Parallel processing in bioinformatics and molecular modelling

Gordon D. Pusch gdpusch at NO.xnet.SPAM.com
Fri Apr 26 19:10:16 EST 2002


howardolson at ausi.com (Howard Olson) writes:

> Are there adequate parallel software systems for bioinformatics work
> in any Cray system?

Crays are ``vector'' machines with a relatively long pipeline, which 
means that they do not perform at all well unless you are performing
=EXACTLY= the same sequence of calculations on every member of a 
large set of numbers, and none of those calculations are conditional 
on any intremediate result. By contrast, nearly everything in bioinformatics 
is ``trivially parallelizable'' rather than vectorizable, but involves 
a lot of conditional branches, e.g., during the backtracking phase of 
a sequence alignment, when you need to choose the path with the best score 
through the alignment matrix. Hence, Crays are the exact =OPPOSITE= 
of what you want for most bioinformatics applications; what you really need
is a ``Beowulf'' style massively parallel cluster of independent processors.


> If not, is there any supercomputer system available commercially with
> such software available.

Timelogic.com <http://Timelogic.com/> sells a special-purpose computer
that has a built-in FPGA-based hardware accelerator. By extracting the
time-critical ``inner loop'' of the bioinformatic algorithm and
implementing it in field-programmable firmware rather than software, 
they can achieve more than a two orders of magnitude speedup.


> I am particularly interested in the quantum biochemistry of the CNS.

I cannot help you there.


-- Gordon D. Pusch   

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