X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=dqsub;h=7fe5f9afd7949fd0d991321c97aec7b36b4b826c;hb=2051f76c3a53881a1d524e7923bb2592798534d4;hp=af930905c2ba33bf1636b5ae04cec47c38b0e522;hpb=25c7a523f17b043a2a8f6abc9715e11e78256b7f;p=uiuc_igb_scripts.git

diff --git a/dqsub b/dqsub
index af93090..7fe5f9a 100755
--- a/dqsub
+++ b/dqsub
@@ -26,6 +26,8 @@ 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-per-job number of array items to handle in each job (default 1)
+   --array-all-in-one-job Run all of the array items in one job
    --ppn processors per node to use
    --mem memory to request
    --dir Directory to run the script in (default current directory)
@@ -79,6 +81,7 @@ dqsub
 
 use IO::File;
 use Cwd qw(getcwd abs_path);
+use POSIX qw(ceil);
 use vars qw($DEBUG);
 
 my %options = (nodes           => 1,
@@ -88,6 +91,7 @@ my %options = (nodes           => 1,
                help            => 0,
                man             => 0,
                interactive     => 0,
+               array_per_job   => 1,
               );
 
 GetOptions(\%options,
@@ -96,6 +100,9 @@ GetOptions(\%options,
            'nodes=i',
            'array=s',
            'array_from|array-from=s',
+           'array_per_job|array-per-job=i',
+           'array_slot_limit|array-slot-limit=i',
+           'array_all_in_one_job|array-all-in-one-job!',
            'ppn|processors-per-node=i',
            'mem|memory=s',
            'dir=s',
@@ -135,7 +142,14 @@ if ($options{interactive}) {
     if ($options{array}) {
         @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_all_in_one_job}) {
+            $options{array_per_job} = scalar @array;
+        } else {
+            push @qsub_options,'-t','1-'. ceil(scalar @array / $options{array_per_job});
+            if ($options{array_slot_limit}) {
+                $qsub_options[$#qsub_options] .= '%'.$options{array_slot_limit};
+            }
+        }
     }
     call_qsub(\@qsub_options,write_qsub_script(\%options,\@ARGV,\@array));
 }
@@ -158,9 +172,12 @@ 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;
 }
 
@@ -199,7 +216,51 @@ sub write_qsub_script {
 # this script was written by dqsub
 EOF
     if (defined $opt->{array}) {
-        die "--array is currently not implemented";
+        my @subshell = ('','');
+        my $array_opt = join("\n",@{$array});
+        my $max_array = scalar @{$array};
+        my $apjm1 = $opt->{array_per_job} - 1;
+        if ($opt->{array_per_job} > 1) {
+            # we will use subshells if there are more than one array
+            # items per job
+            @subshell = ('(',')');
+            $script .= <<EOF;
+for i in \$(seq 1 $opt->{array_per_job}); do
+# in some cases, the jobs aren't going to come out evenly. Handle that.
+JOBNUM=\$(( \${PBS_ARRAYID:=1} * $opt->{array_per_job} + \$i - $opt->{array_per_job} ))
+if [ \$JOBNUM -le $max_array ]; then 
+OPT=\$(sed -n -e "\$JOBNUM p"<<'_HERE_DOC_END_'
+EOF
+        } else {
+            $script .= <<EOF;
+OPT=\$(sed -n -e "\${PBS_ARRAYID:=1} p"<<'_HERE_DOC_END_'
+EOF
+        }
+        $script .= <<EOF;
+$array_opt
+_HERE_DOC_END_
+)
+EOF
+        if ($opt->{array} eq 'chdir') {
+            $script .= <<EOF;
+$subshell[0]
+cd "\$OPT";
+exec ${command};
+$subshell[1]
+EOF
+        } else {
+            $script .= <<EOF;
+$subshell[0]
+exec ${command} "\$OPT";
+$subshell[1]
+EOF
+        }
+        if ($opt->{array_per_job} > 1) {
+            $script .= <<EOF
+fi;
+done;
+EOF
+        }
     } else {
         $script .= <<EOF;
 # there's no array, so just executing the command with arguments