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submit_cycle.sh
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submit_cycle.sh
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#!/bin/bash
#SBATCH --job-name=ufs_land_da
#SBATCH --account=da-cpu
#SBATCH --qos=debug
#SBATCH --nodes=1
#SBATCH --tasks-per-node=6
#SBATCH --cpus-per-task=1
#SBATCH -t 00:06:00
#SBATCH -o log_noahmp.%j.log
#SBATCH -e err_noahmp.%j.err
############################
# loop over time steps
source $analdate
THISDATE=$STARTDATE
date_count=0
while [ $date_count -lt $cycles_per_job ]; do
if [ $THISDATE -ge $ENDDATE ]; then
echo "All done, at date ${THISDATE}" >> $logfile
cd $CYCLEDIR
if [ $KEEPWORKDIR == "NO" ]; then
rm -rf $WORKDIR
fi
exit
fi
echo "starting $THISDATE"
# get DA settings
this_config=DA_config$HH
DA_config=${!this_config}
if [ $DA_config == "openloop" ]; then do_jedi="NO" ; else do_jedi="YES" ; fi
# substringing to get yr, mon, day, hr info
YYYY=`echo $THISDATE | cut -c1-4`
MM=`echo $THISDATE | cut -c5-6`
DD=`echo $THISDATE | cut -c7-8`
HH=`echo $THISDATE | cut -c9-10`
# substringing to get yr, mon, day, hr info for previous cycle
PREVDATE=`${incdate} $THISDATE -6`
YYYP=`echo $PREVDATE | cut -c1-4`
MP=`echo $PREVDATE | cut -c5-6`
DP=`echo $PREVDATE | cut -c7-8`
HP=`echo $PREVDATE | cut -c9-10`
# substring for next cycle
NEXTDATE=`${incdate} $THISDATE $FCSTHR`
nYYYY=`echo $NEXTDATE | cut -c1-4`
nMM=`echo $NEXTDATE | cut -c5-6`
nDD=`echo $NEXTDATE | cut -c7-8`
nHH=`echo $NEXTDATE | cut -c9-10`
############################
# copy restarts to workdir, convert to UFS tile for DA (all members)
mem_ens="mem000"
MEM_WORKDIR=${WORKDIR}/${mem_ens}
MEM_MODL_OUTDIR=${OUTDIR}/${mem_ens}
cd $MEM_WORKDIR
if [[ $do_jedi == "YES" && $atmos_forc == "era5" ]]; then
# copy restarts into work directory
rst_in=${MEM_MODL_OUTDIR}/restarts/vector/ufs_land_restart_back.${YYYY}-${MM}-${DD}_${HH}-00-00.nc
if [[ ! -e ${rst_in} ]]; then
rst_in=${LANDDA_INPUTS}/restarts/${atmos_forc}/ufs_land_restart.${YYYY}-${MM}-${DD}_${HH}-00-00.nc
fi
rst_out=${MEM_WORKDIR}/ufs_land_restart.${YYYY}-${MM}-${DD}_${HH}-00-00.nc
cp ${rst_in} ${rst_out}
echo '************************************************'
echo 'calling vector2tile'
export MEM_WORKDIR
# update vec2tile and tile2vec namelists
cp ${CYCLEDIR}/parm/templates/template.vector2tile vector2tile.namelist
sed -i "s|LANDDA_INPUTS|${LANDDA_INPUTS}|g" vector2tile.namelist
sed -i -e "s/XXYYYY/${YYYY}/g" vector2tile.namelist
sed -i -e "s/XXMM/${MM}/g" vector2tile.namelist
sed -i -e "s/XXDD/${DD}/g" vector2tile.namelist
sed -i -e "s/XXHH/${HH}/g" vector2tile.namelist
sed -i -e "s/XXHH/${HH}/g" vector2tile.namelist
sed -i -e "s/MODEL_FORCING/${atmos_forc}/g" vector2tile.namelist
sed -i -e "s/XXRES/${RES}/g" vector2tile.namelist
sed -i -e "s/XXTSTUB/${TSTUB}/g" vector2tile.namelist
sed -i -e "s#XXTPATH#${TPATH}#g" vector2tile.namelist
# submit vec2tile
echo '************************************************'
echo 'calling vector2tile'
if [[ $BASELINE =~ 'hera.internal' ]]; then
source ${CYCLEDIR}/land_mods
fi
$vec2tileexec vector2tile.namelist
if [[ $? != 0 ]]; then
echo "vec2tile failed"
exit
fi
fi # vector2tile for DA
if [[ $do_jedi == "YES" && $atmos_forc == "gswp3" ]]; then
echo '************************************************'
echo 'calling tile2tile'
export MEM_WORKDIR
# copy restarts into work directory
for tile in 1 2 3 4 5 6
do
rst_in=${MEM_MODL_OUTDIR}/restarts/tile/ufs_land_restart_back.${YYYY}-${MM}-${DD}_${HH}-00-00.nc
if [[ ! -e ${rst_in} ]]; then
rst_in=${LANDDA_INPUTS}/restarts/${atmos_forc}/ufs.cpld.lnd.out.${YYYY}-${MM}-${DD}-00000.tile${tile}.nc
fi
rst_out=${MEM_WORKDIR}/ufs_land_restart.${YYYY}-${MM}-${DD}_${HH}-00-00.tile${tile}.nc
cp ${rst_in} ${rst_out}
done
# update tile2tile namelist
cp ${CYCLEDIR}/parm/templates/template.ufs2jedi ufs2jedi.namelist
sed -i "s|LANDDA_INPUTS|${LANDDA_INPUTS}|g" ufs2jedi.namelist
sed -i -e "s/XXYYYY/${YYYY}/g" ufs2jedi.namelist
sed -i -e "s/XXMM/${MM}/g" ufs2jedi.namelist
sed -i -e "s/XXDD/${DD}/g" ufs2jedi.namelist
sed -i -e "s/XXHH/${HH}/g" ufs2jedi.namelist
sed -i -e "s/XXHH/${HH}/g" ufs2jedi.namelist
sed -i -e "s/MODEL_FORCING/${atmos_forc}/g" ufs2jedi.namelist
sed -i -e "s/XXRES/${RES}/g" ufs2jedi.namelist
sed -i -e "s/XXTSTUB/${TSTUB}/g" ufs2jedi.namelist
sed -i -e "s#XXTPATH#${TPATH}#g" ufs2jedi.namelist
# submit tile2tile
if [[ $BASELINE =~ 'hera.internal' ]]; then
source ${CYCLEDIR}/land_mods
fi
$tile2tileexec ufs2jedi.namelist
if [[ $? != 0 ]]; then
echo "tile2tile failed"
exit
fi
fi # tile2tile for DA
############################
# do DA update
if [[ $do_jedi == "YES" ]]; then
# submit snow DA
echo '************************************************'
echo 'calling snow DA'
cd $WORKDIR
export THISDATE
export EXECdir="${CYCLEDIR}/exec"
$DAscript ${CYCLEDIR}/$DA_config
if [[ $? != 0 ]]; then
echo "land DA script failed"
exit
fi
fi
############################
# convert back to vector/tile
mem_ens="mem000"
MEM_WORKDIR=${WORKDIR}/${mem_ens}
MEM_MODL_OUTDIR=${OUTDIR}/${mem_ens}
cd $MEM_WORKDIR
# convert back to vector, run model (all members) convert back to vector, run model (all members)
if [[ $do_jedi == "YES" && $atmos_forc == "era5" ]]; then
echo '************************************************'
echo 'calling tile2vector'
if [[ $BASELINE =~ 'hera.internal' ]]; then
source ${CYCLEDIR}/land_mods
fi
cp ${CYCLEDIR}/parm/templates/template.tile2vector tile2vector.namelist
sed -i "s|LANDDA_INPUTS|${LANDDA_INPUTS}|g" tile2vector.namelist
sed -i -e "s/XXYYYY/${YYYY}/g" tile2vector.namelist
sed -i -e "s/XXMM/${MM}/g" tile2vector.namelist
sed -i -e "s/XXDD/${DD}/g" tile2vector.namelist
sed -i -e "s/XXHH/${HH}/g" tile2vector.namelist
sed -i -e "s/MODEL_FORCING/${atmos_forc}/g" vector2tile.namelist
sed -i -e "s/XXRES/${RES}/g" tile2vector.namelist
sed -i -e "s/XXTSTUB/${TSTUB}/g" tile2vector.namelist
sed -i -e "s#XXTPATH#${TPATH}#g" tile2vector.namelist
$vec2tileexec tile2vector.namelist
if [[ $? != 0 ]]; then
echo "tile2vector failed"
exit
fi
# save analysis restart
cp ${MEM_WORKDIR}/ufs_land_restart.${YYYY}-${MM}-${DD}_${HH}-00-00.nc ${MEM_MODL_OUTDIR}/restarts/vector/ufs_land_restart_anal.${YYYY}-${MM}-${DD}_${HH}-00-00.nc
fi
# convert back to UFS tile, run model (all members)
if [[ $do_jedi == "YES" && $atmos_forc == "gswp3" ]]; then
echo '************************************************'
echo 'calling tile2tile'
if [[ $BASELINE =~ 'hera.internal' ]]; then
source ${CYCLEDIR}/land_mods
fi
cp ${CYCLEDIR}/parm/templates/template.jedi2ufs jedi2ufs.namelist
sed -i "s|LANDDA_INPUTS|${LANDDA_INPUTS}|g" jedi2ufs.namelist
sed -i -e "s/XXYYYY/${YYYY}/g" jedi2ufs.namelist
sed -i -e "s/XXMM/${MM}/g" jedi2ufs.namelist
sed -i -e "s/XXDD/${DD}/g" jedi2ufs.namelist
sed -i -e "s/XXHH/${HH}/g" jedi2ufs.namelist
sed -i -e "s/MODEL_FORCING/${atmos_forc}/g" jedi2ufs.namelist
sed -i -e "s/XXRES/${RES}/g" jedi2ufs.namelist
sed -i -e "s/XXTSTUB/${TSTUB}/g" jedi2ufs.namelist
sed -i -e "s#XXTPATH#${TPATH}#g" jedi2ufs.namelist
$tile2tileexec jedi2ufs.namelist
if [[ $? != 0 ]]; then
echo "tile2tile failed"
exit
fi
# save analysis restart
for tile in 1 2 3 4 5 6
do
cp ${MEM_WORKDIR}/ufs_land_restart.${YYYY}-${MM}-${DD}_${HH}-00-00.tile${tile}.nc ${MEM_MODL_OUTDIR}/restarts/tile/ufs_land_restart_anal.${YYYY}-${MM}-${DD}_${HH}-00-00.tile${tile}.nc
cp ${MEM_WORKDIR}/ufs_land_restart.${YYYY}-${MM}-${DD}_${HH}-00-00.tile${tile}.nc ${MEM_MODL_OUTDIR}/restarts/tile/ufs.cpld.lnd.out.${YYYY}-${MM}-${DD}-00000.tile${tile}.nc
done
fi
############################
# run the forecast model
if [[ $do_jedi == "YES" && $atmos_forc == "era5" ]]; then
echo '************************************************'
echo 'running the forecast model'
set -x
# update model namelist
cp ${CYCLEDIR}/parm/templates/template.ufs-noahMP.namelist.${atmos_forc} ufs-land.namelist
sed -i "s|LANDDA_INPUTS|${LANDDA_INPUTS}|g" ufs-land.namelist
sed -i -e "s/XXYYYY/${YYYY}/g" ufs-land.namelist
sed -i -e "s/XXMM/${MM}/g" ufs-land.namelist
sed -i -e "s/XXDD/${DD}/g" ufs-land.namelist
sed -i -e "s/XXHH/${HH}/g" ufs-land.namelist
sed -i -e "s/XXFREQ/${FREQ}/g" ufs-land.namelist
sed -i -e "s/XXRDD/${RDD}/g" ufs-land.namelist
sed -i -e "s/XXRHH/${RHH}/g" ufs-land.namelist
# submit model
echo $MEM_WORKDIR
nt=$SLURM_NTASKS
if [[ $BASELINE =~ 'hera.internal' ]]; then
source ${CYCLEDIR}/land_mods
fi
if [[ $BASELINE =~ 'hera.internal' ]]; then
srun '--export=ALL' --label -K -n $nt $LSMexec
else
${MPIEXEC} -n 1 $LSMexec
fi
fi
# no error codes on exit from model, check for restart below instead
if [[ $do_jedi == "YES" && $atmos_forc == "gswp3" ]]; then
set -e
echo '************************************************'
echo 'running the forecast model'
TEST_NAME=datm_cdeps_lnd_gswp3
TEST_NAME_RST=datm_cdeps_lnd_gswp3_rst
PATHRT=${CYCLEDIR}/sorc/ufs_model.fd/tests
RT_COMPILER=${RT_COMPILER:-intel}
ATOL="1e-7"
cp $CYCLEDIR/$TEST_NAME_RST ${PATHRT}/tests/$TEST_NAME_RST
source ${PATHRT}/detect_machine.sh
source ${PATHRT}/rt_utils.sh
source ${PATHRT}/default_vars.sh
source ${PATHRT}/tests/$TEST_NAME_RST
source ${PATHRT}/atparse.bash
BL_DATE=20230816
RTPWD=${RTPWD:-${LANDDA_INPUTS}/NEMSfv3gfs/develop-${BL_DATE}/INTEL/${TEST_NAME}}
INPUTDATA_ROOT=${INPUTDATA_ROOT:-${LANDDA_INPUTS}/NEMSfv3gfs/input-data-20221101}
echo "RTPWD= $RTPWD"
echo "INPUTDATA_ROOT= $INPUTDATA_ROOT"
if [[ ! -d ${INPUTDATA_ROOT} ]] || [[ ! -d ${RTPWD} ]]; then
echo "Error: cannot find either folder for INPUTDATA_ROOT or RTPWD, please check!"
exit 1
fi
# create run folder
RUNDIR=${MEM_MODL_OUTDIR}/noahmp/${TEST_NAME_RST}
[[ -d ${RUNDIR} ]] && echo "Warning: remove old run folder!" && rm -rf ${RUNDIR}
mkdir -p ${RUNDIR}
cd ${RUNDIR}
echo "NoahMP run dir= $RUNDIR"
# modify some env variables - reduce core usage
export ATM_compute_tasks=0
export ATM_io_tasks=1
export LND_tasks=6
export layout_x=1
export layout_y=1
# FV3 executable:
cp ${CYCLEDIR}/exec/ufs_model .
cp ${CYCLEDIR}/fv3_run ./fv3_run
if [[ $DATM_CDEPS = 'true' ]] || [[ $FV3 = 'true' ]] || [[ $S2S = 'true' ]]; then
if [[ $HAFS = 'false' ]] || [[ $FV3 = 'true' && $HAFS = 'true' ]]; then
atparse < ${PATHRT}/parm/${INPUT_NML:-input.nml.IN} > input.nml
fi
fi
atparse < ${PATHRT}/parm/${MODEL_CONFIGURE:-model_configure.IN} > model_configure
compute_petbounds_and_tasks
atparse < ${PATHRT}/parm/${UFS_CONFIGURE:-ufs.configure} > ufs.configure
# diag table
if [[ "Q${DIAG_TABLE:-}" != Q ]] ; then
atparse < ${PATHRT}/parm/diag_table/${DIAG_TABLE} > diag_table
fi
# Field table
if [[ "Q${FIELD_TABLE:-}" != Q ]] ; then
cp ${PATHRT}/parm/field_table/${FIELD_TABLE} field_table
fi
# Field Dictionary
cp ${PATHRT}/parm/fd_ufs.yaml fd_ufs.yaml
# Set up the run directory
source ./fv3_run
if [[ $DATM_CDEPS = 'true' ]]; then
atparse < ${PATHRT}/parm/${DATM_IN_CONFIGURE:-datm_in.IN} > datm_in
atparse < ${PATHRT}/parm/${DATM_STREAM_CONFIGURE:-datm.streams.IN} > datm.streams
fi
# NoahMP table file
cp ${PATHRT}/parm/noahmptable.tbl noahmptable.tbl
# start runs
echo "Start ufs-cdeps-land model run with TASKS: ${TASKS}"
export MPIRUN=${MPIRUN:-`which mpiexec`}
${MPIRUN} -n ${TASKS} ./ufs_model
fi
# no error codes on exit from model, check for restart below instead
############################
# check model ouput (all members)
mem_ens="mem000"
MEM_WORKDIR=${WORKDIR}/${mem_ens}
MEM_MODL_OUTDIR=${OUTDIR}/${mem_ens}
if [[ $atmos_forc == "era5" ]]; then
# if [[ -e ${MEM_WORKDIR}/ufs_land_restart.${nYYYY}-${nMM}-${nDD}_${nHH}-00-00.nc ]]; then
cp ${MEM_WORKDIR}/ufs_land_restart.${nYYYY}-${nMM}-${nDD}_${nHH}-00-00.nc ${MEM_MODL_OUTDIR}/restarts/vector/ufs_land_restart_back.${nYYYY}-${nMM}-${nDD}_${nHH}-00-00.nc
else
for tile in 1 2 3 4 5 6
do
cp ${MEM_WORKDIR}/noahmp_output/${TEST_NAME_RST}/ufs.cpld.lnd.out.${nYYYY}-${nMM}-${nDD}-00000.tile${tile}.nc ${MEM_MODL_OUTDIR}/restarts/tile/ufs_land_restart_back.${nYYYY}-${nMM}-${nDD}_${nHH}-00-00.tile${tile}.nc
done
fi
THISDATE=$NEXTDATE
date_count=$((date_count+1))
done # date_count -lt cycles_per_job
############################
# resubmit script
if [ $THISDATE -lt $ENDDATE ]; then
echo "STARTDATE=${THISDATE}" > ${analdate}
echo "ENDDATE=${ENDDATE}" >> ${analdate}
cd ${CYCLEDIR}
sbatch ${CYCLEDIR}/submit_cycle.sh
fi