X-Git-Url: https://git.donarmstrong.com/?p=uiuc_igb_scripts.git;a=blobdiff_plain;f=dqsub;h=571bc281cd88c45827ae35fa7672844b66a98875;hp=27b8b39c5b43e97a0da442b65e241fd9aa247438;hb=9d5820c033136980f80cccad98a499ba58c0cde5;hpb=e6e19e0274ff4ce9fe45ae9debfd5eebd40a5d69

diff --git a/dqsub b/dqsub
index 27b8b39..571bc28 100755
--- a/dqsub
+++ b/dqsub
@@ -31,6 +31,8 @@ dqsub [options]
    --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
@@ -60,6 +62,20 @@ command run in the current directory.
 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)
@@ -94,10 +110,12 @@ my %options = (nodes           => 1,
                man             => 0,
                interactive     => 0,
                array_per_job   => 1,
+               join            => 1,
               );
 
 GetOptions(\%options,
            'queue|q=s',
+           'batch=s',
            'interactive|I!',
            'nodes=i',
            'array=s',
@@ -105,7 +123,9 @@ GetOptions(\%options,
            '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|processors-per-node=i',
+           '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',
@@ -135,15 +155,44 @@ if ($options{interactive} and @ARGV) {
     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 $JOB_SUBMITTER = 'qsub';
 # OK. Generate the options to qsub which we'll be using
-my @qsub_options = generate_qsub_options(\%options,\@ARGV);
+my @qsub_options;
+if ($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 ($options{array}) {
@@ -158,6 +207,9 @@ if ($options{interactive}) {
             }
         }
     }
+    if ($options{batch} eq 'pbs') {
+        push @qsub_options,'-';
+    }
     call_qsub(\@qsub_options,write_qsub_script(\%options,\@ARGV,\@array));
 }
 
@@ -167,17 +219,15 @@ sub generate_qsub_options{
     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 (defined $options->{account}) {
+        push @qo,'-A',$options->{account};
+    }
     my %l_options =
         (mem => 'vmem',
          time => 'walltime',
@@ -199,7 +249,58 @@ sub generate_qsub_options{
     if ($options->{name}) {
         push @qo,'-N',$options->{name};
     } else {
-        push @qo,'-N',join('_',@{$args}[0..min($#{$args},2)]);
+        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 ($options->{join}) {
+        push @qo,'-j','oe';
     }
     return @qo;
 }
@@ -222,27 +323,43 @@ sub read_array_options{
 sub call_qsub {
     my ($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}) {
         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
@@ -250,13 +367,13 @@ EOF
             $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=\$(( \${PBS_ARRAYID:=1} * $opt->{array_per_job} + \$i - $opt->{array_per_job} ))
+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 "\${PBS_ARRAYID:=1} p"<<'_HERE_DOC_END_'
+OPT=\$(sed -n -e "\${MYARRAYID:=1} p"<<'_HERE_DOC_END_'
 EOF
         }
         $script .= <<EOF;