[gmx-users] Optimal Hardware for Gromacs

Alexey Shvetsov alexxyum at gmail.com
Sun May 2 10:32:50 CEST 2010


Actualy suppermicro offers 4 socket machines with 12-core amd cpus so you
get 48cores in 1U
GROMACS perform well on such hardware =)

In case of using Infiniband you need IB switch of dual port ib cards (to
connect machines as a 1d torus)

2010/4/28 David van der Spoel <spoel at xray.bmc.uu.se>

> 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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Best Regards,
Alexey 'Alexxy' Shvetsov
Petersburg Nuclear Physics Institute, Russia
Department of Molecular and Radiation Biophysics
Gentoo Team Ru
Gentoo Linux Dev
mailto:alexxyum at gmail.com
mailto:alexxy at gentoo.org
mailto:alexxy at omrb.pnpi.spb.ru
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