Optimization Helpby jmmitc06 (Beadle)
|on Aug 01, 2013 at 23:06 UTC||Need Help??|
jmmitc06 has asked for the
wisdom of the Perl Monks concerning the following question:
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.
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.