diff options
Diffstat (limited to 'vest/parallelize.pl')
| -rwxr-xr-x | vest/parallelize.pl | 9 |
1 files changed, 5 insertions, 4 deletions
diff --git a/vest/parallelize.pl b/vest/parallelize.pl index 47b77c79..b4783f91 100755 --- a/vest/parallelize.pl +++ b/vest/parallelize.pl @@ -82,7 +82,7 @@ sub preview_files { my @f=grep { ! ($skipempty && -z $_) } @$l; my $fn=join(' ',map {escape_shell($_)} @f); my $cmd="tail -n $n $fn"; - check_output("$cmd").($footer?"\nNONEMPTY FILES:\n$fn\n":""); + unchecked_output("$cmd").($footer?"\nNONEMPTY FILES:\n$fn\n":""); } sub prefix_dirname($) { #like `dirname but if ends in / then return the whole thing @@ -283,7 +283,8 @@ sub numof_live_jobs { if ($use_fork) { die "not implemented"; } else { - my @livejobs = grep(/$joblist/, split(/\n/, check_output("qstat"))); + # We can probably continue decoding if the qstat error is only temporary + my @livejobs = grep(/$joblist/, split(/\n/, unchecked_output("qstat"))); return ($#livejobs + 1); } } @@ -323,7 +324,7 @@ sub launch_job { } if ($joblist == "") { $joblist = $jobid; } else {$joblist = $joblist . "\|" . $jobid; } - my $cleanfn=check_output("qdel $jobid 2> /dev/null"); + my $cleanfn="qdel $jobid 2> /dev/null"; push(@cleanup_cmds, $cleanfn); } close QOUT; @@ -346,7 +347,7 @@ sub launch_job_fork { my ($fh, $scr_name) = get_temp_script(); print $fh $script; close $fh; - my $todo = "/bin/sh $scr_name 1> $outfile 2> $errorfile"; + my $todo = "/bin/bash -xeo pipefail $scr_name 1> $outfile 2> $errorfile"; print STDERR "EXEC: $todo\n"; my $out = check_output("$todo"); print STDERR "RES: $out\n"; |