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|
#! /usr/bin/perl
# $Id$
use strict;
#######################
#Default parameters
#parameters for submiiting processes through SGE
#NOTE: group name is ws06ossmt (with 2 's') and not ws06osmt (with 1 's')
my $queueparameters="";
# look for the correct pwdcmd
my $pwdcmd = getPwdCmd();
my $workingdir = `$pwdcmd`; chomp $workingdir;
my $tmpdir="$workingdir/tmp$$";
my $jobscript="$workingdir/job$$.sh";
my $qsubout="$workingdir/out.job$$";
my $qsuberr="$workingdir/err.job$$";
$SIG{INT} = \&kill_all_and_quit; # catch exception for CTRL-C
my $help="";
my $dbg="";
my $version="";
my $qsubname="WR$$";
my $cmd="";
my $cmdout=undef;
my $cmderr=undef;
my $parameters="";
my $old_sge = 0; # assume grid engine < 6.0
sub init(){
use Getopt::Long qw(:config pass_through);
GetOptions('version'=>\$version,
'help'=>\$help,
'debug'=>\$dbg,
'qsub-prefix=s'=> \$qsubname,
'command=s'=> \$cmd,
'stdout=s'=> \$cmdout,
'stderr=s'=> \$cmderr,
'queue-parameter=s'=> \$queueparameters,
'old-sge' => \$old_sge,
) or exit(1);
$parameters="@ARGV";
version() if $version;
usage() if $help;
print_parameters() if $dbg;
}
#######################
##print version
sub version(){
# print STDERR "version 1.0 (29-07-2006)\n";
print STDERR "version 1.1 (31-07-2006)\n";
exit(1);
}
#usage
sub usage(){
print STDERR "qsub-wrapper.pl [options]\n";
print STDERR "Options:\n";
print STDERR "-command <file> command to run\n";
print STDERR "-stdout <file> file to save stdout of cmd (optional)\n";
print STDERR "-stderr <file> file to save stderr of cmd (optional)\n";
print STDERR "-qsub-prefix <string> name for sumbitted jobs (optional)\n";
print STDERR "-queue-parameters <string> parameter for the queue (optional)\n";
print STDERR "-old-sge ... assume Sun Grid Engine < 6.0\n";
print STDERR "-debug debug\n";
print STDERR "-version print version of the script\n";
print STDERR "-help this help\n";
exit(1);
}
#printparameters
sub print_parameters(){
print STDERR "command: $cmd\n";
if (defined($cmdout)){ print STDERR "file for stdout: $cmdout\n"; }
else { print STDERR "file for stdout is not defined, stdout is discarded\n"; }
if (defined($cmderr)){ print STDERR "file for stdout: $cmderr\n"; }
else { print STDERR "file for stderr is not defined, stderr is discarded\n"; }
print STDERR "Qsub name: $qsubname\n";
print STDERR "Queue parameters: $queueparameters\n";
print STDERR "parameters directly passed to cmd: $parameters\n";
exit(1);
}
#script creation
sub preparing_script(){
my $scriptheader="\#\!/bin/bash\n# the above line is ignored by qsub, unless parameter \"-b yes\" is set!\n\n";
$scriptheader.="uname -a\n\n";
$scriptheader.="cd $workingdir\n\n";
open (OUT, "> $jobscript");
print OUT $scriptheader;
print OUT "if $cmd $parameters > $tmpdir/cmdout$$ 2> $tmpdir/cmderr$$ ; then
echo 'succeeded'
else
echo failed with exit status \$\?
die=1
fi
";
if (defined $cmdout){
print OUT "mv -f $tmpdir/cmdout$$ $cmdout || echo failed to preserve the log: $tmpdir/cmdout$$\n\n";
}
else{
print OUT "rm -f $tmpdir/cmdout$$\n\n";
}
if (defined $cmderr){
print OUT "mv -f $tmpdir/cmderr$$ $cmderr || echo failed to preserve the log: $tmpdir/cmderr$$\n\n";
}
else{
print OUT "rm -f $tmpdir/cmderr$$\n\n";
}
print OUT "if [ x\$die == 1 ]; then exit 1; fi\n";
close(OUT);
#setting permissions of the script
chmod(oct(755),$jobscript);
}
#######################
#Script starts here
init();
usage() if $cmd eq "";
safesystem("mkdir -p $tmpdir") or die;
preparing_script();
my $maysync = $old_sge ? "" : "-sync y";
# create the qsubcmd to submit to the queue with the parameter "-b yes"
my $qsubcmd="qsub $queueparameters $maysync -V -o $qsubout -e $qsuberr -N $qsubname -b yes $jobscript > $jobscript.log 2>&1";
#run the qsubcmd
safesystem($qsubcmd) or die;
#getting id of submitted job
my $res;
open (IN,"$jobscript.log") or die "Can't read main job id: $jobscript.log";
chomp($res=<IN>);
my @arrayStr = split(/\s+/,$res);
my $id=$arrayStr[2];
die "Failed to get job id from $jobscript.log, got: $res"
if $id !~ /^[0-9]+$/;
close(IN);
print STDERR " res:$res\n";
print STDERR " id:$id\n";
if ($old_sge) {
# need to workaround -sync, add another job that will wait for the main one
# prepare a fake waiting script
my $syncscript = "$jobscript.sync_workaround_script.sh";
safesystem("echo 'date' > $syncscript") or die;
my $checkpointfile = "$jobscript.sync_workaround_checkpoint";
# ensure checkpoint does not exist
safesystem("\\rm -f $checkpointfile") or die;
# start the 'hold' job, i.e. the job that will wait
$cmd="qsub -cwd $queueparameters -hold_jid $id -o $checkpointfile -e /dev/null -N $qsubname.W $syncscript >& $qsubname.W.log";
safesystem($cmd) or die;
# and wait for checkpoint file to appear
my $nr=0;
while (!-e $checkpointfile) {
sleep(10);
$nr++;
print STDERR "w" if $nr % 3 == 0;
}
safesystem("\\rm -f $checkpointfile $syncscript") or die();
print STDERR "End of waiting workaround.\n";
}
my $failure=&check_exit_status();
print STDERR "check_exit_status returned $failure\n";
&kill_all_and_quit() if $failure;
&remove_temporary_files() if !$dbg;
sub check_exit_status(){
my $failure=0;
print STDERR "check_exit_status of submitted job $id\n";
open(IN,"$qsubout") or die "Can't read $qsubout";
while (<IN>){
$failure=1 if (/failed with exit status/);
}
close(IN);
return $failure;
}
sub kill_all_and_quit(){
print STDERR "kill_all_and_quit\n";
print STDERR "qdel $id\n";
safesystem("qdel $id");
print STDERR "The submitted jobs died not correctly\n";
print STDERR "Send qdel signal to the submitted jobs\n";
exit(1);
}
sub remove_temporary_files(){
#removing temporary files
unlink("${jobscript}");
unlink("${jobscript}.log");
unlink("$qsubout");
unlink("$qsuberr");
rmdir("$tmpdir");
}
sub safesystem {
print STDERR "Executing: @_\n";
system(@_);
if ($? == -1) {
print STDERR "Failed to execute: @_\n $!\n";
exit(1);
}
elsif ($? & 127) {
printf STDERR "Execution of: @_\n died with signal %d, %s coredump\n",
($? & 127), ($? & 128) ? 'with' : 'without';
exit(1);
}
else {
my $exitcode = $? >> 8;
print STDERR "Exit code: $exitcode\n" if $exitcode;
return ! $exitcode;
}
}
# look for the correct pwdcmd (pwd by default, pawd if it exists)
# I assume that pwd always exists
sub getPwdCmd(){
my $pwdcmd="pwd";
my $a;
chomp($a=`which pawd 2> /dev/null | head -1 | awk '{print $1}'`);
if ($a && -e $a){ $pwdcmd=$a; }
return $pwdcmd;
}
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