--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
+ --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)
+ --name, -N Name of the job
--debug, -d debugging level (Default 0)
--help, -h display this help
--man, -m display manual
use IO::File;
use Cwd qw(getcwd abs_path);
+use POSIX qw(ceil);
+use List::Util qw(min);
use vars qw($DEBUG);
my %options = (nodes => 1,
help => 0,
man => 0,
interactive => 0,
+ array_per_job => 1,
);
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',
+ 'name=s',
'debug|d+','help|h|?','man|m');
# pod2usage() if $options{help};
print STDERR join("\n",@USAGE_ERRORS) and exit 1 if @USAGE_ERRORS;
# OK. Generate the options to qsub which we'll be using
-my @qsub_options = generate_qsub_options(\%options);
+my @qsub_options = generate_qsub_options(\%options,\@ARGV);
if ($options{interactive}) {
print STDERR 'running: qsub '.join(' ',@qsub_options) if $DEBUG;
if ($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_slot_limit}) {
- $qsub_options[$#qsub_options] .= '%'.$options{array_slot_limit};
+ if ($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] .= '%'.$options{array_slot_limit};
+ }
}
}
call_qsub(\@qsub_options,write_qsub_script(\%options,\@ARGV,\@array));
}
sub generate_qsub_options{
- my ($options) = @_;
+ my ($options,$args) = @_;
my @qo;
if (defined $options->{queue} and length $options->{queue}) {
push @qo,'-q',$options->{queue};
if ($options->{interactive}) {
push @qo,'-I';
}
+ if ($options->{name}) {
+ push @qo,'-N',$options->{name};
+ } else {
+ push @qo,'-N',join('_',@{$args}[0..min($#{$args},2)]);
+ }
return @qo;
}
# this script was written by dqsub
EOF
if (defined $opt->{array}) {
+ 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;
-OPT=\$(sed -n -e "\$PBS_ARRAYID p"<<'_HERE_DOC_END_'
$array_opt
_HERE_DOC_END_
)
EOF
if ($opt->{array} eq 'chdir') {
$script .= <<EOF;
+$subshell[0]
cd "\$OPT";
-exec $command;
+exec ${command};
+$subshell[1]
EOF
} else {
$script .= <<EOF;
-exec $command "\$OPT";
+$subshell[0]
+exec ${command} "\$OPT";
+$subshell[1]
+EOF
+ }
+ if ($opt->{array_per_job} > 1) {
+ $script .= <<EOF
+fi;
+done;
EOF
}
} else {