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- # Function leap days calculates the number of leap days (29th of Februrary) in
- # a time intervall between two dates.
- #
- # Usage leap_days START_DATE END_DATE
- function leap_days()
- {
- local ld=0
- local frstYYYY=$(date -ud "$1" +%Y)
- local lastYYYY=$(date -ud "$2" +%Y)
- set +e
- # Check first year for leap day between start and end date
- $(date -ud "${frstYYYY}-02-29" > /dev/null 2>&1) \
- && (( $(date -ud "$1" +%s) < $(date -ud "${frstYYYY}-03-01" +%s) )) \
- && (( $(date -ud "$2" +%s) > $(date -ud "${lastYYYY}-02-28" +%s) )) \
- && (( ld++ ))
- # Check intermediate years for leap day
- for (( y=(( ${frstYYYY}+1 )); y<=(( ${lastYYYY}-1 )); y++ ))
- do
- $(date -ud "$y-02-29" > /dev/null 2>&1) && (( ld++ ))
- done
- # Check last year (if different from first year) for leap day between start
- # and end date
- (( $lastYYYY > $frstYYYY )) \
- && $(date -ud "${lastYYYY}-02-29" > /dev/null 2>&1) \
- && (( $(date -ud "$1" +%s) < $(date -ud "${frstYYYY}-03-01" +%s) )) \
- && (( $(date -ud "$2" +%s) > $(date -ud "${lastYYYY}-02-28" +%s) )) \
- && (( ld++ ))
- set -e
- echo "$ld"
- }
- [[ $@ == *verbose* ]] && set -x
- module load ${module_list:?}
- export LD_LIBRARY_PATH=${LD_LIBRARY_PATH:+${LD_LIBRARY_PATH}:}"${extralibs_list}"
- mkdir -p ${run_dir}
- cd ${run_dir}
- run_start_epoch=$(date -u -d"${run_start_date}" +%s)
- run_start_date_cos="${run_start_date//-}00"
- run_start_date=$(date -uR -d "${run_start_date}")
- run_end_date="${run_start_date} + ${run_duration:?}"
- run_end_date=$(date -uR -d "${run_end_date}")
- run_end_epoch=$(date -u -d"${run_end_date}" +%s)
- run_end_date_cos="$(date -u -d"${run_end_date}" +%Y%m%d%H)"
- if [[ ${special_rs_nemo} == "true" && ${special_restart} == "true" ]]; then
- echo "ERROR: both special_rs_nemo and special_restart are true. only can be true (at most). exit".
- exit 2
- fi
- for (( ; run_num_legs>0 ; run_num_legs-- ))
- do
- # Check for restart information file and set the current leg start date
- # Ignore restart information file if force_run_from_scratch is true
- if ! [ -r ${info_file} ]
- then
- leg_is_restart=false
- leg_start_date=${run_start_date}
- leg_start_date_cos=${run_start_date_cos}
- leg_number=1
- echo "leg_is_restart=false"
- else
- leg_is_restart=true
- . ./${info_file}
- leg_start_date=${leg_end_date}
- leg_start_date_cos="$(date -u -d"${leg_start_date}" +%Y%m%d%H)"
- leg_number=$((leg_number+1))
- echo "leg_is_restart=true"
- fi
- # Compute the end date of the current leg
- if [ -n "${rst_freq}" ]
- then
- if (($(date -u -d "${leg_start_date:?} + ${rst_freq}" +%s) > $(date -u -d "${leg_start_date:?} + ${run_duration}" +%s) )); then
- rst_freq=$run_duration
- fi
- leg_end_date=$(date -uR -d "${leg_start_date} + ${rst_freq}")
- leg_end_date_cos="$(date -u -d"${leg_end_date}" +%Y%m%d%H)"
- else
- leg_end_date=${run_end_date}
- leg_end_date_cos=${run_end_date_cos}
- fi
- if [ $(date -u -d "${leg_end_date}" +%s) -gt $(date -u -d "${run_end_date}" +%s) ]
- then
- leg_end_date=${run_end_date}
- leg_end_date_cos=${run_end_date_cos}
- fi
- # Some time variables needed later
- leg_start_epoch=$(date -u -d "${leg_start_date}" +%s)
- leg_end_epoch=$(date -u -d "${leg_start_date:?} + ${rst_freq:=$run_duration}" +%s)
- leg_length_sec=$(( $(date -u -d "${leg_end_date}" +%s) - $(date -u -d "${leg_start_date}" +%s) ))
- leg_start_sec=$(( $(date -u -d "${leg_start_date}" +%s) - $(date -u -d "${run_start_date}" +%s) ))
- leg_end_sec=$(( $(date -u -d "${leg_end_date}" +%s) - $(date -u -d "${run_start_date}" +%s) ))
- leg_start_date_yyyymmdd=$(date -u -d "${leg_start_date}" +%Y%m%d)
- leg_start_date_yyyy=$(date -u -d "${leg_start_date}" +%Y)
- leg_end_date_yyyy=$(date -u -d "${leg_end_date}" +%Y)
- echo "leg_number: $leg_number"
- echo "leg_start_date: $leg_start_date"
- echo "leg_end_date: $leg_end_date"
- # Check whether there's actually time left to simulate - exit otherwise
- if [ ${leg_length_sec} -le 0 ]
- then
- info "Leg start date equal to or after end of simulation."
- info "Nothing left to do. Exiting."
- exit 0
- fi
- # -------------------------------------------------------------------------
- # *** Prepare the run directory for a run from scratch
- # -------------------------------------------------------------------------
- if ! $leg_is_restart
- then
- # ---------------------------------------------------------------------
- # *** Check if run dir is empty. If not, and if we are allowed to do so
- # by ${force_run_from_scratch}, remove everything
- # ---------------------------------------------------------------------
- echo "pwd: $PWD"
- if $(ls * >& /dev/null)
- then
- if ${force_run_from_scratch}
- then
- rm -fr ${run_dir}/*
- else
- echo "error: run directory not empty and \$force_run_from_scratch not set."
- exit 0
- fi
- fi
- # ---------------------------------------------------------------------
- # *** Creates some directories
- # ---------------------------------------------------------------------
- mkdir -p ${out_dir}
-
- # ---------------------------------------------------------------------
- # *** Copy executables and coupling-related files
- # ---------------------------------------------------------------------
- cd ${start_dir}
- cp -u xios_config/*xml "${run_dir}"
- cp -u namelists/* "${run_dir}"
- cd ${run_dir}
- cp -u "${nem_exe_file:?}" .
- cp -u "${xio_exe_file:?}" .
- # ---------------------------------------------------------------------
- # *** Link ic, forcing and shared files for NEMO
- # ---------------------------------------------------------------------
- [[ ! -f EMPave_old.dat ]] && echo " 0 0.0000000000000000E+00 0.0000000000000000E+00" > EMPave_old.dat
- for file in "${ic_files[@]}"; do
- [[ ! -e ${file#*> } ]] && ln -sf $(sed 's/ *=> */ /' <<< "${ini_data_dir}/${ic_subdir}/${nem_grid}/$file")
- done
- for file in "${forcing_files[@]}"; do
- [[ ! -e ${file#*> } || "$file" == \** ]] && ln -sf $(sed 's/ *=> */ /' <<< "${ini_data_dir}/${forcing_subdir}/${nem_forcing_set}/$file")
- done
- for file in "${shared_files[@]}"; do
- [[ ! -e ${file#*> } ]] && ln -sf $(sed 's/ *=> */ /' <<< "${shared_dir}/$file")
- done
- # ---------------------------------------------------------------------
- # *** Copy potential special restarts
- # ---------------------------------------------------------------------
- if $special_restart
- then
- ### Getting the right output folders
- leg_start_date_tmp=$leg_start_date
- leg_end_date_tmp=$leg_end_date
- leg_number_tmp=$leg_number
- rsync -avz ${run_dir}/../../${special_restart_from}/rundir/${info_file} ${run_dir}
- special_date=$(date -uR -d "${special_restart_date}")
- sed -i "/$special_date/q" ${run_dir}/${info_file}
- . ${run_dir}/${info_file}
- special_restart_leg=$(printf %03d $((leg_number)))
- echo "special_date: $special_date"
- echo "special_restart_leg: $special_restart_leg"
- echo "special_restart_from: $special_restart_from"
- ### NEMO
- indir="${run_dir}/../../${special_restart_from}/archive/restart/nemo/$(printf %03d $((special_restart_leg)))"
- cd ${indir}
- for f in *.nc; do
- nf=`echo "${f/$special_restart_from/$exp_name}"`
- echo "copy $f to ${run_dir}/$nf"
- cp $f ${run_dir}/$nf
- done
- cd -
- cd ${run_dir}
- echo "pwd: $PWD"
- for f in ${exp_name}_????????_restart_???_????.nc; do
- nf=`echo ${f: -19}`
- echo "linking $f to ${run_dir}/$nf"
- ln -s $f $nf
- done
- cd ${run_dir}
- rm -rf ${info_file}
- leg_start_date=$leg_start_date_tmp
- leg_end_date=$leg_end_date_tmp
- leg_number=$leg_number_tmp
- elif ${special_rs_nemo}
- then
- dir_rs=`dirname ${special_rs_nemo_stencil}`
- base_rs=`basename ${special_rs_nemo_stencil}`
-
- n_oce_rs=`find ${dir_rs} -name "${base_rs}oce_????.nc" | wc -l`
- if(( n_oce_rs != nem_numproc )); then
- echo "in special_rs_nemo, not the right amount of ocean restart files."
- echo "${n_oce_rs} instead of ${nem_numproc}. exiting."
- exit 2
- fi
- n_ice_rs=`find ${dir_rs} -name "${base_rs}ice_????.nc" | wc -l`
- if(( n_ice_rs != nem_numproc )); then
- echo "in special_rs_nemo, not the right amount of ice restart files."
- echo "${n_ice_rs} instead of ${nem_numproc}. exiting."
- exit 2
- fi
-
- for (( n=0 ; n<nem_numproc ; n++ ))
- do
- np=$(printf %04d ${n})
- ln -fs ${special_rs_nemo_stencil}oce_${np}.nc restart_oce_${np}.nc
- ln -fs ${special_rs_nemo_stencil}ice_${np}.nc restart_ice_${np}.nc
- done
- fi # if $special_restart
- else # if ! $leg_is_restart
- # ---------------------------------------------------------------------
- # *** Creates some directories
- # ---------------------------------------------------------------------
- mkdir -p ${out_dir}
- # ---------------------------------------------------------------------
- # *** Copy restart files in run directory
- # ---------------------------------------------------------------------
- cd ${run_dir}
- ### NEMO
- outdir="${archive_dir}/restart/nemo/$(printf %03d $((leg_number-1)))"
-
- ns=$(printf %08d $(( leg_start_sec / nem_time_step_sec )))
- for f in oce ice
- do
- echo "${outdir}/${exp_name}_${ns}_restart_${f}_????.nc"
- ln -sf ${outdir}/${exp_name}_${ns}_restart_${f}_????.nc ${run_dir}
- done
- for (( n=0 ; n<nem_numproc ; n++ ))
- do
- np=$(printf %04d ${n})
- ln -fs ${exp_name}_${ns}_restart_oce_${np}.nc restart_oce_${np}.nc
- ln -fs ${exp_name}_${ns}_restart_ice_${np}.nc restart_ice_${np}.nc
- done
- fi # ! $leg_is_restart
- # -------------------------------------------------------------------------
- # *** Update ocean namelist
- # -------------------------------------------------------------------------
- source build_namelist_cfg.sh > namelist_cfg
- # -------------------------------------------------------------------------
- # *** Launch experiment
- # -------------------------------------------------------------------------
-
- echo "START of mpirun"
- time_begin=$(date +%s)
- mpirun -np "${xio_numproc:?}" "${xio_exe_file:?}" : -np "${nem_numproc:?}" "${nem_exe_file:?}"
- time_end=$(date +%s)
- echo "END of: mpirun"
- # -------------------------------------------------------------------------
- # *** Move output files to archive directory
- # -------------------------------------------------------------------------
- ### NEMO
- outdir="${archive_dir}/output/nemo/$(printf %03d $((leg_number)))"
- mkdir -p ${outdir}
- for v in grid_U grid_V grid_W grid_T icemod SBC scalar SBC_scalar diad_T \
- grid_T_2D grid_U_2D grid_V_2D grid_W_2D grid_T_3D grid_U_3D grid_V_3D grid_W_3D \
- grid_1point grid_T_3D_ncatice vert_sum \
- grid_ptr_W_3basin_3D grid_ptr_T_3basin_2D grid_ptr_T_2D \
- zoom_700_sum zoom_300_sum zoom_2000_sum
- do
- for f in ${exp_name}_*_????????_????????_*${v}*.nc
- do
- test -f $f && mv $f $outdir/
- done
- done
-
- # -------------------------------------------------------------------------
- # *** Move restart files to archive directory
- # -------------------------------------------------------------------------
- ### NEMO
- outdir="${archive_dir}/restart/nemo/$(printf %03d $((leg_number)))"
- mkdir -p ${outdir}
- ns=$(printf %08d $(( leg_end_sec / nem_time_step_sec )))
- for f in oce ice
- do
- mv ${exp_name}_${ns}_restart_${f}_????.nc ${outdir}
- done
- # -------------------------------------------------------------------------
- # *** Move log files to archive directory
- # -------------------------------------------------------------------------
- outdir="${archive_dir}/log/$(printf %03d $((leg_number)))"
- mkdir -p ${outdir}
- for f in \
- ocean.output time.step solver.stat
- do
- test -f ${f} && mv ${f} ${outdir}
- done
- # ---------------------------------------------------------------------
- # *** Remove all leftover output files from previous legs
- # ---------------------------------------------------------------------
- ### NEMO files
- rm -f ${exp_name}_??_????????_????????_{grid_U,grid_V,grid_W,grid_T,icemod,SBC,scalar,SBC_scalar}.nc
- rm -f ${exp_name}_*restart_*nc
- ns=$(printf %08d $(( leg_start_sec / nem_time_step_sec )))
- for (( n=0 ; n<nem_numproc ; n++ ))
- do
- np=$(printf %04d ${n})
- rm -f restart_oce_${np}.nc
- rm -f restart_ice_${np}.nc
- done
- # -------------------------------------------------------------------------
- # *** Write the restart control file
- # -------------------------------------------------------------------------
- shopt -u nullglob
- tr=$(date -d "0 -$time_begin sec + $time_end sec" +%T)
- current_date=$(date +'%F %T')
- {
- echo "#"
- echo "# Finished leg at ${current_date} after ${tr} (hh:mm:ss)"
- echo "leg_number=${leg_number}"
- echo "leg_start_date=\"${leg_start_date}\""
- echo "leg_end_date=\"${leg_end_date}\""
- } | tee -a "${info_file}"
- # Need to reset force_run_from_scratch in order to avoid destroying the next leg
- force_run_from_scratch=false
- special_restart=false
- done # Loop over legs
- cd ${start_dir}
- cd - >/dev/null
- [[ $@ == *noresubmit* ]] && exit 0
- if (( leg_end_epoch < run_end_epoch )) ; then
- echo "Leg end earlier than end of simulation."
- echo "Submitting another job."
- if [[ "$@" == *"local"* ]] ; then
- exec "$0" "$@"
- elif [ "qsub" == *sbatch* ] ; then
- sbatch $0 $@ | awk '{print $4}' >> ${run_dir}/.coral_jobs
- elif [[ $USER == "vsc"* ]]; then
- if [ -f ${PBS_O_WORKDIR-$PWD}/tmp/credits_file ]; then
- credits=`cat ${PBS_O_WORKDIR-$PWD}/tmp/credits_file`
- else
- credits_tmp=`grep "account string:" ${PBS_O_WORKDIR-$PWD}/*.o* -R | sed 's/^.*: //'`
- credits=`echo $credits_tmp | awk '{ print $1 }'`
- cd ${start_dir}
- mkdir -p tmp
- echo ${credits} > tmp/credits_file
- fi
- if [ -f ${PBS_O_WORKDIR-$PWD}/tmp/script_name ]; then
- script_name=`cat ${PBS_O_WORKDIR-$PWD}/tmp/script_name`
- else
- script_name="run.sh"
- fi
- ssh login2 "cd $start_dir; qsub -A $credits $script_name | tee -a coral_jobs"
- sleep 2
- jobid=`cat coral_jobs`
- rm -f coral_jobs
- jobid=${jobid%%.*}
- echo "${jobid}" >> "${run_dir}"/.coral_jobs ;
- else
- "qsub" -v PBS_OPTIONS="$@" "$0" | tee -a coral_jobs
- sleep 2
- jobid=`cat coral_jobs`
- rm -f coral_jobs
- jobid=${jobid%.*}
- echo "${jobid}" >> "${run_dir}"/.coral_jobs
- fi
- else
- if [[ $USER == "vsc"* ]]; then
- rm -rf ${start_dir}/tmp
- fi
- rm -rf ${run_dir}/../cclm_out_tmp
- echo "Nothing left to do. Exiting."
- cat << "EOF"
- _____ _ _ _ _ _ _ _
- / ____(_) | | | | (_) | | | | | |
- | (___ _ _ __ ___ _ _| | __ _| |_ _ ___ _ __ ___ ___ _ __ ___ _ __ | | ___| |_ ___ __| |
- \___ \| | '_ ` _ \| | | | |/ _` | __| |/ _ \| '_ \ / __/ _ \| '_ ` _ \| '_ \| |/ _ \ __/ _ \/ _` |
- ____) | | | | | | | |_| | | (_| | |_| | (_) | | | | | (_| (_) | | | | | | |_) | | __/ || __/ (_| |
- |_____/|_|_| |_| |_|\__,_|_|\__,_|\__|_|\___/|_| |_| \___\___/|_| |_| |_| .__/|_|\___|\__\___|\__,_|
- | |
- |_|
- EOF
- fi
- exit 0
-
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