bkill_pipe

#!/usr/bin/env perl

=head1 Description

This script sends bstop and bkill commands to all jobs
running in a given pipeline. Since it uses a simple 
regex match on a 'bjobs -w' command, it is quite flexible

e.g. bkill_pipe epo_primates_95

=cut

use warnings;
use strict;
use Getopt::Long;

$|++; # turn on auto-flush of stdout buffer

my ( $help, $dry_run );
GetOptions(
    "help"       => \$help,
    "dry_run!"   => \$dry_run,
);

die &helptext if ( $help || !$ARGV[0] );
my $search_term = $ARGV[0];
my @all_bjobs = `bjobs -w`;

my @candidates;
foreach my $job ( @all_bjobs ) {
	chomp $job;
	push( @candidates, $job ) if $job =~ /$search_term/;
}

if (scalar @candidates == 0) {
	print "No '$search_term' jobs found!\n";
	exit(1);
}

if ( $dry_run ) {
	print join("\n", @candidates) . "\n";
	exit 0;
}

my %stop_cmds;
my %kill_cmds;
foreach my $kill_job ( @candidates ) {
	$kill_job =~ /^(\d+)/;
	my $jid = $1;
	die "Cannot get job id from '$kill_job'\n" unless $jid;
	$stop_cmds{"bstop $jid"} = 1 if $kill_job =~ /RUN/;
	$kill_cmds{"bkill $jid"} = 1;
}
# print join("\n", keys %stop_cmds) . "\n\n";
# print join("\n", keys %kill_cmds) . "\n\n";

if ( scalar(keys %stop_cmds) > 0 ) {
	system( join('; ', keys %stop_cmds) . ';' );
	# allow LSF time to stop jobs
	print 'Waiting for jobs to stop';
	foreach my $x ( 1..5 ) {
		print '.';
		sleep 2;
	}
	print "\n";
}
system( join('; ', keys %kill_cmds) . ';' );

sub helptext {
	my $msg = <<HELPEND;

bkill_pipe <hive_pipeline_name> : kill all jobs in the given pipeline

Usage: 

HELPEND
	return $msg;
}