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sethmcgsethmcg
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convenience scripts
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‎date2time‎

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#!/usr/bin/perl
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## This script converts a date string to the corresponding time for a
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## given netcdf file by using the NCL function ut_inv_calendar.
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$usage = "Usage: date2time netcdf-file yyyy-mm-dd [hh:mm]\n";
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if (@ARGV < 2 or @ARGV > 3) {
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die $usage;
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}
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$file = $ARGV[0];
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($year, $month, $day) = split /[-\/]/, $ARGV[1];
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($hour, $minute, $second) = split /\:/, $ARGV[2];
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$hour += 0;
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$minute += 0;
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$second += 0;
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# Check for numeric validity
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if ($year !~ /\d{4}/ or
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$month < 0 or $month > 12 or
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$day < 0 or $day > 31 or
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$hour < 0 or $hour > 24 or
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$minute < 0 or $minute > 60 or
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$second < 0 or $second > 60){
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die "Invalid date specification: $year/$month/$day $hour:$minute:$second (should be YYYY/MM/DD [hh:mm:ss])\n";
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}
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$units = `ncdump -h $file | grep time:units | cut -f 2 -d \\\"`;
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unless ($units) {die "No units found in netcdf file $file.\n";}
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$calendar = `ncdump -h $file | grep time:calendar | cut -f 2 -d \\\"`;
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unless ($calendar) {die "No calendar found in netcdf file $file.\n";}
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chomp $units;
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chomp $calendar;
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$tempfile = ".date2time.$$";
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open(NCL, ">$tempfile");
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$nclscript = <<END;
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c = 0
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c\@calendar = \"$calendar\"
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date = cd_inv_calendar($year,$month,$day,$hour,$minute,$second,\"$units\",c)
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print(sprintf("%.4f",date))
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END
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print NCL "$nclscript";
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close(NCL);
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$result = `ncl -n -Q $tempfile`;
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print "$result";
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`rm $tempfile`;
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# Copyright 2010-2012 Univ. Corp. for Atmos. Research
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# Author: Seth McGinnis, [email protected]

‎extract.R‎

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args<-commandArgs(TRUE)
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library(ncdf4)
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tlat = as.numeric(args[1])
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tlon = as.numeric(args[2])
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infile = args[3]
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outfile = args[4]
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fin<-nc_open(infile)
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lat<-ncvar_get(fin,"lat")
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lon<-ncvar_get(fin,"lon")
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dy = abs(lat - tlat)
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dx = abs(lon%%360 - tlon%%360)
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#image(dx+dy)
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ind = arrayInd(which.min(dx+dy),dim(lat))-1
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xind = paste0("-d xc,", ind[1], ",", ind[1])
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yind = paste0("-d yc,", ind[2], ",", ind[2])
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command = paste("ncks", xind, yind, infile, outfile)
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#print(command)
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system(command)
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‎nclwrap‎

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#!/bin/tcsh -f
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# wrapper script for making passing of arguments to NCL scripts easier.
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# invocation: nclwrap nclscript infile [ [otherfile] outfile]
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if ($#argv < 2) then
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echo Usage: nclwrap nclscript infile \[ \[otherfile\] outfile\]
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exit
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endif
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set ncl = `basename $1 .ncl`
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set var = `basename $2 | cut -f 1 -d _ | cut -f 1 -d .`
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if ($ncl == regrid-rcm2rcm || $ncl == coarsen) then
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set echo
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ncl -Q -n $1 datafile=\"$2\" gridfile=\"$3\" outfile=\"$4\" varname=\"$var\"
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unset echo
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exit
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endif
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if ($ncl == patch-regrid) then
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set echo
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ncl -Q -n $1 infile=\"$2\" wgtfile=\"$3\" outfile=\"$4\" varname=\"$var\"
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unset echo
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exit
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endif
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if ($ncl == aggregate) then
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set echo
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ncl -Q -n $1 infile=\"$2\" outfile=\"$3\" interval=\"$4\" varname=\"$var\" $argv[5-]
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unset echo
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exit
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endif
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if ($ncl == wind-vector-plot) then
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set echo
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ncl -Q -n $1 ufile=\"$2\" vfile=\"$3\" outfile=\"$4\" $argv[5-]
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unset echo
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exit
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endif
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if ($ncl == gap-find ) then
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ncl -Q -n $1 infile=\"$2\" outfile=\"$3\" varname=\"$var\" $argv[4-]
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exit
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endif
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if ($ncl == text2mask ) then
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set echo
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ncl -Q -n $1 infile=\"$2\" $argv[3-]
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unset echo
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exit
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endif
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if ($ncl == datetime ) then
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ncl -Q -n $1 infile=\"$2\" $argv[3-]
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exit
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endif
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if ($#argv == 2) then
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ncl -Q -n $1 varname=\"$var\" infile=\"$2\"
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exit
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endif
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# [should] work for: time-section-plot, plot-timestep, 3d-plots
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set echo
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ncl -Q -n $1 varname=\"$var\" infile=\"$2\" outfile=\"$3\" $argv[4-]
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unset echo
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exit
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endif
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# Copyright 2009-2012 Univ. Corp. for Atmos. Research
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# Author: Seth McGinnis, [email protected]

‎template.pbs‎

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#!/bin/tcsh
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##### parameters for PBS scheduling via qsub
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##### submit jobs as "qsub scriptname"
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# account code to charge to
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#PBS -A P86850057
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# which queue to use
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#PBS -q premium
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# job name
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#PBS -N JOBNAME
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# stdout file
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#PBS -o OUTFILE
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# stderr file
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#PBS -e ERRFILE
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# runtime limit
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#PBS -l walltime=00:10:00
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# CPU resource request
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# ntask = number of lines in file
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# nnode = ceiling(NTASK / 36)
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# ncpus is always set to 36 (use all CPUs in node)
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# mpiprocs is always set to 36 also (1 process per CPU)
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# ompthreads is always set to 1 (1 thread per process)
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#PBS -l select=NNODE:ncpus=36:mpiprocs=36:ompthreads=1
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#source /glade/u/apps/opt/lmod/4.2.1/init/tcsh
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module load mpt
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module load netcdf
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module load R
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module load nco
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module load cdo
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module load ncl
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setenv MPI_SHEPHERD true
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mpiexec_mpt -n NTASK launch_cf.sh CMDFILE

‎vectorize‎

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#!/bin/tcsh -f
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## given a file of commands (one command per line), runs them in
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## parallel on cheyenne using commandfile MPMD approach
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set tmp = `mktemp -d`
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set cmd = $tmp/cmdfile
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set out = $tmp/out
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set err = $tmp/err
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set pbs = $tmp/pbs
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set job = `basename $1`
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## commands need to be wrapped in tcsh shell invocation
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sed "s|\(.*\)|tcsh -c '\1 >>\& $tmp/log'|g" $1 > $cmd
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set nt = `cat $cmd | wc -l`
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set nn = `perl -w -e "use POSIX; print ceil($nt/36)"`
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sed -e "s|NTASK|$nt|; s|NNODE|$nn|; s|JOBNAME|$job|; s|OUTFILE|$out|; s|ERRFILE|$err|; s|CMDFILE|$cmd|" ~/template.pbs > $pbs
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qsub < $pbs &
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# Copyright 2017 Univ. Corp. for Atmos. Research
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# Author: Seth McGinnis, [email protected]

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