[Beowulf] Re: Intro question

Joseph Han jhh3851 at yahoo.com
Fri Dec 5 18:01:10 PST 2008

> Message: 1
> Date: Fri, 5 Dec 2008 08:59:22 -0800
> From: "Lux, James P" <james.p.lux at jpl.nasa.gov>
> Subject: Re: [Beowulf] Intro question
> To: Lawrence Stewart <larry.stewart at sicortex.com>, "Robert G. Brown"
> 	<rgb at phy.duke.edu>
> Cc: Beowulf Mailing List <beowulf at beowulf.org>
> Message-ID: <C55E9DEA.3372%James.P.Lux at jpl.nasa.gov>
> Content-Type: text/plain; charset="iso-8859-1"
> On 12/5/08 8:17 AM, "Lawrence Stewart" <larry.stewart at sicortex.com> wrote:
> > I've been to a couple of DE Shaw talks and I always come away puzzled.
> >
> > It's tempting to conclude that they are just smarter than I am, but
> > maybe they are just wrong.
> >
> > My understanding is they are building a special purpose molecular
> > dynamics machine because it will be far faster than a general purpose
> > machine programmed to do MD.
> >
> > In principle this might work, if you get the problem statement right,
> > and you can design and build the machine before the general purpose
> > machines catch up, and you don't make any mistakes, and after it is
> > built you can keep designing new ones.  In practice it always seems to
> > take longer than you expected and cost more, and maybe that 7 bit ALU
> > really has to be changed to an 8 bit ALU to keep the precision up.
> If the machine is built of reconfigurable FPGAs, then such a change is
> pretty quick.
> If you have a basic hardware infrastructure, and just respin an ASIC, and
> that's a bit more time consuming, but not particularly expensive. e.g. Say
> it costs, in round numbers, $1M to do an ASIC.  That's 2-3 work years labor
> costs, so in the overall scheme of things, it's not very expensive, in a
> relative way.  If your overall research effort is, say, $20M/yr (which is
> big, but not huge), then budgeting for a complete machine rebuild every year
> is only 5-10%.  If that gives you a factor of 3 speed increase, it's
> probably worth it.
> Think about it.. You check out your design in FPGAs to make sure it works,
> then do FPGA>ASIC and crank out a quick 10,000 customized processors, have
> them assembled into boards, fire it up and go. There are all sorts of
> economies of scale possible (if you're building 1000 PC boards, on an
> automated line, it's just not that expensive.  For comparison, we regularly
> have prototype boards made with more than 20 layers and a dozen or so fairly
> high density parts (a couple Xilinx Virtex II FPGAs, RAMs, CPUs, etc.) and
> all the stuff around them.  In single quantities, it might cost around
> $15K-$20K each to do these (parts cost included).  If we were doing 100 of
> them, so we could spread the cost of the pick-and-place programming over all
> of them, etc., it would probably be down in the $5-10K/each range.  Get into
> the 1000 unit quantities where it pays to go to a higher volume house, and
> you might be down in the few hundred bucks each to fab the board, and now
> you're just talking parts cost.
> Consider PC mobos.. The manufacturing cost (including parts) is well under
> $100.
> Now consider using that nifty compchem box to go examine thousands of
> possible drugs.  Get a hit, and it can be a real money maker. Consider that
> Claritin was responsible for about $2B of Schering-Plough's revenue in just
> 2001. Plavix was almost $4B in 2005.  That ED drug that starts with a V that
> we all get mail about was in the $1B/yr area, although its dropping. (One
> article comments that when it comes off patent in 2012 that they'll see a
> bump in sales:"Recreational use of the product could also be expected to
> generate substantial revenues.")
> In this context, spending $100M isn't a huge sum, now, is it.
> Jim

They've actually become quite a bit more transparent lately because I think
that they are close to "releasing" a product.  Their website actually has quite
a bit of detail now:


This paper was a good introduction IMHO:

David E. Shaw, Martin M. Deneroff, Ron O. Dror, Jeffrey S. Kuskin, Richard H.
Larson, John K. Salmon, Cliff Young, Brannon Batson, Kevin J. Bowers, Jack C.
Chao, Michael P. Eastwood, Joseph Gagliardo, J.P. Grossman, C. Richard Ho,
Douglas J. Ierardi, István Kolossváry, John L. Klepeis, Timothy Layman,
Christine McLeavey, Mark A. Moraes, Rolf Mueller, Edward C. Priest, Yibing
Shan, Jochen Spengler, Michael Theobald, Brian Towles, and Stanley C. Wang,
"Anton, A Special-Purpose Machine for Molecular Dynamics Simulation,"
Communications of the ACM, vol. 51, no. 7, July 2008, pp. 91–97. Text

And there is even a free link on their website.


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