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#! /usr/bin/perl
#
# Perl script to generate PBS submission script
#
# Peter Willendrup, 20161031
use POSIX;
use File::Which;
use File::Basename;
use Cwd 'abs_path';
my $nodes = "1";
my $coresprnode = "8";
my $queue = "express";
my $runtime = 1;;
my $name = "McSub_" . $ENV{'USER'} . "_" . POSIX::strftime("%Y%m%d_%H%M%S", localtime);
my $mailrcpt = "none";
my @cmdline;
for($i = 0; $i < @ARGV; $i++) {
if($ARGV[$i] =~ /--help|-h$/) {
$show_help=1;
} elsif($ARGV[$i] =~ /^--nodes=([0-9\-]+)$/) {
$nodes = $1;
} elsif($ARGV[$i] =~ /^--cpn=([0-9\-]+)$/) {
$coresprnode = $1;
} elsif($ARGV[$i] =~ /^--name=([a-zA-Z0-9_]+)$/) {
$name = $1;
} elsif(($ARGV[$i] =~ /^-q([a-zA-Z0-9_]+)$/) ||
($ARGV[$i] =~ /^--queue=([a-zA-Z0-9_]+)$/)) {
$queue = $1;
} elsif(($ARGV[$i] =~ /^-r([0-9]+)$/) ||
($ARGV[$i] =~ /^--runtime=([0-9]+)$/)) {
$runtime = $1;
} elsif(($ARGV[$i] =~ /^-e([0-9a-zA-Z_\.\@]+)$/) ||
($ARGV[$i] =~ /^--email=([0-9a-zA-Z_\.\@]+)$/)) {
$mailrcpt = $1;
} elsif($ARGV[$i] =~ /@MCCODE_PREFIX@run/) {
# strip any reference to @MCCODE_PREFIX@run
} else {
push @cmdline, $ARGV[$i]; }
}
# Figure out which mcstas/mcxtrace is currently loaded
my $mccode_path = which('@FLAVOR@');
my $mccode_version = basename(dirname(dirname(abs_path$mccode_path)));
if (@cmdline == 0) { $show_help=1; }
if ($show_help) {
die "$0 generate PBS submission script
Usage: $0 [options] [@MCCODE_PREFIX@run params]
-h --help Show this help
-rN --runtime=N Specify maximum runtime (hours) [default $runtime]
-qQNAME --queue=QNAME Specify wanted SLURM queue [default '$queue']
-e<mail> --email=<mail> Specify address to notify in reg. sim status [default $mailrcpt]
--nodes=NUM Specify wanted number of nodes [default $nodes]
--coresprnode=NUM Specify wanted number of nodes [default $coresprnode]
--name=NAME Specify openPBS job name [default \"McSub_<USERNAME>_<TIMESTAMP>\"]
\n\nAfter running $0 NAME.batch is ready for submission using the sbatch command\n";
} else {
# Write PBS script to file
open($OUT,"> $name.batch") || die "Could not write to $name.batch!\n";
open($OUT,"> $name.batch") || die "Could not write to $name.batch!\n";
print $OUT "#!/bin/sh\n#\n# PBS queue script generated by $0\n\n";
print $OUT "### Job name\n";
print $OUT "#PBS -N $name\n";
print $OUT "### Number of cpus\n";
print $OUT "#PBS -lncpus=".$nodes*coresprnode."\n";
print $OUT "### Maximum walltime\n";
print $OUT "#PBS -l walltime=$runtime:00:00\n";
print $OUT "### Output\n";
print $OUT "#PBS -o $name.OUT\n";
print $OUT "#PBS -e $name.ERR\n";
print $OUT "### Queue name\n";
print $OUT "#PBS -q $queue\n";
print $OUT "\n\n";
print $OUT "module load @FLAVOR@/$mccode_version\n";
print $OUT "\n";
print $OUT "### Set up @MCCODE_PREFIX@run line\n";
print $OUT "cd \$PBS_O_WORKDIR\n";
print $OUT "@MCCODE_PREFIX@run --mpi=".$nodes*$coresprnode." --machines=\$PBS_NODEFILE ";
print $OUT join(' ',@cmdline);
if (!($mailrcpt eq "none")) {
print $OUT "### Send mail on b)egin e)xit a)bort\n";
print $OUT "#PBS -m abe\n";
print $OUT "#PBS -M $mailrcpt\n";
}
print $OUT "\n### END of McSub script\n";
close($OUT);
print "Your batchfile \n\n--> $name.batch\n\n is now ready for submission using sbatch!\n";
print " \n";
print "Resources:\n";
print " $nodes nodes using all their cores on queue $queue, expected duration $runtime hours \n";
print " \n";
print "@MCCODE_PREFIX@run Command to be submitted: \n";
print " @MCCODE_PREFIX@run --mpi=".$nodes*coresprnode;
print join(' ',@cmdline); print " \n";
print " \n";
print "Output/error messages will go to: \n";
print " $name.stdout and $name.stderr\n";
print " \n";
print "\nNOTE: Please compile your instrumentfile using\n";
print " @MCCODE_PREFIX@run --mpi -c -n0 instrument.instr\n";
print " before submitting!\n";
print " \n";
}
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