only escape if the command contains a space

[uiuc_igb_scripts.git] / dqsub

diff --git a/dqsub b/dqsub
index 89578d0dd003f0a89c25f836bc9e0e4d29b9b1a3..1682d058c4871516720932a1a80f29ef2cd447ad 100755 (executable)
--- a/dqsub
+++ b/dqsub
@@ -31,6 +31,8 @@ dqsub [options]
    --ppn processors per node to use
    --mem memory to request
    --dir Directory to run the script in (default current directory)
+   --account, -A Account name to use
+   --join, -J join error and output streams (default)
    --name, -N Name of the job
    --debug, -d debugging level (Default 0)
    --help, -h display this help
@@ -60,6 +62,15 @@ command run in the current directory.
 File to read array arguments from. If not provided, and B<--array> is
 given, arguments will be read from STDIN.
 
+=item B<--account, -A>
+
+Account name to use
+
+=item B<--join, J>
+
+Whether to join STDOUT and STDERR. On by default; disable with
+C<--nojoin>.
+
 =item B<--debug, -d>
 
 Debug verbosity. (Default 0)
@@ -94,6 +105,7 @@ my %options = (nodes           => 1,
                man             => 0,
                interactive     => 0,
                array_per_job   => 1,
+               join            => 1,
               );
 
 GetOptions(\%options,
@@ -106,7 +118,13 @@ GetOptions(\%options,
            'array_slot_limit|array-slot-limit=i',
            'array_all_in_one_job|array-all-in-one-job!',
            'ppn|processors-per-node=i',
+           'account|A=s',
+           'join|J!',
            'mem|memory=s',
+           'time|walltime=s','cputime|cput=s','host=s',
+           'pmem|process_mem|process-mem=s',
+           'pvmem|process_virtual_mem|process-virtiual-mem=s',
+           'max_file|max-file|file=s',
            'dir=s',
            'name=s',
            'debug|d+','help|h|?','man|m');
@@ -132,7 +150,10 @@ if ($options{interactive} and @ARGV) {
 }
 
 # pod2usage(join("\n",@USAGE_ERRORS)) if @USAGE_ERRORS;
-print STDERR join("\n",@USAGE_ERRORS) and exit 1 if @USAGE_ERRORS;
+if (@USAGE_ERRORS) {
+    print STDERR map {"$_\n"} @USAGE_ERRORS;
+    exit 1;
+}
 
 # OK. Generate the options to qsub which we'll be using
 my @qsub_options = generate_qsub_options(\%options,\@ARGV);
@@ -174,8 +195,22 @@ sub generate_qsub_options{
     if (defined $options->{ppn}) {
         $l[$#l] .= ':ppn='.$options->{ppn};
     }
-    if ($options->{mem}) {
-        push @l,'mem='.$options->{mem};
+    if (defined $options->{account}) {
+        push @qo,'-A',$options->{account};
+    }
+    my %l_options =
+        (mem => 'vmem',
+         time => 'walltime',
+         cputime => 'cput',
+         host    => 'host',
+         pmem => 'pmem',
+         pvmem => 'pvmem',
+         max_file => 'file',
+        );
+    for my $k (keys %l_options) {
+        if ($options->{$k}) {
+            push @l,$l_options{$k}.'='.$options{$k};
+        }
     }
     push @qo,'-l',join(',',@l) if @l;
     if ($options->{interactive}) {
@@ -184,7 +219,13 @@ sub generate_qsub_options{
     if ($options->{name}) {
         push @qo,'-N',$options->{name};
     } else {
-        push @qo,'-N',join('_',@{$args}[0..min($#{$args},2)]);
+        push @qo,'-N',join('_',
+                           map {my $a = $_; $a =~ s/[^a-zA-Z0-9]*//g; $a;}
+                          @{$args}[0..min($#{$args},2)]);
+    }
+    # join error and output streams
+    if ($options->{join}) {
+        push @qo,'-j','oe';
     }
     return @qo;
 }
@@ -219,7 +260,7 @@ sub write_qsub_script {
     my ($opt,$arg,$array) = @_;
 
     my $script = "#!/bin/bash\n";
-    my $command = join(' ',map {qq('$_')} @{$arg});
+    my $command = join(' ',map {$_ =~ /\s/?qq('$_'):$_} @{$arg});
         $script .= <<EOF;
 # this script was written by dqsub
 EOF