[Beowulf] large MPI adopters

Bogdan Costescu Bogdan.Costescu at iwr.uni-heidelberg.de
Wed Oct 8 07:09:36 PDT 2008

On Tue, 7 Oct 2008, Vincent Diepeveen wrote:

> Drug type companies eat typical 0.5% system time.

Could you please explain what you mean here ? That they buy lots of 
CPUs but only use a fraction of them or only for a fraction of time ?

> They are far behind, which is not so logical; i would consider it 
> old fashioned to do experiments on monkeys (Bar-ilan brain 
> experiments on monkeys rings a bell?), so doing everything in 
> software is far more logical.

Maybe your knowledge about the pharma industry is far behind ? "Doing 
everything in software is far more logical" only when you can exactly 
express biological processes in mathematical terms which is not true 
in the great majority of cases. F.e. molecular dynamics (often used to 
simulate interactions at molecular level, f.e. of a drug injected into 
the body) is based on several approximations and the implementations 
are subject to numerical errors. Would you take a drug that was 
produced based only on a simulation with molecular dynamics and found 
to be good enough ?

Similar concerns apply to all levels - the brain, as you mention it, 
is still very much an enigma, otherwise artificial intelligence would 
be all around us (or not, if deemed to dangerous...). And when you 
don't know how an organ or system works, how can you develops drugs 
only by simulations ?

> When someone is really in big need for big calculation power, one 
> makes dedicated cpu's for it.

I tend to agree, provided that the dedicated CPU brings a really big 
advantage, like an order of more of magnitude. F.e., to stay in the 
pharma related field, that's the bussiness case for DEShaw Research's 
molecular dynamics chip (Anton) which is supposed to bring a 
significant increase in speed for MD simulations compared with 
software solutions running on general purpose CPUs (or GPUs).

Bogdan Costescu

IWR, University of Heidelberg, INF 368, D-69120 Heidelberg, Germany
Phone: +49 6221 54 8869/8240, Fax: +49 6221 54 8868/8850
E-mail: bogdan.costescu at iwr.uni-heidelberg.de

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