Merge branch 'master' of github.com:redpony/cdec

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";