[Bioclusters] Parallel blast

Ognen Duzlevski bioclusters@bioinformatics.org
07 Jun 2002 06:31:45 -0600

On Fri, 2002-06-07 at 06:14, Chris Dwan (CCGB) wrote:
> > Is there or is there not a parallel version of blast available
> > somewhere?
> (addressing a different part of the question than Chris D.)
> I'm not aware of an MPI version of BLAST, nor would I use one if it was
> available.  My problem is throughput, not response time on BLAST jobs.  In
> this situation, anything less than a parallel effficiency of one is
> wasting resources.
> NCBI's BLAST has the "-a <NUM_CPUS>" option, which enables threading.  If
> your operating system is intelligent about SMP and you have more than one
> CPU on the board, you can use it to run in parallel.  I haven't studied it
> with any rigor, but thumbnail tests indicate that the parallel
> efficiency is fairly high for NUM_CPU <= 8. 
> This is great for decreasing wait time for web users, but it doesn't
> address my interests at all.  Not to beat it into the ground, but:
> It's throughput that we need.  That's why we're all so fond of queuing
> systems and processing farms, rather than high performance parallel
> machines.

There is a parallel version of Blast based on PVM written by a former
colleague of mine. It was written/tested on our 32-node beowulf cluster.
Instead of posting his email address online, if interested people can
email me and I will make sure they get in touch with him for sharing
experiences / results and possibly obtaining the code (I dont know what
licensing agreements he and our former employer have in place).