Initial code to make qsub accept Grid Engine options.

Bug 2208

RELEASE_NOTES

@@ -50,6 +50,7 @@ HIGHLIGHTS
     If set, the only CPUs available to the job will be those bound to the
     selected GRES (i.e. the CPUs identifed in the gres.conf file will be
     strictly enforced rather than advisory).
+ -- Added Grid Engine options to qsub.
 
 RPMBUILD CHANGES
 ================

contribs/torque/qsub.pl

 #! /usr/bin/perl -w
 ###############################################################################
 #
-# qsub - submit a batch job in familar pbs format.
+# qsub - submit a batch job in familar pbs/Grid Engine format.
 #
 #
 ###############################################################################
+#  Copyright (C) 2015-2016 SchedMD LLC
 #  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>.
+#  Written by Danny Auble <da@schedmd.com>.
 #  CODE-OCEC-09-009. All rights reserved.
 #
 #  This file is part of SLURM, a resource management program.
@@ -62,10 +63,16 @@ my ($start_time,
     $mail_user_list,
     $job_name,
     $out_path,
+    @pe_ev_opts,
     $priority,
+    $requeue,
     $destination,
+    $sbatchline,
     $variable_list,
     @additional_attributes,
+    $wckey,
+    $workdir,
+    $wrap,
     $help,
     $resp,
     $man);
@@ -76,6 +83,8 @@ my $srun = "${FindBin::Bin}/srun";
 
 GetOptions('a=s'      => \$start_time,
 	   'A=s'      => \$account,
+	   'b=s'      => \$wrap,
+	   'cwd'      => sub { warn "option -cwd is the default\n" },
 	   'e=s'      => \$err_path,
 	   'h'        => \$hold,
 	   'I'        => \$interactive,
@@ -88,15 +97,20 @@ GetOptions('a=s'      => \$start_time,
 	   'N=s'      => \$job_name,
 	   'o=s'      => \$out_path,
 	   'p=i'      => \$priority,
+	   'pe=s{2}'  => \@pe_ev_opts,
+	   'P=s'      => \$wckey,
 	   'q=s'      => \$destination,
+	   'r=s'      => \$requeue,
 	   '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,
+	   'wd=s'     => \$workdir,
 	   'W=s'      => \@additional_attributes,
 	   'help|?'   => \$help,
 	   'man'      => \$man,
+	   'sbatchline' => \$sbatchline,
 	   )
 	or pod2usage(2);
 
@@ -182,6 +196,26 @@ if ($resource_list) {
 	}
 }
 
+if (@pe_ev_opts) {
+	my %pe_opts = %{parse_pe_opts(@pe_ev_opts)};
+
+	# while((my $key, my $val) = each(%pe_opts)) {
+	# 	print "$key = ";
+	# 	if($val) {
+	# 		print "$val\n";
+	# 	} else {
+	# 		print "\n";
+	# 	}
+	# }
+
+	# From Stanford: This parallel environment is designed to support
+	# applications that use pthreads to manage multiple threads with
+	# access to a single pool of shared memory.  The SGE PE restricts
+	# the slots used to a threads on a single host, so in this, I think
+	# it is equivalent to the --cpus-per-task option of sbatch.
+	$res_opts{mppdepth} = $pe_opts{shm} if $pe_opts{shm};
+}
+
 my $command;
 
 if($interactive) {
@@ -222,6 +256,8 @@ $command .= " -N$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};
 
+$command .= " -D$workdir" if $workdir;
+
 $command .= " --mincpus=$res_opts{ncpus}"            if $res_opts{ncpus};
 $command .= " --ntasks-per-node=$res_opts{mppnppn}"  if $res_opts{mppnppn};
 
@@ -296,9 +332,21 @@ $command .= " --mail-user=$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 $script;
+$command .= " --wckey=$wckey" if $wckey;
+$command .= " --requeue" if $requeue && $requeue =~ 'y';
+
+if ($script) {
+	if ($wrap && $wrap =~ 'y') {
+		$command .=" --wrap=\"$script\"";
+	} else {
+		$command .= " $script";
+	}
+}
 
-# print "$command\n";
+if ($sbatchline) {
+	print "$command\n";
+	exit;
+}
 
 # Execute the command and capture its stdout, stderr, and exit status. Note
 # that if interactive mode was requested, the standard output and standard
@@ -356,6 +404,8 @@ sub parse_resource_list {
 		   'cput' => "",
 		   'file' => "",
 		   'host' => "",
+		   'h_rt' => "",
+		   'h_vmem' => "",
 		   'mem' => "",
 		   'mpiprocs' => "",
 		   'ncpus' => "",
@@ -400,6 +450,9 @@ sub parse_resource_list {
 		$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});
+	} elsif ($opt{h_rt}) {
+		# GridEngine is in seconds, so convert to minutes.
+		$opt{walltime} = $opt{h_rt} / 60;
 	}
 
 	if($opt{accelerator} && $opt{accelerator} =~ /^[Tt]/ && !$opt{naccelerators}) {
@@ -414,7 +467,10 @@ sub parse_resource_list {
 		$opt{mppnppn} = $opt{mpiprocs};
 	}
 
-	if($opt{mppmem}) {
+	if ($opt{h_vmem}) {
+		# Transfer over the GridEngine value (no conversion)
+		$opt{mem} = $opt{h_vmem};
+	} elsif($opt{mppmem}) {
 		$opt{mem} = convert_mb_format($opt{mppmem});
 	} elsif($opt{mem}) {
 		$opt{mem} = convert_mb_format($opt{mem});
@@ -463,6 +519,19 @@ sub parse_node_opts {
 	return \%opt;
 }
 
+sub parse_pe_opts {
+	my (@pe_array) = @_;
+	my %opt = ('shm' => 0,
+		   );
+	my @keys = keys(%opt);
+
+	foreach my $key (@keys) {
+		$opt{$key} = $pe_array[1] if ($key eq $pe_array[0]);
+	}
+
+	return \%opt;
+}
+
 sub get_minutes {
     my ($duration) = @_;
     $duration = 0 unless $duration;
@@ -522,6 +591,7 @@ B<qsub> - submit a batch job in a familiar PBS format
 
 qsub  [-a start_time]
       [-A account]
+      [-b y|n]
       [-e err_path]
       [-I]
       [-l resource_list]
@@ -529,9 +599,13 @@ qsub  [-a start_time]
       [-N job_name]
       [-o out_path]
       [-p priority]
+      [-pe shm task_cnt]
+      [-P wckey]
       [-q destination]
+      [-r y|n]
       [-v variable_list]
       [-V]
+      [-wd workdir]
       [-W additional_attributes]
       [-h]
       [script]
@@ -552,6 +626,10 @@ Earliest start time of job. Format: [HH:MM][MM/DD/YY]
 
 Specify the account to which the job should be charged.
 
+=item B<-b y|n>
+
+Whether to wrap the command line or not
+
 =item B<-e err_path>
 
 Specify a new path to receive the standard error output for the job.
@@ -588,9 +666,17 @@ Specify the path to a file to hold the standard output from the job.
 
 Specify the priority under which the job should run.
 
-=item B<-p priority>
+=item B<-pe shm cpus-per-task>
 
-Specify the priority under which the job should run.
+Specify the number of cpus per task.
+
+=item B<-P wckey>
+
+Specify the wckey or project of a job.
+
+=item B<-r y|n>
+
+Whether to allow the job to requeue or not.
 
 =item B<-t job_array>
 
@@ -609,6 +695,10 @@ format.
 The -V option to exports the current environment, which is the default mode of
 options unless the -v option is used.
 
+=item B<-wd workdir>
+
+Specify the workdir of a job.  The default is the current work dir.
+
 =item B<-?> | B<--help>
 
 brief help message