[Bioclusters] About the parallel Blast on PVM

Jimmy Wu bioclusters@bioinformatics.org
Mon, 19 Aug 2002 20:23:56 +0800

Dear Ognen:

I just start to study the parallel Blast and get some information about this
topic.  I am interested in the parallel version of Blast on PVM, and I would
like to compare the result with what I have in SMP machine.  Could you
please let me know how to contact with the author or obtain the code to have
a test run?  Thank you for the help!

With Best Regards,


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).