Harnessing the power of multicore

Most of us are working on multi - core processors , but the code we generally write do not utilize the extra cpu given to us. I do lot of "Align EST and genomic DNA sequences" using est2genome from EMBOSS. This is a task which is embarrassingly amenable to parallelization. So how do we go about doing this using PERL? Well following a posting at PerlMonks, I got hold of Parallel::ForkManager:
wget http://search.cpan.org/CPAN/authors/id/D/DL/DLUX/Parallel-ForkManager-0.7.5.tar.gz
and extracted to:
/scratch/misc/parallel/Parallel
[if you have root access to your machine, I would recommend to install this module instead of going for 'use lib'].
Once this is done, all you need is follow the examples and get going :)
For example, I have EST in fasta format files ending with .fas. The genome I am aligning to is NC_010336.fna. For this I can write the following code:

  use strict;
  use warnings;
  use lib '/scratch/misc/parallel/Parallel';
  use LWP::Simple;
  use Parallel::ForkManager;
  system("ls -1 *.fas > list.tmp");
  my $command="est2genome";
  my $genome="NC_010336.fna";
  my @tasks;
  open(F,"list.tmp");
  while(< F >){chomp;push(@tasks,$_);}
  close F;  
  my $tasksize= @tasks;
  print "There are #  $tasksize \n";
  my $pm = new Parallel::ForkManager($tasksize); 
  foreach my $task (@tasks) {
    $pm->start and next; # do the fork
    system("$command $task $genome $task.$genome.out");
    $pm->finish; 
  }
  $pm->wait_all_children;

and store is as est2genome_parallel.pl and run it as:
perl est2genome_parallel.pl
above code can be downloaded from http://sharma.animesh.googlepages.com/est2genome_parallel.pl, enjoy :)