[Bioclusters] mpiBlast and NFS

Joydeep Sen Sarma bioclusters@bioinformatics.org
Mon, 2 Feb 2004 16:06:12 -0800 (PST)

Hi folks,

I work on file systems and am doing some research into

NFS issues when running Blast. I have read a number of

posts on the bioclusters mailing list regarding usage 
of local disks being better.

However, after reading the mpiBlast white paper, I
got the impression that mpiBlast would avoid nfs read
io after the server caches are warmed up. (Of course
as long as the data fits in the server memory pool).

So I guess i am a little curious as to whether people
still feel nfs is not suited for mpiBlast and if so,
why ? Do you have multiple databases against which 
searches are performed (so that the cache is purged
periodically ?). Or does the database not fit into the
combined memory of a typical cluster ?

thanks in advance for your response,


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