X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=dqsub;h=245f11ece72bca05abcc6736ba2c37badbaa5150;hb=6ff8280b017eb99c4ce759895d460bcb76646f4c;hp=1d3dd1b801bc8d39efa013dea43ebdceea544278;hpb=056bec558a499c31f31f7f3e346d2bdac2f77f90;p=uiuc_igb_scripts.git

diff --git a/dqsub b/dqsub
old mode 100644
new mode 100755
index 1d3dd1b..245f11e
--- a/dqsub
+++ b/dqsub
@@ -10,7 +10,7 @@ use warnings;
 use strict;
 
 use Getopt::Long;
-use Pod::Usage;
+# use Pod::Usage;
 
 =head1 NAME
 
@@ -26,6 +26,7 @@ dqsub [options]
    --nodes nodes to use
    --array array mode (one of 'chdir' or 'xargs' or '')
    --array-from file to read arrays from (default STDIN)
+   --array-slot-limit
    --ppn processors per node to use
    --mem memory to request
    --dir Directory to run the script in (default current directory)
@@ -96,13 +97,14 @@ GetOptions(\%options,
            'nodes=i',
            'array=s',
            'array_from|array-from=s',
+           'array_slot_limit|array-slot-limit=i',
            'ppn|processors-per-node=i',
            'mem|memory=s',
            'dir=s',
            'debug|d+','help|h|?','man|m');
 
-pod2usage() if $options{help};
-pod2usage({verbose=>2}) if $options{man};
+# pod2usage() if $options{help};
+# pod2usage({verbose=>2}) if $options{man};
 
 $DEBUG = $options{debug};
 
@@ -121,13 +123,14 @@ if ($options{interactive} and @ARGV) {
     push @USAGE_ERRORS,"Don't provide commands when you're asking for an interactive shell";
 }
 
-pod2usage(join("\n",@USAGE_ERRORS)) if @USAGE_ERRORS;
+# pod2usage(join("\n",@USAGE_ERRORS)) if @USAGE_ERRORS;
+print STDERR join("\n",@USAGE_ERRORS) and exit 1 if @USAGE_ERRORS;
 
 # OK. Generate the options to qsub which we'll be using
 my @qsub_options = generate_qsub_options(\%options);
 
 if ($options{interactive}) {
-    print STDERR 'running: qsub '.join(' ',@qsub_options) if $DEBUG:
+    print STDERR 'running: qsub '.join(' ',@qsub_options) if $DEBUG;
     exec('qsub',@qsub_options);
 } else {
     my @array = ();
@@ -135,6 +138,9 @@ if ($options{interactive}) {
         @array = read_array_options(\%options) if $options{array};
         # the -t option gives the range of elements for an array job
         push @qsub_options,'-t','1-'. scalar @array;
+        if ($options{array_slot_limit}) {
+            $qsub_options[$#qsub_options] .= '%'.$options{array_slot_limit};
+        }
     }
     call_qsub(\@qsub_options,write_qsub_script(\%options,\@ARGV,\@array));
 }
@@ -157,9 +163,13 @@ sub generate_qsub_options{
         $l[$#l] .= ':ppn='.$options->{ppn};
     }
     if ($options->{mem}) {
-        push @l,'mem=',$options->{mem};
+        push @l,'mem='.$options->{mem};
     }
     push @qo,'-l',join(',',@l) if @l;
+    if ($options->{interactive}) {
+        push @qo,'-I';
+    }
+    return @qo;
 }
 
 sub read_array_options{
@@ -169,7 +179,7 @@ sub read_array_options{
         $fh = IO::File->new(defined $options->{array_from}) or
             die "Unable to open $options->{array_from} for reading: $!";
     }
-    my @arrah;
+    my @array;
     for (<$fh>) {
         chomp;
         push @array,$_;
@@ -197,7 +207,23 @@ sub write_qsub_script {
 # this script was written by dqsub
 EOF
     if (defined $opt->{array}) {
-        die "--array is currently not implemented";
+        my $array_opt = join("\n",@{$array});
+        $script .= <<EOF;
+OPT=\$(sed -n -e "\$PBS_ARRAYID p"<<'_HERE_DOC_END_'
+$array_opt
+_HERE_DOC_END_
+)
+EOF
+        if ($opt->{array} eq 'chdir') {
+            $script .= <<EOF;
+cd "\$OPT";
+exec $command;
+EOF
+        } else {
+            $script .= <<EOF;
+exec $command "\$OPT";
+EOF
+        }
     } else {
         $script .= <<EOF;
 # there's no array, so just executing the command with arguments