# 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" } # Function for loading modules function load_modules_isfcpl () { if [[ ${USER} == "vsc"????? ]]; then # quick and dirty patch - only BRENIAC will work while waiting for something to distinguish between both machines (include on computing nodes) # if [[ ${HOSTNAME} == "tier2"* ]]; then # if [[ "${name_icesheet_model}" == "fETISh" ]]; then # module purge # module load Python # PYTHONPATH="${HOME}/.local/bin:${HOME}/.local/lib/python3.7/site-packages:\${PYTHONPATH}" # module load CDO # echo ${PYTHONPATH} > ${start_dir}/ppath # echo "genius and fetish detected" > ${start_dir}/tmpout # else # echo "On Genius, ice sheet models other than fETISh not implemented yet" > ${start_dir}/tmpout # exit 2 # fi # elif [[ ${HOSTNAME} == "login"? ]]; then if [[ "${name_icesheet_model}" == "fETISh" ]]; then module purge module load Python/3.7.2-intel-2018a CDO/1.9.5-intel-2018a [ ! -d "${VSC_HOME}/.local/lib/python3.7/site-packages/netCDF4" ] && pip install --user netCDF4 [ ! -d "${VSC_HOME}/.local/lib/python3.7/site-packages/numpy" ] && pip install --target=${VSC_HOME}/.local/lib/python3.7/site-packages numpy [ ! -d "${VSC_HOME}/.local/lib/python3.7/site-packages/gsw" ] && pip install --user gsw PYTHONPATH="${HOME}/.local/bin:${HOME}/.local/lib/python3.7/site-packages:\${PYTHONPATH}" echo ${PYTHONPATH} > ${start_dir}/ppath echo "breniac and fetish detected" > ${start_dir}/tmpout else echo "On Breniac, ice sheet models other than fETISh not implemented yet" > ${start_dir}/tmpout exit 2 fi # else # echo "You seem to be on a VSC machine that is neither Genius nor BRENIAC. This has not been implemented yet. Exiting" # exit 2 # fi elif [[ ${HOSTNAME} == "lm3"* ]]; then if [[ "${name_icesheet_model}" == "fETISh" ]]; then echo "lemaitre3 and fetish detected" > ${start_dir}/tmpout module purge module load releases/2018a CDO/1.8.2-intel-2018a Python/3.6.4-intel-2018a else echo "On lemaitre3, ice sheet models other than fETISh not implemented yet" > ${start_dir}/tmpout exit 2 fi else echo "hostname undetected. not implemented yet." > ${start_dir}/tmpout exit 2 fi } [[ $@ == *verbose* ]] && set -x module load ${module_list:?} export LD_LIBRARY_PATH=${LD_LIBRARY_PATH:+${LD_LIBRARY_PATH}:}"${extralibs_list}" mkdir -p ${run_dir} cd ${run_dir} # Prepare iscpl if [ "${isfcpl}" == "1" ]; then if [[ ${USER} == "vsc"????? ]]; then if [[ ${VSC_INSTITUTE_CLUSTER} == "breniac" ]]; then echo "BRENIAC and iscpl detected. OK." else echo "VSC clusters other than BRENIAC not supported for isfcpl." exit 2 fi elif [[ ${HOSTNAME} == "lm3"* ]]; then echo "Lemaitre3 and iscpl detected. OK." else echo "You have asked for iscpl, but I have not recognized genius nor lemaitre3. Exiting." exit 2 fi if [ "${name_icesheet_model}" != "fETISh" ]; then echo "only \"fETISh\" is known as an ice sheet model. exiting." exit 2 fi length_cut_pref=$(( ${#exp_name} + 4 )) rebuild_nemo_exe=${nemo_src_dir}/TOOLS/REBUILD_NEMO/rebuild_nemo if [ -f ${start_dir}/isfcpl.track ]; then source ${start_dir}/isfcpl.track fi iscpl_nm=.true. if [[ ${xio_exe_file} == *"xios-2"* ]]; then is_xios2=1 else is_xios2=0 fi else iscpl_nm=.false. fi run_start_epoch=$(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: $leg_end_date" # Additional time variables for iscpl if (( isfcpl == 1 )); then leg_beforestart_epoch=$(( ${leg_start_epoch} - 43200 )) leg_beforestart_date=$(date -uR -d@"${leg_beforestart_epoch}") leg_almostend_epoch=$(( ${leg_end_epoch} - 43200 )) leg_almostend_date=$(date -uR -d@"${leg_almostend_epoch}") nextleg_start_epoch=$(( ${leg_end_epoch} + 43200 )) nextleg_start_date=$(date -uR -d@"${nextleg_start_epoch}") run_start_date_yyyymmdd=$(date -u -d "${run_start_date}" +%Y%m%d) # FIXME appears unused run_end_date_yyyymmdd=$(date -u -d "${run_end_date}" +%Y%m%d) # FIXME appears unused leg_start_date_yyyymmdd=$(date -u -d "${leg_start_date}" +%Y%m%d) # FIXME appears unused leg_almostend_date_yyyymmdd=$(date -u -d "${leg_almostend_date}" +%Y%m%d) # FIXME appears unused nextleg_start_date_yyyymmdd=$(date -u -d "${nextleg_start_date}" +%Y%m%d) # FIXME appears unused leg_beforestart_date_yyyymmdd=$(date -u -d "${leg_beforestart_date}" +%Y%m%d) # FIXME appears unused fi # 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:?}" . if (( isfcpl == 1 )) ; then cp -u ${icesheet_exe_file} . cp -u ${isfcpl_dir}/* . ln -sf ${start_dir}/isfcpl.track ${run_dir} mkdir -p ${out_dir}/isfcpl_tmp fi # --------------------------------------------------------------------- # *** Link ic, forcing and shared files for NEMO # --------------------------------------------------------------------- [[ ! -f EMPave_old.dat ]] && echo " 0 0.0000000000000000E+00 0.0000000000000000E+00" > EMPave_old.dat for file in "${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}/$file") done # --------------------------------------------------------------------- # *** Prepare NEMO - ice shelf coupling # --------------------------------------------------------------------- if [ "${isfcpl}" == "1" ]; then if (( leg_number == 1 )); then mkdir -p ${archive_dir}/isfcpl mkdir -p ${archive_dir}/${name_icesheet_model} rm -f ${start_dir}/isfcpl.track isfcpl_window_days=$(echo "(${n_res_perisfcpl} * ${leg_length_sec}) / 86400" | bc) isfcpl_d30=$(echo "${isfcpl_window_days} / 30" | bc -l) n_month_isfcpl=$(echo ${isfcpl_d30} | awk '{print int($1+0.5)}') n_month_full_run=$(( $(( 12 * $(( ${run_end_date_yyyymmdd::4} - ${run_start_date_yyyymmdd::4} )) )) + $(( ${run_end_date_yyyymmdd:4:2} - ${run_start_date_yyyymmdd:4:2} )) )) if (( $(( ${n_month_full_run} % ${n_month_isfcpl} )) != 0 )); then echo "n_month_full_run=${n_month_full_run} is not a multiple of n_month_isfcpl=${n_month_isfcpl}." exit 2 else n_isfcpl_window=$(echo "${n_month_full_run} / ${n_month_isfcpl}" | bc) fi tmp=`readlink -f isf_draft_meter.nc` tmp2=`readlink -f bathy_meter.nc` if [ "${tmp}" != "${tmp2}" ]; then echo "Error. At initialization, isf_draft_meter.nc and bathy_meter.nc do not point to the same file." exit 1 fi init_bathy_file=`basename ${tmp}` cp -f ${tmp} ${archive_dir}/isfcpl cp -f ${tmp} ${run_dir}/init_NEMO_bathy.nc ln -sf ${icesheet_files_dir}/* ./ ln -sf ${isfcpl_files_dir}/* ./ date_beg_isfcpl="${run_start_date_yyyymmdd}" printf "# Information for the ice sheet model\n" > ${start_dir}/isfcpl.track printf "run_name=${exp_name}\n" >> ${start_dir}/isfcpl.track printf "initial_date=${run_start_date_yyyymmdd}\n" >> ${start_dir}/isfcpl.track printf "n_month_isfcpl=${n_month_isfcpl}\n" >> ${start_dir}/isfcpl.track printf "n_isfcpl_window=${n_isfcpl_window}\n" >> ${start_dir}/isfcpl.track printf "date_beg_isfcpl=${date_beg_isfcpl}\n" >> ${start_dir}/isfcpl.track printf "date_end_isfcpl=YYYYMMDD\n" >> ${start_dir}/isfcpl.track printf "ice_atm_cpl=${ice_atm_cpl}\n\n" >> ${start_dir}/isfcpl.track printf "# Information for NEMO to keep up\n" >> ${start_dir}/isfcpl.track printf "init_bathy=1\n" >> ${start_dir}/isfcpl.track printf "curr_bathy_file=${init_bathy_file}\n" >> ${start_dir}/isfcpl.track init_bathy=1 curr_bathy_file=${init_bathy_file} fi ln -sf ${curr_bathy_file} ${run_dir}/bathy_meter.nc ln -sf ${curr_bathy_file} ${run_dir}/isf_draft_meter.nc fi # if [ "${iscpl}" == 1 ] # --------------------------------------------------------------------- # *** 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 namelist_cfg # ------------------------------------------------------------------------- # *** Build ice sheet launch # ------------------------------------------------------------------------- if (( isfcpl == 1)); then source ${icesheet_launch_template} > launch_icesheet.sh chmod +x launch_icesheet.sh fi # ------------------------------------------------------------------------- # *** Launch experiment # ------------------------------------------------------------------------- echo "START of mpirun" time_begin=$(date +%s) mpirun -np "${xio_numproc:?}" "${xio_exe_file:?}" : -np "${nem_numproc:?}" "${nem_exe_file:?}" time_end=$(date +%s) echo "END of: mpirun" # ------------------------------------------------------------------------- # *** Ice sheet coupling # ------------------------------------------------------------------------- if (( isfcpl == 1 )); then cnt_res_isfcpl=$(( $(( ${leg_number} - 1 )) % ${n_res_perisfcpl} )) fmt_res_isfcpl=$(printf "%02d" ${cnt_res_isfcpl}) in_fwfisf_stencil="${exp_name}_${frequency_fwfisf}_${leg_start_date_yyyymmdd}_${leg_almostend_date_yyyymmdd}_${suffix_fwfisf}" out_fwfisf_stencil="${exp_name}_fwfisf_res" out_fwfisf_curr="${out_fwfisf_stencil}${fmt_res_isfcpl}" if (( is_xios2 == 0 )); then module purge module load ${module_list:?} export LD_LIBRARY_PATH=${LD_LIBRARY_PATH:+${LD_LIBRARY_PATH}:}"${extralibs_list}" /bin/bash ${rebuild_nemo_exe} ${in_fwfisf_stencil} ${xio_numproc} module purge load_modules_isfcpl cdo selname,${name_var_fwfisf} ${in_fwfisf_stencil}.nc tmp_fwfisf.nc cdo monmean tmp_fwfisf.nc ${out_fwfisf_curr}.nc rm -f ${in_fwfisf_stencil}.nc tmp_fwfisf.nc else cdo selname,${name_var_fwfisf} ${in_fwfisf_stencil}.nc tmp_fwfisf.nc cdo monmean tmp_fwfisf.nc ${out_fwfisf_curr}.nc rm -f tmp_fwfisf.nc fi mv -f ${out_fwfisf_curr}.nc ${out_dir}/isfcpl_tmp/ if (( ${leg_number} % ${n_res_perisfcpl} == 0 )); then date_end_isfcpl=${leg_almostend_date_yyyymmdd} sed -i "s/.*date_end_isfcpl=.*/date_end_isfcpl=${date_end_isfcpl}/" ${start_dir}/isfcpl.track module purge module load ${module_list:?} export LD_LIBRARY_PATH=${LD_LIBRARY_PATH:+${LD_LIBRARY_PATH}:}"${extralibs_list}" /bin/bash ${rebuild_nemo_exe} mesh_mask ${nem_numproc} module purge load_modules_isfcpl infile_ocean2ice="${exp_name}_ocean2ice_raw_${date_beg_isfcpl}-${date_end_isfcpl}.nc" outfile_ocean2ice="${exp_name}_ocean2ice_${date_beg_isfcpl}-${date_end_isfcpl}.nc" fwfisf_records="" for((rs2=0; rs2 ./pp_nemo_to_${name_icesheet_model}.py python pp_nemo_to_${name_icesheet_model}.py mv -f ${infile_ocean2ice} ${archive_dir}/isfcpl/ mv -f mesh_mask.nc ${archive_dir}/isfcpl/${exp_name}_mesh_mask_${date_beg_isfcpl}-${date_end_isfcpl}.nc module purge module load ${icesheet_modules} if [ "${icesheet_library_path}" != "" ]; then export LD_LIBRARY_PATH="${icesheet_library_path}" fi /bin/bash ./launch_icesheet.sh mv -f ${outfile_ocean2ice} ${archive_dir}/isfcpl if (( ice_atm_cpl == 1 )); then mv -f ${outfile_atm2ice} ${archive_dir}/isfcpl fi if [[ "${name_icesheet_model}" == "fETISh" ]]; then find . -type l -name "${exp_name}_${name_icesheet_model}Run_??????_toto.mat" -exec rm -f {} \; mv -f ${exp_name}_${name_icesheet_model}Run_??????_toto.mat ${archive_dir}/${name_icesheet_model} ln -sf ${archive_dir}/${name_icesheet_model}/${exp_name}_${name_icesheet_model}Run_${date_end_isfcpl::-2}_toto.mat else # GVAN EDIT HERE; DO THE SAME FOR BISICLES OUTPUT NOMENCLATURE echo "Ice-sheet models other than fETISh not implemented yet." exit 2 fi curr_geom_file="${exp_name}_ice2ocean_${date_end_isfcpl}.nc" new_bathy_file="${exp_name}_bathymetry_isfdraft_${date_end_isfcpl}.nc" source build_pp_icesheet_to_nemo.sh > pp_${name_icesheet_model}_to_nemo.py if [ "${init_bathy}" == 0 ]; then mv -f ${curr_bathy_file} ${archive_dir}/isfcpl else init_bathy=0 cp -f ${curr_bathy_file} ${archive_dir}/isfcpl fi module purge load_modules_isfcpl python pp_${name_icesheet_model}_to_nemo.py mv -f ${curr_geom_file} ${archive_dir}/isfcpl curr_bathy_file=${new_bathy_file} ln -sf ${curr_bathy_file} ${run_dir}/bathy_meter.nc ln -sf ${curr_bathy_file} ${run_dir}/isf_draft_meter.nc printf "# Information for the ice sheet model\n" > ${start_dir}/isfcpl.track printf "run_name=${exp_name}\n" >> ${start_dir}/isfcpl.track printf "initial_date=${run_start_date_yyyymmdd}\n" >> ${start_dir}/isfcpl.track printf "n_month_isfcpl=${n_month_isfcpl}\n" >> ${start_dir}/isfcpl.track printf "n_isfcpl_window=${n_isfcpl_window}\n" >> ${start_dir}/isfcpl.track printf "date_beg_isfcpl=${nextleg_start_date_yyyymmdd}\n" >> ${start_dir}/isfcpl.track printf "date_end_isfcpl=YYYYMMDD\n" >> ${start_dir}/isfcpl.track printf "ice_atm_cpl=${ice_atm_cpl}\n\n" >> ${start_dir}/isfcpl.track printf "# Information for NEMO to keep up\n" >> ${start_dir}/isfcpl.track printf "init_bathy=${init_bathy}\n" >> ${start_dir}/isfcpl.track printf "curr_bathy_file=${curr_bathy_file}\n" >> ${start_dir}/isfcpl.track module purge module load ${module_list:?} export LD_LIBRARY_PATH=${LD_LIBRARY_PATH:+${LD_LIBRARY_PATH}:}"${extralibs_list}" fi fi # ------------------------------------------------------------------------- # *** 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/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