[Bioclusters] Questions on mpiBLAST

Hrishikesh Deshmukh hdeshmuk at gmail.com
Thu Feb 3 13:09:18 EST 2005

I am no authority on BLAST, i guess you see a linear speedup increase
only when the problem is huge, for 20 odd sequences mpiblast doesn't
play, your ncbi blast is good enough! Just curious are the results for
ncbi and mpiblast for the same dataset (input) match exactly?!

I am tryting to get BLAST and mpiBLAST running on Sun Grid, right now
BLAST works in serial mode and mpiBLAST is kinds stuck!


On Thu, 03 Feb 2005 11:45:45 -0500, Xiaowu Gai <xgai at genome.chop.edu> wrote:
> Hi Everyone:
> We have a 16-node Xserve cluster, with 2GB memory on each node and dual
> processors.  I was able to install mpiBLAST on it, along with LAM/MPI.
> However, the performance that I saw with some test runs has not been that
> good and quite confusing.  Here is what I did:
> 1.) I formatted the nt database:
> mpiformatdb -N 16 -i nt
> 2.) I ran the mpiblast on one, two, five, ten, twenty, and more sequences
> (about 500bp each) and with the command:
> time mpirun N mpiblast -p blastn -d nt -i single.fa -o blast_results.
> Here are the numbers:
> Single: 1m39.054s
> Two: 0m11.009s
> Five: 0m16.021s
> Ten: 0m46.591s
> twenty: 3m7.541s
> ..
> I am all confused.  First of all, the performance is not that impressive.
> Secondly, the numbers are very confusing to me.  Why is that a single
> sequence query takes so much more time than a two (BTW, I reran the query of
> a single sequence right after the query of two and got similar results)? And
> query of five takes only 5 seconds more than the query of two and  so on..
> I am afraid that I have done something wrong and would really appreciate any
> thoughts.
> Thanks
> Xiaowu
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