slurm-wlm-torque 15.08.7-1build1 / usr / bin / qsub

#! /usr/bin/perl -w
###############################################################################
#
# qsub - submit a batch job in familar pbs format.
#
#
###############################################################################
#  Copyright (C) 2007 The Regents of the University of California.
#  Produced at Lawrence Livermore National Laboratory (cf, DISCLAIMER).
#  Written by Danny Auble <auble1@llnl.gov>.
#  CODE-OCEC-09-009. All rights reserved.
#
#  This file is part of SLURM, a resource management program.
#  For details, see <http://slurm.schedmd.com/>.
#  Please also read the included file: DISCLAIMER.
#
#  SLURM is free software; you can redistribute it and/or modify it under
#  the terms of the GNU General Public License as published by the Free
#  Software Foundation; either version 2 of the License, or (at your option)
#  any later version.
#
#  In addition, as a special exception, the copyright holders give permission
#  to link the code of portions of this program with the OpenSSL library under
#  certain conditions as described in each individual source file, and
#  distribute linked combinations including the two. You must obey the GNU
#  General Public License in all respects for all of the code used other than
#  OpenSSL. If you modify file(s) with this exception, you may extend this
#  exception to your version of the file(s), but you are not obligated to do
#  so. If you do not wish to do so, delete this exception statement from your
#  version.  If you delete this exception statement from all source files in
#  the program, then also delete it here.
#
#  SLURM is distributed in the hope that it will be useful, but WITHOUT ANY
#  WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
#  FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
#  details.
#
#  You should have received a copy of the GNU General Public License along
#  with SLURM; if not, write to the Free Software Foundation, Inc.,
#  51 Franklin Street, Fifth Floor, Boston, MA 02110-1301  USA.
#
###############################################################################

use strict;
use FindBin;
use Getopt::Long 2.24 qw(:config no_ignore_case require_order);
use lib qw(/usr/lib/x86_64-linux-gnu/perl/5.22.1);
use autouse 'Pod::Usage' => qw(pod2usage);
use Slurm ':all';
use Switch;
use English;

my ($start_time,
    $account,
    $array,
    $err_path,
    $export_env,
    $interactive,
    $hold,
    $resource_list,
    $mail_options,
    $mail_user_list,
    $job_name,
    $out_path,
    $priority,
    $destination,
    $variable_list,
    @additional_attributes,
    $help,
    $resp,
    $man);

my $sbatch = "${FindBin::Bin}/sbatch";
my $salloc = "${FindBin::Bin}/salloc";
my $srun = "${FindBin::Bin}/srun";

GetOptions('a=s'      => \$start_time,
	   'A=s'      => \$account,
	   'e=s'      => \$err_path,
	   'h'        => \$hold,
	   'I'        => \$interactive,
	   'j:s'      => sub { warn "option -j is the default, " .
				    "stdout/stderr go into the same file\n" },
	   'J=s'      => \$array,
	   'l=s'      => \$resource_list,
	   'm=s'      => \$mail_options,
	   'M=s'      => \$mail_user_list,
	   'N=s'      => \$job_name,
	   'o=s'      => \$out_path,
	   'p=i'      => \$priority,
	   'q=s'      => \$destination,
	   'S=s'      => sub { warn "option -S is ignored, " .
				    "specify shell via #!<shell> in the job script\n" },
	   't=s'      => \$array,
	   'v=s'      => \$variable_list,
	   'V'        => \$export_env,
	   'W=s'      => \@additional_attributes,
	   'help|?'   => \$help,
	   'man'      => \$man,
	   )
	or pod2usage(2);

# Display usage if necessary
pod2usage(0) if $help;
if ($man) {
        if ($< == 0) {   # Cannot invoke perldoc as root
		my $id = eval { getpwnam("nobody") };
		$id = eval { getpwnam("nouser") } unless defined $id;
		$id = -2                          unless defined $id;
		$<  = $id;
        }
        $> = $<;                         # Disengage setuid
        $ENV{PATH} = "/bin:/usr/bin";    # Untaint PATH
        delete @ENV{'IFS', 'CDPATH', 'ENV', 'BASH_ENV'};
        if ($0 =~ /^([-\/\w\.]+)$/) { $0 = $1; }    # Untaint $0
        else { die "Illegal characters were found in \$0 ($0)\n"; }
        pod2usage(-exitstatus => 0, -verbose => 2);
}

# Use sole remaining argument as jobIds
my $script;
if ($ARGV[0]) {
	foreach (@ARGV) {
	        $script .= "$_ ";
	}
}
my $block="false";
my $depend;
my $group_list;
my $job_id;
my %res_opts;
my %node_opts;

# remove PBS_NODEFILE environment as passed in to qsub.
if ($ENV{PBS_NODEFILE}) {
	delete $ENV{PBS_NODEFILE};
}

# Process options provided with the -W name=value syntax.
my $W;
foreach $W (@additional_attributes) {
	my($name, $value) = split('=', $W);
	if ($name eq 'umask') {
		$ENV{SLURM_UMASK} = $value;
	} elsif ($name eq 'depend') {
		$depend = $value;
	} elsif ($name eq 'group_list') {
		$group_list = $value;
	} elsif (lc($name) eq 'block') {
		if (defined $value) {
			$block = $value;
		}
#	} else {
#		print("Invalid attribute: $W!");
#		exit(1);
	}
}

if ($resource_list) {
	%res_opts = %{parse_resource_list($resource_list)};

# 	while((my $key, my $val) = each(%res_opts)) {
# 		print "$key = ";
# 		if($val) {
# 			print "$val\n";
# 		} else {
# 			print "\n";
# 		}
# 	}

	if($res_opts{nodes}) {
		%node_opts =  %{parse_node_opts($res_opts{nodes})};
	}
	if ($res_opts{select} && (!$node_opts{node_cnt} || ($res_opts{select} > $node_opts{node_cnt}))) {
		$node_opts{node_cnt} = $res_opts{select};
	}
	if ($res_opts{select} && $res_opts{ncpus} && $res_opts{mpiprocs}) {
		my $cpus_per_task = int ($res_opts{ncpus} / $res_opts{mppnppn});
		if (!$res_opts{mppdepth} || ($cpus_per_task > $res_opts{mppdepth})) {
			$res_opts{mppdepth} = $cpus_per_task;
		}
	}
}

my $command;

if($interactive) {
	$command = "$salloc";

#	Always want at least one node in the allocation
	if (!$node_opts{node_cnt}) {
		$node_opts{node_cnt} = 1;
	}

#	Calculate the task count based of the node cnt and the amount
#	of ppn's in the request
	if ($node_opts{task_cnt}) {
		$node_opts{task_cnt} *= $node_opts{node_cnt};
	}

	if (!$node_opts{node_cnt} && !$node_opts{task_cnt} && !$node_opts{hostlist}) {
		$node_opts{task_cnt} = 1;
	}
} else {
	if (!$script) {
		pod2usage(2);
	}

	$command = "$sbatch";

	$command .= " -e $err_path" if $err_path;
	$command .= " -o $out_path" if $out_path;

#	The job size specification may be within the batch script,
#	Reset task count if node count also specified
	if ($node_opts{task_cnt} && $node_opts{node_cnt}) {
		$node_opts{task_cnt} *= $node_opts{node_cnt};
	}
}

$command .= " -N$node_opts{node_cnt}" if $node_opts{node_cnt};
$command .= " -n$node_opts{task_cnt}" if $node_opts{task_cnt};
$command .= " -w$node_opts{hostlist}" if $node_opts{hostlist};

$command .= " --mincpus=$res_opts{ncpus}"            if $res_opts{ncpus};
$command .= " --ntasks-per-node=$res_opts{mppnppn}"  if $res_opts{mppnppn};

if($res_opts{walltime}) {
	$command .= " -t$res_opts{walltime}";
} elsif($res_opts{cput}) {
	$command .= " -t$res_opts{cput}";
} elsif($res_opts{pcput}) {
	$command .= " -t$res_opts{pcput}";
}

if ($variable_list) {
	if ($interactive) {
		$variable_list =~ s/\'/\"/g;
		my @parts = $variable_list =~ m/(?:(?<=")[^"]*(?=(?:\s*"\s*,|\s*"\s*$)))|(?<=,)(?:[^",]*(?=(?:\s*,|\s*$)))|(?<=^)(?:[^",]+(?=(?:\s*,|\s*$)))|(?<=^)(?:[^",]*(?=(?:\s*,)))/g;
		foreach my $part (@parts) {
			my ($key, $value) = $part =~ /(.*)=(.*)/;
			if (defined($key) && defined($value)) {
				$ENV{$key} = $value;
			}
		}
	} else {
		if ($export_env) {
			$command .= " --export=all";
		} else {
			$command .= " --export=none";
		}

#		The logic below ignores quoted commas, but the quotes must be escaped
#		to be forwarded from the shell to Perl. For example:
#		qsub -v foo=\"b,ar\" tmp
		$variable_list =~ s/\'/\"/g;
		my @parts = $variable_list =~ m/(?:(?<=")[^"]*(?=(?:\s*"\s*,|\s*"\s*$)))|(?<=,)(?:[^",]*(?=(?:\s*,|\s*$)))|(?<=^)(?:[^",]+(?=(?:\s*,|\s*$)))|(?<=^)(?:[^",]*(?=(?:\s*,)))/g;
		foreach my $part (@parts) {
			my ($key, $value) = $part =~ /(.*)=(.*)/;
			if (defined($key) && defined($value)) {
				$command .= ",$key=$value";
			} elsif (defined($ENV{$part})) {
				$command .= ",$part=$ENV{$part}";
			}
		}
	}
} elsif ($export_env && ! $interactive) {
	$command .= " --export=all";
}

$command .= " --account='$group_list'" if $group_list;
$command .= " --array='$array'" if $array;
$command .= " --constraint='$res_opts{proc}'" if $res_opts{proc};
$command .= " --dependency=$depend"   if $depend;
$command .= " --tmp=$res_opts{file}"  if $res_opts{file};
$command .= " --mem=$res_opts{mem}"   if $res_opts{mem};
$command .= " --nice=$res_opts{nice}" if $res_opts{nice};

$command .= " --gres=gpu:$res_opts{naccelerators}"  if $res_opts{naccelerators};

# Cray-specific options
$command .= " -n$res_opts{mppwidth}"		    if $res_opts{mppwidth};
$command .= " -w$res_opts{mppnodes}"		    if $res_opts{mppnodes};
$command .= " --cpus-per-task=$res_opts{mppdepth}"  if $res_opts{mppdepth};

$command .= " --begin=$start_time" if $start_time;
$command .= " --account=$account" if $account;
$command .= " -H" if $hold;

if($mail_options) {
	$command .= " --mail-type=FAIL" if $mail_options =~ /a/;
	$command .= " --mail-type=BEGIN" if $mail_options =~ /b/;
	$command .= " --mail-type=END" if $mail_options =~ /e/;
}
$command .= " --mail-user=$mail_user_list" if $mail_user_list;
$command .= " -J $job_name" if $job_name;
$command .= " --nice=$priority" if $priority;
$command .= " -p $destination" if $destination;
$command .= " $script" if $script;

# print "$command\n";

# Execute the command and capture its stdout, stderr, and exit status. Note
# that if interactive mode was requested, the standard output and standard
# error are _not_ captured.
if ($interactive) {
	my $ret = system($command);
	exit ($ret >> 8);
} else {
	# Capture stderr from the command to the stdout stream.
	$command .= ' 2>&1';

	# Execute the command and capture the combined stdout and stderr.
	my @command_output = `$command 2>&1`;

	# Save the command exit status.
	my $command_exit_status = $CHILD_ERROR;

	# If available, extract the job ID from the command output and print
	# it to stdout, as done in the PBS version of qsub.
	if ($command_exit_status == 0) {
		my @spcommand_output=split(" ", $command_output[$#command_output]);
		$job_id= $spcommand_output[$#spcommand_output];
		print "$job_id\n";
	} else {
		print("There was an error running the SLURM sbatch command.\n" .
		      "The command was:\n" .
		      "'$command'\n" .
		      "and the output was:\n" .
		      "'@command_output'\n");
	}

	# If block is true wait for the job to finish
	my($resp, $count);
	my $slurm = Slurm::new();
	if ( (lc($block) eq "true" ) and ($command_exit_status == 0) ) {
		sleep 2;
		my($job) = $slurm->load_job($job_id);
		$resp = $$job{'job_array'}[0]->{job_state};
		while ( $resp < JOB_COMPLETE ) {
			$job = $slurm->load_job($job_id);
			$resp = $$job{'job_array'}[0]->{job_state};
			sleep 1;
		}
	}

	# Exit with the command return code.
	exit($command_exit_status >> 8);
}

sub parse_resource_list {
	my ($rl) = @_;
	my %opt = ('accelerator' => "",
		   'arch' => "",
		   'block' => "",
		   'cput' => "",
		   'file' => "",
		   'host' => "",
		   'mem' => "",
		   'mpiprocs' => "",
		   'ncpus' => "",
		   'nice' => "",
		   'nodes' => "",
		   'naccelerators' => "",
		   'opsys' => "",
		   'other' => "",
		   'pcput' => "",
		   'pmem' => "",
		   'proc' => '',
		   'pvmem' => "",
		   'select' => "",
		   'software' => "",
		   'vmem' => "",
		   'walltime' => "",
		   # Cray-specific resources
		   'mppwidth' => "",
		   'mppdepth' => "",
		   'mppnppn' => "",
		   'mppmem' => "",
		   'mppnodes' => ""
		   );
	my @keys = keys(%opt);

#	The select option uses a ":" separator rather than ","
#	This wrapper currently does not support multiple select options

#	Protect the colons used to separate elements in walltime=hh:mm:ss.
#	Convert to NNhNNmNNs format.
	$rl =~ s/walltime=(\d{1,2}):(\d{2}):(\d{2})/walltime=$1h$2m$3s/;

	$rl =~ s/:/,/g;
	foreach my $key (@keys) {
		#print "$rl\n";
		($opt{$key}) = $rl =~ m/$key=([\w:\+=+]+)/;

	}

#	If needed, un-protect the walltime string.
	if ($opt{walltime}) {
		$opt{walltime} =~ s/(\d{1,2})h(\d{2})m(\d{2})s/$1:$2:$3/;
#		Convert to minutes for SLURM.
		$opt{walltime} = get_minutes($opt{walltime});
	}

	if($opt{accelerator} && $opt{accelerator} =~ /^[Tt]/ && !$opt{naccelerators}) {
		$opt{naccelerators} = 1;
	}

	if($opt{cput}) {
		$opt{cput} = get_minutes($opt{cput});
	}

	if ($opt{mpiprocs} && (!$opt{mppnppn} || ($opt{mpiprocs} > $opt{mppnppn}))) {
		$opt{mppnppn} = $opt{mpiprocs};
	}

	if($opt{mppmem}) {
		$opt{mem} = convert_mb_format($opt{mppmem});
	} elsif($opt{mem}) {
		$opt{mem} = convert_mb_format($opt{mem});
	}

	if($opt{file}) {
		$opt{file} = convert_mb_format($opt{file});
	}

	return \%opt;
}

sub parse_node_opts {
	my ($node_string) = @_;
	my %opt = ('node_cnt' => 0,
		   'hostlist' => "",
		   'task_cnt' => 0
		   );
	while($node_string =~ /ppn=(\d+)/g) {
		$opt{task_cnt} += $1;
	}

	my $hl = Slurm::Hostlist::create("");

	my @parts = split(/\+/, $node_string);
	foreach my $part (@parts) {
		my @sub_parts = split(/:/, $part);
		foreach my $sub_part (@sub_parts) {
			if($sub_part =~ /ppn=(\d+)/) {
				next;
			} elsif($sub_part =~ /^(\d+)/) {
				$opt{node_cnt} += $1;
			} else {
				if(!Slurm::Hostlist::push($hl, $sub_part)) {
					print "problem pushing host $sub_part onto hostlist\n";
				}
			}
		}
	}

	$opt{hostlist} = Slurm::Hostlist::ranged_string($hl);

	my $hl_cnt = Slurm::Hostlist::count($hl);
	$opt{node_cnt} = $hl_cnt if $hl_cnt > $opt{node_cnt};

	return \%opt;
}

sub get_minutes {
    my ($duration) = @_;
    $duration = 0 unless $duration;
    my $minutes = 0;

    # Convert [[HH:]MM:]SS to duration in minutes
    if ($duration =~ /^(?:(\d+):)?(\d*):(\d+)$/) {
        my ($hh, $mm, $ss) = ($1 || 0, $2 || 0, $3);
	$minutes += 1 if $ss > 0;
        $minutes += $mm;
        $minutes += $hh * 60;
    } elsif ($duration =~ /^(\d+)$/) {  # Convert number in minutes to seconds
	    my $mod = $duration % 60;
	    $minutes = int($duration / 60);
	    $minutes++ if $mod;
    } else { # Unsupported format
        die("Invalid time limit specified ($duration)\n");
    }

    return $minutes;
}

sub convert_mb_format {
	my ($value) = @_;
	my ($amount, $suffix) = $value =~ /(\d+)($|[KMGT])/i;
	return if !$amount;
	$suffix = lc($suffix);

	if (!$suffix) {
		$amount /= 1048576;
	} elsif ($suffix eq "k") {
		$amount /= 1024;
	} elsif ($suffix eq "m") {
		#do nothing this is what we want.
	} elsif ($suffix eq "g") {
		$amount *= 1024;
	} elsif ($suffix eq "t") {
		$amount *= 1048576;
	} else {
		print "don't know what to do with suffix $suffix\n";
		return;
	}

	$amount .= "M";

	return $amount;
}
##############################################################################

__END__

=head1 NAME

B<qsub> - submit a batch job in a familiar PBS format

=head1 SYNOPSIS

qsub  [-a start_time]
      [-A account]
      [-e err_path]
      [-I]
      [-l resource_list]
      [-m mail_options] [-M user_list]
      [-N job_name]
      [-o out_path]
      [-p priority]
      [-q destination]
      [-v variable_list]
      [-V]
      [-W additional_attributes]
      [-h]
      [script]

=head1 DESCRIPTION

The B<qsub> submits batch jobs. It is aimed to be feature-compatible with PBS' qsub.

=head1 OPTIONS

=over 4

=item B<-a>

Earliest start time of job. Format: [HH:MM][MM/DD/YY]

=item B<-A account>

Specify the account to which the job should be charged.

=item B<-e err_path>

Specify a new path to receive the standard error output for the job.

=item B<-I>

Interactive execution.

=item B<-J job_array>

Job array index values. The -J and -t options are equivalent.

=item B<-l resource_list>

Specify an additional list of resources to request for the job.

=item B<-m mail_options>

Specify a list of events on which email is to be generated.

=item B<-M user_list>

Specify a list of email addresses to receive messages on specified events.

=item B<-N job_name>

Specify a name for the job.

=item B<-o out_path>

Specify the path to a file to hold the standard output from the job.

=item B<-p priority>

Specify the priority under which the job should run.

=item B<-p priority>

Specify the priority under which the job should run.

=item B<-t job_array>

Job array index values. The -J and -t options are equivalent.

=item B<-v> [variable_list]

Export only the specified environment variables. This option can also be used
with the -V option to add newly defined environment variables to the existing
environment. The variable_list is a comma delimited list of existing environment
variable names and/or newly defined environment variables using a name=value
format.

=item B<-V>

The -V option to exports the current environment, which is the default mode of
options unless the -v option is used.

=item B<-?> | B<--help>

brief help message

=item B<--man>

full documentation

=back

=cut