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lib/HPC/Runner/Command/submit_jobs/Plugin/SGE.pm  view on Meta::CPAN

        return $filename;
    },
    predicate => 'has_template_file',
    clearer   => 'clear_template_file',
    documentation =>
      q{Path to Slurm template file if you do not wish to use the default}
);

=head2 Subroutines

=cut

=head3 submit_jobs

Submit jobs to slurm queue using PBS.

Format is

 "Your job <job_id> ("<job_name>") has been submitted"

=cut

sub submit_jobs {
    my $self = shift;

    my ( $exitcode, $stdout, $stderr ) =
      $self->submit_to_scheduler(
        $self->submit_command . " " . $self->slurmfile );
    sleep(5);

    if ( $exitcode != 0 ) {
        $self->log->fatal("Job was not submitted successfully");
        $self->log->warn( "STDERR: " . $stderr ) if $stderr;
        $self->log->warn( "STDOUT: " . $stdout ) if $stdout;
    }

    # my $jobid = $stdout;
    my $jobid;
    ($jobid) = $stdout =~ m/Your job (\d.*) \(/;

    if ( !$jobid ) {
        $self->job_failure;
    }
    else {
        $self->log->debug(
            "Submited job " . $self->slurmfile . "\n\tWith SGE jobid $jobid" );
    }

    return $jobid;
}

=head3 update_job_deps

Update the job dependencies if using job_array (not batches)

NOTE - Task dependencies may not be supported.


=cut

sub update_job_deps {
    my $self = shift;

    return unless $self->has_array_deps;

    $self->log->warn('Task dependencies in SGE is still very experimental!');
    $self->log->warn( 'Please raise any problems as an issue at github.' . "\n"
          . "\thttp://github.com/biosails/HPC-Runner-Command" );

    while ( my ( $current_task, $v ) = each %{ $self->array_deps } ) {

        my $cmd;
        if ( $self->use_batches ) {
            my $dep_tasks = join( ':', @$v );
            $cmd = "qalter -hold_jid \"$dep_tasks\" $current_task ";
        }
        else {
            foreach my $tv ( @{$v} ) {
                my @tmp = split( '_', $tv );
                $tv = $tmp[0] . '[' . $tmp[1] . ']';
            }

            my @tmp = split( '_', $current_task );
            $current_task = $tmp[0] . '[' . $tmp[1] . ']';

            my $dep_tasks = join( ':', @$v );
            $cmd = "qalter -hold_jid \"$dep_tasks\" \"$current_task\" ";
        }

        $self->submit_to_scheduler($cmd);
    }
}

1;