Enable cycling atmosphere DA in 3DEnVar mode with coupled ensemble.

jobs/JGLOBAL_ARCHIVE

@@ -13,9 +13,10 @@ YMD=${PDY} HH=${cyc} generate_com -rx COM_ATMOS_ANALYSIS COM_ATMOS_BUFR COM_ATMO
   COM_ATMOS_GENESIS COM_ATMOS_HISTORY COM_ATMOS_INPUT COM_ATMOS_MASTER COM_ATMOS_RESTART \
   COM_ATMOS_TRACK COM_ATMOS_WMO \
   COM_CHEM_HISTORY \
-  COM_ICE_HISTORY COM_ICE_INPUT \
+  COM_MED_RESTART \
+  COM_ICE_HISTORY COM_ICE_INPUT COM_ICE_RESTART \
   COM_OBS COM_TOP \
-  COM_OCEAN_HISTORY COM_OCEAN_INPUT COM_OCEAN_XSECT COM_OCEAN_2D COM_OCEAN_3D \
+  COM_OCEAN_HISTORY COM_OCEAN_INPUT COM_OCEAN_RESTART COM_OCEAN_XSECT COM_OCEAN_2D COM_OCEAN_3D \
   COM_WAVE_GRID COM_WAVE_HISTORY COM_WAVE_STATION
 
 for grid in "0p25" "0p50" "1p00"; do

jobs/JGLOBAL_FORECAST

@@ -30,10 +30,10 @@ fi
 
 # Ignore possible spelling error (nothing is misspelled)
 # shellcheck disable=SC2153
-GDATE=$(${NDATE} -"${assim_freq}" "${PDY}${cyc}")
+declare -rx GDATE=$(date -d "${PDY} ${cyc} - ${assim_freq} hours" +%Y%m%d%H)
 # shellcheck disable=
-declare -x gPDY="${GDATE:0:8}"
-declare -x gcyc="${GDATE:8:2}"
+declare -rx gPDY="${GDATE:0:8}"
+declare -rx gcyc="${GDATE:8:2}"
 
 # Construct COM variables from templates (see config.com)
 YMD=${PDY} HH=${cyc} generate_com -rx COM_ATMOS_RESTART COM_ATMOS_INPUT COM_ATMOS_ANALYSIS \

jobs/rocoto/coupled_ic.sh

@@ -1,45 +1,27 @@
 #! /usr/bin/env bash
 
-source "$HOMEgfs/ush/preamble.sh"
+source "${HOMEgfs}/ush/preamble.sh"
 
-###############################################################
-## Abstract:
-## Copy initial conditions from BASE_CPLIC to ROTDIR for coupled forecast-only runs
-## HOMEgfs   : /full/path/to/workflow
-## EXPDIR : /full/path/to/config/files
-## CDUMP  : cycle name (gdas / gfs)
-## PDY    : current date (YYYYMMDD)
-## cyc    : current cycle (HH)
-###############################################################
-
-###############################################################
 # Source FV3GFS workflow modules
 . ${HOMEgfs}/ush/load_fv3gfs_modules.sh
 status=$?
 [[ ${status} -ne 0 ]] && exit ${status}
-err=0
 
-###############################################################
-# Source relevant configs
-configs="base coupled_ic wave"
-for config in ${configs}; do
-    . ${EXPDIR}/config.${config}
-    status=$?
-    [[ ${status} -ne 0 ]] && exit ${status}
-done
+export job="coupled_ic"
+export jobid="${job}.$$"
 
-###############################################################
-# Source machine runtime environment
-. ${BASE_ENV}/${machine}.env config.coupled_ic
-status=$?
-[[ ${status} -ne 0 ]] && exit ${status}
+# Execute the JJOB
+
+source "${HOMEgfs}/ush/jjob_header.sh" -e "coupled_ic" -c "base coupled_ic"
 
-###############################################################
 # Locally scoped variables and functions
 GDATE=$(date -d "${PDY} ${cyc} - ${assim_freq} hours" +%Y%m%d%H)
 gPDY="${GDATE:0:8}"
 gcyc="${GDATE:8:2}"
 
+# Initialize return code
+err=0
+
 error_message(){
     echo "FATAL ERROR: Unable to copy ${1} to ${2} (Error code ${3})"
 }
@@ -78,10 +60,9 @@ if [[ "${DO_OCN:-}" = "YES" ]]; then
   [[ ${rc} -ne 0 ]] && error_message "${source}" "${target}" "${rc}"
   err=$((err + rc))
   case "${OCNRES}" in
-    "500") 
-      echo "Do not have Mom.res_*.nc files for 5 deg ocean"
-      ;;
-    "025")
+    "500" | "100")  # Only 5 degree or 1 degree ocean does not have MOM.res_[1-4].nc files
+    ;;
+    "025")  # Only 1/4 degree ocean has MOM.res_[1-4].nc files
       for nn in $(seq 1 4); do
         source="${BASE_CPLIC}/${CPL_OCNIC}/${PDY}${cyc}/ocn/${OCNRES}/MOM.res_${nn}.nc"
         if [[ -f "${source}" ]]; then
@@ -101,9 +82,9 @@ if [[ "${DO_OCN:-}" = "YES" ]]; then
   esac
 fi
 
-# Stage ice initial conditions to ROTDIR (cold start as these are SIS2 generated)
+# Stage ice initial conditions to ROTDIR (warm start)
 if [[ "${DO_ICE:-}" = "YES" ]]; then
-  YMD=${PDY} HH=${cyc} generate_com -r COM_ICE_RESTART
+  YMD=${gPDY} HH=${gcyc} generate_com -r COM_ICE_RESTART
   [[ ! -d "${COM_ICE_RESTART}" ]] && mkdir -p "${COM_ICE_RESTART}"
   ICERESdec=$(echo "${ICERES}" | awk '{printf "%0.2f", $1/100}')
   source="${BASE_CPLIC}/${CPL_ICEIC}/${PDY}${cyc}/ice/${ICERES}/cice5_model_${ICERESdec}.res_${PDY}${cyc}.nc"
@@ -137,4 +118,4 @@ fi
 
 ##############################################################
 # Exit cleanly
-exit 0
+exit "${err}"

parm/config/gfs/config.base.emc.dyn

@@ -167,7 +167,7 @@ case "${CASE}" in
         export waveGRD='glo_500'
         ;;
     "C96")
-        export OCNRES=100
+        export OCNRES=500
         export waveGRD='glo_200'
         ;;
     "C192")

parm/config/gfs/config.efcs

@@ -5,17 +5,17 @@
 
 echo "BEGIN: config.efcs"
 
-# TODO: the _ENKF counterparts need to be defined in config.base
-export DO_AERO=${DO_AERO_ENKF:-"NO"}
-export DO_OCN=${DO_OCN_ENKF:-"NO"}
-export DO_ICE=${DO_ICE_ENKF:-"NO"}
-export DO_WAVE=${DO_WAVE_ENKF:-"NO"}
+# TODO: the _ENKF counterparts need to be defined in config.base; for now inherit from config.base
+export DO_AERO=${DO_AERO_ENKF:-${DO_AERO:-"NO"}}
+export DO_OCN=${DO_OCN_ENKF:-${DO_OCN:-"NO"}}
+export DO_ICE=${DO_ICE_ENKF:-${DO_ICE:-"NO"}}
+export DO_WAVE=${DO_WAVE_ENKF:-${DO_WAVE:-"NO"}}
 
 # TODO: Possibly need OCNRES_ENKF, ICERES_ENKF, WAVRES_ENKF too
 if [[ ${DO_OCN} == "YES" ]]; then
   case "${CASE_ENS}" in
     "C48") export OCNRES=500;;
-    "C96") export OCNRES=100;;
+    "C96") export OCNRES=500;;
     "C192") export OCNRES=050;;
     "C384") export OCNRES=025;;
     "C768") export OCNRES=025;;
@@ -81,18 +81,4 @@ else
   export restart_interval="6"
 fi
 
-# wave model
-export cplwav=.false.
-
-# ocean model resolution
-case "${CASE_ENS}" in
-    "C48") export OCNRES=500;;
-    "C96") export OCNRES=100;;
-    "C192") export OCNRES=050;;
-    "C384") export OCNRES=025;;
-    "C768") export OCNRES=025;;
-    *) export OCNRES=025;;
-esac
-export ICERES=${OCNRES}
-
 echo "END: config.efcs"

scripts/exgdas_enkf_fcst.sh

@@ -18,58 +18,34 @@
 ####
 ################################################################################
 
-source "$HOMEgfs/ush/preamble.sh"
-
-# Directories.
-export FIX_DIR=${FIX_DIR:-$HOMEgfs/fix}
-export FIX_AM=${FIX_AM:-$FIX_DIR/am}
-
-# Utilities
-export NCP=${NCP:-"/bin/cp -p"}
-export NMV=${NMV:-"/bin/mv"}
-export NLN=${NLN:-"/bin/ln -sf"}
-
-# Scripts.
-FORECASTSH=${FORECASTSH:-$HOMEgfs/scripts/exglobal_forecast.sh}
+source "${HOMEgfs}/ush/preamble.sh"
 
 # Enemble group, begin and end
 ENSGRP=${ENSGRP:-1}
 ENSBEG=${ENSBEG:-1}
 ENSEND=${ENSEND:-1}
 
-# Model builds
-export FCSTEXECDIR=${FCSTEXECDIR:-$HOMEgfs/sorc/fv3gfs.fd/BUILD/bin}
-export FCSTEXEC=${FCSTEXEC:-fv3gfs.x}
-
-# Get DA specific diag table.
-export PARM_FV3DIAG=${PARM_FV3DIAG:-$HOMEgfs/parm/parm_fv3diag}
-export DIAG_TABLE=${DIAG_TABLE_ENKF:-${DIAG_TABLE:-$PARM_FV3DIAG/diag_table_da}}
-
 # Re-run failed members, or entire group
 RERUN_EFCSGRP=${RERUN_EFCSGRP:-"YES"}
 
 # Recenter flag and increment file prefix
 RECENTER_ENKF=${RECENTER_ENKF:-"YES"}
 export PREFIX_ATMINC=${PREFIX_ATMINC:-""}
 
-# Ops related stuff
-SENDECF=${SENDECF:-"NO"}
-SENDDBN=${SENDDBN:-"NO"}
-
 ################################################################################
 # Preprocessing
-cd $DATA || exit 99
-DATATOP=$DATA
+cd "${DATA}" || exit 99
+DATATOP=${DATA}
 
 ################################################################################
 # Set output data
 EFCSGRP="${COM_TOP}/efcs.grp${ENSGRP}"
-if [ -f $EFCSGRP ]; then
-   if [ $RERUN_EFCSGRP = "YES" ]; then
-      rm -f $EFCSGRP
+if [[ -f ${EFCSGRP} ]]; then
+   if [[ ${RERUN_EFCSGRP} = "YES" ]]; then
+      rm -f "${EFCSGRP}"
    else
-      echo "RERUN_EFCSGRP = $RERUN_EFCSGRP, will re-run FAILED members only!"
-      $NMV $EFCSGRP ${EFCSGRP}.fail
+      echo "RERUN_EFCSGRP = ${RERUN_EFCSGRP}, will re-run FAILED members only!"
+      ${NMV} "${EFCSGRP}" "${EFCSGRP}.fail"
    fi
 fi
 
@@ -119,7 +95,7 @@ export FHZER=${FHZER_ENKF:-${FHZER:-6}}
 export FHCYC=${FHCYC_ENKF:-${FHCYC:-6}}
 
 # Set PREFIX_ATMINC to r when recentering on
-if [ $RECENTER_ENKF = "YES" ]; then
+if [[ ${RECENTER_ENKF} = "YES" ]]; then
    export PREFIX_ATMINC="r"
 fi
 
@@ -132,21 +108,21 @@ declare -x gcyc="${GDATE:8:2}"
 ################################################################################
 # Run forecast for ensemble member
 rc=0
-for imem in $(seq $ENSBEG $ENSEND); do
+for imem in $(seq "${ENSBEG}" "${ENSEND}"); do
 
-   cd $DATATOP
+   cd "${DATATOP}"
 
-   cmem=$(printf %03i $imem)
+   cmem=$(printf %03i "${imem}")
    memchar="mem${cmem}"
 
-   echo "Processing MEMBER: $cmem"
+   echo "Processing MEMBER: ${cmem}"
 
    ra=0
 
    skip_mem="NO"
-   if [ -f ${EFCSGRP}.fail ]; then
-      memstat=$(cat ${EFCSGRP}.fail | grep "MEMBER $cmem" | grep "PASS" | wc -l)
-      [[ $memstat -eq 1 ]] && skip_mem="YES"
+   if [[ -f ${EFCSGRP}.fail ]]; then
+      memstat=$(cat "${EFCSGRP}.fail" | grep "MEMBER ${cmem}" | grep "PASS" | wc -l)
+      [[ ${memstat} -eq 1 ]] && skip_mem="YES"
    fi
 
    # Construct COM variables from templates (see config.com)
@@ -177,70 +153,70 @@ for imem in $(seq $ENSBEG $ENSEND); do
    fi
 
 
-   if [ $skip_mem = "NO" ]; then
+   if [[ ${skip_mem} = "NO" ]]; then
 
       ra=0
 
-      export MEMBER=$imem
+      export MEMBER=${imem}
       export DATA="${DATATOP}/${memchar}"
-      if [ -d $DATA ]; then rm -rf $DATA; fi
-      mkdir -p $DATA
-      $FORECASTSH
+      if [[ -d ${DATA} ]]; then rm -rf "${DATA}"; fi
+      mkdir -p "${DATA}"
+      ${FORECASTSH}
       ra=$?
 
       # Notify a member forecast failed and abort
-      if [ $ra -ne 0 ]; then
-         err_exit "FATAL ERROR:  forecast of member $cmem FAILED.  Aborting job"
+      if [[ ${ra} -ne 0 ]]; then
+         err_exit "FATAL ERROR:  forecast of member ${cmem} FAILED.  Aborting job"
       fi
 
       rc=$((rc+ra))
 
    fi
 
-   if [ $SENDDBN = YES ]; then
-     fhr=$FHOUT
-     while [ $fhr -le $FHMAX ]; do
-       FH3=$(printf %03i $fhr)
-       if [ $(expr $fhr % 3) -eq 0 ]; then
+   if [[ ${SENDDBN} = YES ]]; then
+     fhr=${FHOUT}
+     while [[ ${fhr} -le ${FHMAX} ]]; do
+       FH3=$(printf %03i "${fhr}")
+       if (( fhr % 3 == 0 )); then
          "${DBNROOT}/bin/dbn_alert" MODEL GFS_ENKF "${job}" "${COM_ATMOS_HISTORY}/${RUN}.t${cyc}z.sfcf${FH3}.nc"
        fi
        fhr=$((fhr+FHOUT))
      done
    fi
 
-   cd $DATATOP
+   cd "${DATATOP}"
 
-   if [ -s $EFCSGRP ]; then
-       $NCP $EFCSGRP log_old
+   if [[ -s ${EFCSGRP} ]]; then
+       ${NCP} "${EFCSGRP}" log_old
    fi
    [[ -f log ]] && rm log
    [[ -f log_new ]] && rm log_new
-   if [ $ra -ne 0 ]; then
-      echo "MEMBER $cmem : FAIL" > log
+   if [[ ${ra} -ne 0 ]]; then
+      echo "MEMBER ${cmem} : FAIL" > log
    else
-      echo "MEMBER $cmem : PASS" > log
+      echo "MEMBER ${cmem} : PASS" > log
    fi
-   if [ -s log_old ] ; then
+   if [[ -s log_old ]] ; then
        cat log_old log > log_new
    else
        cat log > log_new
    fi
-   $NCP log_new $EFCSGRP
+   ${NCP} log_new "${EFCSGRP}"
 
 done
 
 ################################################################################
 # Echo status of ensemble group
-cd $DATATOP
-echo "Status of ensemble members in group $ENSGRP:"
-cat $EFCSGRP
-[[ -f ${EFCSGRP}.fail ]] && rm ${EFCSGRP}.fail
+cd "${DATATOP}"
+echo "Status of ensemble members in group ${ENSGRP}:"
+cat "${EFCSGRP}"
+[[ -f ${EFCSGRP}.fail ]] && rm "${EFCSGRP}".fail
 
 ################################################################################
 # If any members failed, error out
-export err=$rc; err_chk
+export err=${rc}; err_chk
 
 ################################################################################
 #  Postprocessing
 
-exit $err
+exit "${err}"