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@@ -37,19 +37,34 @@ function leap_days()
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}
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-function mlpy () {
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+function ml_pp_ice () {
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+ if [[ ${USER} == "vsc"????? ]]; then
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+ if [[ "${name_icesheet_model}" == "fETISh" ]]; then
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+ module purge
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+ module load Python
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+ PYTHONPATH="${HOME}/.local/bin:${HOME}/.local/lib/python3.7/site-packages:\${PYTHONPATH}"
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+ module load CDO
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+ echo ${PYTHONPATH} > ${start_dir}/ppath
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+ echo "genius and fetish detected" > ${start_dir}/tmpout
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+ else
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+ echo "On Genius, ice sheet models other than fETISh not implemented yet" > ${start_dir}/tmpout
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+ exit 2
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+ fi
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+ elif [[ ${HOSTNAME} == "lm3"* ]]; then
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+ if [[ "${name_icesheet_model}" == "fETISh" ]]; then
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+ echo "lemaitre3 and fetish detected" > ${start_dir}/tmpout
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+ module purge
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+ module load releases/2018a CDO/1.8.2-intel-2018a Python/3.6.4-intel-2018a
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+ # PYTHONPATH="${HOME}/.local/lib/python3.6/site-packages:${PYTHONPATH}"
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+ # module load NCO CDO
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+ else
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+ echo "On lemaitre3, ice sheet models other than fETISh not implemented yet" > ${start_dir}/tmpout
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+ exit 2
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+ fi
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- if [[ `hostname` == "ozone" ]]; then
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- module purge
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- module load Python
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- PYTHONPATH="/elic/home/pelletie/.local/lib/python3.6/site-packages:${PYTHONPATH}"
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- elif [[ ${USER} == "vsc"????? ]]; then
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- module purge
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- module load Python
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- PYTHONPATH="/user/leuven/327/vsc32749/.local/bin:/user/leuven/327/vsc32749/.local/lib/python3.7/site-packages:${PYTHONPATH}"
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else
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- echo "Nothing detected ${USER}" > ${start_dir}/tmpout
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- exit 0
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+ echo "hostname undetected. not implemented yet." > ${start_dir}/tmpout
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+ exit 2
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fi
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}
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@@ -101,6 +116,10 @@ cd "${run_dir}"
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# cp -u "${nem_exe_file:?}" .
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# cp -u "${xio_exe_file:?}" .
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+# nem_exe_bn=`basename ${nem_exe_file}`
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+# xio_exe_bn=`basename ${xio_exe_file}`
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+
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+
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# Write fake file for previous fresh water budget adjustment (nn_fwb==2 in namelist)
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[[ ! -f EMPave_old.dat ]] && echo " 0 0.0000000000000000E+00 0.0000000000000000E+00" > EMPave_old.dat
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#TODO: Enquiry about this
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@@ -122,6 +141,20 @@ done
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if [ "${isfcpl}" == "1" ]; then
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+ if [[ ${USER} == "vsc"????? ]]; then
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+ echo "Genius and iscpl detected. OK."
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+ elif [[ ${HOSTNAME} == "lm3"* ]]; then
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+ echo "Lemaitre3 and iscpl detected. OK."
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+ else
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+ echo "You have asked for iscpl, but I have not recognized genius nor lemaitre3. Exiting."
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+ exit 2
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+ fi
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+
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+ if [ "${name_icesheet_model}" != "fETISh" ]; then
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+ echo "only \"fETISh\" is known as an ice sheet model. exiting."
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+ exit 2
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+ fi
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+
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length_cut_pref=$(( ${#exp_name} + 4 ))
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rebuild_nemo_exe=${nemo_src_dir}/TOOLS/REBUILD_NEMO/rebuild_nemo
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if [ -f ${start_dir}/isfcpl.track ]; then
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@@ -129,8 +162,10 @@ if [ "${isfcpl}" == "1" ]; then
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# printf "\n" >> isfcpl.track
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# rm -f isfcpl.track
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fi
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+
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+ ln -sf ${start_dir}/isfcpl.track ${run_dir}
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- cp -f ${fetish_src_dir}/* ${run_dir}
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+ cp -f ${icesheet_src_dir}/* ${run_dir}
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iscpl_nm=.true.
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else
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iscpl_nm=.false.
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@@ -173,10 +208,14 @@ do
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leg_almostend_epoch=$(( ${leg_end_epoch} - 43200 ))
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leg_almostend_date=$(date -uR -d@"${leg_almostend_epoch}")
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+ nextleg_start_epoch=$(( ${leg_end_epoch} + 43200 ))
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+ nextleg_start_date=$(date -uR -d@"${nextleg_start_epoch}")
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+
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run_start_date_yyyymmdd=$(date -u -d "${run_start_date}" +%Y%m%d) # FIXME appears unused
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run_end_date_yyyymmdd=$(date -u -d "${run_end_date}" +%Y%m%d) # FIXME appears unused
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leg_start_date_yyyymmdd=$(date -u -d "${leg_start_date}" +%Y%m%d) # FIXME appears unused
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leg_almostend_date_yyyymmdd=$(date -u -d "${leg_almostend_date}" +%Y%m%d) # FIXME appears unused
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+ nextleg_start_date_yyyymmdd=$(date -u -d "${nextleg_start_date}" +%Y%m%d) # FIXME appears unused
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leg_beforestart_date_yyyymmdd=$(date -u -d "${leg_beforestart_date}" +%Y%m%d) # FIXME appears unused
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# run_start_date_yyyymm="${run_start_date_yyyymmdd::-2}"
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@@ -201,20 +240,23 @@ do
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if (( leg_number == 1 )); then
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mkdir -p ${archive_dir}/isfcpl
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+ mkdir -p ${archive_dir}/${name_icesheet_model}
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rm -f ${start_dir}/isfcpl.track
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- # Counter for the number of restart since last file exchange with fETISh.
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+ # Counter for the number of restart since last file exchange with the ice sheet model.
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cnt_res_isfcpl=0
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isfcpl_window_days=$(echo "(${n_res_perisfcpl} * ${leg_length_sec}) / 86400" | bc)
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-
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- if (( isfcpl_window_days >= 28 && isfcpl_window_days <= 31 )); then
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- n_month_isfcpl=1
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- elif (( isfcpl_window_days >= 336 && isfcpl_window_days <= 372 )); then
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- n_month_isfcpl=12
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- else
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- echo "Can't figure out how many month long is the coupling window."
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- exit 2
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- fi
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+ isfcpl_d30=$(echo "${isfcpl_window_days} / 30" | bc -l)
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+ n_month_isfcpl=$(echo ${isfcpl_d30} | awk '{print int($1+0.5)}')
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+
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+ # if (( isfcpl_window_days >= 28 && isfcpl_window_days <= 31 )); then
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+ # n_month_isfcpl=1
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+ # elif (( isfcpl_window_days >= 336 && isfcpl_window_days <= 372 )); then
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+ # n_month_isfcpl=12
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+ # else
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+ # echo "Can't figure out how many month long is the coupling window."
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+ # exit 2
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+ # fi
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n_month_full_run=$(( $(( 12 * $(( ${run_end_date_yyyymmdd::4} - ${run_start_date_yyyymmdd::4} )) )) + $(( ${run_end_date_yyyymmdd:4:2} - ${run_start_date_yyyymmdd:4:2} )) ))
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@@ -236,13 +278,20 @@ do
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init_bathy_file=`basename ${tmp}`
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cp -f ${tmp} ${archive_dir}/isfcpl
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cp -f ${tmp} ${run_dir}/init_NEMO_bathy.nc
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+
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+ date_beg_isfcpl="${run_start_date_yyyymmdd}"
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+ init_geom=1
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+ init_bathy=1
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+ curr_bathy_file=${init_bathy_file}
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+ ln -sf ${run_dir}/${icesheet_init_geom_file} ${run_dir}/${name_icesheet_model}_8km_geometry_curr.nc
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+
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printf "# Information for the ice sheet model\n" > ${start_dir}/isfcpl.track
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printf "run_name=${exp_name}\n" >> ${start_dir}/isfcpl.track
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printf "initial_date=${run_start_date_yyyymmdd}\n" >> ${start_dir}/isfcpl.track
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printf "n_month_isfcpl=${n_month_isfcpl}\n" >> ${start_dir}/isfcpl.track
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printf "n_isfcpl_window=${n_isfcpl_window}\n" >> ${start_dir}/isfcpl.track
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- printf "date_beg_isfcpl=YYYYMMDD\n" >> ${start_dir}/isfcpl.track
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+ printf "date_beg_isfcpl=${date_beg_isfcpl}\n" >> ${start_dir}/isfcpl.track
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printf "date_end_isfcpl=YYYYMMDD\n\n" >> ${start_dir}/isfcpl.track
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printf "# Information for NEMO to keep up\n" >> ${start_dir}/isfcpl.track
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@@ -251,59 +300,15 @@ do
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printf "init_bathy=1\n" >> ${start_dir}/isfcpl.track
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printf "curr_bathy_file=${init_bathy_file}\n" >> ${start_dir}/isfcpl.track
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- init_geom=1
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- init_bathy=1
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-
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- curr_bathy_file=${init_bathy_file}
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- ln -sf ${run_dir}/fETISh_8km_geometry_init.nc ${run_dir}/fETISh_8km_geometry_curr.nc
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+
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fi
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ln -sf ${curr_bathy_file} ${run_dir}/bathy_meter.nc
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ln -sf ${curr_bathy_file} ${run_dir}/isf_draft_meter.nc
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- if (( $(( ${leg_number} - 1 )) % ${n_res_perisfcpl} == 0 )); then
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-
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- date_beg_isfcpl=${leg_start_date_yyyymmdd}
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- sed -i "s/.*date_beg_isfcpl=.*/date_beg_isfcpl=${date_beg_isfcpl}/" ${start_dir}/isfcpl.track
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-
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- if (( leg_number > 1 )); then
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- # leg number at which NEMO is supposed to receive updated geometry from fETISh.
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- # We need to pre-treat fETISh outputs in order to make them readable by NEMO.
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-
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- # new fETISh output should be ${run_dir}/fETISh_8km_geometry_curr.nc
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- module purge
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- mlpy
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- module load CDO
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- ${pp_fetish_call}
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-
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- # Copy (for initial) or move (non initial) previous bathymetry file to archive and link new one to what NEMO will read.
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- new_bathy_file="fETISh_eORCA025-SO_bathymetry_${leg_beforestart_date_yyyymmdd}.nc"
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- mv -f fETISh_new_8km_eORCA025-bathymetry_curr.nc ${new_bathy_file}
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-
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- old_bathy=`readlink -f ${run_dir}/bathy_meter.nc`
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- if [ "${init_bathy}" == 0 ]; then
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- mv -f ${old_bathy} ${archive_dir}/isfcpl
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- else
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- init_bathy=0
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- sed -i "s/^init_bathy=.*$/init_bathy=0/g" ${start_dir}/isfcpl.track
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- cp -f ${old_bathy} ${archive_dir}/isfcpl
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- fi
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- curr_bathy_file=${new_bathy_file}
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- sed -i "s/.*curr_bathy_file=.*/curr_bathy_file=${curr_bathy_file}/" ${start_dir}/isfcpl.track
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- ln -sf ${new_bathy_file} ${run_dir}/bathy_meter.nc
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- ln -sf ${new_bathy_file} ${run_dir}/isf_draft_meter.nc
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-
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- module purge
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- module load ${module_list:?}
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- export LD_LIBRARY_PATH=${LD_LIBRARY_PATH:+${LD_LIBRARY_PATH}:}"${extralibs_list}"
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-
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- fi
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- fi
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-
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fi
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-
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# Correct for leap days because NEMO standalone uses no-leap calendar
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if (( leap_years == 0 )); then
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@@ -360,7 +365,7 @@ do
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#
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if [[ "$@" == *"dbg"* ]]; then
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- echo $HOSTNAME
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+ echo $HOSTNAME > ${start_dir}/log
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sleep 10000000000000
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fi
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@@ -368,10 +373,17 @@ do
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mpirun -np "${xio_numproc:?}" "${xio_exe_file:?}" : -np "${nem_numproc:?}" "${nem_exe_file:?}"
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time_end=$(date +%s)
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+ echo "dbg cp made it past mpirun"
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+
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if (( isfcpl == 1 )); then
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- module purge
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- module load CDO
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+ # NEMO restart index within ice sheet / ocean coupling window
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+ cnt_res_isfcpl=$(( $(( ${leg_number} - 1 )) % ${n_res_perisfcpl} ))
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+ sed -i "s/.*cnt_res_isfcpl=.*/cnt_res_isfcpl=${cnt_res_isfcpl}/" ${start_dir}/isfcpl.track
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+
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+
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+ # module purge
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+ # module load CDO
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fmt_res_isfcpl=$(printf "%02d" ${cnt_res_isfcpl})
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in_stencil="${exp_name}_1m_${leg_start_date_yyyymmdd}_${leg_almostend_date_yyyymmdd}_icesheet"
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@@ -390,46 +402,57 @@ do
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module load ${module_list:?}
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export LD_LIBRARY_PATH=${LD_LIBRARY_PATH:+${LD_LIBRARY_PATH}:}"${extralibs_list}"
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- ${rebuild_nemo_exe} ${out_stencil} ${xio_numproc}
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- rm -f ${out_stencil}_????.nc
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+ echo "dbg cp before rebuild"
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+ /bin/bash ${rebuild_nemo_exe} ${out_stencil} ${xio_numproc}
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+ rm -f ${out_stencil}_????.nc
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- # Counter increase (NEMO restart index within ice sheet / ocean coupling window).
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- cnt_res_isfcpl=$(( ${cnt_res_isfcpl} + 1 ))
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- sed -i "s/.*cnt_res_isfcpl=.*/cnt_res_isfcpl=${cnt_res_isfcpl}/" ${start_dir}/isfcpl.track
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+ echo "dbg cp after rebuild"
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+
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+
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if (( ${leg_number} % ${n_res_perisfcpl} == 0 )); then
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# We have just ended one NEMO leg which closes an ice sheet / ocean coupling window.
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date_end_isfcpl=${leg_almostend_date_yyyymmdd}
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sed -i "s/.*date_end_isfcpl=.*/date_end_isfcpl=${date_end_isfcpl}/" ${start_dir}/isfcpl.track
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- cp -f ${start_dir}/isfcpl.track ${start_dir}/isfcpl.old
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- ${rebuild_nemo_exe} mesh_mask ${nem_numproc}
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+ echo "dbg cp before rebuild mesh"
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+ /bin/bash ${rebuild_nemo_exe} mesh_mask ${nem_numproc}
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+ echo "dbg cp after rebuild mesh"
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- module purge; module load CDO
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+
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+ module purge
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+ ml_pp_ice
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+
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# Concatenate all icesheet files from all legs contained within this coupling window
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tmpfile_eos80="curr_ocean2ice_EOS80.nc"
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tmpfile_teos10="curr_ocean2ice_TEOS10.nc"
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outfile="${exp_name}_ocean2ice_${date_beg_isfcpl}-${date_end_isfcpl}.nc"
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- cdo -O copy "${out_stencil::-2}??.nc" ${tmpfile_teos10}
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+ cdo -O copy ${out_stencil::-2}??.nc ${tmpfile_teos10}
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+ rm -f ${out_stencil::-2}??.nc
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+ echo "dbg cp after cdo copy, before pp nemo to fetish"
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+
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+
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module purge
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- mlpy
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- ${pp_nemo_to_fetish_call}
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-
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+ ml_pp_ice
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+ ${pp_nemo_to_icesheet_call}
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mv -f ${tmpfile_eos80} ${outfile}
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- mv -f mesh_mask.nc ${archive_dir}/isfcpl/mesh_mask_${date_beg_isfcpl}-${date_end_isfcpl}.nc
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+ mv -f mesh_mask.nc ${archive_dir}/isfcpl/${exp_name}_mesh_mask_${date_beg_isfcpl}-${date_end_isfcpl}.nc
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+
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+ echo "dbg cp after pp nemo to fetish, before fetish"
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- # CALL FETISH
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+ # CALL ICE SHEET MODEL
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module purge
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- cp -f ${start_dir}/isfcpl.track ${run_dir}
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- module load ${fetish_modules}
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- ${fetish_call}
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+ module load ${icesheet_modules}
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+ ${icesheet_call}
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- mv -f ${exp_name}_fETISh*.mat ${archive_dir}/isfcpl
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- ln -sf ${archive_dir}/isfcpl/*.mat ./
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+ echo "dbg cp after fetish"
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+
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+ find . -type f -name "*.mat" -exec mv -f {} ${archive_dir}/${name_icesheet_model} \;
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+ ln -sf ${archive_dir}/${name_icesheet_model}/*.mat ./
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module purge
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# mv ocean2ice file to arch dir
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@@ -437,11 +460,7 @@ do
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new_geom_file="${exp_name}_ice2ocean_${date_end_isfcpl}.nc"
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- # module load NCO
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- # ncks -C -v B ${init_fetish_file} -A ${new_geom_file}
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- # module purge
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-
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- old_geom=`readlink -f fETISh_8km_geometry_curr.nc`
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+ old_geom=`readlink -f ${name_icesheet_model}_8km_geometry_curr.nc`
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if [ "${init_geom}" == 0 ]; then
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mv -f ${old_geom} ${archive_dir}/isfcpl
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else
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@@ -450,16 +469,45 @@ do
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cp -f ${old_geom} ${archive_dir}/isfcpl
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fi
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- ln -sf ${new_geom_file} fETISh_8km_geometry_curr.nc
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+ ln -sf ${new_geom_file} ${name_icesheet_model}_8km_geometry_curr.nc
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- cnt_res_isfcpl=0
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+ # leg number at which NEMO is supposed to receive updated geometry from the ice sheet model.
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+ # We need to pre-treat fETISh outputs in order to make them readable by NEMO.
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+
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+ # new fETISh output should be ${run_dir}/fETISh_8km_geometry_curr.nc
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+ module purge
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+ ml_pp_ice
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+ ${pp_icesheet_to_nemo_call}
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+
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+ # Copy (for initial) or move (non initial) previous bathymetry file to archive and link new one to what NEMO will read.
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+ new_bathy_file="${name_icesheet_model}_eORCA025-SO_bathymetry_${date_end_isfcpl}.nc"
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+ mv -f ${name_icesheet_model}_new_8km_eORCA025-bathymetry_curr.nc ${new_bathy_file}
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+
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+ old_bathy=`readlink -f ${run_dir}/bathy_meter.nc`
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+ if [ "${init_bathy}" == 0 ]; then
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+ mv -f ${old_bathy} ${archive_dir}/isfcpl
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+ else
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+ init_bathy=0
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+ sed -i "s/^init_bathy=.*$/init_bathy=0/g" ${start_dir}/isfcpl.track
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+ cp -f ${old_bathy} ${archive_dir}/isfcpl
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+ fi
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+ curr_bathy_file=${new_bathy_file}
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+ sed -i "s/.*curr_bathy_file=.*/curr_bathy_file=${curr_bathy_file}/" ${start_dir}/isfcpl.track
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+
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+ ln -sf ${new_bathy_file} ${run_dir}/bathy_meter.nc
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+ ln -sf ${new_bathy_file} ${run_dir}/isf_draft_meter.nc
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+
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+ module purge
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+ module load ${module_list:?}
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+ export LD_LIBRARY_PATH=${LD_LIBRARY_PATH:+${LD_LIBRARY_PATH}:}"${extralibs_list}"
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+
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printf "# Information for the ice sheet model\n" > ${start_dir}/isfcpl.track
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printf "run_name=${exp_name}\n" >> ${start_dir}/isfcpl.track
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printf "initial_date=${run_start_date_yyyymmdd}\n" >> ${start_dir}/isfcpl.track
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printf "n_month_isfcpl=${n_month_isfcpl}\n" >> ${start_dir}/isfcpl.track
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printf "n_isfcpl_window=${n_isfcpl_window}\n" >> ${start_dir}/isfcpl.track
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- printf "date_beg_isfcpl=YYYYMMDD\n" >> ${start_dir}/isfcpl.track
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+ printf "date_beg_isfcpl=${nextleg_start_date_yyyymmdd}\n" >> ${start_dir}/isfcpl.track
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printf "date_end_isfcpl=YYYYMMDD\n\n" >> ${start_dir}/isfcpl.track
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printf "# Information for NEMO to keep up\n" >> ${start_dir}/isfcpl.track
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printf "cnt_res_isfcpl=0\n" >> ${start_dir}/isfcpl.track
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Charles Pelletier