cycle=t${cyc}z
 fi
 
 ####################################
@@ -71,51 +58,79 @@ export PARMgefs=${PARMgefs:-$HOMEgefs/parm}
 ##############################################
 # Define COM directories
 ##############################################
-ver=${ver:-$(echo ${gefs_ver}|cut -c1-5)}
-export COMIN=${COMIN:-$(compath.py $envir/com/$NET/${ver})/${RUN}.${PDY}/$cyc}
-export COMOUT=${COMOUT:-$(compath.py -o $NET/${ver})/${RUN}.${PDY}/$cyc}
-export GESIN=${GESIN:-$(compath.py $envir/com/$NET/${ver})/${RUN}.${PDY}/$cyc/nwges}
-export GESOUT=${GESOUT:-$(compath.py -o $NET/${ver})/${RUN}.${PDY}/$cyc/nwges}
+ver=${gefs_ver:0:5}
+export ROTDIR=${ROTDIR:-$(compath.py $envir/com/$NET/${ver})}
 
 #############################
 # Source relevant config files
 #############################
-configs="gefs gefs_wave gefs_fcst"
-config_path=$PARMgefs
+export CDATE=$PDY$cyc
+configs="base fcst efcs"
+config_path=${PARMgefs}/config
 for config in $configs; do
-    . $config_path/$config.parm
-    export err=$?
-    if [[ $err != 0 ]]; then
-    	echo "FATAL ERROR in ${.sh.file}: Error while loading parm file $config_path/$config.parm"
-    	exit $err
-    fi
+  . ${config_path}/config.${config}
+  export err=$?
+  if [[ $err != 0 ]]; then
+    echo "FATAL ERROR in ${BASH_SOURCE[0]}: Error while loading parm file ${config_path}/config.${config}"
+    exit $err
+  fi
 done
 
+export APRUN_UFS=${APRUN_UFS:-"${launcher:-'mpiexec -l'} -n ${npe_fcst} -ppn ${npe_node_fcst} --cpu-bind depth --depth ${NTHREADS_FV3}"}
+
 if [[ $cplchm = ".true." ]]; then
-    COMPONENT="chem"
-fi
-if [[ $cplwav = ".true." ]]; then
-    # Set location of wave restart from last cycle
-    last_date=$($NDATE -$WAVHCYC $CDATE)
-    last_PDY=$(echo $last_date | cut -c1-8)
-    last_cyc=$(echo $last_date | cut -c9-10)
-    export WRDIR=${WRDIR:-$(compath.py $envir/com/$NET/${ver})}/${RUN}.${last_PDY}/$last_cyc/wave/restart
+  COMPONENT="chem"
 fi
 
 export COMPONENT=${COMPONENT:-atmos}
 
 echo "Environment before calling script"
 env | sort
 
+# Ignore possible spelling error (nothing is misspelled)
+# shellcheck disable=SC2153
+GDATE=$(${NDATE} -"${assim_freq}" "${PDY}${cyc}")
+# shellcheck disable=
+declare -x gPDY="${GDATE:0:8}"
+declare -x gcyc="${GDATE:8:2}"
+
+# Construct COM variables from templates (see config.com)
+declare -rx memchar=${RUNMEM:2:3}
+
+MEMDIR="${memchar}" YMD=${PDY} HH=${cyc} generate_com -rx COM_ATMOS_RESTART COM_ATMOS_INPUT COM_ATMOS_ANALYSIS \
+  COM_ATMOS_HISTORY COM_ATMOS_MASTER
+
+RUN=${rCDUMP} MEMDIR="${memchar}" YMD="${gPDY}" HH="${gcyc}" generate_com -rx COM_ATMOS_RESTART_PREV:COM_ATMOS_RESTART_TMPL
+
+if [[ ${DO_WAVE} == "YES" ]]; then
+  MEMDIR="${memchar}" YMD=${PDY} HH=${cyc} generate_com -rx COM_WAVE_RESTART COM_WAVE_PREP COM_WAVE_HISTORY
+  RUN=${rCDUMP} MEMDIR="${memchar}" YMD="${gPDY}" HH="${gcyc}" generate_com -rx COM_WAVE_RESTART_PREV:COM_WAVE_RESTART_TMPL
+fi
+
+if [[ ${DO_OCN} == "YES" ]]; then
+  MEMDIR="${memchar}" YMD=${PDY} HH=${cyc} generate_com -rx COM_MED_RESTART COM_OCEAN_RESTART \
+    COM_OCEAN_INPUT COM_OCEAN_HISTORY COM_OCEAN_ANALYSIS
+  RUN=${rCDUMP} MEMDIR="${memchar}" YMD="${gPDY}" HH="${gcyc}" generate_com -rx COM_OCEAN_RESTART_PREV:COM_OCEAN_RESTART_TMPL
+fi
+
+if [[ ${DO_ICE} == "YES" ]]; then
+   MEMDIR="${memchar}" YMD=${PDY} HH=${cyc} generate_com -rx COM_ICE_HISTORY
+   RUN=${rCDUMP} MEMDIR="${memchar}" YMD="${gPDY}" HH="${gcyc}" generate_com -rx COM_ICE_RESTART_PREV:COM_ICE_RESTART_TMPL
+fi
+
+if [[ ${DO_AERO} == "YES" ]]; then
+  MEMDIR="${memchar}" YMD=${PDY} HH=${cyc} generate_com -rx COM_CHEM_HISTORY
+fi
+
 #############################################################
 # Execute the script
 $HOMEgefs/scripts/exgefs_forecast.sh
 export err=$?
 if [[ $err == 0 ]]; then
-    echo "$job completed normally!"
+  echo "$job completed normally!"
 else
-    echo "FATAL ERROR in ${.sh.file}: $job failed!"
-    exit $err
+  echo "FATAL ERROR in ${BASH_SOURCE[0]}: $job failed!"
+  exit $err
 fi
 #############################################################
 
@@ -125,6 +140,4 @@ fi
 cd $DATAROOT
 if [ ${KEEPDATA:-NO} = NO ] ; then rm -rf $DATA ; fi
 
-echo "$(date -u) end ${.sh.file}"
-
 exit $err

parm/.gitignore

@@ -3,4 +3,6 @@ post
 product
 prep_chem_sources.inp.IN
 
-config
+config/config.nsst
+config/config.com
+config/config.defaults.s2sw

parm/parm_gefs/gefs.parm → parm/config/config.base

@@ -50,10 +50,9 @@ esac
 memberlist="c00"
 
 imem=1
-while [[ imem -le $npert ]];
-do
+while [[ imem -le $npert ]]; do
   memberlist="$memberlist p$(printf %02i $imem)"
-  (( imem++ ))
+  ((imem++))
 done
 export memberlist
 
@@ -62,26 +61,26 @@ if [[ ${RUNMEM:-none} = "geaer" ]]; then cplchm=".true."; fi
 export cplchm=${cplchm:-.false.}
 
 if [[ $cplchm = ".true." ]]; then
-	# Override forecast length
-	export fhmaxh=$fhmax_aer
-	export fhmax=$fhmax_aer
+  # Override forecast length
+  export fhmaxh=$fhmax_aer
+  export fhmax=$fhmax_aer
 
-	export AEROSOL_INIT_TYPE=${AEROSOL_INIT_TYPE:-"warm"}
+  export AEROSOL_INIT_TYPE=${AEROSOL_INIT_TYPE:-"warm"}
 
-	export cplwav=".false." # Running both chem and waves is not yet supported
+  export cplwav=".false." # Running both chem and waves is not yet supported
 fi
 
 export fhmax
-if (( fhmax <= fhmaxh )); then export fhmaxh=$fhmax; fi
-if (( FHMAXHF > fhmaxh )); then export FHMAXHF=$fhmaxh; fi
+if ((fhmax <= fhmaxh)); then export fhmaxh=$fhmax; fi
+if ((FHMAXHF > fhmaxh)); then export FHMAXHF=$fhmaxh; fi
 
-export restart_interval=${fhrestart:-12}
+export restart_interval_gfs=${fhrestart:-12}
 export restart_interval_aer=${restart_interval_aer:-12}
 export other_restart_time=${other_restart_time:-6}
 
 if [[ $cplchm = ".true." ]]; then
-	export restart_interval=$restart_interval_aer
-	export other_restart_time=${other_restart_time:-$gefs_cych}
+  export restart_interval_gfs=$restart_interval_aer
+  export other_restart_time=${other_restart_time:-$gefs_cych}
 fi
 
 #pass these variables to gefs_wave.parm
@@ -135,21 +134,24 @@ export IDVC=${IDVC:-2}
 export HOMEgefs=${HOMEgefs:-${PACKAGEROOT}/gefs.${gefs_ver}}
 export EXECgefs=${EXECgefs:-${HOMEgefs}/exec}
 export USHgefs=${USHgefs:-${HOMEgefs}/ush}
-#export FIXgefs=${FIXgefs:-${HOMEgefs}/fix/fix_gefs}
 export PARMgefs=${PARMgefs:-${HOMEgefs}/parm}
 
 export HOMEgfs=${HOMEgfs:-${HOMEgefs}}
 export PARMgfs=${HOMEgfs}/parm
 export EXPDIR=${PARMgfs}/config
-#export FIXgfs=${HOMEgfs}/fix
-#export USHgfs=${HOMEgfs}/ush
-#export UTILgfs=${HOMEgfs}/util
-#export EXECgfs=${HOMEgfs}/exec
-#export SCRgfs=${HOMEgfs}/scripts
+export FIXgfs=${HOMEgfs}/fix
+export USHgfs=${HOMEgfs}/ush
+export UTILgfs=${HOMEgfs}/util
+export EXECgfs=${HOMEgfs}/exec
+export SCRgfs=${HOMEgfs}/scripts
 
-#export FIXcice=${HOMEgfs}/fix/cice
-#export FIXmom=${HOMEgfs}/fix/mom6
-#export FIXreg2grb2=${HOMEgfs}/fix/reg2grb2
+export FIXcice=${HOMEgfs}/fix/cice
+export FIXmom=${HOMEgfs}/fix/mom6
+export FIXreg2grb2=${HOMEgfs}/fix/reg2grb2
+
+
+export ERRSCRIPT=${ERRSCRIPT:-'eval [[ $err = 0 ]]'}
+export LOGSCRIPT=${LOGSCRIPT:-""} #=startmsg
 
 ####################################
 # CONVENIENT utility scripts and other environment parameters
@@ -182,6 +184,23 @@ export VERBOSE=${VERBOSE:-YES}
 # Get all the COM path templates
 source "${PARMgefs:-${PARMgfs}}/config/config.com"
 
+#------
+# APP settings
+export APP=${APP:-"ATM"} # ATM, S2SW
+
+# Defaults:
+export DO_ATM="YES"
+export DO_COUPLED="NO"
+export DO_WAVE="NO"
+export DO_OCN="NO"
+export DO_ICE="NO"
+export DO_AERO="NO"
+export CCPP_SUITE=${CCPP_SUITE:-"FV3_GFS_v17_p8"} #FV3_GFS_v16"}
+export WAVE_CDUMP=""                           # When to include wave suite: gdas, gfs, or both
+export DOBNDPNT_WAVE="NO"
+export cplwav2atm=".false."
+export FRAC_GRID=".true."
+
 # These are the currently available grid-combinations
 case "${CASE}" in
   "C48") export OCNRES=500;;
@@ -192,6 +211,71 @@ case "${CASE}" in
   *) export OCNRES=025;;
 esac
 export ICERES=${OCNRES}
+export waveGRD='gnh_10m aoc_9km gsh_15m'
+
+case "${APP}" in
+  ATM)
+    export confignamevarfornems="atm"
+    ;;
+  ATMA)
+    export DO_AERO="YES"
+    export confignamevarfornems="atm_aero"
+    ;;
+  ATMW)
+    export DO_COUPLED="YES"
+    export DO_WAVE="YES"
+    export WAVE_CDUMP="both"
+    export confignamevarfornems="leapfrog_atm_wav"
+    ;;
+  NG-GODAS)
+    export DO_ATM="NO"
+    export DO_OCN="YES"
+    export DO_ICE="YES"
+    ;;
+  S2S*)
+    export DO_COUPLED="YES"
+    export DO_OCN="YES"
+    export DO_ICE="YES"
+    export CCPP_SUITE="FV3_GFS_v17_coupled_p8"
+    export confignamevarfornems="cpld"
+
+    if [[ "${APP}" =~ A$ ]]; then
+        export DO_AERO="YES"
+        export confignamevarfornems="${confignamevarfornems}_aero"
+    fi
+
+    if [[ "${APP}" =~ ^S2SW ]]; then
+        export DO_WAVE="YES"
+        export WAVE_CDUMP="both"
+        export cplwav2atm=".true."
+        export confignamevarfornems="${confignamevarfornems}_outerwave"
+    fi
+
+    source ${EXPDIR}/config.defaults.s2sw
+
+    ;;
+  *)
+    echo "Unrecognized APP: ${APP}"
+    exit 1
+    ;;
+esac
+
+# Surface cycle update frequency
+export FHCYC=24
+
+# IAU related parameters
+export DOIAU="NO" # Enable 4DIAU for control with 3 increments
+export IAU_OFFSET=0
+export IAU_DELTHRS=0
+export IAU_FHROT=0
+
+# turned on nsst in anal and/or fcst steps, and turn off rtgsst
+export DONST="YES"
+if [[ ${DONST} = "YES" ]]; then export FNTSFA="        "; fi
+
+# The switch to apply SST elevation correction or not
+export nst_anl=.true.
+#-----
 
 # Microphysics Options: 99-ZhaoCarr, 8-Thompson; 6-WSM6, 10-MG, 11-GFDL
 export imp_physics=${imp_physics:-"8"}