From 3dfa575d202c9277060bc43a7af9351702da9f12 Mon Sep 17 00:00:00 2001
From: Jonathan Clark <jon.h.clark@gmail.com>
Date: Fri, 11 Mar 2011 09:05:04 -0500
Subject: fix my dumb bug that killed qsub functionality

---
 vest/parallelize.pl | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'vest/parallelize.pl')

diff --git a/vest/parallelize.pl b/vest/parallelize.pl
index 47b77c79..2798a303 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
@@ -323,7 +323,7 @@ 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;
-- 
cgit v1.2.3


From 6b25a85dd45af5982e07577b33c64e3b577579c3 Mon Sep 17 00:00:00 2001
From: Jonathan Clark <jon.h.clark@gmail.com>
Date: Fri, 11 Mar 2011 10:27:43 -0500
Subject: dont fail on possibly temporary qstat errors

---
 vest/parallelize.pl | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

(limited to 'vest/parallelize.pl')

diff --git a/vest/parallelize.pl b/vest/parallelize.pl
index 2798a303..c2526503 100755
--- a/vest/parallelize.pl
+++ b/vest/parallelize.pl
@@ -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);
   }
 }
-- 
cgit v1.2.3


From eda8d83cd957463d32980da7c60085a820f7eae0 Mon Sep 17 00:00:00 2001
From: Jonathan Clark <jon.h.clark@gmail.com>
Date: Fri, 11 Mar 2011 11:06:48 -0500
Subject: be more verbose when running each child decoder process when forking.
 also, avoid some non-bash errors

---
 vest/parallelize.pl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'vest/parallelize.pl')

diff --git a/vest/parallelize.pl b/vest/parallelize.pl
index c2526503..b4783f91 100755
--- a/vest/parallelize.pl
+++ b/vest/parallelize.pl
@@ -347,7 +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";
-- 
cgit v1.2.3