From d4e4120ca1e21e356ae529e3be815b2bf3f2ef97 Mon Sep 17 00:00:00 2001
From: kiran <kiran@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 12 Feb 2010 00:18:34 +0000
Subject: [PATCH] Some useful changes that I've had laying around for a while -
 deletes files from failed runs, automatically adds a memory limit to java
 commands where one isn't specified, and touches files on the local machine
 after command completion to get around the problem with the times not being
 perfectly synchronized across LSF nodes.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2829 348d0f76-0448-11de-a6fe-93d51630548a
---
 perl/DistributedMake.pm | 33 +++++++++++++++++++++++----------
 1 file changed, 23 insertions(+), 10 deletions(-)

diff --git a/perl/DistributedMake.pm b/perl/DistributedMake.pm
index f844ad677..e784c4292 100644
--- a/perl/DistributedMake.pm
+++ b/perl/DistributedMake.pm
@@ -55,9 +55,9 @@ sub new {
         'hostindex'          => 0,
     );
 
-    $self{'makefile'}  = new File::Temp(TEMPLATE => "/broad/hptmp/DistributedMake_XXXXXX", SUFFIX => ".makefile", UNLINK => $self{'unlink'}),
+    $self{'makefile'}  = new File::Temp(TEMPLATE => "/tmp/DistributedMake_XXXXXX", SUFFIX => ".makefile", UNLINK => $self{'unlink'}),
     $self{'hostarray'} = &parseHostsString($self{'hosts'});
-    $self{'jobName'}   = basename($self{'makefile'});
+    $self{'projectName'}   = basename($self{'makefile'});
 
 	bless \%self, $class;
 
@@ -84,7 +84,7 @@ sub addRule {
         my %bja = (
             'queue' => $self->{'queue'},
             'memLimit' => $self->{'memLimit'},
-            'jobName' => $self->{'jobName'},
+            'projectName' => $self->{'projectName'},
             'outputFile' => $self->{'outputFile'},
             'mailTo' => $self->{'mailTo'},
             'wait' => $self->{'wait'},
@@ -99,17 +99,29 @@ sub addRule {
         my $wait = $bja{'wait'} ? "-K" : "";
 
         my $logdir = dirname($bja{'outputFile'});
-        my $mklogdircmd = "\@test \"! -d $logdir\" && mkdir -p $logdir";
-        push(@prepcmds, $mklogdircmd);
+        if (!-e $logdir) {
+            my $mklogdircmd = "\@test \"! -d $logdir\" && mkdir -p $logdir";
+            push(@prepcmds, $mklogdircmd);
+        }
 
-        $cmdprefix = "bsub -q $bja{'queue'} -M $bja{'memLimit'} -J $bja{'jobName'} -o $bja{'outputFile'} -u $bja{'mailTo'} $wait $rerunnable $migrationThreshold $bja{'extra'}    ";
+        # A quick check to make sure that java commands being dispatched to the farm are instructed to run under a default memory limit
+        for (my $i = 0; $i <= $#cmds; $i++) {
+            if ($cmds[$i] =~ /^java / && $cmds[$i] =~ / -jar / && $cmds[$i] !~ / -Xmx/) {
+                $cmds[$i] =~ s/^java /java -Xmx2048m /;
+            }
+        }
+
+        $cmdprefix = "bsub -q $bja{'queue'} -M $bja{'memLimit'} -P $bja{'projectName'} -o $bja{'outputFile'} -u $bja{'mailTo'} $wait $rerunnable $migrationThreshold $bja{'extra'}    ";
     }
 
     my $rootdir = dirname($targets[0]);
-    my $mkdircmd = "\@test \"! -d $rootdir\" && mkdir -p $rootdir";
-    push(@prepcmds, $mkdircmd);
+    if (!-e $rootdir) {
+        my $mkdircmd = "\@test \"! -d $rootdir\" && mkdir -p $rootdir";
+        push(@prepcmds, $mkdircmd);
+    }
 
-    print { $self->{'makefile'} } "$targets[0]: " . join(" ", @dependencies) . "\n\t" . join("\n\t", @prepcmds) . "\n\t$cmdprefix" . join("\n\t$cmdprefix", @cmds) . "\n";
+    # We have to touch the final file just in case the time between different nodes on the farm are not synchronized.
+    print { $self->{'makefile'} } "$targets[0]: " . join(" ", @dependencies) . "\n\t" . join("\n\t", @prepcmds) . "\n\t$cmdprefix" . join("\n\t$cmdprefix", @cmds) . "\n\ttouch -c $targets[0]\n\n\n";
 
     push(@{$self->{'targets'}}, $targets[0]);
 }
@@ -117,7 +129,8 @@ sub addRule {
 sub execute {
     my ($self, %overrides) = @_;
 
-    print { $self->{'makefile'} } "all: " . join(" ", @{$self->{'targets'}}) . "\n";
+    print { $self->{'makefile'} } "all: " . join(" ", @{$self->{'targets'}}) . "\n\n";
+    print { $self->{'makefile'} } ".DELETE_ON_ERROR:\n";
 
 	my %makeargs = (
         'dryRun'         => $self->{'dryRun'},