It should. Basically mpiblast partitions the input and the databases. NCBI blast could use partitioned databases. NCBI threads each search, rather than across searches that MPIblast does. -- Joseph Landman, Ph.D Scalable Informatics LLC, email: landman at scalableinformatics.com web : http://scalableinformatics.com phone: +1 734 612 4615 ---------- Original Message ----------- From: Jithesh <p.jithesh at qub.ac.uk> To: "Clustering, compute " farming & distributed computing in life science informatics <bioclusters at bioinformatics.org> Cc: mpiblast <mpiblast-users at lists.sourceforge.net>, Mike Muratet <muratem at eng.uah.edu> Sent: 16 Mar 2005 18:24:40 +0000 Subject: Re: [Bioclusters] mpiblast on SGI Altix > Does mpiblast provide adavantage over the normal threaded version of > NCBI BLAST on shared memory machines? > > Jithesh > > On Wed, 2005-03-16 at 17:48, Aaron Darling wrote: > > Since XFS seems to provide these machines with extremely fast shared > > storage I would suggest setting your "Local" directory equal to the > > "Shared" storage directory. Then you can avoid all the fragment copy > > overhead. > > > > Also, a google for mpiblast sgi altix > > (http://www.google.com/search?q=mpiblast+sgi+altix) reveals what appears > > to be some excellent work done by folks at ORNL and NCSU to optimize > > mpiblast for the altix architecture. It may be worthwhile to contact > > them for more info... > > They benchmarked version 1.2.1. It would be interesting to see how > > their mpiblast benchmark results improve on an altix with shared and > > local set identical and with the --disable-mpi-db flag. > > > > -Aaron > > > > Joe Landman wrote: > > > > >Hi Mike: > > > > > > Make sure you configure mpiblast to use the shared memory device (ch_shmem) > > >rather than the ethernet (ch_p4), or similar devices if you are using MPICH. > > >Dont worry about assignments of partitions to nodes, that should not be an issue > > >for this machine. > > > > > >Joe > > > > > >-- > > >Joseph Landman, Ph.D > > >Scalable Informatics LLC, > > >email: landman at scalableinformatics.com > > >web : http://scalableinformatics.com > > >phone: +1 734 612 4615 > > > > > > > > >---------- Original Message ----------- > > >From: Mike Muratet <muratem at eng.uah.edu> > > >To: mpiblast-users at sourceforge.net, bioclusters at bioinformatics.org > > >Sent: Wed, 16 Mar 2005 11:13:28 -0600 (CST) > > >Subject: [Bioclusters] mpiblast on SGI Altix > > > > > > > > > > > >>Greetings > > >> > > >>Does anyone have any experience with mpiblast on the SGI Altix and can > > >>you offer any suggestions for configuring jobs? The Altix 350 has 16- > > >>CPU nodes with shared memory. The machine I'm using has 56 total CPUs. > > >>Can anyone offer any advice for how many database partitions to use, > > >>and how they get assigned to nodes/CPUs? > > >> > > >>Thanks > > >> > > >>Mike > > >> > > >>_______________________________________________ > > >>Bioclusters maillist - Bioclusters at bioinformatics.org > > >>https://bioinformatics.org/mailman/listinfo/bioclusters > > >> > > >> > > >------- End of Original Message ------- > > > > > >_______________________________________________ > > >Bioclusters maillist - Bioclusters at bioinformatics.org > > >https://bioinformatics.org/mailman/listinfo/bioclusters > > > > > > > > _______________________________________________ > > Bioclusters maillist - Bioclusters at bioinformatics.org > > https://bioinformatics.org/mailman/listinfo/bioclusters > > _______________________________________________ > Bioclusters maillist - Bioclusters at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bioclusters ------- End of Original Message -------