#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=# # NEMO postlude # Revised NEMO history file pattens to be consistent with those in AGCM # - Jan/2018, D.Yang #=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=# #=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=# #=#=#=# Post processing #=#=#=# #=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=# echo " " echo "#################### NEMO post processing #################" # bail_prefix is used in the error exit function bail (defined in nemo_prelude) bail_prefix="nemo postlude" # The job name cn_exp=$runid # Part of the input ocean restart name (default restart) # The input ocean restart file name will be ${cn_ocerst_in}_MMMM.nc # where MMMM is the MPI task number (I4.4) cn_ocerst_in="restart" # Part of output ocean restart name (default restart) # The output ocean restart file name will be ${cn_exp}_NNNNNNNN_${cn_ocerst_out}_MMMM.nc # where NNNNNNNN is the time step (I8.8) and MMMM is the MPI task number (I4.4) cn_ocerst_out="restart" # Part of input ice restart name (default restart_ice_in) # The input ice restart file name will be ${cn_icerst_in}_MMMM.nc # where MMMM is the MPI task number (I4.4) cn_icerst_in="restart_ice_in" # Part of output ice restart name (default restart_ice) # The output ice restart file name will be ${cn_exp}_NNNNNNNN_${cn_icerst_out}_NNNN.nc # where NNNNNNNN is the time step (I8.8) and MMMM is the MPI task number (I4.4) cn_icerst_out="restart_ice" # Part of input pisces restart name (default restart_trc_in) # The input pisces restart file name will be ${cn_trcrst_in}_MMMM.nc # where MMMM is the MPI task number (I4.4) cn_trcrst_in="restart_trc_in" # Part of output pisces restart name (default restart_trc) # The output pisces restart file name will be ${cn_exp}_NNNNNNNN_${cn_trcrst_out}_NNNN.nc # where NNNNNNNN is the time step (I8.8) and MMMM is the MPI task number (I4.4) cn_trcrst_out="restart_trc" # After the job has run remove input restart files (if any) [ -s input_ocn_restart_file_names ] && cat input_ocn_restart_file_names | xargs rm -f [ -s input_ice_restart_file_names ] && cat input_ice_restart_file_names | xargs rm -f [ -s input_trc_restart_file_names ] && cat input_trc_restart_file_names | xargs rm -f ######## Save history and restart files ####### # Should we save the NEMO restart to DATAPATH nemo_save_rs=${nemo_save_rs:-on} ToF nemo_save_rs # tarlist contains a list of additional files to add to the restart archive tarlist='' # The file saved_history_file_names will contain a list of saved files to be archived. # Since "save" will blindly transpose all file name characters to lower case before # saving to DATAPATH, we must keep track of the case of these files in some way. # The file saved_history_FILE_NAMES will contain the same list of file names that # saved_history_file_names contains but it will preserve case. (Large pita) rm -f saved_history_file_names touch saved_history_file_names rm -f saved_history_FILE_NAMES touch saved_history_FILE_NAMES # History file suffix and frequency lists nemo_hist_file_suffix_list_save=${nemo_hist_file_suffix_list_save} nemo_hist_file_freq_list_save=${nemo_hist_file_freq_list_save} nemo_hist_file_suffix_list_array_save=($nemo_hist_file_suffix_list_save) nemo_hist_file_freq_list_array_save=($nemo_hist_file_freq_list_save) # Check that the lists are the same length. Use this number to loop below.. n_suffix=${#nemo_hist_file_suffix_list_array_save[@]} n_freq=${#nemo_hist_file_freq_list_array_save[@]} if [ "$n_suffix" -ne "$n_freq" ]; then bail "ERROR: nemo_hist_file_suffix_list_array_save and nemo_hist_file_freq_list_array_save MUST have the same number of elements." fi # Collect history files into directories and save nemo_save_hist=${nemo_save_hist:-on} ToF nemo_save_hist if [ $nemo_save_hist -eq 1 ] ; then # Define the list of history files to rebuild for i in $(seq 0 $(($n_suffix-1))); do sfx=${nemo_hist_file_suffix_list_array_save[$i]} freq=${nemo_hist_file_freq_list_array_save[$i]} pfx=${cn_exp}_${freq}_${nemo_start_date}_${nemo_stop_date}_$sfx echo $pfx fnpatt=${pfx}_0000.nc if [ -s "$fnpatt" ]; then echo "found $fnpatt" rm -rf $pfx mkdir $pfx mv ${pfx}_[0-9]*.nc $pfx ncsave=${cn_exp}_${nemo_start_year}_m${nemo_start_mon}_${freq}_${sfx} save $pfx ${uxxx}_$ncsave && echo "${uxxx}_$ncsave" >> saved_history_FILE_NAMES elif [ -s "${pfx}.nc" ]; then echo "found ${pfx}.nc" ncsave=${cn_exp}_${nemo_start_year}_m${nemo_start_mon}_${freq}_${sfx} save ${pfx}.nc ${uxxx}_${ncsave}.nc && echo "${uxxx}_${ncsave}.nc" >> saved_history_FILE_NAMES fi done # Add the mesh_mask file created by the model, if present if [ -s mesh_mask_0000.nc ]; then rm -f rs_mesh_mask.nc pfx=mesh_mask rm -rf $pfx mkdir $pfx mv $pfx*.nc $pfx ncsave=${cn_exp}_${nemo_start_year}_m${nemo_start_mon}_mesh_mask save $pfx ${uxxx}_$ncsave && echo "${uxxx}_$ncsave" >> saved_history_FILE_NAMES fi fi if [ -s saved_history_FILE_NAMES ]; then # Once files have been rebuilt and saved to DATAPATH create a file that is # equivalent to the file saved_history_FILE_NAMES except that all file names # contained therein are lower case. rm -f saved_history_file_names cat saved_history_FILE_NAMES | tr '[A-Z]' '[a-z]' > saved_history_file_names fi #=#=#=# Save the current restart files. if [ $nemo_save_rs -eq 1 ]; then # Collect up the current restarts and save them to DATAPATH rm -rf NEXT_RESTART_ARC mkdir NEXT_RESTART_ARC # Identify the last NEMO timestep, which will be in the rs names end_step=$(echo $nn_itend | awk '{printf "%8.8d",$1}') eval ofnpatt=${cn_exp}_${end_step}_${cn_ocerst_out}_\[0-9\]\[0-9\]\[0-9\]\[0-9\].nc found_rs=`(ls -1 $ofnpatt || : ) 2>/dev/null` if [ -z "$found_rs" ]; then # No ocean restart files exist bail "Attempting to save restarts but no ocean restart files exist. Looking for $ofnpatt" else mv $found_rs NEXT_RESTART_ARC fi if [ $nemo_trc -eq 1 ] || [ $nemo_carbon -eq 1 ]; then # Deal with Pisces restarts eval pfnpatt=${cn_exp}_${end_step}_${cn_trcrst_out}_\[0-9\]\[0-9\]\[0-9\]\[0-9\].nc found_rs=`(ls -1 $pfnpatt || : ) 2>/dev/null` if [ -z "$found_rs" ]; then # No pisces restart files exist bail "Attempting to save restarts but no pisces restart files exist. Looking for $pfnpatt" else mv $found_rs NEXT_RESTART_ARC fi fi if [ $with_ice -eq 1 ]; then # Anything but CICE eval ifnpatt=${cn_exp}_${end_step}_${cn_icerst_out}_\[0-9\]\[0-9\]\[0-9\]\[0-9\].nc found_rs=`(ls -1 $ifnpatt || : ) 2>/dev/null` if [ -z "$found_rs" ]; then # No ice restart files exist bail "Attempting to save restarts but no ice restart files exist. Looking for $ifnpatt" else mv $found_rs NEXT_RESTART_ARC fi fi # tarlist contains a list of additional files to add to the restart archive tarlist='' # Create copies of the namelists used and include them in the tar file cp -f namelist rs_namelist || : [ -s rs_namelist ] && tarlist="$tarlist rs_namelist" cp -f namelist_top rs_namelist_top || : [ -s rs_namelist_top ] && tarlist="$tarlist rs_namelist_top" case $nn_ice in 0) ;; # no ice boundary condition 1) ;; # use observed ice cover 2) # LIM2 ice-model cp -f namelist_ice rs_namelist_ice || : [ -s rs_namelist_ice ] && tarlist="$tarlist rs_namelist_ice" ;; 3) # LIM3 ice-model cp -f namelist_ice rs_namelist_ice || : [ -s rs_namelist_ice ] && tarlist="$tarlist rs_namelist_ice" ;; 4) # CICE ice-model cp -f ice_in rs_ice_in || : [ -s rs_ice_in ] && tarlist="$tarlist rs_ice_in" ;; *) bail "Invalid value for nn_ice = $nn_ice" ;; esac if [ $nemo_carbon -eq 1 ]; then cp -f namelist_pisces rs_namelist_pisces || : [ -s rs_namelist_pisces ] && tarlist="$tarlist rs_namelist_pisces" if [ $nemo_cmoc -eq 1 ]; then cp -f namelist_cmoc rs_namelist_cmoc || : if [ -s rs_namelist_cmoc ]; then chmod u+rw rs_namelist_cmoc tarlist="$tarlist rs_namelist_cmoc" fi fi fi # Save a copy of the executable that was just run to the restart archive cp -f nemo.exe rs_nemo_exec || : [ -s rs_nemo_exec ] && tarlist="$tarlist rs_nemo_exec" # Add a file containing the time step cp -f time.step rs_time.step || : [ -s rs_time.step ] && tarlist="$tarlist rs_time.step" # Add ocean output and timing info cp -f ocean.output rs_ocean.output || : [ -s rs_ocean.output ] && tarlist="$tarlist rs_ocean.output" cp -f timing.output rs_timing.output || : [ -s rs_timing.output ] && tarlist="$tarlist rs_timing.output" cp -f saved_history_file_names rs_saved_history_file_names || : [ -s rs_saved_history_file_names ] && tarlist="$tarlist rs_saved_history_file_names" cp -f xnemo_access_log rs_xnemo_access_log || : [ -s rs_xnemo_access_log ] && tarlist="$tarlist rs_xnemo_access_log" cp -f nemo_prelude rs_nemo_prelude || : [ -s rs_nemo_prelude ] && tarlist="$tarlist rs_nemo_prelude" cp -f nemo_postlude rs_nemo_postlude || : [ -s rs_nemo_postlude ] && tarlist="$tarlist rs_nemo_postlude" [ -s rs_mesh_mask.nc ] && tarlist="$tarlist rs_mesh_mask.nc" mv -f $tarlist NEXT_RESTART_ARC || : if [ -n "$model_rs" ]; then # Assume we are running from gcmrun rs_out=${model_rs}nemors elif [ -n "$model" ]; then # Assume we are running from gcmjcl rs_out=${model_rs}nemors else rs_out=${uxxx}_${cn_exp}_${nemo_stop_date}_restart.tar fi save NEXT_RESTART_ARC $rs_out release NEXT_RESTART_ARC fi # Echo ocean output to stdout, if requested nemo_write_stdout=on ToF nemo_write_stdout if [ $nemo_write_stdout -eq 1 ]; then if [ -s ocean.output ]; then echo " " echo "########################## ocean output ##########################" echo " " cat ocean.output fi fi