From: Don Armstrong <don@donarmstrong.com>
Date: Wed, 5 Aug 2015 16:36:27 +0000 (-0700)
Subject: add start of dqsub
X-Git-Url: https://git.donarmstrong.com/?p=uiuc_igb_scripts.git;a=commitdiff_plain;h=056bec558a499c31f31f7f3e346d2bdac2f77f90

add start of dqsub
---

diff --git a/dqsub b/dqsub
new file mode 100644
index 0000000..1d3dd1b
--- /dev/null
+++ b/dqsub
@@ -0,0 +1,211 @@
+#!/usr/bin/perl
+# dqsub submits jobs using qsub with better options
+# and is released under the terms of the GNU GPL version 3, or any
+# later version, at your option. See the file README and COPYING for
+# more information.
+# Copyright 2014 by Don Armstrong <don@donarmstrong.com>.
+
+
+use warnings;
+use strict;
+
+use Getopt::Long;
+use Pod::Usage;
+
+=head1 NAME
+
+dqsub - submits jobs using qsub with better options
+
+=head1 SYNOPSIS
+
+dqsub [options]
+
+ Options:
+   --queue, -q Queue to use
+   --interactive, -I call qsub interactively
+   --nodes nodes to use
+   --array array mode (one of 'chdir' or 'xargs' or '')
+   --array-from file to read arrays from (default STDIN)
+   --ppn processors per node to use
+   --mem memory to request
+   --dir Directory to run the script in (default current directory)
+   --debug, -d debugging level (Default 0)
+   --help, -h display this help
+   --man, -m display manual
+
+=head1 OPTIONS
+
+=over
+
+=item B<--array>
+
+This describes how dqsub will generate array jobs.
+
+If no B<--array> is given, then the command and any additional
+arguments given will be run using qsub.
+
+If B<--array> is C<chdir>, then each line of the input given in
+B<--array-from> will be used as a directory and the command and any
+additional arguments given will run in each directory.
+
+IF B<--array> is C<xargs>, then each line of the input given will be
+considered to be an additional argument which will be given to the
+command run in the current directory.
+
+=item B<--array-from>
+
+File to read array arguments from. If not provided, and B<--array> is
+given, arguments will be read from STDIN.
+
+=item B<--debug, -d>
+
+Debug verbosity. (Default 0)
+
+=item B<--help, -h>
+
+Display brief usage information.
+
+=item B<--man, -m>
+
+Display this manual.
+
+=back
+
+=head1 EXAMPLES
+
+dqsub
+
+=cut
+
+use IO::File;
+use Cwd qw(getcwd abs_path);
+use vars qw($DEBUG);
+
+my %options = (nodes           => 1,
+               ppn             => 2,
+               mem             => '2G',
+               debug           => 0,
+               help            => 0,
+               man             => 0,
+               interactive     => 0,
+              );
+
+GetOptions(\%options,
+           'queue|q=s',
+           'interactive|I!',
+           'nodes=i',
+           'array=s',
+           'array_from|array-from=s',
+           'ppn|processors-per-node=i',
+           'mem|memory=s',
+           'dir=s',
+           'debug|d+','help|h|?','man|m');
+
+pod2usage() if $options{help};
+pod2usage({verbose=>2}) if $options{man};
+
+$DEBUG = $options{debug};
+
+my @USAGE_ERRORS;
+if (not @ARGV and not $options{interactive}) {
+    push @USAGE_ERRORS,"You must provide a command to run";
+}
+if (defined $options{array} and $options{array} !~ /^(?:|chdir|xargs)$/i) {
+    push @USAGE_ERRORS,"--array must be one of chdir, xargs or '' if provided";
+    $options{array} = lc($options{array});
+    if ($options{array} eq '') {
+        $options{array} = undef;
+    }
+}
+if ($options{interactive} and @ARGV) {
+    push @USAGE_ERRORS,"Don't provide commands when you're asking for an interactive shell";
+}
+
+pod2usage(join("\n",@USAGE_ERRORS)) if @USAGE_ERRORS;
+
+# OK. Generate the options to qsub which we'll be using
+my @qsub_options = generate_qsub_options(\%options);
+
+if ($options{interactive}) {
+    print STDERR 'running: qsub '.join(' ',@qsub_options) if $DEBUG:
+    exec('qsub',@qsub_options);
+} else {
+    my @array = ();
+    if ($options{array}) {
+        @array = read_array_options(\%options) if $options{array};
+        # the -t option gives the range of elements for an array job
+        push @qsub_options,'-t','1-'. scalar @array;
+    }
+    call_qsub(\@qsub_options,write_qsub_script(\%options,\@ARGV,\@array));
+}
+
+sub generate_qsub_options{
+    my ($options) = @_;
+    my @qo;
+    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='.$options->{ppn};
+    }
+    if ($options->{mem}) {
+        push @l,'mem=',$options->{mem};
+    }
+    push @qo,'-l',join(',',@l) if @l;
+}
+
+sub read_array_options{
+    my ($options) = @_;
+    my $fh = \*STDIN;
+    if (defined $options->{array_from}) {
+        $fh = IO::File->new(defined $options->{array_from}) or
+            die "Unable to open $options->{array_from} for reading: $!";
+    }
+    my @arrah;
+    for (<$fh>) {
+        chomp;
+        push @array,$_;
+    }
+    return @array;
+}
+
+sub call_qsub {
+    my ($qsub_options,$script) = @_;
+    my $qsub_fh;
+    open $qsub_fh,'|-','qsub',@{$qsub_options},'-' or
+        die "Unable to start qsub: $!";
+    print {$qsub_fh} $script or
+        die "Unable to print to qsub: $!";
+    close($qsub_fh) or
+        die "Unable to close qsub filehandle: $!";
+}
+
+sub write_qsub_script {
+    my ($opt,$arg,$array) = @_;
+
+    my $script = "#!/bin/bash\n";
+    my $command = join(' ',map {qq('$_')} @{$arg});
+        $script .= <<EOF;
+# this script was written by dqsub
+EOF
+    if (defined $opt->{array}) {
+        die "--array is currently not implemented";
+    } else {
+        $script .= <<EOF;
+# there's no array, so just executing the command with arguments
+exec $command;
+EOF
+    }
+    return $script;
+}
+
+
+__END__