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, Jim 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). Ognen