[Bioperl-l] Bio-Perl and multiple cores of CPU

[Dave Messina]

On May 7, 2010, at 11:46 PM, Chris Fields wrote:

> With legacy BLAST this is -a 8, with BLAST+ I think this is -num_threads 8 (with the explicit caveat I haven't tried the latter much, so no guarantees, we're not liable for explosions and such).

Once other caveat if you use BLAST+: be sure you have the latest version 2.2.23. In my informal testing, the num_threads option wasn't working correctly in 2.2.22.

Blast parsing will still be single-threaded, by the way. BioPerl programs, like everything else unfortunately, need to explicitly spawn multiple threads or forks to take advantage of multiple cores.

While I've never done it myself, I ran across this post which may be helpful in case you want to try it:

http://computationalbiologynews.blogspot.com/2008/07/harnessing-power-of-multicore.html



Dave