[Bioclusters] a dedicated cluster to mpiblast the nr database

Mike Cariaso bioclusters@bioinformatics.org
Thu, 4 Dec 2003 15:10:36 -0800 (PST)

I'm looking to put together a small cluster for a very
large number of blasts against a local copy of the the
ncbi nr database.

I am under the impression the best thing I can do is
to get it all in memory, for which I'm estimating 24GB
should cover me. 

I've found a vendor for 3 dual 2.4G Xenon each with
8GB (ram: DDR 8x1G ecc pc2100). The total price is
about $12k for the 3 of them.

would mpiblast benefit from a 64 bit platform, or will
32 bits perform reasonably close. 

I hope to just add 1 more machine in the future as nr

Given this config what might be my bottleneck?

Any advice, experience, or warnings would be greatly appreciated.

Mike Cariaso