diff options
Diffstat (limited to 'vest')
| -rwxr-xr-x | vest/dist-vest.pl | 12 | ||||
| -rwxr-xr-x | vest/parallelize.pl | 9 |
2 files changed, 12 insertions, 9 deletions
diff --git a/vest/dist-vest.pl b/vest/dist-vest.pl index 973a29ef..d17d7de1 100755 --- a/vest/dist-vest.pl +++ b/vest/dist-vest.pl @@ -194,7 +194,6 @@ sub modbin { my $src=$$_; $$_="$bindir/".basename($src); check_call("cp -p $src $$_"); - die "cp $src $$_ failed: $!" unless $? == 0; } } sub dirsize { @@ -372,13 +371,12 @@ while (1){ if ($first_shard) { print STDERR "$script\n"; $first_shard=0; } $nmappers++; - my $qcmd = "QSUB_CMD -N $client_name -o /dev/null -e $logdir/$client_name.ER $script_file"; + my $qcmd = "$QSUB_CMD -N $client_name -o /dev/null -e $logdir/$client_name.ER $script_file"; my $jobid = check_output("$qcmd"); - die "qsub failed: $!\nCMD was: $qcmd" unless $? == 0; chomp $jobid; $jobid =~ s/^(\d+)(.*?)$/\1/g; $jobid =~ s/^Your job (\d+) .*$/\1/; - push(@cleanupcmds, check_output("qdel $jobid 2> /dev/null")); + push(@cleanupcmds, "qdel $jobid 2> /dev/null"); print STDERR " $jobid"; if ($joblist == "") { $joblist = $jobid; } else {$joblist = $joblist . "\|" . $jobid; } @@ -398,7 +396,7 @@ while (1){ print STDERR "Waiting for mappers to complete...\n"; while ($nmappers > 0) { sleep 5; - my @livejobs = grep(/$joblist/, split(/\n/, check_output("qstat | grep -v ' C '"))); + my @livejobs = grep(/$joblist/, split(/\n/, unchecked_output("qstat | grep -v ' C '"))); $nmappers = scalar @livejobs; } print STDERR "All mappers complete.\n"; @@ -575,7 +573,11 @@ sub enseg { while (my $line=<SRC>){ chomp $line; if ($line =~ /^\s*<seg/i) { + if($line =~ /id="[0-9]+"/) { print NEWSRC "$line\n"; + } else { + die "When using segments with pre-generated <seg> tags, you must include a zero-based id attribute"; + } } else { print NEWSRC "<seg id=\"$i\">$line</seg>\n"; } 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"; |