[Bioclusters] mpiblast on SGI Altix

[Jithesh]

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
> >  
> >
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