From 658d5dd88ffbf3a4fb6f37b587f10a32eb2c1eec Mon Sep 17 00:00:00 2001
From: Glenn Proctor <gp1@sanger.ac.uk>
Date: Mon, 7 Mar 2005 11:43:38 +0000
Subject: [PATCH] Use double-fork (not Open3) to communicate with LSF
processes. More reliable and no quoting strangeness.
---
.../XrefMapper/Methods/ExonerateBasic.pm | 66 ++++++++++++-------
1 file changed, 44 insertions(+), 22 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateBasic.pm b/misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateBasic.pm
index aeb8b80fbe..368e6420ff 100644
--- a/misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateBasic.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateBasic.pm
@@ -94,14 +94,10 @@ sub submit_exonerate {
my $output = $self->get_class_name() . "_" . $ensembl_type . "_" . "\$LSB_JOBINDEX.map";
- my @main_bsub = ( 'bsub', '-J', $unique_name . "[1-$num_jobs]", '-o', "$prefix.%J-%I.out", '-e', "$prefix.%J-%I.err");
+ my @main_bsub = ( 'bsub', '-J' . $unique_name . "[1-$num_jobs]", '-o', "$prefix.%J-%I.out", '-e', "$prefix.%J-%I.err");
#print "bsub command: " . join(" ", @main_bsub) . "\n\n";
- # Use IPC::Open3 to open the process so that we can read and write from/to its stdout/stderr
- my ($wtr, $rtr, $etr, $pid);
- $pid = open3($wtr, $rtr, $etr, @main_bsub) || die "Cannot call bsub command";
-
# Create actual execute script to be executed with LSF, and write to pipe
my $main_job = <<EOF;
. /usr/local/lsf/conf/profile.lsf
@@ -120,24 +116,50 @@ lsrcp /tmp/$output ecs1a:$root_dir/$output
rm -f /tmp/\$LSB_JOBINDEX.$queryfile /tmp/\$LSB_JOBINDEX.$targetfile /tmp/$output
EOF
- # TODO make sure query/target are the right way round
-
- print $wtr $main_job;
-
- #print "Job:\n" . $main_job . "\n\n";
-
- close($wtr);
-
- # Wait until bsub has actually run - will print to its stdout ($rtr) and then close it
- my $jobid;
- while (<$rtr>) {
- if (/Job <([0-9]+)> is/) {
- $jobid = $1;
- print "LSF job ID for main mapping job: $jobid (job array with $num_jobs jobs)\n"
+ # now submit it
+ my $jobid = 0;
+
+ eval {
+ my $pid;
+ my $reader;
+
+ local *BSUB;
+ local *BSUB_READER;
+
+ if (($reader = open(BSUB_READER, '-|'))) {
+ while (<BSUB_READER>) {
+ if (/^Job <(\d+)> is submitted/) {
+ $jobid = $1;
+ print "LSF job ID for main mapping job: $jobid (job array with $num_jobs jobs)\n"
+ }
+ }
+ close(BSUB_READER);
+ } else {
+ die("Could not fork : $!\n") unless (defined($reader));
+ open(STDERR, ">&STDOUT");
+ if (($pid = open(BSUB, '|-'))) {
+
+ print BSUB $main_job;
+ close BSUB;
+ if ($? != 0) {
+ die("bsub exited with non-zero status - job not submitted\n");
+ }
+ } else {
+ if (defined($pid)) {
+ exec(@main_bsub);
+ die("Could not exec bsub : $!\n");
+ } else {
+ die("Could not fork : $!\n");
+ }
+ }
+ exit(0);
}
- }
- if (!defined($jobid)) {
- print STDERR "Error: could not get LSF job ID for mapping job\n";
+ };
+
+ if ($@) {
+ # Something went wrong
+ warn("Job submission failed:\n$@\n");
+ return 0;
}
return $unique_name;
--
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