NCBI BLAST Performance

While looking at the performance of the new computational core in BLAST 2.2.14, I noticed that the precompiled version for SPARC Solaris is compiled using an old compiler (Studio 8). Building your own version from the source code (also available on the website) appears to improve performance noticeably -- about 15% (results observed on a 1GHz T1000 running the NCBI benchmark queries). It's likely that further gains are feasible by altering the default compiler flags -- although the default flags look reasonable (-fast etc).

Posted on: Sep 05, 2006

Posted by: sprack

Category: General

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Comments:

For compiler flags, would profile based optimisation make much difference?

PS Would be interesting to see the performance relative to Opteron, Xeon etc.

Posted by Chris Rijk on September 05, 2006 at 04:05 PM PDT #

Feedback profile doesn't seem to make much performance difference (tested on T2000).

Posted by Lawrence Spracklen on September 07, 2006 at 06:26 PM PDT #

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