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