diff --git a/contribs/torque/qalter.pl b/contribs/torque/qalter.pl
old mode 100644
new mode 100755
index e5ac6a462b24809f0fc0b0cf353683b3d25f4a4e..d8c9fbed5f3d99655169761c4a09111fccb39a5c
--- a/contribs/torque/qalter.pl
+++ b/contribs/torque/qalter.pl
@@ -1,232 +1,232 @@
-#! /usr/bin/perl -w
-###############################################################################
-#
-# qalter - PBS wrapper for changing job status using scontrol
-#
-###############################################################################
-
-use strict;
-use FindBin;
-use Getopt::Long 2.24 qw(:config no_ignore_case);
-use lib "${FindBin::Bin}/../lib/perl";
-use autouse 'Pod::Usage' => qw(pod2usage);
-use Slurm ':all';
-use Slurmdb ':all'; # needed for getting the correct cluster dims
-use Switch;
-
-# ------------------------------------------------------------------
-# This makes the assumption job_id will always be the last argument
-# -------------------------------------------------------------------
-my $job_id = $ARGV[$#ARGV];
-my (
- $err,
- $new_name,
- $output,
- $rerun,
- $resp,
- $slurm,
- $man,
- $help
-);
-
-# Remove this
-my $scontrol = "/usr/slurm/bin/scontrol";
-
-# ------------------------------
-# Parse Command Line Arguments
-# ------------------------------
-GetOptions(
- 'N=s' => \$new_name,
- 'r=s' => \$rerun,
- 'o=s' => \$output,
- 'help|?' => \$help,
- 'man' => \$man
- )
- or pod2usage(2);
-
-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);
-}
-
-# ----------------------
-# Check input arguments
-# ----------------------
-if (@ARGV < 1) {
- pod2usage(-message=>"Missing Job ID", -verbose=>0);
-} else {
- $slurm = Slurm::new();
- $resp = $slurm->get_end_time($job_id);
- if (not defined($resp)) {
- pod2usage(-message=>"Job id $job_id not valid!", -verbose=>0);
- }
- if ((not defined($new_name)) and (not defined($rerun)) and (not defined($output))) {
- pod2usage(-message=>"no argument given!", -verbose=>0);
- }
-}
-
-# --------------------------------------------
-# Use Slurm's Perl API to change name of a job
-# --------------------------------------------
-if ($new_name) {
- my %update = ();
-
- $update{job_id} = $job_id;
- $update{name} = $new_name;
- if (Slurm->update_job(\%update)) {
- $err = Slurm->get_errno();
- $resp = Slurm->strerror($err);
- pod2usage(-message=>"Job id $job_id name change error: $resp", -verbose=>0);
- exit(1);
- }
-}
-
-# ---------------------------------------------------
-# Use Slurm's Perl API to change the requeue job flag
-# ---------------------------------------------------
-if ($rerun) {
- my %update = ();
-
- $update{job_id} = $job_id;
- if (($rerun eq "n") || ($rerun eq "N")) {
- $update{requeue} = 0;
- } else {
- $update{requeue} = 1;
- }
- if (Slurm->update_job(\%update)) {
- $err = Slurm->get_errno();
- $resp = Slurm->strerror($err);
- pod2usage(-message=>"Job id $job_id requeue error: $resp", -verbose=>0);
- exit(1);
- }
-}
-
-# ------------------------------------------------------------
-# Use Slurm's Perl API to change Comment string
-# Comment is used to relocate an output log file
-# ------------------------------------------------------------
-if ($output) {
- # Example:
- # $comment="on:16337,stdout=/gpfsm/dhome/lgerner/tmp/slurm-16338.out,stdout=~lgerner/tmp/new16338.out";
- #
- my $comment;
- my %update = ();
-
- # ---------------------------------------
- # Get current comment string from job_id
- # ---------------------------------------
- my($job) = $slurm->load_job($job_id);
- $comment = $$job{'job_array'}[0]->{comment};
-
- # ----------------
- # Split at stdout
- # ----------------
- if ($comment) {
- my(@outlog) = split("stdout", $comment);
-
- # ---------------------------------
- # Only 1 stdout argument add a ','
- # ---------------------------------
- if ($#outlog < 2) {
- $outlog[1] .= ","
- }
-
- # ------------------------------------------------
- # Add new log file location to the comment string
- # ------------------------------------------------
- $outlog[2] = "=".$output;
- $comment = join("stdout", @outlog);
- } else {
- $comment = "stdout=$output";
- }
-
- # -------------------------------------------------
- # Make sure that "%j" is changed to current $job_id
- # -------------------------------------------------
- $comment =~ s/%j/$job_id/g ;
-
- # -----------------------------------------------------
- # Update comment and print usage if there is a response
- # -----------------------------------------------------
- $update{job_id} = $job_id;
- $update{comment} = $comment;
- if (Slurm->update_job(\%update)) {
- $err = Slurm->get_errno();
- $resp = Slurm->strerror($err);
- pod2usage(-message=>"Job id $job_id comment change error: $resp", -verbose=>0);
- exit(1);
- }
-}
-exit(0);
-
-##############################################################################
-
-__END__
-
-=head1 NAME
-
-B<qalter> - alter a job name, the job rerun flag or the job output file name.
-
-=head1 SYNOPSIS
-
-qalter [-N Name]
- [-r y|n]
- [-o output file]
- <job ID>
-
-=head1 DESCRIPTION
-
-The B<qalter> updates job name, job rerun flag or job output(stdout) log location.
-
-It is aimed to be feature-compatible with PBS' qsub.
-
-=head1 OPTIONS
-
-=over 4
-
-=item B<-N>
-
-Update job name in the queue
-
-=item B<-r>
-
-Alter a job rerunnable flag. "y" will allow a qrerun to be issued. "n" disable qrerun option.
-
-=item B<-o>
-
-Alter a job output log file name (stdout).
-
-The job log will be move/rename after the job has B<terminated>.
-
-=item B<-?> | B<--help>
-
-brief help message
-
-=item B<-man>
-
-full documentation
-
-=back
-
-=head1 SEE ALSO
-
-qrerun(1) qsub(1)
-=cut
-
+#! /usr/bin/perl -w
+###############################################################################
+#
+# qalter - PBS wrapper for changing job status using scontrol
+#
+###############################################################################
+
+use strict;
+use FindBin;
+use Getopt::Long 2.24 qw(:config no_ignore_case);
+use lib "${FindBin::Bin}/../lib/perl";
+use autouse 'Pod::Usage' => qw(pod2usage);
+use Slurm ':all';
+use Slurmdb ':all'; # needed for getting the correct cluster dims
+use Switch;
+
+# ------------------------------------------------------------------
+# This makes the assumption job_id will always be the last argument
+# -------------------------------------------------------------------
+my $job_id = $ARGV[$#ARGV];
+my (
+ $err,
+ $new_name,
+ $output,
+ $rerun,
+ $resp,
+ $slurm,
+ $man,
+ $help
+);
+
+# Remove this
+my $scontrol = "/usr/slurm/bin/scontrol";
+
+# ------------------------------
+# Parse Command Line Arguments
+# ------------------------------
+GetOptions(
+ 'N=s' => \$new_name,
+ 'r=s' => \$rerun,
+ 'o=s' => \$output,
+ 'help|?' => \$help,
+ 'man' => \$man
+ )
+ or pod2usage(2);
+
+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);
+}
+
+# ----------------------
+# Check input arguments
+# ----------------------
+if (@ARGV < 1) {
+ pod2usage(-message=>"Missing Job ID", -verbose=>0);
+} else {
+ $slurm = Slurm::new();
+ $resp = $slurm->get_end_time($job_id);
+ if (not defined($resp)) {
+ pod2usage(-message=>"Job id $job_id not valid!", -verbose=>0);
+ }
+ if ((not defined($new_name)) and (not defined($rerun)) and (not defined($output))) {
+ pod2usage(-message=>"no argument given!", -verbose=>0);
+ }
+}
+
+# --------------------------------------------
+# Use Slurm's Perl API to change name of a job
+# --------------------------------------------
+if ($new_name) {
+ my %update = ();
+
+ $update{job_id} = $job_id;
+ $update{name} = $new_name;
+ if (Slurm->update_job(\%update)) {
+ $err = Slurm->get_errno();
+ $resp = Slurm->strerror($err);
+ pod2usage(-message=>"Job id $job_id name change error: $resp", -verbose=>0);
+ exit(1);
+ }
+}
+
+# ---------------------------------------------------
+# Use Slurm's Perl API to change the requeue job flag
+# ---------------------------------------------------
+if ($rerun) {
+ my %update = ();
+
+ $update{job_id} = $job_id;
+ if (($rerun eq "n") || ($rerun eq "N")) {
+ $update{requeue} = 0;
+ } else {
+ $update{requeue} = 1;
+ }
+ if (Slurm->update_job(\%update)) {
+ $err = Slurm->get_errno();
+ $resp = Slurm->strerror($err);
+ pod2usage(-message=>"Job id $job_id requeue error: $resp", -verbose=>0);
+ exit(1);
+ }
+}
+
+# ------------------------------------------------------------
+# Use Slurm's Perl API to change Comment string
+# Comment is used to relocate an output log file
+# ------------------------------------------------------------
+if ($output) {
+ # Example:
+ # $comment="on:16337,stdout=/gpfsm/dhome/lgerner/tmp/slurm-16338.out,stdout=~lgerner/tmp/new16338.out";
+ #
+ my $comment;
+ my %update = ();
+
+ # ---------------------------------------
+ # Get current comment string from job_id
+ # ---------------------------------------
+ my($job) = $slurm->load_job($job_id);
+ $comment = $$job{'job_array'}[0]->{comment};
+
+ # ----------------
+ # Split at stdout
+ # ----------------
+ if ($comment) {
+ my(@outlog) = split("stdout", $comment);
+
+ # ---------------------------------
+ # Only 1 stdout argument add a ','
+ # ---------------------------------
+ if ($#outlog < 2) {
+ $outlog[1] .= ","
+ }
+
+ # ------------------------------------------------
+ # Add new log file location to the comment string
+ # ------------------------------------------------
+ $outlog[2] = "=".$output;
+ $comment = join("stdout", @outlog);
+ } else {
+ $comment = "stdout=$output";
+ }
+
+ # -------------------------------------------------
+ # Make sure that "%j" is changed to current $job_id
+ # -------------------------------------------------
+ $comment =~ s/%j/$job_id/g ;
+
+ # -----------------------------------------------------
+ # Update comment and print usage if there is a response
+ # -----------------------------------------------------
+ $update{job_id} = $job_id;
+ $update{comment} = $comment;
+ if (Slurm->update_job(\%update)) {
+ $err = Slurm->get_errno();
+ $resp = Slurm->strerror($err);
+ pod2usage(-message=>"Job id $job_id comment change error: $resp", -verbose=>0);
+ exit(1);
+ }
+}
+exit(0);
+
+##############################################################################
+
+__END__
+
+=head1 NAME
+
+B<qalter> - alter a job name, the job rerun flag or the job output file name.
+
+=head1 SYNOPSIS
+
+qalter [-N Name]
+ [-r y|n]
+ [-o output file]
+ <job ID>
+
+=head1 DESCRIPTION
+
+The B<qalter> updates job name, job rerun flag or job output(stdout) log location.
+
+It is aimed to be feature-compatible with PBS' qsub.
+
+=head1 OPTIONS
+
+=over 4
+
+=item B<-N>
+
+Update job name in the queue
+
+=item B<-r>
+
+Alter a job rerunnable flag. "y" will allow a qrerun to be issued. "n" disable qrerun option.
+
+=item B<-o>
+
+Alter a job output log file name (stdout).
+
+The job log will be move/rename after the job has B<terminated>.
+
+=item B<-?> | B<--help>
+
+brief help message
+
+=item B<-man>
+
+full documentation
+
+=back
+
+=head1 SEE ALSO
+
+qrerun(1) qsub(1)
+=cut
+
diff --git a/contribs/torque/qrerun.pl b/contribs/torque/qrerun.pl
old mode 100644
new mode 100755
index 2cc1c5419ddc132b00e38e2649c4594fdc908473..67b9681f0421e2943eb05f047c33e6ca63f804eb
--- a/contribs/torque/qrerun.pl
+++ b/contribs/torque/qrerun.pl
@@ -1,134 +1,134 @@
-#! /usr/bin/perl -w
-###############################################################################
-#
-# qrerun - PBS wrapper to cancel and resubmit a job
-#
-###############################################################################
-# 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.
-#
-# Based off code with permission copyright 2006, 2007 Cluster Resources, Inc.
-###############################################################################
-use strict;
-use FindBin;
-use Getopt::Long 2.24 qw(:config no_ignore_case);
-use lib "${FindBin::Bin}/../lib/perl";
-use autouse 'Pod::Usage' => qw(pod2usage);
-use Slurm ':all';
-use Slurmdb ':all'; # needed for getting the correct cluster dims
-use Switch;
-
-# Parse Command Line Arguments
-my (
- $help, $man,
- $err, $pid, $resp
-);
-
-GetOptions(
- 'help|?' => \$help,
- '--man' => \$man,
- ) or pod2usage(2);
-
-pod2usage(2) if $help;
-# Handle man page flag
-if ($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);
-}
-
-
-# This makes the assumption JOBID will always be the last argument
-my $job_id = $ARGV[$#ARGV];
-
-if (@ARGV < 1) {
- pod2usage(-message=>"Invalid Argument", -verbose=>1);
- exit(1);
-}
-
-if (Slurm->requeue($job_id)) {
- $err = Slurm->get_errno();
- $resp = Slurm->strerror($err);
- pod2usage(-message=>"Job id $job_id rerun error: $resp", -verbose=>0);
- exit(1);
-}
-exit(0);
-
-__END__
-
-=head1 NAME
-
-B<qrerun> - To rerun a job is to terminate the job and return the job to the queued state in the execution queue in which the job currently resides.
-If a job is marked as not rerunable then the rerun request will fail for that job.
-
-See the option on the qsub and qalter commands.
-
-It is aimed to be feature-compatible with PBS' qsub.
-
-=head1 SYNOPSIS
-
-B<qrerun> [-? | --help] [--man] [--verbose] <job_id>
-
-=head1 DESCRIPTION
-
-The B<qrerun> command directs that the specified job is to be rerun if possible.
-
-=head1 OPTIONS
-
-=over 4
-
-=item B<-? | --help>
-
-a brief help message
-
-=item B<--man>
-
-full documentation
-
-=back
-
-=head1 EXIT STATUS
-
-On success, B<qrerun> will exit with a value of zero. On failure, B<qrerun> will exit with a value greater than zero.
-
-=head1 SEE ALSO
-
-qalter(1) qsub(1)
-=cut
+#! /usr/bin/perl -w
+###############################################################################
+#
+# qrerun - PBS wrapper to cancel and resubmit a job
+#
+###############################################################################
+# 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.
+#
+# Based off code with permission copyright 2006, 2007 Cluster Resources, Inc.
+###############################################################################
+use strict;
+use FindBin;
+use Getopt::Long 2.24 qw(:config no_ignore_case);
+use lib "${FindBin::Bin}/../lib/perl";
+use autouse 'Pod::Usage' => qw(pod2usage);
+use Slurm ':all';
+use Slurmdb ':all'; # needed for getting the correct cluster dims
+use Switch;
+
+# Parse Command Line Arguments
+my (
+ $help, $man,
+ $err, $pid, $resp
+);
+
+GetOptions(
+ 'help|?' => \$help,
+ '--man' => \$man,
+ ) or pod2usage(2);
+
+pod2usage(2) if $help;
+# Handle man page flag
+if ($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);
+}
+
+
+# This makes the assumption JOBID will always be the last argument
+my $job_id = $ARGV[$#ARGV];
+
+if (@ARGV < 1) {
+ pod2usage(-message=>"Invalid Argument", -verbose=>1);
+ exit(1);
+}
+
+if (Slurm->requeue($job_id)) {
+ $err = Slurm->get_errno();
+ $resp = Slurm->strerror($err);
+ pod2usage(-message=>"Job id $job_id rerun error: $resp", -verbose=>0);
+ exit(1);
+}
+exit(0);
+
+__END__
+
+=head1 NAME
+
+B<qrerun> - To rerun a job is to terminate the job and return the job to the queued state in the execution queue in which the job currently resides.
+If a job is marked as not rerunable then the rerun request will fail for that job.
+
+See the option on the qsub and qalter commands.
+
+It is aimed to be feature-compatible with PBS' qsub.
+
+=head1 SYNOPSIS
+
+B<qrerun> [-? | --help] [--man] [--verbose] <job_id>
+
+=head1 DESCRIPTION
+
+The B<qrerun> command directs that the specified job is to be rerun if possible.
+
+=head1 OPTIONS
+
+=over 4
+
+=item B<-? | --help>
+
+a brief help message
+
+=item B<--man>
+
+full documentation
+
+=back
+
+=head1 EXIT STATUS
+
+On success, B<qrerun> will exit with a value of zero. On failure, B<qrerun> will exit with a value greater than zero.
+
+=head1 SEE ALSO
+
+qalter(1) qsub(1)
+=cut