Hi, I am interested in this as well. I have NCBI blast running twice = faster on a 2-processor Intel Linux box than 4-processor UltraSparc = server(SUN E3500, Solaris 8). It is not using more than 1 processor on = the solaris server even when we specify 4 or more for the -a parameter, = as it does on the Linux server. Is there any known implementation that = takes advantange of the 64-bit architecture of Sun servers? Please let = me know if you have any useful info on this. Filatei=20 > -----Original Message----- > From: Jimmy Wu [mailto:jimwu@ms25.url.com.tw] > Sent: Monday, August 19, 2002 8:24 AM > To: bioclusters@bioinformatics.org > Subject: [Bioclusters] About the parallel Blast on PVM >=20 >=20 > Dear Ognen: >=20 > I just start to study the parallel Blast and get some=20 > information about this > topic. I am interested in the parallel version of Blast on=20 > 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=20 > the code to have > a test run? Thank you for the help! >=20 > With Best Regards, >=20 > Jim >=20 > 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=20 > one if it was > > available. My problem is throughput, not response time on=20 > 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=20 > threading. If > > your operating system is intelligent about SMP and you have=20 > more than one > > CPU on the board, you can use it to run in parallel. I=20 > haven't studied it > > with any rigor, but thumbnail tests indicate that the parallel > > efficiency is fairly high for NUM_CPU <=3D 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=20 > of queuing > > systems and processing farms, rather than high performance parallel > > machines. >=20 > 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=20 > 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=20 > know what > licensing agreements he and our former employer have in place). >=20 > Ognen >=20 >=20 >=20 > _______________________________________________ > Bioclusters maillist - Bioclusters@bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bioclusters >=20