#!/bin/sh #======================================================================= # Run NEMO --- xnemo --- #======================================================================= # keyword :: xnemo # description :: Run NEMO set -a . betapath2 # * ........................... Parmsub Parameters ............................ jobname=xnemo; time="10800" ; memory="25000mb" ; uxxx=xx; runid=job000; year=1; mon=1; nqsprfx="${runid}_${year}m${mon}_"; nqsext=''; crawork="${runid}_job"; username="acrnxxx"; user="XXX"; nemo_jpni=4 nemo_jpnj=4 nemo_jpnij=`expr $nemo_jpni \* $nemo_jpnj` # Number of MPI tasks nnodex=$nemo_jpnij # Number of openmp tasks nprocx=1 # Number of physical nodes to map the job to phys_nodex=1 # The name of a tar file containing the NEMO restart files # This must be set for the first job of a run unless nemo_from_rest = on # nemo_restart should be unset or null otherwise nemo_restart='' # nemo_from_rest is used to flag starting nemo from rest rather than a restart # If this is set "on" then the user must also supply namelist files via the # variables nemo_namelist and nemo_namelist_ice nemo_from_rest=off # nemo_exec identifies the nemo executable # This can be a file that is "save"d on DATAPATH or # a full pathname to a user supplied binary nemo_exec='' # Identify files containing namelist input for NEMO (namelist) and LIM (namelist_ice) nemo_namelist=nemo_3.4_orca2_lim_namelist nemo_namelist_ice=nemo_3.4_orca2_lim_namelist_ice # Normally user suppled namelist files are only required when starting the model # from rest. Otherwise the namelist files are stored in the restart archive and # read from the archive at each restart. Setting nemo_force_namelist = on will # over ride this behaviour and allow the namelists defined by the variables # nemo_namelist and nemo_namelist_ice to be used at the start of each new string. nemo_force_namelist=off # If set, nemo_nn_it000 will define the initial time step. # Normally the initial time step is read from the restart and so nemo_nn_it000 # should normally be null or unset. # Only set this if you are absolutely sure this is what you want. # If defined, nemo_nn_it000 must always be set to an integer greater than zero. nemo_nn_it000='' # If set then delete the previous restart from DATAPATH after it is copied to the execution dir nemo_del_rs='' # Alternate path to a directory where .queue/.crawork will be found JHOME='' if [ -n "$JHOME" -a x"$JHOME" != x"$HOME" ]; then # Allow optional reset of DATAPATH/RUNPATH JHOME_DATA='' DATAPATH=${JHOME_DATA:=$DATAPATH} RUNPATH=${JHOME_DATA:=$RUNPATH} # Allow optional reset of CCRNTMP JHOME_RUN='' CCRNTMP=${JHOME_RUN:=$CCRNTMP} fi # * ............................ Condef Parameters ............................ nextjob=on noprint=on openmp=off coupled=off debug=off # * ............................. Deck Definition ............................. . comjcl.cdk cat > Execute_Script <<'end_of_script' # ---Start_submit_ignore_code---- set -a # Add job specific functions, definitions etc : ; . local_defs # These variables are set when the job string is created previous_year=NotSet previous_month=NotSet current_year=NotSet current_month=NotSet next_year=NotSet next_month=NotSet run_start_year=NotSet run_start_month=NotSet run_stop_year=NotSet run_stop_month=NotSet # This invocation of make_file_name_list will process the *_year and *_months # variables defined above and output a file containing definitions for # start_year, start_mon, stop_year, stop_mon tmp_file_list="xnemo_date_list_${runid}_${stamp}" make_file_name_list --dates_only $tmp_file_list >>$error_out 2>&1 || bail "Problem in make_file_name_list --dates_only $tmp_file_list" rm -f $error_out # Verify that the output list is not empty [ ! -s "$tmp_file_list" ] && bail "Unable to create file list" # A file list was created ...source it # This will add the following variables to the current envoronment # start_year, start_mon, stop_year, stop_mon, days_in_job : ; . $tmp_file_list rm -f $tmp_file_list # Set a flag if this is the last job in the run is_last_job=0 if [ $run_stop_year -eq $stop_year ]; then if [ $run_stop_month -eq $stop_mon ]; then # Assume this is the last job in the run is_last_job=1 fi fi # Determine run start and stop dates run_start_day=1 run_start_date=`echo $run_start_year $run_start_month $run_start_day|\ awk '{printf "%4.4d%2.2d%2.2d",$1,$2,$3}' -` days_in_month $run_stop_month run_stop_day=$days_this_month run_stop_date=`echo $run_stop_year $run_stop_month $run_stop_day|\ awk '{printf "%4.4d%2.2d%2.2d",$1,$2,$3}' -` # refdate is a reference date used to calculate first time step # given the start_year and start_mon for the current job refdate="${run_start_year}:${run_start_month}" # Determine the number of days since the reference date (start of run) # The reference date is normally define by run_start_(year/month) # but may be overridden by the user # This will be the number of days to the start of start_(year/mon) days_since_run_start=`days_since --quiet --ref="$refdate" "${start_year}:${start_mon}" || bail "Error in days_since calculating days_since_run_start."` # Currently start_day is always 1 start_day=1 # Determine the number of days in the last month of the run case $stop_mon in 1|01) stop_day=31 ;; 2|02) stop_day=28 ;; 3|03) stop_day=31 ;; 4|04) stop_day=30 ;; 5|05) stop_day=31 ;; 6|06) stop_day=30 ;; 7|07) stop_day=31 ;; 8|08) stop_day=31 ;; 9|09) stop_day=30 ;; 10) stop_day=31 ;; 11) stop_day=30 ;; 12) stop_day=31 ;; *) bail "stop_mon=$stop_mon is out of range" ;; esac # First and last calendar date YYYYMMDD determined from user input start/stop start_date=`echo $start_year $start_mon $start_day|awk '{printf "%4.4d%2.2d%2.2d",$1,$2,$3}' -` stop_date=`echo $stop_year $stop_mon $stop_day|awk '{printf "%4.4d%2.2d%2.2d",$1,$2,$3}' -` # Determine the year and month of the previous restart, if any if [ $start_mon -eq 1 ]; then rs_mon=12 if [ $start_year -eq 1 ]; then rs_year=0 else rs_year=`expr $start_year - 1` fi else rs_mon=`expr $start_mon - 1` rs_year=$start_year fi # Determine the number of days in the last month of the previous restart case $rs_mon in 1|01) rs_day=31 ;; 2|02) rs_day=28 ;; 3|03) rs_day=31 ;; 4|04) rs_day=30 ;; 5|05) rs_day=31 ;; 6|06) rs_day=30 ;; 7|07) rs_day=31 ;; 8|08) rs_day=31 ;; 9|09) rs_day=30 ;; 10) rs_day=31 ;; 11) rs_day=30 ;; 12) rs_day=31 ;; *) bail "rs_mon=$rs_mon is out of range" ;; esac # Calendar date (YYYYMMDD) for the previous restart rs_date=`echo $rs_year $rs_mon $rs_day|awk '{printf "%4.4d%2.2d%2.2d",$1,$2,$3}' -` # Restart file name # This name will be used in all jobs except, possibly, the first job in the string rs_file=${uxxx}_${runid}_${rs_date}_restart.tar # nemo_rs is the restart file name that will be used below # It will be the same as rs_file unless nemo_restart is defined nemo_rs=${nemo_restart:-$rs_file} # time step for the dynamics (and tracer if nn_acc=0) rn_rdt=5760. # Number of time steps per day steps_per_day=`echo $rn_rdt|awk '{s=86400./$1; printf "%d",s}' -` # Total number of time steps in the current job [ -z "$days_in_job" ] && bail "days_in_job must be defined" steps_in_job=`echo $steps_per_day $days_in_job|awk '{printf "%d",$1*$2}' -` # The following parameters are used to define restart file names # The job name cn_exp=$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" # nn_ice =0 no ice boundary condition # =1 use observed ice-cover # =2 lim2 ice-model used # =3 lim3 ice-model used # =4 cice ice-model used nn_ice=2 # Ignore missing ice restart files when with_ice = off if [ $nn_ice -ge 2 ]; then with_ice=on else with_ice=off fi ToF with_ice nemo_del_rs=${nemo_del_rs:=off} ToF nemo_del_rs # Configure namelist parameters etc appropriate for continuing from a restart or not nemo_from_rest=${nemo_from_rest:=off} ToF nemo_from_rest if [ $nemo_from_rest -eq 1 ]; then #=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=# #=#=#=# Start from rest #=#=#=# #=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=# ln_rstart=.false. [ -n "$nemo_restart" ] && bail "nemo_from_rest = on and nemo_restart = ${nemo_restart}. These are mutually exclusive." echo "###############################" echo "### Starting from rest. ###" echo "###############################" # job number nn_no=1 # first time step # This will correspond with the beginning of ${start_year}:${start_mon} [ -z "$days_since_run_start" ] && bail "Cannot determine days_since_run_start" nn_it000=`echo $steps_per_day $days_since_run_start|awk '{printf "%d",1+$1*$2}' -` # Initial date prev_date0="010101" # Use input namelist files from a user supplied location # The input ocean namelist is hard coded as "namelist" in nemo source [ -z "$nemo_namelist" ] && bail "nemo_namelist is not defined" acc_cp namelist $nemo_namelist # The input ice namelist is hard coded as "namelist_ice" in nemo source [ -z "$nemo_namelist_ice" ] && bail "nemo_namelist_ice is not defined" acc_cp namelist_ice $nemo_namelist_ice # Get a local copy of the NEMO executable [ -z "$nemo_exec" ] && bail "nemo_exec must be defined." acc_cp nemo.exe $nemo_exec nocp=no else #=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=# #=#=#=# Start from a restart #=#=#=# #=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=# ln_rstart=.true. # Extract restart and namelist files from the tar archive [ -z "$nemo_rs" ] && bail "No restart file name provided. Define nemo_restart." echo "##########################" echo "### Restarting from file $nemo_rs" echo "##########################" rm -f RESTART_ARC acc_cp RESTART_ARC $nemo_rs tar xf RESTART_ARC || bail "Cannot extract files from $nemo_rs" # Rename each task specific output restart file from the previous run # as the equivalent task specific input restart for the current run # When starting a new run from an existing restart the ocean and ice restart # file names found in the restart tar file will be prefixed with the runid used # in the previous run. # Ocean restart files found_rs=`(ls -1 *_${cn_ocerst_out}_[0-9][0-9][0-9][0-9].nc || : ) 2>/dev/null` [ -z "$found_rs" ] && bail "No ocean restart files were found in $nemo_rs" rm -f input_ocn_restart_file_names touch input_ocn_restart_file_names for rsfile in $found_rs; do sfx=`echo $rsfile|sed 's/^.*\(_[0-9][0-9][0-9][0-9].nc\).*$/\1/'` mv $rsfile ${cn_ocerst_in}$sfx echo "${cn_ocerst_in}$sfx" >> input_ocn_restart_file_names done # Ice restart files rm -f input_ice_restart_file_names touch input_ice_restart_file_names found_rs=`(ls -1 *_${cn_icerst_out}_[0-9][0-9][0-9][0-9].nc || : ) 2>/dev/null` if [ -z "$found_rs" ]; then [ $nn_ice -ge 2 ] && bail "No ice restart files were found in $nemo_rs" with_ice=off else for rsfile in $found_rs; do sfx=`echo $rsfile|sed 's/^.*\(_[0-9][0-9][0-9][0-9].nc\).*$/\1/'` mv $rsfile ${cn_icerst_in}$sfx echo "${cn_icerst_in}$sfx" >> input_ice_restart_file_names done fi # Get a local copy of the NEMO executable rm -f nemo.exe if [ -z "$nemo_exec" ]; then # If nemo_exec is not defined then use the executable found in the restart archive [ ! -s rs_nemo_exec ] && bail "rs_nemo_exec is missing from $nemo_rs" mv rs_nemo_exec nemo.exe else # Otherwise use the executable pointed to by nemo_exec acc_cp nemo.exe $nemo_exec nocp=no fi [ ! -s nemo.exe ] && bail "Unable to find nemo executable." ToF nemo_force_namelist if [ $nemo_force_namelist -eq 1 ]; then # Override the namelist files found in the restart archive with # files supplied by the user # The input ocean namelist is hard coded as "namelist" in nemo source [ -z "$nemo_namelist" ] && bail "nemo_namelist is not defined" acc_cp namelist $nemo_namelist nocp=no # The input ice namelist is hard coded as "namelist_ice" in nemo source [ -z "$nemo_namelist_ice" ] && bail "nemo_namelist_ice is not defined" acc_cp namelist_ice $nemo_namelist_ice nocp=no else # Use the namelist files found in the restart archive [ ! -s rs_namelist ] && bail "Missing rs_namelist from $nemo_rs" [ ! -s rs_namelist_ice ] && bail "Missing rs_namelist_ice from $nemo_rs" # The input ocean namelist is hard coded as "namelist" in nemo source cp -f rs_namelist namelist # The input ice namelist is hard coded as "namelist_ice" in nemo source cp -f rs_namelist_ice namelist_ice fi # job number # Increment the job number from the previous namelist file prev_no=`sed -n '/^ *nn_no *=/p' rs_namelist|sed 's/^.*= *\([^ \t\!]*\).*/\1/'` nn_no=`expr $prev_no + 1` # Current beginning time step # get this from the time.step file that was saved in the restart prev_itend=`cat rs_time.step` nn_it000=`expr $prev_itend + 1` # Date stamp from the previous restart # Increment the job number from the previous namelist file prev_date0=`sed -n '/^ *nn_date0 *=/p' rs_namelist|sed 's/^.*= *\([^ \t\!]*\).*/\1/'` fi # The user may override the initial time step value by setting nemo_nn_it000 [ -n "$nemo_nn_it000" ] && nn_it000=$nemo_nn_it000 # Always use nn_it000 and nn_date0 from the namelist file # nn_rstctl is restart control; activated only if ln_rstart = T # = 0 nn_date0 read in namelist ; nn_it000 : read in namelist # = 1 nn_date0 read in namelist ; nn_it000 : check consistancy between namelist and restart # = 2 nn_date0 read in restart ; nn_it000 : check consistancy between namelist and restart nn_rstctl=0 # last time step # This will correspond with the end of ${stop_year}:${stop_mon} nn_itend=`echo $nn_it000 $steps_in_job|awk '{printf "%d",$1+$2-1}' -` # initial calendar date yymmdd nn_date0=`echo $start_year $start_mon $start_day|awk '{printf "%2.2d%2.2d%2.2d",$1,$2,$3}' -` # Leap year calendar (1) or not (0) nn_leapy=0 # output the initial state (1) or not (0) nn_istate=0 # frequency of creation of a restart file (modulo referenced to 1) nn_stock=$nn_itend # frequency of write in the output file (modulo referenced to nn_it000) nn_write=$steps_in_job # DIMG file format: 1 file for all processors (F) or by processor (T) ln_dimgnnn=.false. # mask land points in NetCDF outputs (costly: + ~15%) ln_mskland=.false. # clobber (overwrite) an existing file ln_clobber=.false. # chunksize (bytes) for NetCDF file (works only with iom_nf90 routines) nn_chunksz=0 ###### "nammpp_dyndist" Namelist parameters ##### ###### Massively Parallel Distribution for AGRIF zoom ("key_agrif" && "key_mpp_dyndist") # jpni number of processors following i jpni=$nemo_jpni # jpnj number of processors following j jpnj=$nemo_jpnj # jpnij number of local domains jpnij=$nemo_jpnij # &namctl # Control prints & Benchmark # Set ln_ctl = T and nn_print = 1 to get debugging output # Set ln_ctl = F and nn_print = 0 to get normal output ln_ctl=.false. # trends control print (expensive!) nn_print=0 # level of print (0 no extra print) # Modify specified parameter values in the input ocean namelist mod_nl namelist nn_it000 nn_itend nn_stock nn_write jpni jpnj jpnij \ rn_rdt cn_exp nn_date0 ln_rstart nn_rstctl nn_no cn_ocerst_in cn_ocerst_out \ ln_ctl nn_print nn_ice # Modify specified parameter values in the input ice namelist mod_nl namelist_ice cn_icerst_in cn_icerst_out # Write selected namelists from the namelist file # sed -n '/^&namrun/,/^\//p' namelist # sed -n '/^&nammpp/,/^\//p' namelist # sed -n '/^&namdom/,/^\//p' namelist # sed -n '/^&namnc4/,/^\//p' namelist # sed -n '/^&namctl/,/^\//p' namelist # Access or copy files required to run NEMO nemo_iodef=nemo_3.4_orca2_lim_iodef_xml nemo_xmlio_server_def=nemo_3.4_orca2_lim_xmlio_server_def nemo_ahmcoef=nemo_3.3_orca2_ahmcoef nemo_coordinates=nemo_3.3_orca2_coordinates.nc nemo_bathy_meter=nemo_3.3_orca2_bathy_meter.nc nemo_mask_itf=nemo_3.3_orca2_mask_itf.nc nemo_M2rowdrg=nemo_3.3_orca2_m2rowdrg.nc nemo_K1rowdrg=nemo_3.3_orca2_k1rowdrg.nc nemo_geothermal_heating=nemo_3.3_orca2_geothermal_heating.nc nemo_runoff_core_monthly=nemo_3.3_orca2_runoff_core_monthly.nc nemo_sss_data=nemo_3.3_orca2_sss_data.nc nemo_sst_data=nemo_3.3_orca2_sst_data.nc nemo_chlorophyll=nemo_3.3_orca2_chlorophyll.nc nemo_subbains=nemo_3.4_orca2_lim_subbasins.nc acc_cp iodef.xml $nemo_iodef acc_cp xmlio_server.def $nemo_xmlio_server_def acc_cp ahmcoef $nemo_ahmcoef acc_cp coordinates.nc $nemo_coordinates acc_cp bathy_meter.nc $nemo_bathy_meter acc_cp mask_itf.nc $nemo_mask_itf acc_cp M2rowdrg.nc $nemo_M2rowdrg acc_cp K1rowdrg.nc $nemo_K1rowdrg acc_cp geothermal_heating.nc $nemo_geothermal_heating acc_cp runoff_core_monthly.nc $nemo_runoff_core_monthly acc_cp sss_data.nc $nemo_sss_data acc_cp sst_data.nc $nemo_sst_data acc_cp chlorophyll.nc $nemo_chlorophyll acc_cp subbasins.nc $nemo_subbains nemo_data_1m_potential_temperature_nomask=nemo_3.3_orca2_data_1m_potential_temperature_nomask.nc nemo_data_1m_salinity_nomask=nemo_3.3_orca2_data_1m_salinity_nomask.nc acc_cp data_1m_potential_temperature_nomask.nc $nemo_data_1m_potential_temperature_nomask acc_cp data_1m_salinity_nomask.nc $nemo_data_1m_salinity_nomask nemo_t=nemo_3.3_orca2_t_10.15june2009_orca2.nc nemo_u=nemo_3.3_orca2_u_10.15june2009_orca2.nc nemo_v=nemo_3.3_orca2_v_10.15june2009_orca2.nc nemo_q=nemo_3.3_orca2_q_10.15june2009_orca2.nc nemo_qsw=nemo_3.3_orca2_ncar_rad.15june2009_orca2.nc nemo_qlw=nemo_3.3_orca2_ncar_rad.15june2009_orca2.nc nemo_precip=nemo_3.3_orca2_ncar_precip.15june2009_orca2.nc nemo_snow=nemo_3.3_orca2_ncar_precip.15june2009_orca2.nc nemo_weights_bicubic1=nemo_3.4_weights_grid02_bicubic_orca1.nc nemo_weights_bilinear1=nemo_3.4_weights_grid02_bilinear_orca1.nc nemo_weights_bicubic2=nemo_3.4_weights_grid03_bicubic_orca1.nc nemo_weights_bilinear2=nemo_3.4_weights_grid03_bilinear_orca1.nc acc_cp tair10m.nc $nemo_t acc_cp uwnd10m.nc $nemo_u acc_cp vwnd10m.nc $nemo_v acc_cp humi10m.nc $nemo_q acc_cp qsw.nc $nemo_qsw acc_cp qlw.nc $nemo_qlw acc_cp precip.nc $nemo_precip acc_cp snow.nc $nemo_snow acc_cp weights_bic1.nc $nemo_weights_bicubic1 acc_cp weights_bil1.nc $nemo_weights_bilinear1 acc_cp weights_bic2.nc $nemo_weights_bicubic2 acc_cp weights_bil2.nc $nemo_weights_bilinear2 nemo_utau=mc_ncq_5d_06360101_06361231_grid_ufl_mean.nc nemo_vtau=mc_ncq_5d_06360101_06361231_grid_vfl_mean.nc nemo_qtot=mc_ncq_5d_06360101_06361231_grid_hfl_mean.nc nemo_qsr=mc_ncq_5d_06360101_06361231_grid_hfl_mean.nc nemo_emp=mc_ncq_5d_06360101_06361231_grid_hfl_mean.nc nemo_weights_bicubic3=nemo_3.4_weights_grid02_bicubic_orca2.nc nemo_weights_bilinear3=nemo_3.4_weights_grid02_bilinear_orca2.nc acc_cp utau.nc $nemo_utau acc_cp vtau.nc $nemo_vtau acc_cp qtot.nc $nemo_qtot acc_cp qsr.nc $nemo_qsr acc_cp emp.nc $nemo_emp acc_cp weights_bic3.nc $nemo_weights_bicubic3 acc_cp weights_bil3.nc $nemo_weights_bilinear3 # acc_cp t_10.15JUNE2009_orca2.nc nemo_3.3_orca2_t_10.15june2009_orca2.nc # acc_cp u_10.15JUNE2009_orca2.nc nemo_3.3_orca2_u_10.15june2009_orca2.nc # acc_cp v_10.15JUNE2009_orca2.nc nemo_3.3_orca2_v_10.15june2009_orca2.nc # acc_cp q_10.15JUNE2009_orca2.nc nemo_3.3_orca2_q_10.15june2009_orca2.nc # acc_cp ncar_rad.15JUNE2009_orca2.nc nemo_3.3_orca2_ncar_rad.15june2009_orca2.nc # acc_cp ncar_precip.15JUNE2009_orca2.nc nemo_3.3_orca2_ncar_precip.15june2009_orca2.nc #=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=# #=#=#=# Run the program #=#=#=# #=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=# : ; . run_nemo #=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=# #=#=#=# Post processing #=#=#=# #=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=# # 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 nemo_save_hist=on ToF nemo_save_hist if [ $nemo_save_hist -eq 1 ]; then #=#=#=# Combine output files that were written one file per MPI task #=#=#=# into a single file containing data from all MPI tasks nemo_rebuild_exec=nemo_3.4_orca2_lim_flio_rbld_exe nemo_rebuild_sh=nemo_3.4_orca2_lim_rebuild_sh # Verify the rebuild executable variables are defined [ -z "$nemo_rebuild_exec" ] && bail "nemo_rebuild_exec is not defined" [ -z "$nemo_rebuild_sh" ] && bail "nemo_rebuild_sh is not defined" acc_cp flio_rbld.exe $nemo_rebuild_exec nocp=no acc_cp REBUILD $nemo_rebuild_sh nocp=no chmod u+x REBUILD # 1 year save interval nemo_save_1y_data=on ToF nemo_save_1y_data if [ $nemo_save_1y_data -eq 1 ]; then nemo_1y_suffix_list="grid_T" for sfx in $nemo_1y_suffix_list; do pfx=${cn_exp}_1y_${start_date}_${stop_date}_$sfx ncout=${uxxx}_${pfx}.nc if [ -s "${pfx}.nc" ]; then # The output file already exists # Assume that there are no task specific files and therefore # no need to combine them into a single file # Note file names must be transposed to lower case letters since # the "save" will blindly do so cp ${pfx}.nc $ncout save $ncout $ncout && echo "$ncout" >> saved_history_FILE_NAMES else eval fnpatt=${pfx}_\[0-9\]\[0-9\]\[0-9\]\[0-9\].nc found_file=`(ls -1 $fnpatt || : ) 2>/dev/null` if [ -n "$found_file" ]; then # At least 1 file name matches the current pattern REBUILD -o $ncout $fnpatt && save $ncout $ncout && echo "$ncout" >> saved_history_FILE_NAMES fi fi done fi # 1 month save interval nemo_save_1m_data=on ToF nemo_save_1m_data if [ $nemo_save_1m_data -eq 1 ]; then nemo_1m_suffix_list="grid_T" for sfx in $nemo_1m_suffix_list; do pfx=${cn_exp}_1m_${start_date}_${stop_date}_$sfx ncout=${uxxx}_${pfx}.nc if [ -s "${pfx}.nc" ]; then # The output file already exists # Assume that there are no task specific files and therefore # no need to combine them into a single file # Note file names must be transposed to lower case letters since # the "save" will blindly do so cp ${pfx}.nc $ncout save $ncout $ncout && echo "$ncout" >> saved_history_FILE_NAMES else eval fnpatt=${pfx}_\[0-9\]\[0-9\]\[0-9\]\[0-9\].nc found_file=`(ls -1 $fnpatt || : ) 2>/dev/null` if [ -n "$found_file" ]; then # At least 1 file name matches the current pattern REBUILD -o $ncout $fnpatt && save $ncout $ncout && echo "$ncout" >> saved_history_FILE_NAMES fi fi done fi # 1 day save interval nemo_save_1d_data=on ToF nemo_save_1d_data if [ $nemo_save_1d_data -eq 1 ]; then nemo_1d_suffix_list="grid_T grid_T_0n180w diaptr" for sfx in $nemo_1d_suffix_list; do pfx=${cn_exp}_1d_${start_date}_${stop_date}_$sfx ncout=${uxxx}_${pfx}.nc if [ -s "${pfx}.nc" ]; then # The output file already exists # Assume that there are no task specific files and therefore # no need to combine them into a single file # Note file names must be transposed to lower case letters since # the "save" will blindly do so cp ${pfx}.nc $ncout save $ncout $ncout && echo "$ncout" >> saved_history_FILE_NAMES else eval fnpatt=${pfx}_\[0-9\]\[0-9\]\[0-9\]\[0-9\].nc found_file=`(ls -1 $fnpatt || : ) 2>/dev/null` if [ -n "$found_file" ]; then # At least 1 file name matches the current pattern REBUILD -o $ncout $fnpatt && save $ncout $ncout && echo "$ncout" >> saved_history_FILE_NAMES fi fi done fi # 5 day save interval nemo_save_5d_data=on ToF nemo_save_5d_data if [ $nemo_save_5d_data -eq 1 ]; then nemo_5d_suffix_list="icemod grid_T grid_U grid_V grid_W" for sfx in $nemo_5d_suffix_list; do pfx=${cn_exp}_5d_${start_date}_${stop_date}_$sfx ncout=${uxxx}_${pfx}.nc if [ -s "${pfx}.nc" ]; then # The output file already exists # Assume that there are no task specific files and therefore # no need to combine them into a single file # Note file names must be transposed to lower case letters since # the "save" will blindly do so cp ${pfx}.nc $ncout save $ncout $ncout && echo "$ncout" >> saved_history_FILE_NAMES else eval fnpatt=${pfx}_\[0-9\]\[0-9\]\[0-9\]\[0-9\].nc found_file=`(ls -1 $fnpatt || : ) 2>/dev/null` if [ -n "$found_file" ]; then # At least 1 file name matches the current pattern REBUILD -o $ncout $fnpatt && save $ncout $ncout && echo "$ncout" >> saved_history_FILE_NAMES fi fi done 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 else echo "No history files were saved to DATAPATH." fi fi #=#=#=# Run time diagnostics rm -f archived_rtd_files touch archived_rtd_files if [ $nemo_save_hist -eq 1 -a -s saved_history_FILE_NAMES ]; then # Run time diagnostics can only be created when history files have been # recombined, which is done in the "if nemo_save_hist -eq 1" block above # We do the run time diags here so that the restart file gets created # and saved even if there is a failure during the rtd calculation. # Determine the name of the rtd file nemo_with_rtd=on ToF nemo_with_rtd if [ $nemo_with_rtd -eq 1 ]; then # Specify the location of some NCO tools # These are required for manipulation of the netcdf files NCOBIN=/users/tor/acrn/rls/local/aix64/bin NCRCAT="$NCOBIN/ncrcat" test -x "$NCRCAT" || bail "$NCRCAT does not have execute permission" NCWA="$NCOBIN/ncwa" test -x "$NCWA" || bail "$NCWA does not have execute permission" NCKS="$NCOBIN/ncks" test -x "$NCKS" || bail "$NCKS does not have execute permission" #=#=# Yearly data #=#=# nemo_rtd_file_1y=sc_${runid}_1y_rtd.nc nemo_with_rtd_1y=on ToF nemo_with_rtd_1y if [ $nemo_with_rtd_1y -eq 1 ]; then # Loop over all rebuilt files looking for yearly data test -z "$nemo_rtd_file_1y" && bail "nemo_with_rtd is on but nemo_rtd_file_1y is undefined" rm -f TMP_RTDFILE.nc # Use the version of the saved history file list that does not have all # characters transposed to lower case cat saved_history_FILE_NAMES | while read fname; do [ -z "$fname" ] && continue case $fname in *_1y_*.nc) ;; # Allow *) continue ;; # Disallow anything else esac # Spatially average this file and remove nav_lon and nav_lat $NCWA -O -h -a x,y -x -v nav_lon,nav_lat $fname XXX.nc # Append any variables in the current file to the tmp file $NCKS -A -h XXX.nc TMP_RTDFILE.nc rm -f XXX.nc done if test -s TMP_RTDFILE.nc; then # Get a local copy if a saved version exists rm -f RTDFILE access RTDFILE $nemo_rtd_file_1y nocp=no na rm -f NEW_RTDFILE if [ -s RTDFILE ]; then # Append to an existing file $NCRCAT -h RTDFILE TMP_RTDFILE.nc NEW_RTDFILE else # Create a new file cp TMP_RTDFILE.nc NEW_RTDFILE fi test ! -s NEW_RTDFILE && bail "Unable to create run time diagnostics file." rm -f TMP_RTDFILE.nc if [ $is_last_job -eq 1 ]; then # This is the last job in the current string... archive the rtd file saved_name=`echo $nemo_rtd_file_1y | tr '[A-Z]' '[a-z]'` new_name=`echo $saved_name | sed 's/^\(.*\)_rtd.nc.*$/\1_'${run_stop_date}'_rtd.nc/'` cp NEW_RTDFILE $new_name save $new_name $new_name && echo "$new_name" >> archived_rtd_files fi # Save the rtd file, deleting any previous version test -s RTDFILE && delete RTDFILE save NEW_RTDFILE $nemo_rtd_file_1y else echo "Unable to find annual data to create run time diagnostics." fi fi #=#=# Monthly data #=#=# nemo_rtd_file_1m=sc_${runid}_1m_rtd.nc nemo_with_rtd_1m=on ToF nemo_with_rtd_1m if [ $nemo_with_rtd_1m -eq 1 ]; then # Loop over all rebuilt files looking for monthly data test -z "$nemo_rtd_file_1m" && bail "nemo_with_rtd is on but nemo_rtd_file_1m is undefined" rm -f TMP_RTDFILE.nc # Use the version of the saved history file list that does not have all # characters transposed to lower case cat saved_history_FILE_NAMES | while read fname; do [ -z "$fname" ] && continue case $fname in *_1m_*.nc) ;; # Allow *) continue ;; # Disallow anything else esac # Spatially average this file and remove nav_lon and nav_lat $NCWA -O -h -a x,y -x -v nav_lon,nav_lat $fname XXX.nc # Append any variables in the current file to the tmp file $NCKS -A -h XXX.nc TMP_RTDFILE.nc rm -f XXX.nc done if test -s TMP_RTDFILE.nc; then # Get a local copy if a saved version exists rm -f RTDFILE access RTDFILE $nemo_rtd_file_1m nocp=no na rm -f NEW_RTDFILE if [ -s RTDFILE ]; then # Append to an existing file $NCRCAT -h RTDFILE TMP_RTDFILE.nc NEW_RTDFILE else # Create a new file cp TMP_RTDFILE.nc NEW_RTDFILE fi test ! -s NEW_RTDFILE && bail "Unable to create run time diagnostics file." rm -f TMP_RTDFILE.nc if [ $is_last_job -eq 1 ]; then # This is the last job in the current string... archive the rtd file saved_name=`echo $nemo_rtd_file_1m | tr '[A-Z]' '[a-z]'` new_name=`echo $saved_name | sed 's/^\(.*\)_rtd.nc.*$/\1_'${run_stop_date}'_rtd.nc/'` cp NEW_RTDFILE $new_name save $new_name $new_name && echo "$new_name" >> archived_rtd_files fi # Save the rtd file, deleting any previous version test -s RTDFILE && delete RTDFILE save NEW_RTDFILE $nemo_rtd_file_1m else echo "Unable to find monthly data to create run time diagnostics." fi fi #=#=# Daily data #=#=# nemo_rtd_file_1d=sc_${runid}_1d_rtd.nc nemo_with_rtd_1d=on ToF nemo_with_rtd_1d if [ $nemo_with_rtd_1d -eq 1 ]; then # Loop over all rebuilt files looking for daily data test -z "$nemo_rtd_file_1d" && bail "nemo_with_rtd is on but nemo_rtd_file_1d is undefined" rm -f TMP_RTDFILE.nc # Use the version of the saved history file list that does not have all # characters transposed to lower case cat saved_history_FILE_NAMES | while read fname; do [ -z "$fname" ] && continue case $fname in *_1d_*_grid_T_0n180w.nc) continue ;; # Disallow *_1d_*.nc) ;; # Allow *) continue ;; # Disallow anything else esac # Spatially average this file and remove nav_lon and nav_lat $NCWA -O -h -a x,y -x -v nav_lon,nav_lat $fname XXX.nc # Append any variables in the current file to the tmp file $NCKS -A -h XXX.nc TMP_RTDFILE.nc rm -f XXX.nc done if test -s TMP_RTDFILE.nc; then # Get a local copy if a saved version exists rm -f RTDFILE access RTDFILE $nemo_rtd_file_1d nocp=no na rm -f NEW_RTDFILE if [ -s RTDFILE ]; then # Append to an existing file $NCRCAT -h RTDFILE TMP_RTDFILE.nc NEW_RTDFILE else # Create a new file cp TMP_RTDFILE.nc NEW_RTDFILE fi test ! -s NEW_RTDFILE && bail "Unable to create run time diagnostics file." rm -f TMP_RTDFILE.nc if [ $is_last_job -eq 1 ]; then # This is the last job in the current string... archive the rtd file saved_name=`echo $nemo_rtd_file_1d | tr '[A-Z]' '[a-z]'` new_name=`echo $saved_name | sed 's/^\(.*\)_rtd.nc.*$/\1_'${run_stop_date}'_rtd.nc/'` cp NEW_RTDFILE $new_name save $new_name $new_name && echo "$new_name" >> archived_rtd_files fi # Save the rtd file, deleting any previous version test -s RTDFILE && delete RTDFILE save NEW_RTDFILE $nemo_rtd_file_1d else echo "Unable to find daily data to create run time diagnostics." fi fi #=#=# 5 day data #=#=# nemo_rtd_file_5d=sc_${runid}_5d_rtd.nc nemo_with_rtd_5d=on ToF nemo_with_rtd_5d if [ $nemo_with_rtd_5d -eq 1 ]; then # Loop over all rebuilt files looking for 5 day data test -z "$nemo_rtd_file_5d" && bail "nemo_with_rtd is on but nemo_rtd_file_5d is undefined" rm -f TMP_RTDFILE.nc # Use the version of the saved history file list that does not have all # characters transposed to lower case cat saved_history_FILE_NAMES | while read fname; do [ -z "$fname" ] && continue case $fname in *_5d_*.nc) ;; # Allow *) continue ;; # Disallow anything else esac # Spatially average this file and remove nav_lon and nav_lat $NCWA -O -h -a x,y -x -v nav_lon,nav_lat $fname XXX.nc # Append any variables in the current file to the tmp file $NCKS -A -h XXX.nc TMP_RTDFILE.nc rm -f XXX.nc done if test -s TMP_RTDFILE.nc; then # Get a local copy if a saved version exists rm -f RTDFILE access RTDFILE $nemo_rtd_file_5d nocp=no na rm -f NEW_RTDFILE if [ -s RTDFILE ]; then # Append to an existing file $NCRCAT -h RTDFILE TMP_RTDFILE.nc NEW_RTDFILE else # Create a new file cp TMP_RTDFILE.nc NEW_RTDFILE fi test ! -s NEW_RTDFILE && bail "Unable to create run time diagnostics file." rm -f TMP_RTDFILE.nc if [ $is_last_job -eq 1 ]; then # This is the last job in the current string... archive the rtd file saved_name=`echo $nemo_rtd_file_5d | tr '[A-Z]' '[a-z]'` new_name=`echo $saved_name | sed 's/^\(.*\)_rtd.nc.*$/\1_'${run_stop_date}'_rtd.nc/'` cp NEW_RTDFILE $new_name save $new_name $new_name && echo "$new_name" >> archived_rtd_files fi # Save the rtd file, deleting any previous version test -s RTDFILE && delete RTDFILE save NEW_RTDFILE $nemo_rtd_file_5d else echo "Unable to find 5 day data used to create run time diagnostics." fi fi fi fi if [ -s archived_rtd_files ]; then # Prepend the list of rtd files to be archived to the list of saved history files # Do this for both copies of the history file (lower case and mixed case) cat archived_rtd_files saved_history_file_names > XXX mv XXX saved_history_file_names cat archived_rtd_files saved_history_FILE_NAMES > XXX mv XXX saved_history_FILE_NAMES fi if [ -s saved_history_file_names -a -s saved_history_FILE_NAMES ]; then # Reorder the list of files that were saved so that # the file names appear in order of descending size [ ! -f reorder_list ] && bail "reorder_list is missing." chmod u+x reorder_list reorder_list saved_history_FILE_NAMES > XXX mv XXX saved_history_FILE_NAMES [ ! -s saved_history_FILE_NAMES ] && bail "Empty file --> saved_history_FILE_NAMES <-- after reorder." rm -f saved_history_file_names cat saved_history_FILE_NAMES | tr '[A-Z]' '[a-z]' > saved_history_file_names fi if [ -s saved_history_file_names ]; then echo " " echo "###########################" echo "Ocean files to be archived:" echo "###########################" cat saved_history_file_names echo " " fi #=#=#=# Save the restart file # 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 nemo_save_rs=on ToF nemo_save_rs if [ $nemo_save_rs -eq 1 ]; then # tar up the current restarts and save them to DATAPATH # Make sure that at least 1 restart file is present eval ofnpatt=${cn_exp}_\*_${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." fi if [ $with_ice -eq 1 ]; then eval ifnpatt=${cn_exp}_\*_${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." fi else ifnpatt='' 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 || : cp -f namelist_ice rs_namelist_ice || : [ -s rs_namelist ] && tarlist="$tarlist rs_namelist" [ -s rs_namelist_ice ] && tarlist="$tarlist rs_namelist_ice" # 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" rm -f NEXT_RESTART_ARC tar cf NEXT_RESTART_ARC $tarlist $ofnpatt $ifnpatt || bail "Unable to create restart archive" rs_out=${uxxx}_${cn_exp}_${stop_date}_restart.tar save NEXT_RESTART_ARC $rs_out fi if [ $nemo_del_rs -eq 1 ]; then mmrs=`echo $nemo_rs|sed 's/^.*_\([0-9][0-9]*\)_restart\.tar$/\1/'|cut -c 5-6` ddrs=`echo $nemo_rs|sed 's/^.*_\([0-9][0-9]*\)_restart\.tar$/\1/'|cut -c 7-8` if [ x"$mmrs" = "x12" -a "x$ddrs" = "x31" ]; then # Simply release the previous restart release RESTART_ARC else # Delete the previous restart from DATAPATH delete RESTART_ARC fi else # Simply release the previous restart release 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 # ---Stop_submit_ignore_code---- end_of_script cat >local_defs << 'end_local_defs' # Miscelaneous local definitions # ---Start_submit_ignore_code---- stamp=`date "+%j%H%M%S"$$` # Use -e option if recognized by echo (enable backslash escapes) if [ "X`echo -e`" = "X-e" ]; then echo_e() { echo ${1+"$@"}; } else echo_e() { echo -e ${1+"$@"}; } fi # bail is a simple error exit routine this_host=`hostname|cut -d'.' -f1` error_out="${JHOME:-$HOME}/.queue/error_xnemo_${runid}_${this_host}_$stamp" [ ! -z "$error_out" ] && rm -f $error_out bail(){ echo_e `date`" $this_host $runid --- xnemo: $*" echo_e `date`" $this_host $runid --- xnemo: $*" >>$error_out exit 1 } # Name a file to contain debugging info # This file will survive even when stdout goes missing dbg_out="${JHOME:-$HOME}/.queue/dbg_xnemo_${runid}_${this_host}_$stamp" [ ! -z "$dbg_out" ] && rm -f $dbg_out ToF(){ # usage: ToF var_name # purpose: Possibly reset the value of var_name to "0" (false) or "1" (true) # If var_name is null or has a value of "off" or "no" then reset to "0" # If var_name has a value of "on" or "yes" then reset to "1" # Otherwise return with var_name unchanged [ -z "$1" ] && bail "ToF requires a variable name as an argument" eval ToF_var\=\$$1 XXX=`echo $ToF_var|sed 's/ //g'` eval ToF_var\=$XXX if [ -n "$ToF_var" ]; then if [ "$ToF_var" = 'on' ]; then eval ToF_var\=1 elif [ "$ToF_var" = 'off' ]; then eval ToF_var\=0 elif [ "$ToF_var" = 'yes' ]; then eval ToF_var\=1 elif [ "$ToF_var" = 'no' ]; then eval ToF_var\=0 else eval ToF_var\=\$$1 fi else eval ToF_var\=0 fi eval $1=$ToF_var } # mod_nl is used to change namelist values for the current job mod_nl(){ # Modify a text file containing namelists # Each variable definition in this input namelist file must be on a line by itself # and be the of the form var =.* which will be replaced with var = value # # Usage: mod_nl namelist_file var1 [var2 ...] # namelist_file_in ...is an existing text file containing the namelists # var1 var2 ... ...names of variables to be changed # these variables must be defined in the current environment # [ -z "$1" ] && bail "mod_nl requires a namelist file as the first arg" [ -z "$2" ] && bail "mod_nl requires at least 1 variable name on the command line" nlfile=$1 [ ! -s $nlfile ] && bail "mod_nl input namelist file --> $nlfile <-- is missing or empty" shift # Create a backup copy of the input namelist file, overwriting any existing backup cp -f $nlfile ${nlfile}.bak # Write a sed program to make the requested substitutions sprog=mod_nl_cmd rm -f $sprog touch $sprog for var in $*; do eval val=\$$var [ -z "$val" ] && bail "mod_nl $var is not defined or null" if [ x`echo $var|sed -n '/^ *c/p'` != x ]; then # This is a character variable that needs to be quoted # This assumes the nemo naming convention (char variables start with "c") vsub='s/^ *'$var' *=.*/'" ${var} = \"$val\""'/' else vsub='s/^ *'$var' *=.*/'" ${var} = $val"'/' fi # Add this command to the file # Note, the quotes are required to preserve white space echo "$vsub" >> $sprog # Echo the changes to stdout (useful for debugging runs) echo "${nlfile}: RESET $var = $val" done # Make the substitutions in situ, overwriting the input file sed -f $sprog $nlfile > mod_nl_tmp mv mod_nl_tmp $nlfile rm $sprog } from_com_file(){ # The first arg is a file name [ -z "$1" ] && bail "from_com_file requires a file name as the first arg" [ ! -s $1 ] && bail "from_com_file input file --> $1 <-- is missing or empty" # The second arg is a variable name [ -z "$2" ] && bail "from_com_file requires a variable name as the second arg" # The input file should contain one variable definition per line of the form # var = value # with whitespace optional everywhere but the value cannot contain whitespace # Any line that does not begin with the variable name (excluding whitespace) # is ignored. Only the last definition found in the file is returned. echo 's/^ *'$2' *= *\([^ \!#]*\).*/\\1/p' > from_com_file_cmd sed -n -f from_com_file_cmd $1 | tail -1 rm -f from_com_file_cmd >/dev/null >&2 || : } acc_cp() { # Attempt to access a file and if that fails attempt to copy it [ -z "$1" ] && bail "--> acc_cp <-- requires a local file name as the first arg" local_file=$1 [ -z "$2" ] && bail "--> acc_cp $1 <-- requires a remote file name as the second arg" remote_file=$2 shift 2 # Alternate path to a directory where .queue/.crawork will be found JHOME='' if [ -n "$JHOME" -a x"$JHOME" != x"$HOME" ]; then # Allow optional reset of DATAPATH/RUNPATH JHOME_DATA='' DATAPATH=${JHOME_DATA:=$DATAPATH} RUNPATH=${JHOME_DATA:=$RUNPATH} # Allow optional reset of CCRNTMP JHOME_RUN='' CCRNTMP=${JHOME_RUN:=$CCRNTMP} fi access $local_file $remote_file $* || cp $remote_file $local_file || bail "--> acc_cp $local_file $remote_file $* <-- Unable to locate $remote_file" } days_in_month() { # Determine the number of days in a given month (assuming 365 day year) [ -z "$1" ] && bail "--> days_in_month <-- requires an integer as the first arg" case $1 in 1|01) days_this_month=31 ;; 2|02) days_this_month=28 ;; 3|03) days_this_month=31 ;; 4|04) days_this_month=30 ;; 5|05) days_this_month=31 ;; 6|06) days_this_month=30 ;; 7|07) days_this_month=31 ;; 8|08) days_this_month=31 ;; 9|09) days_this_month=30 ;; 10) days_this_month=31 ;; 11) days_this_month=30 ;; 12) days_this_month=31 ;; *) days_this_month=0 bail "month = $1 is out of range" ;; esac } # ---Stop_submit_ignore_code---- end_local_defs cat >reorder_list << 'end_reorder_list' #!/usr/bin/env perl # ---Start_submit_ignore_code---- # Process input file which must contain valid file names, one name per line # Only the first white space separated word in each line is used while ($flist = shift) { open(FLIST,$flist) or die "reorder_list: Cannot open input file $flist\n"; while () { chomp; # Ignore blank lines and comment lines next if /^\s*$/; next if /^\s*#/; # Only the first word on the line is significant ($fin) = split; # This must be a valid non-empty file die "reorder_list: $fin is missing or empty.\n" unless -s $fin; $list{$fin} = -s $fin; } } die "reorder_list: No valid file names found.\n" unless defined %list; # Sort in ascending order by size and print the reordered list to stdout foreach (sort {$list{$a} <=> $list{$b}} keys %list) { print "$_\n"; } # ---Stop_submit_ignore_code---- end_reorder_list cat >run_nemo << 'end_run_nemo' # Used to time the executable TIMEME=${TIMEME:='hpmcount'} : ; . gcm_parallel_setup.cdk # Overwrite the poe.cmdfile so that it executes the NEMO binary echo '#!/usr/bin/ksh93' > poe.cmdfile if [ "$openmp" = 'on' ] ; then echo "env OMP_NUM_THREADS=${nprocx} nemo.exe" >> poe.cmdfile else echo "nemo.exe" >> poe.cmdfile fi chmod u+x poe.cmdfile # echo "NEMO run start" >>$dbg_out if [ "$nnode" -gt 1 ] ; then if [ "$TIMEME" = 'hpmcount' ] ; then (rm -f hpmcount_out* || : ) poe $TIMEME -o hpmcount_out poe.cmdfile ( cat hpmcount_out* || : ) (rm -f hpmcount_out* || : ) else poe $TIMEME poe.cmdfile fi else $TIMEME nemo.exe fi # echo "NEMO run complete" >>$dbg_out end_run_nemo cat >new_run_nemo << 'end_new_run_nemo' # ---Start_submit_ignore_code---- # Used to time the executable TIMEME=${TIMEME:='hpmcount'} this_mach=`uname -n|awk -F\. '{print \$1}' -` case $this_mach in ha|ha*) this_mach=hadar ;; sp|sp*) this_mach=spica ;; c1*) this_mach=spica ;; c2*) this_mach=hadar ;; za|ze*) this_mach=zeta ;; sa|sa*) this_mach=saiph ;; c6*) this_mach=saiph ;; c7*) this_mach=zeta ;; *) bail "$this_mach is not a valid machine name." ;; esac nprocx=${nprocx:=1} nnodex=${nnodex:=0} nproc=${nproc:=$nprocx} nnode=${nnode:=$nnodex} if [ "$openmp" = 'on' ]; then OMP_NUM_THREADS=$nproc export OMP_NUM_THREADS if [ "$nproc" -gt 1 ]; then XLSMPOPTS="stack=134217728" # 128MB export XLSMPOPTS fi fi if [ "$OS" = 'AIX' ] ; then MP_COREFILE_SIGTERM=yes ; export MP_COREFILE_SIGTERM MP_COREFILE_FORMAT=STDERR ; export MP_COREFILE_FORMAT if [ "$nnode" -gt 1 ] ; then # default MP_PULSE is 600 seconds MP_PULSE=60; export MP_PULSE MP_S_DEBUG=4; export MP_S_DEBUG if [ -z "$geometry" ] ; then MP_NODES=$nnode export MP_NODES else MP_PROCS=$nnode export MP_PROCS fi MP_SHARED_MEMORY=YES # The MP_BUFFER_MEM environment variable specifies the size of the Early Arrival # buffer that is used by the communication subsystem to buffer eagerly sent # point-to-point messages that arrive before there is a matching receive posted. # This value can also be specified with the -buffer_mem command line flag. # The command line flag overrides a value set with the environment variable. # The maximum allowable value is 256MB. MP_BUFFER_MEM=256M SPINLOOPTIME=5000 LLAPIERRORMSGS=yes ; export LLAPIERRORMSGS ### Enable the next 6 lines for higher debug level and set MP_INFOLEVEL >= 4 LAPI_DEBUG_PERF=yes ; export LAPI_DEBUG_PERF LAPI_DEBUG_TIMEOUT=yes ; export LAPI_DEBUG_TIMEOUT LAPI_DEBUG_TIMEOUT_SECONDS=300 ; export LAPI_DEBUG_TIMEOUT_SECONDS MP_PMDLOG=yes ; export MP_PMDLOG ; POE_LL_DEBUG_FILE=/tmp/lldebug.log ; export POE_LL_DEBUG_FILE MP_RM_TIMEOUT=45 ; export MP_RM_TIMEOUT LAPI_DEBUG_STRIPE_ENABLE_PING=no ; export LAPI_DEBUG_STRIPE_ENABLE_PING ### MP_INFOLEVEL=4 MP_STDOUTMODE=ordered ; MP_STDOUTMODE=unordered ; MP_LABELIO=yes ; export MP_STDOUTMODE MP_LABELIO MP_EUILIB=us if [ "$this_mach" = "spica" -o "$this_mach" = "hadar" ]; then MP_EUIDEVICE=sn_all else MP_EUIDEVICE=csss fi if [ "$this_mach" = "spica" -o "$this_mach" = "hadar" ]; then if [ "$this_mach" = "spica" ] ; then MP_EUILIBPATH=/fs/dev/hpcs/aspgasd/pmr67302 ; export MP_EUILIBPATH MP_S_FINALIZE=120 ; export MP_S_FINALIZE elif [ "$this_mach" = "hadar" ] ; then MP_EUILIBPATH=/fs/dev/hpcs/aspgasd/pmr67302 ; export MP_EUILIBPATH MP_S_FINALIZE=120 ; export MP_S_FINALIZE fi MP_INFOLEVEL=5 ; export MP_INFOLEVEL LAPI_ITRC=yes ; export LAPI_ITRC LAPI_ITRC_MASK=all-lock ; export LAPI_ITRC_MASK LAPI_ITRC_FILE="/fs/dev/crb/LAPI_TRACE_DIR/trc.${LOADL_STEP_ID}.`hostname`.$$" export LAPI_ITRC_FILE fi export MP_SHARED_MEMORY SPINLOOPTIME MP_STDOUTMODE export MP_EUILIB MP_EUIDEVICE MP_INFOLEVEL export MP_BUFFER_MEM # Allow enabling MCM provided not in "coupled" mode. if [ "$CCCMA_MCM" = 'on' -a "$coupled" != 'on' ] ; then MP_TASK_AFFINITY=MCM MEMORY_AFFINITY=MCM export MP_TASK_AFFINITY MEMORY_AFFINITY fi MP_USE_BULK_XFER=YES ; export MP_USE_BULK_XFER fi fi MP_PGMMODEL=spmd MP_CMDFILE='poe.cmdfile' export MP_PGMMODEL MP_CMDFILE # Create the poe.cmdfile to execute the NEMO binary echo '#!/usr/bin/ksh93' > poe.cmdfile echo "nemo.exe" >> poe.cmdfile chmod u+x poe.cmdfile ### # Create a function to run poe and handle an error exit ### poe () { ### set -x ### poe_xt_st=255 ### echo "MP_PULSE = $MP_PULSE" ### /bin/poe $* && ### poe_xt_st=$? || ### poe_xt_st=$? ### if [ $poe_xt_st -ne 0 -a $poe_xt_st -ne 192 ] ; then ### noprint=off ### fi ### echo "poe function: poe_xt_st=$poe_xt_st" ### if [ $poe_xt_st -ne 0 ] ; then ### (exit $poe_xt_st) ### else ### : ### fi || (exit $poe_xt_st) ; ### } # echo "NEMO run start" >>$dbg_out if [ "$nnode" -gt 1 ] ; then if [ "$TIMEME" = 'hpmcount' ] ; then (rm -f hpmcount_out* || : ) poe $TIMEME -o hpmcount_out poe.cmdfile poe_status=$? echo "poe_status = $poe_status" [ $poe_status -ne 0 ] && bail "NEMO run time error." ( cat hpmcount_out* || : ) (rm -f hpmcount_out* || : ) else poe $TIMEME poe.cmdfile || bail "NEMO run time error." fi else $TIMEME nemo.exe || bail "NEMO run time error." fi # echo "NEMO run complete" >>$dbg_out # ---Stop_submit_ignore_code---- end_new_run_nemo . endjcl.cdk #end_of_job