Dear Monks:

I am a bioinformatics programmer and I am currently running a very large calculation looking for subgraph isomorphisms. I have optimized it to the best of my abilities (I'm limited to the scale of my rewriting since the underlying objects/modules are used in much of my other code)

Below is a subroutine that currently consumes 74% of the time in my multiday calculation, even when using a cluster with torque. I have tried various different things, but I cannot beat what I have and any improvement would save me considerable time. 

sub equate2
  {
  my ($self, $other, $mapping) = @_;
  foreach my $row_index (0..$#$mapping)
    {
    return 0 if (grep { $$self{Matrix}[$row_index][$_] != $$other{Matr
+ix}[$$mapping[$row_index]][$$mapping[$_]]); } (0..$#$mapping));
    }
  return 1;
  }

[download]

I can provide more information if necessary, but in short this subroutine finds if elements of two matrices, i and j determined by a vector: $mapping.

Any advice and any tips for improving performance would be greatly appreciated. I have tried switching out the grep and foreach with for statements to no avail.

Thanks to all the monks for the help you have given in the past.

In reply to Optimization Help by jmmitc06

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