[Bioclusters] Parallel blast

Chris Dwan (CCGB) bioclusters@bioinformatics.org
Fri, 7 Jun 2002 07:14:27 -0500 (CDT)

> 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