[gmx-developers] Gromacs hardware

David spoel at xray.bmc.uu.se
Mon Apr 25 22:17:41 CEST 2005

On Mon, 2005-04-25 at 13:27 -0700, Brendan Moran wrote:
> Brendan Moran wrote:
> >  The benefit is parallelism, and preprogramming.  The opteron is going 
> > to be doing a lot of pushing variables around, and that takes time.  
> > An FPGA based processor might be able to handle that portion better, 
> > though it will never compare with the raw power available from a true 
> > CPU.
> I should point out that I never thought that the coprocessor would be 
> doing all the work.  It would just be a tool to operate the most time 
> consuming part of the gmx algorithm, as outlined by Erik

I don't want to discourage you, but you are probably aware of what the
competition looks like: I'm about to order some new Dual Opteron boxes,
with Dual Core chips. That'll give me 4 chips @ 2GHz in a 1U box. Such a
box would cost roughly $4000, depending on clock speed...

Assuming 1 FPGA does 1 flop per clock, you'd need roughly 15 of them to
be competitive with the 4 way Opteron box. So let's say you have the
design ready and it can go into production. How much would it cost to
produce a board with those? How many can you fit in on a regular PCI

You may also want to check the following hardware implementation:
> --
> Brendan Moran
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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