task actions for #911

jobs/JGLOBAL_STAGE_IC

@@ -0,0 +1,24 @@
+#! /usr/bin/env bash
+
+source "${HOMEgfs}/ush/preamble.sh"
+source "${HOMEgfs}/ush/jjob_header.sh" -e "stage_ic" -c "base stage stage_ic"
+
+
+# Set COM Paths
+YMD=${PDY} HH=${cyc} generate_com -rx COM_STAGE_IC COM_ATM_INPUT
+
+if [[ ! -d "${COM_STAGE_IC}" ]]; then mkdir -p "${COM_STAGE_IC}"; fi
+
+
+
+# Execute the Script
+${HOMEgfs}/scripts/exglobal_stage_ic.sh
+
+##########################################
+# Remove the Temporary working directory
+##########################################
+cd ${DATAROOT}
+[[ ${KEEPDATA} = "NO" ]] && rm -rf ${DATA}
+
+
+exit 0

jobs/rocoto/coupled_ic.sh → jobs/rocoto/stage_ic.sh

@@ -7,12 +7,12 @@ source "${HOMEgfs}/ush/preamble.sh"
 status=$?
 [[ ${status} -ne 0 ]] && exit ${status}
 
-export job="coupled_ic"
+export job="stage_ic"
 export jobid="${job}.$$"
 
 # Execute the JJOB
 
-source "${HOMEgfs}/ush/jjob_header.sh" -e "coupled_ic" -c "base coupled_ic"
+source "${HOMEgfs}/ush/jjob_header.sh" -e "stage_ic" -c "base stage_ic"
 
 # Locally scoped variables and functions
 GDATE=$(date -d "${PDY} ${cyc} - ${assim_freq} hours" +%Y%m%d%H)
@@ -29,6 +29,26 @@ error_message(){
 ###############################################################
 # Start staging
 
+# Stage the initial conditions
+YMD=${PDY} HH=${cyc} generate_com -r COM_STAGE_IC
+[[ ! -d "${COM_STAGE_IC}" ]] && mkdir -p "${COM_STAGE_IC}"
+source="${BASE_CPLIC}/${CPL_ATMIC}/${PDY}${cyc}/${CDUMP}/${CASE}/INPUT/gfs_ctrl.nc"
+target="${COM_ATMOS_INPUT}/gfs_ctrl.nc"
+${NCP} "${source}" "${target}"
+rc=$?
+[[ ${rc} -ne 0 ]] && error_message "${source}" "${target}" "${rc}"
+err=$((err + rc))
+for ftype in gfs_data sfc_data; do
+  for tt in $(seq 1 6); do
+    source="${BASE_CPLIC}/${CPL_ATMIC}/${PDY}${cyc}/${CDUMP}/${CASE}/INPUT/${ftype}.tile${tt}.nc"
+    target="${COM_STAGE_IC}/${ftype}.tile${tt}.nc"
+    ${NCP} "${source}" "${target}"
+    rc=$?
+    [[ ${rc} -ne 0 ]] && error_message "${source}" "${target}" "${rc}"
+    err=$((err + rc))
+  done
+done
+
 # Stage the FV3 initial conditions to ROTDIR (cold start)
 YMD=${PDY} HH=${cyc} generate_com -r COM_ATMOS_INPUT
 [[ ! -d "${COM_ATMOS_INPUT}" ]] && mkdir -p "${COM_ATMOS_INPUT}"

scripts/exglobal_stage_ic.sh

@@ -0,0 +1,141 @@
+#! /usr/bin/env bash
+
+source "${HOMEgfs}/ush/preamble.sh"
+
+# Source FV3GFS workflow modules
+. ${HOMEgfs}/ush/load_fv3gfs_modules.sh
+status=$?
+[[ ${status} -ne 0 ]] && exit ${status}
+
+export job="stage_ic"
+export jobid="${job}.$$"
+
+# Execute the JJOB
+
+source "${HOMEgfs}/ush/jjob_header.sh" -e "stage_ic" -c "base stage_ic"
+
+# Locally scoped variables and functions
+GDATE=$(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 ${3})"
+}
+
+###############################################################
+# Start staging
+
+# Stage the initial conditions 
+YMD=${PDY} HH=${cyc} generate_com -r COM_STAGE_IC
+[[ ! -d "${COM_STAGE_IC}" ]] && mkdir -p "${COM_STAGE_IC}"
+source="${BASE_CPLIC}/${CPL_ATMIC}/${PDY}${cyc}/${CDUMP}/${CASE}/INPUT/gfs_ctrl.nc"
+target="${COM_ATMOS_INPUT}/gfs_ctrl.nc"
+${NCP} "${source}" "${target}"
+rc=$?
+[[ ${rc} -ne 0 ]] && error_message "${source}" "${target}" "${rc}"
+err=$((err + rc))
+for ftype in gfs_data sfc_data; do
+  for tt in $(seq 1 6); do
+    source="${BASE_CPLIC}/${CPL_ATMIC}/${PDY}${cyc}/${CDUMP}/${CASE}/INPUT/${ftype}.tile${tt}.nc"
+    target="${COM_STAGE_IC}/${ftype}.tile${tt}.nc"
+    ${NCP} "${source}" "${target}"
+    rc=$?
+    [[ ${rc} -ne 0 ]] && error_message "${source}" "${target}" "${rc}"
+    err=$((err + rc))
+  done
+done
+
+# Stage the FV3 initial conditions to ROTDIR (cold start)
+YMD=${PDY} HH=${cyc} generate_com -r COM_ATMOS_INPUT
+[[ ! -d "${COM_ATMOS_INPUT}" ]] && mkdir -p "${COM_ATMOS_INPUT}"
+source="${BASE_CPLIC}/${CPL_ATMIC}/${PDY}${cyc}/${CDUMP}/${CASE}/INPUT/gfs_ctrl.nc"
+target="${COM_ATMOS_INPUT}/gfs_ctrl.nc"
+${NCP} "${source}" "${target}"
+rc=$?
+[[ ${rc} -ne 0 ]] && error_message "${source}" "${target}" "${rc}"
+err=$((err + rc))
+for ftype in gfs_data sfc_data; do
+  for tt in $(seq 1 6); do
+    source="${BASE_CPLIC}/${CPL_ATMIC}/${PDY}${cyc}/${CDUMP}/${CASE}/INPUT/${ftype}.tile${tt}.nc"
+    target="${COM_ATMOS_INPUT}/${ftype}.tile${tt}.nc"
+    ${NCP} "${source}" "${target}"
+    rc=$?
+    [[ ${rc} -ne 0 ]] && error_message "${source}" "${target}" "${rc}"
+    err=$((err + rc))
+  done
+done
+
+# Stage ocean initial conditions to ROTDIR (warm start)
+if [[ "${DO_OCN:-}" = "YES" ]]; then
+  YMD=${gPDY} HH=${gcyc} generate_com -r COM_OCEAN_RESTART
+  [[ ! -d "${COM_OCEAN_RESTART}" ]] && mkdir -p "${COM_OCEAN_RESTART}"
+  source="${BASE_CPLIC}/${CPL_OCNIC}/${PDY}${cyc}/ocn/${OCNRES}/MOM.res.nc"
+  target="${COM_OCEAN_RESTART}/${PDY}.${cyc}0000.MOM.res.nc"
+  ${NCP} "${source}" "${target}"
+  rc=$?
+  [[ ${rc} -ne 0 ]] && error_message "${source}" "${target}" "${rc}"
+  err=$((err + rc))
+  case "${OCNRES}" in
+    "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
+          target="${COM_OCEAN_RESTART}/${PDY}.${cyc}0000.MOM.res_${nn}.nc"
+          ${NCP} "${source}" "${target}"
+          rc=$?
+          [[ ${rc} -ne 0 ]] && error_message "${source}" "${target}" "${rc}"
+          err=$((err + rc))
+        fi
+      done
+    ;;
+    *)
+      echo "FATAL ERROR: Unsupported ocean resolution ${OCNRES}"
+      rc=1
+      err=$((err + rc))
+    ;;
+  esac
+fi
+
+# Stage ice initial conditions to ROTDIR (warm start)
+if [[ "${DO_ICE:-}" = "YES" ]]; then
+  YMD=${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}${cyc}.nc"
+  target="${COM_ICE_RESTART}/${PDY}.${cyc}0000.cice_model.res.nc"
+  ${NCP} "${source}" "${target}"
+  rc=$?
+  [[ ${rc} -ne 0 ]] && error_message "${source}" "${target}" "${rc}"
+  err=$((err + rc))
+fi
+
+# Stage the WW3 initial conditions to ROTDIR (warm start; TODO: these should be placed in $RUN.$gPDY/$gcyc)
+if [[ "${DO_WAVE:-}" = "YES" ]]; then
+  YMD=${PDY} HH=${cyc} generate_com -r COM_WAVE_RESTART
+  [[ ! -d "${COM_WAVE_RESTART}" ]] && mkdir -p "${COM_WAVE_RESTART}"
+  for grdID in ${waveGRD}; do  # TODO: check if this is a bash array; if so adjust
+    source="${BASE_CPLIC}/${CPL_WAVIC}/${PDY}${cyc}/wav/${grdID}/${PDY}.${cyc}0000.restart.${grdID}"
+    target="${COM_WAVE_RESTART}/${PDY}.${cyc}0000.restart.${grdID}"
+    ${NCP} "${source}" "${target}"
+    rc=$?
+    [[ ${rc} -ne 0 ]] && error_message "${source}" "${target}" "${rc}"
+    err=$((err + rc))
+  done
+fi
+
+###############################################################
+# Check for errors and exit if any of the above failed
+if  [[ "${err}" -ne 0 ]] ; then
+  echo "FATAL ERROR: Unable to copy ICs from ${BASE_CPLIC} to ${ROTDIR}; ABORT!"
+  exit "${err}"
+fi
+
+##############################################################
+# Exit cleanly
+exit "${err}"