[Computational-biology] Re: processor system

Kevin Karplus karplus at soe.ucsc.edu
Mon Apr 24 15:00:54 EST 2006


There has been some interest in parallel processing for bioinformatics
applications, but most bioinformatics applications are "embarassingly
parallel"---that is they consist of doing thousands of independent
computations, so simple clusters work fine.  Most "high performance
computing" projects are designed by and for physicists---the tight
coupling they need for handling differential equations on large grids
are simply irrelevant to most bioinformatics applications.

The big problem is not multi-processing, but properly distributing and
maintaining data.  You can't afford to have 1000 processors hitting on
a single file server---even 40 processors will bring most servers to
their knees.  But making 1000s of copies of terabytes of data is also
impractical. 

The real problems in computer architecture for bioinformatics have to
do with handling the data, not the computation.  We need
high-performance data architectures, which the computer engineering
community has not paid nearly enough attention to.

Kevin Karplus
------------------------------------------------------------
Kevin Karplus 	karplus at soe.ucsc.edu	http://www.soe.ucsc.edu/~karplus
Professor of Biomolecular Engineering, University of California, Santa Cruz
(formerly a Computer Engineering professor)



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