tools/lh3misc/sys/asub

   1 #!/usr/bin/perl -w
   2
   3 # Author: lh3
   4
   5 use strict;
   6 use warnings;
   7 use Getopt::Std;
   8 use Cwd qw/abs_path/;
   9 use Sys::Hostname qw/hostname/;
  10
  11 my $version = "0.1.8";
  12
  13 my %opts = (R=>'', j=>'', k=>0, q=>'', c=>'', w=>'', M=>'', n=>'', m=>'', W=>'');
  14 getopts('R:j:k:q:c:pw:M:n:m:W:', \%opts);
  15 &usage if (-t STDIN && @ARGV == 0);
  16 my $is_run = ($opts{k} > 0 && $opts{j})? 1 : 0;
  17 if (!$is_run) { # prepare to run
  18   my $is_sge = &which('bsub')? 0 : 1;
  19   $opts{j} ||= sprintf("asub_$$%.3d", rand(1000));
  20   my ($fh, $K);
  21   $K = 0;
  22   open($fh, ">$opts{j}.sh") || die;
  23   while (<>) {
  24         s/&\s*$//; # remove "&" at the end of the command
  25         next if (/^\s*$/);
  26         print $fh $_;
  27         ++$K;
  28   }
  29   close($fh);
  30   $_ = $opts{j};
  31   my $cmd;
  32   $opts{c} = $K if ($opts{c} && $opts{c} > $K);
  33   $opts{q} = qq/-q $opts{q}/ if ($opts{q});
  34   if (!$is_sge) { # LSF
  35         $opts{R} = qq/-R "$opts{R}"/ if ($opts{R});
  36         $opts{c} = qq/\%$opts{c}/ if ($opts{c});
  37         $opts{w} = qq/-w "$opts{w}"/ if ($opts{w});
  38         $opts{n} = qq/-n $opts{n}/ if ($opts{n});
  39         $opts{m} = qq/-m $opts{m}/ if ($opts{m});
  40         $opts{W} = qq/-W $opts{W}/ if ($opts{W});
  41         if ($opts{n}) {
  42           if ($opts{R}) {
  43                 chop($opts{R}); # chop the tailing "
  44                 $opts{R} .= qq/ span[hosts=1]"/;
  45           } else {
  46                 $opts{R} = qq/-R "span[hosts=1]"/;
  47           }
  48         }
  49         if ($opts{M}) {
  50           if ($opts{R}) {
  51                 chop($opts{R}); # chop the tailing "
  52                 $opts{R} .= qq/ select[mem>$opts{M}] rusage[mem=$opts{M}]"/;
  53           } else {
  54                 $opts{R} = qq/-R "select[mem>$opts{M}] rusage[mem=$opts{M}]"/;
  55           }
  56           $opts{R} .= ' -M ' . ($opts{M}*1000);
  57         }
  58         $cmd = qq(mkdir -p $_.out $_.err && echo '$0 -j $_.sh -k \${LSB_JOBINDEX}' | bsub -J$_)
  59           . qq("[1-$K]$opts{c}" -o $_.out/\%I.out -e $_.err/\%I.err $opts{n} $opts{R} $opts{q} $opts{w} $opts{m} $opts{W});
  60   } else { # SGE
  61         $opts{R} = qq/-l "$opts{R}"/ if ($opts{R});
  62         $opts{w} = qq/-hold_jid $opts{w}/ if ($opts{w});
  63         my $asub = abs_path($0);
  64         $cmd = qq(mkdir -p $_.out $_.err && echo '$asub -j $_.sh -k \${SGE_TASK_ID}' | qsub -N $_ -cwd )
  65           . qq(-t 1-$K -o '$_.out/\$TASK_ID.out' -e '$_.err/\$TASK_ID.err' $opts{R} $opts{q} $opts{w});
  66   }
  67   defined($opts{p})? (print "$cmd\n") : system($cmd);
  68 } else { # run the command
  69   warn("[asub] Hostname: ".hostname.", Arch-OS: ".&get_cpu_sys."\n");
  70   my $fh;
  71   my $k = 0;
  72   open($fh, $opts{j}) || die;
  73   while (<$fh>) {
  74         chomp;
  75         last if ((++$k) == $opts{k});
  76   }
  77   my $cmd = $_;
  78   close($fh);
  79   warn("[asub] Command: $_\n");
  80   warn("[asub] --- BEGIN OF COMMAND STDERR ---\n");
  81   my $ret = system($_);
  82   warn("[asub] --- END OF COMMAND STDERR ---\n");
  83   warn("[asub] Return value: $ret\n");
  84   exit($ret);
  85 }
  86
  87 sub get_cpu_sys {
  88   my $dir = `uname -p 2>/dev/null`;
  89   $dir = `uname -m 2>/dev/null` if (!$dir || $dir =~ "unknown");
  90   $dir .= '-'.`uname -s`;
  91   $dir = lc($dir);
  92   $dir =~ s/\s//g;
  93   return $dir;
  94 }
  95
  96 sub which {
  97   my $file = shift;
  98   my $path = (@_)? shift : $ENV{PATH};
  99   return if (!defined($path));
 100   foreach my $x (split(":", $path)) {
 101         $x =~ s/\/$//;
 102         return "$x/$file" if (-x "$x/$file");
 103   }
 104   return;
 105 }
 106
 107 sub usage {
 108   die qq(
 109 Program: asub (Array Job submission with bsub/qsub)
 110 Version: $version
 111 Contact: Heng Li <lh3\@sanger.ac.uk>\n
 112 Usage:   asub [options] <cmd_file>\n
 113 Options: -R STR    resources string [null]
 114          -w STR    job dependency [null]
 115          -q STR    queue name [default queue]
 116          -j STR    job name [auto]
 117          -c INT    number of processors (LSF only) [max]
 118          -M INT    maximum memory in MB (Sanger LSF only) [null]
 119          -W INT    runtime limit (LSF only) [none]
 120          -n INT    # CPUs for a parallel job (LSF only) [null]
 121          -m STR    host group (LSF only) [null]
 122          -p        print the submission command only
 123
 124 Note: For option -R and -w, SGE and LSF have different syntax. Please
 125       check SGE/LSF manual page for details. Here are some examples for
 126       LSF:
 127
 128         -R "select[type==X86_64&&mem>800] rusage[mem=800]"
 129         -w "done(my_job_001)"
 130
 131       And for SGE:
 132
 133         -R h_cpu=86400,h_data=1000000000
 134         -w my_job_001
 135
 136 );
 137 }