Commit 8a3eb697 authored by Jessica Severin's avatar Jessica Severin
Browse files

removed -m lsf option and replaced with a general

-lsf_options <string>
which passes whatever is specified in the string to the bsub command
thus allowing the user complete flexibility
parent 2d7324e7
......@@ -36,6 +36,7 @@ my $local=undef;
$self->{'overdue_limit'} = 75; #minutes
$self->{'show_analysis_stats'} = undef;
$self->{'show_worker_stats'} = undef;
$self->{'lsf_options'} = "";
GetOptions('help' => \$help,
'url=s' => \$url,
......@@ -45,9 +46,10 @@ GetOptions('help' => \$help,
'dbuser=s' => \$user,
'dbpass=s' => \$pass,
'dbname=s' => \$dbname,
'local' => \$local,
'local' => \$local,
'lsf' => \$self->{'lsf_mode'},
'dead' => \$self->{'check_for_dead'},
'killworker=i' => \$self->{'kill_worker_id'},
'killworker=i' => \$self->{'kill_worker_id'},
'overdue' => \$self->{'overdue_limit'},
'alldead' => \$self->{'all_dead'},
'run' => \$self->{'run'},
......@@ -64,7 +66,7 @@ GetOptions('help' => \$help,
'failed_jobs' => \$self->{'show_failed_jobs'},
'reset_job_id=i' => \$self->{'reset_job_id'},
'reset_all_jobs_for_analysis_id=i' => \$self->{'reset_all_jobs_for_analysis_id'},
'm=s' => \$self->{'lsf_machine_option'},
'lsf_options=s' => \$self->{'lsf_options'},
);
if ($help) { usage(); }
......@@ -170,8 +172,8 @@ sub usage {
print " -loop : run autonomously, loops and sleeps\n";
print " -local : run jobs on local CPU (fork)\n";
print " -lsf : run jobs on LSF compute resource (bsub)\n";
print " -lsf_options <string> : passes <string> to LSF bsub command as <options>\n";
print " -no_pend : don't adjust needed workers by pending workers\n";
print " -m <string> : passes <string> to LSF bsub -m option\n";
print " -sleep <num> : when looping, sleep <num> minutes (default 3min)\n";
print " -wlimit <num> : max # workers to create per loop\n";
print " -analysis_stats : show status of each analysis\n";
......@@ -412,12 +414,12 @@ sub run_autonomously {
if($self->{'beekeeper_type'} eq 'LSF') {
if($count>1) { $cmd = "bsub -JHL$loopCount\[1-$count\]";}
else { $cmd = "bsub -JHL$loopCount";}
$cmd .= " -m '" . $self->{'lsf_machine_option'} ."'" if($self->{'lsf_machine_option'});
$cmd .= " " . $self->{'lsf_options'} if($self->{'lsf_options'});
$cmd .= " ".$worker_cmd;
} elsif(($self->{'beekeeper_type'} eq 'LOCAL') and
($self->get_local_running_count() < $self->{'local_cpus'}))
{
$cmd = "$worker_cmd &";
$cmd = "$worker_cmd &";
}
if($cmd) {
......
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