[gmx-users] Optimal Hardware for Gromacs

David van der Spoel spoel at xray.bmc.uu.se
Wed Apr 28 10:03:38 CEST 2010

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 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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