#!/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) # -i High resolution mode (Only used with -f) # -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 # -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/p/cesm/cseg/inputdata fi #---------------------------------------------------------------------- # Usage subroutine usage() { echo "" echo "**********************" echo "usage:" 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_ctsm.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 (and run with mpi). 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 directly to the batch system" echo "[-i|--hires]" echo " Output maps are high resolution and large file support should be used" 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 "[-h|--help] " echo " Displays this help message" echo "[-v|--verbose]" echo " Toggle verbose usage -- log more information on what is happening " echo "[--fast]" echo " Toggle fast maps only -- only create the maps that can be done quickly " echo "" echo " You can also set the following env variables:" echo " ESMFBIN_PATH - Path to ESMF binaries " echo " (default is determined by machine running on)" echo " CSMDATA ------ Path to CESM input data" echo " (default is $CSMDATA)" echo " MPIEXEC ------ Name of mpirun executable" echo " (default is determined by machine running on)" echo " REGRID_PROC -- Number of MPI processors to use" echo " (default is $REGRID_PROC)" echo "" echo "**defaults can be determined on the machines: cheyenne or casper" echo "" echo "**pass environment variables by preceding above commands " echo " with 'env var1=setting var2=setting '" echo "**********************" } #---------------------------------------------------------------------- # runcmd subroutine #---------------------------------------------------------------------- runcmd() { cmd=$@ 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" phys="clm4_5" verbose="no" list="no" outgrid="" gridfile="default" fast="no" netcdfout="none" while [ $# -gt 0 ]; do case $1 in -v|-V) verbose="YES" ;; -b|--batch) interactive="NO" ;; -d|--debug) debug="YES" ;; --fast) fast="YES" ;; -i|--hires) netcdfout="64bit_offset" ;; -l|--list) debug="YES" list="YES" ;; -r|--res) res=$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 " QUERY="$QUERY -justvalue -options sim_year=2000 -csmdata $CSMDATA" echo "query command is $QUERY" echo "" DST_EXTRA_ARGS="" if [ "$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 # For now, maked the assumption about user-specified grids -- # that they are SCRIP format. In the future we may want to # provide a command-line options to allow the user to # override that default. DST_LRGFIL=$netcdfout DST_TYPE="SCRIP" else if [ "$res" = "default" ]; then res=$default_res fi QUERYARGS="-res $res -options lmask=nomask" # Find the output grid file for this resolution using the XML database QUERYFIL="$QUERY -var scripgriddata $QUERYARGS -onlyfiles" if [ "$verbose" = "YES" ]; then echo $QUERYFIL fi GRIDFILE=`$QUERYFIL` echo "Using default scrip grid file: $GRIDFILE" # Determine extra information about the destination grid file DST_LRGFIL=`$QUERY -var scripgriddata_lrgfile_needed $QUERYARGS` DST_TYPE=`$QUERY -var scripgriddata_type $QUERYARGS` if [ "$DST_TYPE" = "UGRID" ]; then # For UGRID, we need extra information: the meshname variable dst_meshname=`$QUERY -var scripgriddata_meshname $QUERYARGS` DST_EXTRA_ARGS="$DST_EXTRA_ARGS --dst_meshname $dst_meshname" fi fi if [ "$type" = "global" ] && [ `echo "$res" | grep -c "1x1_"` = 1 ]; then echo "This is a regional resolution and yet it is being run as global, set type with '-t' option\n"; exit 1 fi if [ "$type" = "global" ] && [ `echo "$res" | grep -c "5x5_"` = 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: $GRIDFILE\n"; echo "Make sure CSMDATA environment variable is set correctly" exit 1 fi #---------------------------------------------------------------------- # Determine all input grid files and output file names #---------------------------------------------------------------------- if [ "$phys" = "clm4_5" ]; then grids=( \ "0.5x0.5_AVHRR" \ "0.25x0.25_MODIS" \ "0.5x0.5_MODIS" \ "3x3min_LandScan2004" \ "3x3min_MODIS-wCsp" \ "3x3min_USGS" \ "5x5min_nomask" \ "5x5min_IGBP-GSDP" \ "5x5min_ISRIC-WISE" \ "5x5min_ORNL-Soil" \ "10x10min_nomask" \ "10x10min_IGBPmergeICESatGIS" \ "3x3min_GLOBE-Gardner" \ "3x3min_GLOBE-Gardner-mergeGIS" \ "0.9x1.25_GRDC" \ "360x720cru_cruncep" \ "1km-merge-10min_HYDRO1K-merge-nomask" \ ) else echo "ERROR: Unknown value for phys: $phys" exit 1 fi # Set timestamp for names below CDATE="c"`date +%y%m%d` # Set name of each output mapping file # 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#*_} QUERYARGS="-res $grid -options lmask=$lmask,glc_nec=10 " QUERYFIL="$QUERY -var scripgriddata $QUERYARGS -onlyfiles" if [ "$verbose" = "YES" ]; then echo $QUERYFIL fi INGRID[nfile]=`$QUERYFIL` if [ "$list" = "YES" ]; then echo "ingrid = ${INGRID[nfile]}" echo "ingrid = ${INGRID[nfile]}" >> $outfilelist fi OUTFILE[nfile]=map_${grid}_${lmask}_to_${res}_nomask_aave_da_$CDATE.nc # Determine extra information about the source grid file SRC_EXTRA_ARGS[nfile]="" SRC_LRGFIL[nfile]=`$QUERY -var scripgriddata_lrgfile_needed $QUERYARGS` SRC_TYPE[nfile]=`$QUERY -var scripgriddata_type $QUERYARGS` if [ "${SRC_TYPE[nfile]}" = "UGRID" ]; then # For UGRID, we need extra information: the meshname variable src_meshname=`$QUERY -var scripgriddata_meshname $QUERYARGS` SRC_EXTRA_ARGS[nfile]="${SRC_EXTRA_ARGS[nfile]} --src_meshname $src_meshname" fi nfile=nfile+1 done #---------------------------------------------------------------------- # Determine supported machine specific stuff #---------------------------------------------------------------------- hostname=`hostname` if [ -n "$NERSC_HOST" ]; then hostname=$NERSC_HOST fi echo "Hostname = $hostname" case $hostname in ##cheyenne cheyenne* | r* ) . /glade/u/apps/ch/opt/lmod/7.2.1/lmod/lmod/init/bash if [ -z "$REGRID_PROC" ]; then REGRID_PROC=36 fi esmfvers=7.1.0r intelvers=18.0.5 # Could also use intel/19.0.2 EBK 10/4/2019 module purge module load intel/$intelvers module load esmf_libs/$esmfvers module load ncl module load nco if [[ $REGRID_PROC > 1 ]]; then mpi=mpi else mpi=uni fi module load esmf-${esmfvers}-ncdfio-${mpi}-O if [ -z "$ESMFBIN_PATH" ]; then ESMFBIN_PATH=`grep ESMF_APPSDIR $ESMFMKFILE | awk -F= '{print $2}'` fi if [ -z "$MPIEXEC" ]; then MPIEXEC="mpiexec_mpt -np $REGRID_PROC" fi ;; ## DAV pronghorn* | casper* ) . /glade/u/apps/ch/opt/lmod/7.2.1/lmod/lmod/init/bash if [ -z "$REGRID_PROC" ]; then REGRID_PROC=8 fi echo "REGRID_PROC=$REGRID_PROC" esmfvers=7.1.0r intelvers=17.0.1 module purge module load intel/$intelvers if [ $? != 0 ]; then echo "Error doing module load: intel/$intelvers" exit 1 fi module load ncl module load nco module load netcdf module load ncarcompilers module load esmflibs/$esmfvers if [ $? != 0 ]; then echo "Error doing module load: esmflibs/$esmfvers" exit 1 fi if [[ $REGRID_PROC > 1 ]]; then mpi=mpi echo "MPI option is NOT currently available" exit 1 else mpi=uni fi module load esmf-${esmfvers}-ncdfio-${mpi}-O if [ $? != 0 ]; then echo "Error doing module load: esmf-${esmfvers}-ncdfio-${mpi}-O" exit 1 fi if [ -z "$ESMFBIN_PATH" ]; then ESMFBIN_PATH=`grep ESMF_APPSDIR $ESMFMKFILE | awk -F= '{print $2}'` fi echo "ESMFMKFILE: $ESMFMKFILE" echo "LD_LIBRARY_PATH: $LD_LIBRARY_PATH" if [ -z "$MPIEXEC" ]; then MPIEXEC="mpiexec -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: $ESMFBIN_PATH" echo "Set the environment variable: ESMFBIN_PATH" exit 1 fi #---------------------------------------------------------------------- # Generate the mapping files needed for surface dataset generation #---------------------------------------------------------------------- # Resolve interactive or batch mode command # NOTE - if you want to run in batch mode - you need to have a separate # batch file that calls this script interactively - you cannot submit # this script to the batch system if [ "$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: $GRIDFILE" echo " " if [ -z "${INGRID[nfile]}" ] || [ -z "$GRIDFILE" ] || [ -z "${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: ${INGRID[nfile]}" if [ ! "$list" = "YES" ]; then exit 2 fi fi if [ ! -f "$GRIDFILE" ]; then echo "Output grid file does NOT exist: $GRIDFILE" exit 3 fi # Determine what (if any) large file support is needed. Use the # most extreme large file support needed by either the source file # or the destination file. if [ "$DST_LRGFIL" = "netcdf4" ] || [ "${SRC_LRGFIL[nfile]}" = "netcdf4" ]; then lrgfil="--netcdf4" elif [ "$DST_LRGFIL" = "64bit_offset" ] || [ "${SRC_LRGFIL[nfile]}" = "64bit_offset" ]; then lrgfil="--64bit_offset" elif [ "$DST_LRGFIL" = "none" ] && [ "${SRC_LRGFIL[nfile]}" = "none" ]; then lrgfil="" else echo "Unknown LRGFIL type:" echo "DST_LRGFIL = $DST_LRGFIL" echo "SRC_LRGFIL = ${SRC_LRGFIL[nfile]}" exit 4 fi # Skip if file already exists if [ -f "${OUTFILE[nfile]}" ]; then echo "Skipping creation of ${OUTFILE[nfile]} as already exists" # Skip if large file and Fast mode is on elif [ "$fast" = "YES" ] && [ "${SRC_LRGFIL[nfile]}" = "netcdf4" ]; then echo "Skipping creation of ${OUTFILE[nfile]} as fast mode is on so skipping large files in NetCDF4 format" else cmd="$mpirun $ESMF_REGRID --ignore_unmapped -s ${INGRID[nfile]} " cmd="$cmd -d $GRIDFILE -m conserve -w ${OUTFILE[nfile]}" if [ $type = "regional" ]; then cmd="$cmd --dst_regional" fi cmd="$cmd --src_type ${SRC_TYPE[nfile]} ${SRC_EXTRA_ARGS[nfile]} --dst_type $DST_TYPE $DST_EXTRA_ARGS" cmd="$cmd $lrgfil" runcmd $cmd if [ "$debug" != "YES" ] && [ ! -f "${OUTFILE[nfile]}" ]; then echo "Output mapping file was NOT created: ${OUTFILE[nfile]}" exit 6 fi # add some metadata to the file HOST=`hostname` history="$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 $dir/rmdups.ncl" if [ -f "$newfile" ]; then runcmd "mv $newfile ${OUTFILE[nfile]}" fi fi nfile=nfile+1 done echo "Successffully created needed mapping files for $res" exit 0