[Bioclusters] mpi-blast performance on a 256-core cluster

Li Liu liliu at biotech.ufl.edu
Thu Jan 3 16:51:31 EST 2008

Dear biocluster members,

We've been struggling with the performance of mpi-blast 1.4 on our  
256-core cluster for almost a month. What we tried to do is to run  
blastx search against NCBI NR database for 600K 454 reads. It ran for  
a few days and stopped without giving any error message. I'm  
wondering if any of you have any suggestions on

1. Any alternative parallel blast program?
2. Did anybody observe frequent I/O operations with mpi-blast? Isn't  
it supposed to load the database into memory and access the memory  
from then on, rather than keep asking disk for database fragment?

Many thanks in advance.



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