Raw content of Bio::EnsEMBL::Pipeline::BatchSubmission::GridEngine
<![CDATA[# Ensembl Pipeline module for handling job submission via Sun Grid Engine
# load sharing software
#
# Cared for by Steve Searle
#
# Copyright Steve Searle
#
# You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code
=pod
=head1 NAME
Bio::EnsEMBL::Pipeline::BatchSubmission::GridEngine
=head1 SYNOPSIS
my $batchjob = Bio::EnsEMBL::Pipeline::BatchSubmission::LSF->new(
-STDOUT => $stdout_file,
-STDERR => $stderr_file,
-PARAMETERS => @args,
-PRE_EXEC => $pre_exec,
-QUEUE => $queue,
-JOBNAME => $jobname,
-NODES => $nodes,
-RESOURCE => $resource
);
$batch_job->construct_command_line('test.pl');
$batch_job->open_command_line();
=head1 DESCRIPTION
This module provides an interface to the Sun Grid Engine load sharing softwa
re and its commands. It implements the method construct_command_line which is
not defined in the base class and which enables the pipeline to submit jobs
in a distributed environment using Sun Grid Engine.
See base class Bio::EnsEMBL::Pipeline::BatchSubmission for more info
=head1 CONTACT
Post general queries to B<ensembl-dev@ebi.ac.uk>
=head1 APPENDIX
The rest of the documentation details each of the object methods. Interna
l
methods are usually preceded with a _
=cut
package Bio::EnsEMBL::Pipeline::BatchSubmission::GridEngine;
use Bio::EnsEMBL::Pipeline::BatchSubmission;
use vars qw(@ISA);
use strict;
@ISA = qw(Bio::EnsEMBL::Pipeline::BatchSubmission);
sub new{
my ($class, @args) = @_;
my $self = $class->SUPER::new(@args);
return $self;
}
##################
#accessor methods#
##################
sub qsub {
my ($self,$qsub_line) = @_;
if (defined($qsub_line)) {
$self->{_qsub} = $qsub_line;
}
return $self->{_qsub};
}
##other accessor are in base class##
######################
#command line methods#
######################
sub construct_command_line{
my($self, $command, $stdout, $stderr) = @_;
#print STDERR "creating the command line\n";
#command must be the first argument then if stdout or stderr aren't definhed the objects own can be used
if(!$command){
$self->throw("cannot create qsub if nothing to submit to it : $!\n");
}
my $qsub_line;
$self->command($command);
if($stdout){
$qsub_line = "qsub -V -cwd -v FINAL_STDOUT=".$stdout;
}else{
$qsub_line = "qsub -V -cwd -v FINAL_STDOUT=".$self->stdout_file;
}
if($stderr){
$qsub_line .= " -v FINAL_STDERR=".$stderr;
}else{
$qsub_line .= " -v FINAL_STDERR=".$self->stderr_file;
}
$qsub_line .= " -o /tmp -e /tmp";
# Depends on queues being made for each node with name node.q
if($self->nodes){
my $nodes = $self->nodes;
# $nodes needs to be a space-delimited list
$nodes =~ s/,/.q,/;
$qsub_line .= " -q ".$nodes." ";
}
if (defined($self->queue) && $self->queue ne "") {$qsub_line .= " -l ".$self->queue;}
$qsub_line .= " -N ".$self->jobname if defined $self->jobname;
$qsub_line .= " ".$self->parameters." " if defined $self->parameters;
$qsub_line .= " -v PREEXEC=\"".$self->pre_exec."\"" if defined $self->pre_exec;
## must ensure the prexec is in quotes ##
my $ge_wrapper = "ge_wrapper.pl";
unless (-x $ge_wrapper) {
$ge_wrapper = __FILE__;
$ge_wrapper =~ s:GridEngine.pm:../../../../../scripts/ge_wrapper.pl:;
print $ge_wrapper . "\n";
my $caller = caller(0);
$self->throw("ge_wrapper not found - needs to be set in $caller\n") unless -x $ge_wrapper;
}
$qsub_line .= " $ge_wrapper \"".$command . "\"";
$self->qsub($qsub_line);
#print "have command line\n";
}
sub open_command_line{
my ($self)= @_;
print STDERR $self->qsub."\n";
print STDERR "opening command line\n";
open(SUB, $self->qsub." 2>&1 |");
my $geid;
while(<SUB>){
if (/your job (\d+)/) {
$geid = $1;
}
}
print STDERR "have opened ".$self->qsub."\n";
print STDERR "geid ".$geid."\n";
$self->id($geid);
close(SUB);
}
]]>