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Commit bfa7e79f authored by Yu Watanabe's avatar Yu Watanabe Committed by Morris Jette
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qalter and qrerun have wrong end-of-line encoding 

qalter and qrerun have wrong end-of-line encoding: \r\n rather than \n.

To fix it, please run
sed -e 's/\r$//' -i contribs/torque/qalter.pl
sed -e 's/\r$//' -i contribs/torque/qrerun.pl

Note that these two files have different permission (644) compare to other .pl files (755).
bug 2409
parent 76350de6
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contribs/torque/qalter.pl 100644 → 100755
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View file @ bfa7e79f
#! /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
contribs/torque/qrerun.pl 100644 → 100755
+ 134
− 134
View file @ bfa7e79f
#! /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
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