#!/bin/bash #---------------------------------------------------------------------- # # mkmapdata.sh # # Create needed mapping files for mksurfdata_map and CLM. # # Example to run for an output resolution of 4x5 # # mkmapdata.sh -r 4x5 # # valid arguments: # -f Input grid filename # -t Output type, supported values are [regional, global] # -r Output resolution # -b use batch mode (not default) # -l list mapping files required (so can use check_input_data to get them) # -d debug usage -- display mkmapdata that will be run but don't execute them # -o Also map to the input ocean-grid resolution" # -v verbose usage -- log more information on what is happening # -h displays this help message # # You can also set the following env variables: # # ESMFBIN_PATH - Path to ESMF binaries # CSMDATA ------ Path to CESM input data # MPIEXEC ------ Name of mpirun executable # REGRID_PROC -- Number of MPI processors to use # #---------------------------------------------------------------------- echo $0 dir=${0%/*} if [ "$dir" = "$0" ];then dir="." fi outfilelist="clm.input_data_list" default_res="10x15" #---------------------------------------------------------------------- # SET SOME DEFAULTS -- if not set via env variables outside if [ -z "$CSMDATA" ]; then CSMDATA=/glade/proj3/cseg/inputdata fi if [ -z "$REGRID_PROC" ]; then REGRID_PROC=8 fi #---------------------------------------------------------------------- # Usage subroutine usage() { echo "" echo "**********************" echo "usage on bluefire:" echo "./mkmapdata.sh" echo "" echo "valid arguments: " echo "[-f|--gridfile ] " echo " Full pathname of model SCRIP grid file to use " echo " This variable should be set if this is not a supported grid" echo " This variable will override the automatic generation of the" echo " filename generated from the -res argument " echo " the filename is generated ASSUMING that this is a supported " echo " grid that has entries in the file namelist_defaults_clm.xml" echo " the -r|--res argument MUST be specied if this argument is specified" echo "[-r|--res ]" echo " Model output resolution (default is $default_res)" echo "[-t|--gridtype ]" echo " Model output grid type" echo " supported values are [regional,global], (default is global)" echo "[-b|--batch]" echo " Toggles batch mode usage. If you want to run in batch mode" echo " you need to have a separate batch script for a supported machine" echo " that calls this script interactively - you cannot submit this" echo " script directory to the batch system" echo "[-l|--list]" echo " List mapping files required (use check_input_data to get them)" echo " also writes data to $outfilelist" echo "[-d|--debug]" echo " Toggles debug-only (don't actually run mkmapdata just echo what would happen)" echo "[-o|--ocn] " echo " Also map to the input ocean-grid resolution" echo "[-h|--help] " echo " Displays this help message" echo "[-v|--verbose]" echo " Toggle verbose usage -- log more information on what is happening " echo "" echo " You can also set the following env variables:" echo " ESMFBIN_PATH - Path to ESMF binaries " echo " (default is /contrib/esmf-5.3.0-64-O/bin)" echo " CSMDATA ------ Path to CESM input data" echo " (default is /glade/proj3/cseg/inputdata)" echo " MPIEXEC ------ Name of mpirun executable" echo " (default is mpirun.lsf)" echo " REGRID_PROC -- Number of MPI processors to use" echo " (default is 8)" echo "" echo "**pass environment variables by preceding above commands " echo " with 'env var1=setting var2=setting '" echo "**********************" } #---------------------------------------------------------------------- # runcmd subroutine #---------------------------------------------------------------------- runcmd() { cmd=$@ if [ -z "$cmd" ]; then echo "No command given to the runcmd function" exit 3 fi if [ "$verbose" = "YES" ]; then echo "$cmd" fi if [ "$debug" != "YES" ]; then ${cmd} rc=$? else rc=0 fi if [ $rc != 0 ]; then echo "Error status returned from mkmapdata script" exit 4 undo fi return 0 } #---------------------------------------------------------------------- # Process input arguments #---------------------------------------------------------------------- interactive="YES" debug="no" res="default" type="global" verbose="no" ocean="no" list="no" outgrid="" gridfile="default" while [ $# -gt 0 ]; do case $1 in -v|-V) verbose="YES" ;; -b|--batch) interactive="NO" ;; -d|--debug) debug="YES" ;; -l|--list) debug="YES" list="YES" ;; -r|--res) res=$2 shift ;; -o|--ocn) ocn=$2 shift ;; -f|--gridfile) gridfile=$2 shift ;; -t|--gridtype) type=$2 shift ;; -h|--help ) usage exit 0 ;; * ) echo "ERROR:: invalid argument sent in: $2" usage exit 1 ;; esac shift done echo "Script to create mapping files required by mksurfdata_map" #---------------------------------------------------------------------- # Determine output scrip grid file #---------------------------------------------------------------------- # Set general query command used below QUERY="$dir/../../bld/queryDefaultNamelist.pl -silent -namelist clmexp -onlyfiles " QUERY="$QUERY -justvalue -options sim_year=2000 -csmdata $CSMDATA" echo "query command is $QUERY" echo "" if [ "$gridfile" != "default" ]; then GRIDFILE=$gridfile echo "Using user specified scrip grid file: $GRIDFILE" if [ "$res" = "default" ]; then echo "When user specified grid file is given you MUST set the resolution (as the name of your grid)\n"; exit 1 fi else if [ "$res" = "default" ]; then res=$default_res fi # Find the output grid file for this resolution using the XML database QUERYFIL="$QUERY -var scripgriddata -res $res -options lmask=nomask" if [ "$verbose" = "YES" ]; then echo $QUERYFIL fi GRIDFILE=`$QUERYFIL` echo "Using default scrip grid file: $GRIDFILE" fi if [ "$type" = "global" ] && [ `echo "$res" | grep -c "1x1_"` = 1 ]; then echo "This is a regional resolution and yet it is being run as global, set type with '-t' option\n"; exit 1 fi echo "Output grid resolution is $res" if [ -z "$GRIDFILE" ]; then echo "Output grid file was NOT found for this resolution: $res\n"; exit 1 fi if [ "$list" = "YES" ]; then echo "outgrid = $GRIDFILE" echo "outgrid = $GRIDFILE" > $outfilelist elif [ ! -f "$GRIDFILE" ]; then echo "Input SCRIP grid file does NOT exist: $GRIDFILE\n"; echo "Make sure CSMDATA environment variable is set correctly" exit 1 fi #---------------------------------------------------------------------- # Determine all input grid files and output file names #---------------------------------------------------------------------- grids=( \ "1.9x2.5_nomask" \ "0.5x0.5_USGS" \ "0.5x0.5_AVHRR" \ "0.5x0.5_MODIS" \ "3x3min_LandScan2004" \ "3x3min_MODIS" \ "3x3min_USGS" \ "5x5min_nomask" \ "5x5min_IGBP-GSDP" \ "5x5min_ISRIC-WISE" \ "10x10min_nomask" \ "3x3min_GLOBE-Gardner" \ "3x3min_GLOBE-Gardner-mergeGIS" ) # Set timestamp for names below CDATE="c"`date +%y%m%d` # Set name of each output mapping file OTHER than RTM # First determine the name of the input scrip grid file # for each of the above grids declare -i nfile=1 for gridmask in ${grids[*]} do grid=${gridmask%_*} lmask=${gridmask#*_} QUERYFIL="$QUERY -var scripgriddata -res $grid -options lmask=$lmask" if [ "$verbose" = "YES" ]; then echo $QUERYFIL fi INGRID[nfile]=`$QUERYFIL` if [ "$list" = "YES" ]; then echo "ingrid = ${INGRID[nfile]}" echo "ingrid = ${INGRID[nfile]}" >> $outfilelist fi if [[ "$gridmask" = "3x3min_MODIS" || "$gridmask" = "3x3min_LandScan2004" || "$gridmask" = "3x3min_GLOBE-Gardner" || "$gridmask" = "3x3min_GLOBE-Gardner-mergeGIS" ]]; then LRGFIL[nfile]="yes" else LRGFIL[nfile]="no" fi GRIDFILE[nfile]=$GRIDFILE OUTFILE[nfile]=map_${grid}_${lmask}_to_${res}_nomask_aave_da_$CDATE.nc nfile=nfile+1 done # Add main mapping file from ocean to atmosphere if [ "$ocean" != "no" ]; then INGRID[nfile]=`$QUERY -var scripgriddata -options hgrid=$ocean,lmask=$ocean` OUTGRID[nfile]=$GRIDFILE OUTFILE[nfile]=map_${ocean}_to_${res}_aave_da_$CDATE.nc nfile=nfile+1 fi # Set name of RTM output mapping file if [ "$type" = "global" ]; then grid=0.5x0.5 lmask=nomask INGRID[nfile]=$GRIDFILE QUERYFIL="$QUERY -var scripgriddata -res $grid -options lmask=$lmask" if [ "$verbose" = "YES" ]; then echo $QUERYFIL fi GRIDFILE[nfile]=`$QUERYFIL` OUTFILE[nfile]=map_${res}_${lmask}_to_${grid}_${lmask}_aave_da_$CDATE.nc if [ "$list" = "YES" ]; then echo "ingrid = ${GRIDFILE[nfile]}" echo "ingrid = ${GRIDFILE[nfile]}" >> $outfilelist echo "Succesffully found and listed all required mapping files" exit 0 fi nfile=nfile+1 fi #---------------------------------------------------------------------- # Determine supported machine specific stuff #---------------------------------------------------------------------- hostname=`hostname` case $hostname in ##bluefire be* ) source /contrib/Modules/3.2.6/init/bash module load netcdf/4.1.3_seq if [ -z "$ESMFBIN_PATH" ]; then if [ "$type" = "global" ]; then ESMFBIN_PATH=/contrib/esmf-5.2.0rp1bs09-64/bin else ESMFBIN_PATH=/contrib/esmf-5.3.0-64-O-mpiuni-netcdf4.1.3/bin fi fi if [ -z "$MPIEXEC" ]; then MPIEXEC="mpirun.lsf" fi if [ "$interactive" != "NO" ]; then # Bluefire specific commands to prepare to run interactively export MP_PROCS=$REGRID_PROC export MP_EUILIB=ip hostname > hostfile declare -i p=2 until ((p>$MP_PROCS)); do hostname >> hostfile p=p+1 done export MP_HOSTFILE=hostfile fi ;; ##jaguarpf ## NOTE that for jaguarpf there is no batch script for now jaguarpf* ) if [ -z "$ESMFBIN_PATH" ]; then module load esmf/5.2.0-p1_with-netcdf_g ESMFBIN_PATH=$ESMF_BINDIR fi if [ -z "$MPIEXEC" ]; then MPIEXEC="aprun -n $REGRID_PROC" fi ;; ##no other machine currently supported *) echo "Machine $hostname NOT recognized" ;; esac # Error checks if [ ! -d "$ESMFBIN_PATH" ]; then echo "Path to ESMF binary directory does NOT exist: $ESMFBIN_PATH" echo "Set the environment variable: ESMFBIN_PATH" exit 1 fi #---------------------------------------------------------------------- # Generate the mapping files needed for surface dataset generation # and the RTM run time mapping #---------------------------------------------------------------------- # Resolve interactive or batch mode command # NOTE - if you want to run in batch mode - you need to have a separate # batch file that calls this script interactively - you cannot submit # this script to the batch system if [ "$interactive" = "NO" ]; then echo "Running in batch mode using MPI" if [ -z "$MPIEXEC" ]; then echo "Name of MPI exec to use was NOT set" echo "Set the environment variable: MPIEXEC" exit 1 fi if [ ! -x `which $MPIEXEC` ]; then echo "The MPIEXEC pathname given is NOT an executable: $MPIEXEC" echo "Set the environment variable: MPIEXEC or run in interactive mode without MPI" exit 1 fi mpirun=$MPIEXEC echo "Running in batch mode" else mpirun="" fi ESMF_REGRID="$ESMFBIN_PATH/ESMF_RegridWeightGen" if [ ! -x "$ESMF_REGRID" ]; then echo "ESMF_RegridWeightGen does NOT exist in ESMF binary directory: $ESMFBIN_PATH\n" echo "Upgrade to a newer version of ESMF with this utility included" echo "Set the environment variable: ESMFBIN_PATH" exit 1 fi # Remove previous log files rm PET*.Log # # Now run the mapping for each file, checking that input files exist # and then afterwards that the output mapping file exists # declare -i nfile=1 until ((nfile>${#INGRID[*]})); do echo "Creating mapping file: ${OUTFILE[nfile]}" echo "From input grid: ${INGRID[nfile]}" echo "For output grid: ${GRIDFILE[nfile]}" echo " " if [ -z "${INGRID[nfile]}" ] || [ -z "${GRIDFILE[nfile]}" ] || [ -z "${OUTFILE[nfile]}" ]; then echo "Either input or output grid or output mapping file is NOT set" exit 3 fi if [ ! -f "${INGRID[nfile]}" ]; then echo "Input grid file does NOT exist: ${INGRID[nfile]}" exit 2 fi if [ ! -f "${GRIDFILE[nfile]}" ]; then echo "Output grid file does NOT exist: ${GRIDFILE[nfile]}" exit 3 fi cmd="$mpirun $ESMF_REGRID --ignore_unmapped -s ${INGRID[nfile]} " cmd="$cmd -d ${GRIDFILE[nfile]} -m conserve -w ${OUTFILE[nfile]}" if [ $type = "regional" ]; then cmd="$cmd --dst_regional" fi if [ "${LRGFIL[nfile]}" = "yes" ]; then cmd="$cmd --64bit_offset " fi runcmd $cmd if [ "$debug" != "YES" ] && [ ! -f "${OUTFILE[nfile]}" ]; then echo "Output mapping file was NOT created: ${OUTFILE[nfile]}" exit 4 fi # add some metadata to the file HOST=`hostname` history="$ESMF_REGRID" runcmd "ncatted -a history,global,a,c,"$history" ${OUTFILE[nfile]}" runcmd "ncatted -a hostname,global,a,c,$HOST -h ${OUTFILE[nfile]}" runcmd "ncatted -a logname,global,a,c,$LOGNAME -h ${OUTFILE[nfile]}" # check for duplicate mapping weights newfile="rmdups_${OUTFILE[nfile]}" runcmd "rm -f $newfile" runcmd "env MAPFILE=${OUTFILE[nfile]} NEWMAPFILE=$newfile ncl rmdups.ncl" if [ -f "$newfile" ]; then runcmd "mv $newfile ${OUTFILE[nfile]}" fi nfile=nfile+1 done echo "Successffully created needed mapping files for $res" exit 0