[gmx-users] Optimal Hardware for Gromacs

[David van der Spoel]

On 4/28/10 9:38 AM, Igor Leontyev wrote:
> Hi,
> there is a question for hardware experts. What is the optimal hardware to
> achieve better scalability in parallel MD simulations of 10K-100K atoms?
>
> Probably, it should be a cluster of multi-cpu, multi-core units with fast
> interconnection. In this case, what is the optimal=performance/price
> configuration for the units? Or in greater details the choice should be:
> 1) Intel or AMD?
> 2) Server cpus (Xeon/Opteron) or Desktop cpus (i7/Phenom)?
> (The problem is that for the cheaper option (Desktop cpus) there is no
> multi-cpu
> motherboards available on a market. May be somebody knows the
> appropriate MB
> model.)
> 3) 4-, 6- or 8-core cpus? See Opteron 6134 which has 8 cores of 2.3 Ghz.
> 4) Is there network solution faster than 1 Gbps for a reasonable price?
>
> Or may be the optimum is some preassembled workstation or cluster
> available on a market for a reasonable price.
>
> Resuming the subject: what is the optimal hardware with a budget ~$10K?
> April 2010
>
Try finding a local vendor to sell you Supermicro based machines. $10k 
should get you roughly 4 dual quad core Intel or AMD with Infiniband 
network, 32 cores altogether in a rack (with some haggling). The 
machines with more cores per chip are usually overprized.

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Professor of Biology
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://folding.bmc.uu.se
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