--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)
+ --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
--man, -m display manual
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<--batch>
+
+Which batch system to use. If sbatch exists, assume it's slurm,
+otherwise, PBS.
+
=item B<--debug, -d>
Debug verbosity. (Default 0)
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,
+ join => 1,
);
GetOptions(\%options,
'queue|q=s',
+ 'batch=s',
'interactive|I!',
'nodes=i',
'array=s',
'array_from|array-from=s',
- 'ppn|processors-per-node=i',
+ '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|cpus|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');
# pod2usage() if $options{help};
push @USAGE_ERRORS,"Don't provide commands when you're asking for an interactive shell";
}
+if (not defined $options{batch}) {
+ qx/which sbatch/;
+ if ($?) {
+ $options{batch} = 'slurm'
+ } else {
+ $options{batch} = 'pbs'
+ }
+}
+
+if ($options{batch} !~ /^pbs|slurm$/) {
+ push @USAGE_ERRORS,"Unsupported batch system '$options{batch}'; ".
+ "supported systems are pbs or slurm";
+}
+
# 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;
+}
+
+my $JOB_SUBMITTER = 'qsub';
# OK. Generate the options to qsub which we'll be using
-my @qsub_options = generate_qsub_options(\%options);
+my @qsub_options;
+if ($options{batch} eq 'pbs') {
+ @qsub_options = generate_qsub_options(\%options,\@ARGV);
+ $JOB_SUBMITTER = 'qsub';
+} elsif ($options{batch} eq 'slurm') {
+ @qsub_options = generate_slurm_options(\%options,\@ARGV);
+ $JOB_SUBMITTER = 'sbatch';
+} else {
+ die "Unsupported batch system '$options{batch}'";
+}
+
if ($options{interactive}) {
print STDERR 'running: qsub '.join(' ',@qsub_options) if $DEBUG;
- exec('qsub',@qsub_options);
+ exec($JOB_SUBMITTER,@qsub_options);
} else {
my @array = ();
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] .= '%'.$options{array_slot_limit};
+ }
+ }
+ }
+ if ($options{batch} eq 'pbs') {
+ push @qsub_options,'-';
}
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 (defined $options->{dir}) {
- push @qo,'-d',abs_path($options->{dir});
- } else {
- push @qo,'-d',getcwd;
- }
## handle the -l options
my @l;
push @l, 'nodes='.$options->{nodes};
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}) {
+ push @qo,'-I';
+ }
+ if ($options->{name}) {
+ push @qo,'-N',$options->{name};
+ } else {
+ 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 ($options->{join}) {
+ push @qo,'-j','oe';
+ }
+ return @qo;
+}
+
+sub generate_slurm_options{
+ my ($options,$args) = @_;
+ my @qo;
+ if (defined $options->{queue} and length $options->{queue}) {
+ push @qo,'-p',$options->{queue};
+ }
+ ## handle the -l options
+ if (defined $options->{account}) {
+ push @qo,'-A',$options->{account};
+ }
+ my %options_map =
+ (mem => 'mem',
+ ppn => 'cpus-per-task',
+ time => 'time',
+ cputime => 'cput',
+ host => 'host',
+ pmem => 'pmem',
+ pvmem => 'pvmem',
+ max_file => 'file',
+ );
+ for my $k (keys %options_map) {
+ if ($options->{$k}) {
+ push @qo,'--'.$options_map{$k}.'=',$options{$k};
+ }
+ }
+ if ($options{mem}) {
+ push @qo,'--mem=',$options{mem};
+ }
+ if ($options->{interactive}) {
+ push @qo,'-I';
+ }
+ if ($options->{name}) {
+ push @qo,'-J',$options->{name};
+ } else {
+ push @qo,'-J',join('_',
+ map {my $a = $_; $a =~ s/[^a-zA-Z0-9]*//g; $a;}
+ @{$args}[0..min($#{$args},2)]);
+ }
+ # join error and output streams
+ if ($options->{join}) {
+ push @qo,'-j','oe';
+ }
+ return @qo;
}
sub read_array_options{
sub call_qsub {
my ($qsub_options,$script) = @_;
my $qsub_fh;
- open $qsub_fh,'|-','qsub',@{$qsub_options},'-' or
- die "Unable to start qsub: $!";
+ open $qsub_fh,'|-',$JOB_SUBMITTER,@{$qsub_options} or
+ die "Unable to start $JOB_SUBMITTER: $!";
print {$qsub_fh} $script or
- die "Unable to print to qsub: $!";
+ die "Unable to print to $JOB_SUBMITTER: $!";
close($qsub_fh) or
- die "Unable to close qsub filehandle: $!";
+ die "Unable to close $JOB_SUBMITTER filehandle: $!";
}
sub write_qsub_script {
my ($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
+ my $directory = getcwd;
+ if (defined $opt->{dir}) {
+ $directory = abs_path($opt->{dir});
+ }
+ # we really should be quoting this instead
+ $script .=<<EOF;
+# change to the working directory
+cd "$directory";
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;
+ $script .= <<EOF;
+if [ -n "\$PBS_ARRAYID" ]; then
+ MYARRAYID="\${PBS_ARRAYID:=1}"
+else
+ MYARRAYID="\${SLURM_ARRAY_TASK_ID:=1}"
+fi;
+EOF
+ if ($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=\$(( \${MYARRAYID:=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 "\${MYARRAYID:=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
projects / uiuc_igb_scripts.git / blobdiff