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clean-up exglobal_atmos_sfcanl.sh and update the j-job for COMIN/COMOUT #2

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Merged
CoryMartin-NOAA merged 3 commits into from
May 24, 2024
Merged

clean-up exglobal_atmos_sfcanl.sh and update the j-job for COMIN/COMOUT #2

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30bd93e
clean-up exglobal_atmos_sfcanl.sh and update the j-job for COMIN/COMOUT
aerorahul May 24, 2024
a625a11
shellcheck j-job
aerorahul May 24, 2024
15ec7f1
shellcheck exscript
aerorahul May 24, 2024
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40 changes: 17 additions & 23 deletions jobs/JGLOBAL_ATMOS_SFCANL
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Original file line number Diff line number Diff line change
Expand Up @@ -4,40 +4,34 @@ source "${HOMEgfs}/ush/preamble.sh"
source "${HOMEgfs}/ush/jjob_header.sh" -e "sfcanl" -c "base sfcanl"


##############################################
# Set variables used in the script
##############################################
export CDUMP="${RUN/enkf}"


##############################################
# Begin JOB SPECIFIC work
##############################################
# Ignore possible spelling error (nothing is misspelled)
# shellcheck disable=SC2153
GDATE=$(${NDATE} -"${assim_freq}" "${PDY}${cyc}")
# shellcheck disable=
gPDY=${GDATE:0:8}
gcyc=${GDATE:8:2}
export GDUMP="gdas"
GDATE=$(date --utc -d "${PDY} ${cyc} - ${assim_freq} hours" +%Y%m%d%H)

RUN="gdas" YMD=${GDATE:0:8} HH=${GDATE:8:2} declare_from_tmpl -rx \
COMIN_OBS_PREV:COM_OBS_TMPL \
COMIN_ATMOS_RESTART_PREV:COM_ATMOS_RESTART_TMPL

YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
COMIN_OBS:COM_OBS_TMPL \
COMIN_ATMOS_ANALYSIS:COM_ATMOS_ANALYSIS_TMPL \
COMIN_SNOW_ANALYSIS:COM_SNOW_ANALYSIS_TMPL

export OPREFIX="${CDUMP}.t${cyc}z."
export GPREFIX="${GDUMP}.t${gcyc}z."
export APREFIX="${CDUMP}.t${cyc}z."
YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
COMOUT_ATMOS_RESTART:COM_ATMOS_RESTART_TMPL

YMD=${PDY} HH=${cyc} declare_from_tmpl -rx COM_OBS COM_ATMOS_ANALYSIS COM_ATMOS_RESTART \
COM_SNOW_ANALYSIS
mkdir -p "${COMOUT_ATMOS_RESTART}"

RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} declare_from_tmpl -rx \
COM_OBS_PREV:COM_OBS_TMPL \
COM_ATMOS_RESTART_PREV:COM_ATMOS_RESTART_TMPL

###############################################################
# Run relevant script

${SFCANALSH:-${SCRgfs}/exglobal_atmos_sfcanl.sh}
status=$?
[[ ${status} -ne 0 ]] && exit ${status}
(( status != 0 )) && exit "${status}"


##############################################
Expand All @@ -48,14 +42,14 @@ status=$?
# Final processing
##############################################
if [[ -e "${pgmout}" ]] ; then
cat ${pgmout}
cat "${pgmout}"
fi

##########################################
# Remove the Temporary working directory
##########################################
cd ${DATAROOT}
[[ ${KEEPDATA} = "NO" ]] && rm -rf ${DATA}
cd "${DATAROOT}"
[[ "${KEEPDATA}" == "NO" ]] && rm -rf "${DATA}"


exit 0
216 changes: 72 additions & 144 deletions scripts/exglobal_atmos_sfcanl.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -22,200 +22,128 @@
source "${USHgfs}/preamble.sh"

# Directories.
pwd=$(pwd)
cd "${DATA}" || exit 99

# Derived base variables
# Ignore possible spelling error (nothing is misspelled)
# shellcheck disable=SC2153
GDATE=$(${NDATE} -"${assim_freq}" "${PDY}${cyc}")
BDATE=$(${NDATE} -3 "${PDY}${cyc}")
bPDY=${BDATE:0:8}
bcyc=${BDATE:8:2}

# Utilities
export CHGRP_CMD=${CHGRP_CMD:-"chgrp ${group_name:-rstprod}"}
export NCLEN=${NCLEN:-${USHgfs}/getncdimlen}
COMPRESS=${COMPRESS:-gzip}
UNCOMPRESS=${UNCOMPRESS:-gunzip}
APRUNCFP=${APRUNCFP:-""}

# IAU
DOIAU=${DOIAU:-"NO"}
export IAUFHRS=${IAUFHRS:-"6"}
GDATE=$(date --utc -d "${PDY} ${cyc} - ${assim_freq} hours" +%Y%m%d%H)

# Surface cycle related parameters
# Dependent Scripts and Executables
CYCLESH=${CYCLESH:-${USHgfs}/global_cycle.sh}
export CYCLEXEC=${CYCLEXEC:-${EXECgfs}/global_cycle}
NTHREADS_CYCLE=${NTHREADS_CYCLE:-24}
APRUN_CYCLE=${APRUN_CYCLE:-${APRUN:-""}}

# Surface cycle related parameters
export SNOW_NUDGE_COEFF=${SNOW_NUDGE_COEFF:-'-2.'}
export CYCLVARS=${CYCLVARS:-""}
export FHOUR=${FHOUR:-0}
export DELTSFC=${DELTSFC:-6}

# FV3 specific info (required for global_cycle)
export CASE=${CASE:-"C384"}
ntiles=${ntiles:-6}

# IAU
DOIAU=${DOIAU:-"NO"}
export IAUFHRS=${IAUFHRS:-"6"}

# Dependent Scripts and Executables
export NTHREADS_CALCINC=${NTHREADS_CALCINC:-1}
export APRUN_CALCINC=${APRUN_CALCINC:-${APRUN:-""}}
export APRUN_CALCANL=${APRUN_CALCANL:-${APRUN:-""}}
export APRUN_CHGRES=${APRUN_CALCANL:-${APRUN:-""}}

export CALCANLEXEC=${CALCANLEXEC:-${EXECgfs}/calc_analysis.x}
export CHGRESNCEXEC=${CHGRESNCEXEC:-${EXECgfs}/enkf_chgres_recenter_nc.x}
export CHGRESINCEXEC=${CHGRESINCEXEC:-${EXECgfs}/interp_inc.x}
export NTHREADS_CHGRES=${NTHREADS_CHGRES:-1}
CALCINCPY=${CALCINCPY:-${USHgfs}/calcinc_gfs.py}
CALCANLPY=${CALCANLPY:-${USHgfs}/calcanl_gfs.py}

export APRUN_CHGRES=${APRUN_CALCANL:-${APRUN:-""}}
CHGRESEXEC=${CHGRESEXEC:-${EXECgfs}/enkf_chgres_recenter.x}

# OPS flags
RUN=${RUN:-""}
SENDECF=${SENDECF:-"NO"}
SENDDBN=${SENDDBN:-"NO"}
# Other info used in this script
RUN_GETGES=${RUN_GETGES:-"NO"}
GETGESSH=${GETGESSH:-"getges.sh"}
export gesenvir=${gesenvir:-${envir}}
GPREFIX="gdas.t${GDATE:8:2}z."
OPREFIX="${RUN/enkf}.t${cyc}z."
APREFIX="${RUN/enkf}.t${cyc}z."

# Observations
OPREFIX=${OPREFIX:-""}
OSUFFIX=${OSUFFIX:-""}

# Guess files
GPREFIX=${GPREFIX:-""}
ntiles=6

# Analysis files
export APREFIX=${APREFIX:-""}
DTFANL=${DTFANL:-${COM_ATMOS_ANALYSIS}/${APREFIX}dtfanl.nc}

##############################################################
# Get dimension information based on CASE
res=$(echo ${CASE} | cut -c2-)
res="${CASE:1}"
JCAP_CASE=$((res*2-2))
LATB_CASE=$((res*2))
LONB_CASE=$((res*4))

################################################################################
# Preprocessing
mkdata=NO
if [[ ! -d ${DATA} ]]; then
mkdata=YES
mkdir -p ${DATA}
fi

cd ${DATA} || exit 99

if [[ ${DONST} = "YES" ]]; then
export NSSTBF="${COM_OBS}/${OPREFIX}nsstbufr"
${NLN} ${NSSTBF} nsstbufr
fi


##############################################################
# Required model guess files


##############################################################
# Output files
if [[ ${DONST} = "YES" ]]; then
${NLN} ${DTFANL} dtfanl
fi


##############################################################
# Update surface fields in the FV3 restart's using global_cycle
mkdir -p "${COM_ATMOS_RESTART}"

# Global cycle requires these files
export FNTSFA=${FNTSFA:-${COM_OBS}/${OPREFIX}rtgssthr.grb}
export FNACNA=${FNACNA:-${COM_OBS}/${OPREFIX}seaice.5min.blend.grb}
export FNSNOA=${FNSNOA:-${COM_OBS}/${OPREFIX}snogrb_t${JCAP_CASE}.${LONB_CASE}.${LATB_CASE}}
[[ ! -f ${FNSNOA} ]] && export FNSNOA="${COM_OBS}/${OPREFIX}snogrb_t1534.3072.1536"
FNSNOG=${FNSNOG:-${COM_OBS_PREV}/${GPREFIX}snogrb_t${JCAP_CASE}.${LONB_CASE}.${LATB_CASE}}
[[ ! -f ${FNSNOG} ]] && FNSNOG="${COM_OBS_PREV}/${GPREFIX}snogrb_t1534.3072.1536"
export FNTSFA=${FNTSFA:-${COMIN_OBS}/${OPREFIX}rtgssthr.grb}
export FNACNA=${FNACNA:-${COMIN_OBS}/${OPREFIX}seaice.5min.blend.grb}
export FNSNOA=${FNSNOA:-${COMIN_OBS}/${OPREFIX}snogrb_t${JCAP_CASE}.${LONB_CASE}.${LATB_CASE}}
[[ ! -f ${FNSNOA} ]] && export FNSNOA="${COMIN_OBS}/${OPREFIX}snogrb_t1534.3072.1536"
FNSNOG=${FNSNOG:-${COMIN_OBS_PREV}/${GPREFIX}snogrb_t${JCAP_CASE}.${LONB_CASE}.${LATB_CASE}}
[[ ! -f ${FNSNOG} ]] && FNSNOG="${COMIN_OBS_PREV}/${GPREFIX}snogrb_t1534.3072.1536"

# Set CYCLVARS by checking grib date of current snogrb vs that of prev cycle
if [[ ${RUN_GETGES} = "YES" ]]; then
snoprv=$(${GETGESSH} -q -t snogrb_${JCAP_CASE} -e ${gesenvir} -n ${GDUMP} -v ${GDATE})
snoprv=$(${GETGESSH} -q -t "snogrb_${JCAP_CASE}" -e "${gesenvir}" -n "${GDUMP}" -v "${GDATE}")
else
snoprv=${snoprv:-${FNSNOG}}
snoprv=${snoprv:-${FNSNOG}}
fi

if [[ $(${WGRIB} -4yr ${FNSNOA} 2>/dev/null | grep -i snowc | awk -F: '{print $3}' | awk -F= '{print $2}') -le \
$(${WGRIB} -4yr ${snoprv} 2>/dev/null | grep -i snowc | awk -F: '{print $3}' | awk -F= '{print $2}') ]] ; then
export FNSNOA=" "
export CYCLVARS="FSNOL=99999.,FSNOS=99999.,"
if [[ $(${WGRIB} -4yr "${FNSNOA}" 2>/dev/null | grep -i snowc | awk -F: '{print $3}' | awk -F= '{print $2}') -le \
$(${WGRIB} -4yr "${snoprv}" 2>/dev/null | grep -i snowc | awk -F: '{print $3}' | awk -F= '{print $2}') ]] ; then
export FNSNOA=" "
export CYCLVARS="FSNOL=99999.,FSNOS=99999.,"
else
export SNOW_NUDGE_COEFF=${SNOW_NUDGE_COEFF:-0.}
export CYCLVARS="FSNOL=${SNOW_NUDGE_COEFF},${CYCLVARS}"
export CYCLVARS="FSNOL=${SNOW_NUDGE_COEFF},${CYCLVARS}"
fi

if [[ ${DONST} = "YES" ]]; then
export NST_FILE=${GSI_FILE:-${COM_ATMOS_ANALYSIS}/${APREFIX}dtfanl.nc}
# determine where the input snow restart files come from
if [[ "${DO_JEDISNOWDA:-}" == "YES" ]]; then
COMIN="${COMIN_SNOW_ANALYSIS}"
else
export NST_FILE="NULL"
COMIN="${COMIN_ATMOS_RESTART_PREV}"
fi

# determine where the input snow restart files come from
if [[ ${DO_JEDISNOWDA:-"NO"} = "YES" ]]; then
src_dir="${COM_SNOW_ANALYSIS}"
# global_cycle executable specific variables
export APRUNCY=${APRUN_CYCLE}
export OMP_NUM_THREADS_CY=${NTHREADS_CYCLE}
export MAX_TASKS_CY=${ntiles}

# Copy fix files required by global_cycle to DATA just once
for (( nn=1; nn <= ntiles; nn++ )); do
${NCP} "${FIXgfs}/orog/${CASE}/${CASE}_grid.tile${nn}.nc" "${DATA}/fngrid.00${nn}"
${NCP} "${FIXgfs}/orog/${CASE}/${CASE}.mx${OCNRES}_oro_data.tile${nn}.nc" "${DATA}/fnorog.00${nn}"
done

# Copy the NSST analysis file for global_cycle
# There is only a single NSST analysis at the middle of the window
# For now use/assume it is the same at the beginning of the window if doing IAU
if [[ "${DONST}" == "YES" ]]; then
${NCP} "${COMIN_ATMOS_ANALYSIS}/${APREFIX}dtfanl.nc" "${DATA}/dtfanl"
export NST_FILE="dtfanl"
else
src_dir="${COM_ATMOS_RESTART_PREV}"
export NST_FILE="NULL"
fi

if [[ ${DOIAU} = "YES" ]]; then
# update surface restarts at the beginning of the window, if IAU
# For now assume/hold dtfanl.nc valid at beginning of window
for n in $(seq 1 ${ntiles}); do
${NCP} "${src_dir}/${bPDY}.${bcyc}0000.sfc_data.tile${n}.nc" \
"${COM_ATMOS_RESTART}/${bPDY}.${bcyc}0000.sfcanl_data.tile${n}.nc"
${NLN} "${src_dir}/${bPDY}.${bcyc}0000.sfc_data.tile${n}.nc" "${DATA}/fnbgsi.00${n}"
${NLN} "${COM_ATMOS_RESTART}/${bPDY}.${bcyc}0000.sfcanl_data.tile${n}.nc" "${DATA}/fnbgso.00${n}"
${NLN} "${FIXgfs}/orog/${CASE}/${CASE}_grid.tile${n}.nc" "${DATA}/fngrid.00${n}"
${NLN} "${FIXgfs}/orog/${CASE}/${CASE}.mx${OCNRES}_oro_data.tile${n}.nc" "${DATA}/fnorog.00${n}"
done

export APRUNCY=${APRUN_CYCLE}
export OMP_NUM_THREADS_CY=${NTHREADS_CYCLE}
export MAX_TASKS_CY=${ntiles}

CDATE="${PDY}${cyc}" ${CYCLESH}
export err=$?; err_chk
# Collect the dates in the window to update surface restarts
gcycle_dates=("${PDY}${cyc}") # Always update surface restarts at middle of window
if [[ "${DOIAU:-}" == "YES" ]]; then # Update surface restarts at beginning of window
half_window=$(( assim_freq / 2 ))
BDATE=$(date --utc -d "${PDY} ${cyc} - ${half_window} hours" +%Y%m%d%H)
gcycle_dates+=("${BDATE}")
fi

# Update surface restarts at middle of window
for n in $(seq 1 ${ntiles}); do
${NCP} "${src_dir}/${PDY}.${cyc}0000.sfc_data.tile${n}.nc" \
"${COM_ATMOS_RESTART}/${PDY}.${cyc}0000.sfcanl_data.tile${n}.nc"
${NLN} "${src_dir}/${PDY}.${cyc}0000.sfc_data.tile${n}.nc" "${DATA}/fnbgsi.00${n}"
${NLN} "${COM_ATMOS_RESTART}/${PDY}.${cyc}0000.sfcanl_data.tile${n}.nc" "${DATA}/fnbgso.00${n}"
${NLN} "${FIXgfs}/orog/${CASE}/${CASE}_grid.tile${n}.nc" "${DATA}/fngrid.00${n}"
${NLN} "${FIXgfs}/orog/${CASE}/${CASE}.mx${OCNRES}_oro_data.tile${n}.nc" "${DATA}/fnorog.00${n}"
done
# Loop over the dates in the window to update the surface restarts
for gcycle_date in "${gcycle_dates[@]}"; do

export APRUNCY=${APRUN_CYCLE}
export OMP_NUM_THREADS_CY=${NTHREADS_CYCLE}
export MAX_TASKS_CY=${ntiles}
echo "Updating surface restarts for ${gcycle_date} ..."

CDATE="${PDY}${cyc}" ${CYCLESH}
export err=$?; err_chk
datestr="${gcycle_date:0:8}.${gcycle_date:8:2}0000"

# Copy inputs from COMIN to DATA
for (( nn=1; nn <= ntiles; nn++ )); do
${NCP} "${COMIN}/${datestr}.sfc_data.tile${nn}.nc" "${DATA}/fnbgsi.00${nn}"
${NCP} "${COMIN}/${datestr}.sfc_data.tile${nn}.nc" "${DATA}/fnbgso.00${nn}"
done

################################################################################
# Postprocessing
cd ${pwd}
[[ ${mkdata} = "YES" ]] && rm -rf ${DATA}
CDATE="${gcyle_date}" ${CYCLESH}
export err=$?; err_chk

# Copy outputs from DATA to COMOUT
for (( nn=1; nn <= ntiles; nn++ )); do
${NCP} "${DATA}/fnbgso.00${nn}" "${COMOUT_ATMOS_RESTART}/${datestr}.sfcanl_data.tile${nn}.nc"
done

done


################################################################################

exit ${err}
exit "${err}"

################################################################################