[gmx-users] hybrid CPU/GPU nodes

Gloria Saracino glosara at yahoo.it
Mon Feb 24 09:09:09 CET 2014

We would get one/two nodes completely dedicated to molecular dynamics with GPU
and we had originally thought to 

2 x Xeon 6-Core E5-2630v2 2,6Ghz 15MB + 2 x NVIDIA Tesla K20C
but probably the CPU cores should be doubled and 

In addition one/two nodes completely CPU
for other software that does not use GPU but still suitable for molecular dynamics
with 4 x AMD Opteron 16-Core 6272 2,1Ghz 115W.
All nodes would be connected with infiniband.



 Da: Szilárd Páll <pall.szilard at gmail.com>
A: Gloria Saracino <glosara at yahoo.it>; Discussion list for GROMACS users <gmx-users at gromacs.org> 
Inviato: Venerdì 21 Febbraio 2014 16:05
Oggetto: Re: [gmx-users] hybrid CPU/GPU nodes

Please keep the discussion on the mailing list.

You have still not described what exactly you want to accomplish. Get
new nodes? Upgrading machines with GPUs?

On Fri, Feb 21, 2014 at 10:12 AM, Gloria Saracino <glosara at yahoo.it> wrote:
> Thank you very much for your suggestions ... we have to have to keep an eye
> on expenses.
> The vendor proposed us to mount two GPU on the same node, but having
> multiple GPUs on the same node could be beneficial?

Multiple GPUs in a node can be beneficial.

> In this case the number of CPUcores should be increased accordingly?

In fact, typically one GPU per CPU (socket) is a good balance, but as
I said before, this greatly depends on the kind of CPUs and GPUs used.

> We would like to use these nodes to simulate large multi-molecules systems
> in explicit water and treating electrostatic interactions with PME. The aim
> is to gradually increase dimensions and simulation times starting from about
> 200.000 grains of CG force field that is about 800.000 atoms in all-atom ff.

That sounds like a decent candidate for running on GPUs. However, you
did not mention what network you have either.


> Bye,
> Gloria
> ________________________________
> Da: Szilárd Páll <pall.szilard at gmail.com>
> A: Discussion list for GROMACS users <gmx-users at gromacs.org>; Gloria
> Saracino <glosara at yahoo.it>
> Inviato: Venerdì 21 Febbraio 2014 1:10
> Oggetto: Re: [gmx-users] hybrid CPU/GPU nodes
> Hi,
> Unfortunately the answer is not as simple as "use 6-8 cores and you'll
> be fine". Balanced hardware from the GROMACS perspective depends
> greatly on what kind of CPUs and GPUs are used as on the type of
> simulations you plan to run (system size, cut-off, single-node or
> multi-node, etc.).
> If budget is not a strong limiting factor, I'd suggest dual-socket
> Xeon Ivy Bridge nodes with 8-12 cores and Tesla K20/K40 or if you want
> to avoid spending $5k on a single card Geforce TITAN Black and 780 Ti
> can match and even beat the Teslas.
> No advertisement intended, but one thing that can help you is to try
> the "GPU Test drive" which will allow you to test actual hardware.
> AFAIK they even have pre-installed GROMACS, but I can't vouch for the
> correctness of the installations.
> Feel free to post concrete hardware specs you are considering and log
> files of test too if you'll have any.
> Cheers,
> --
> Szilárd
> On Thu, Feb 20, 2014 at 2:44 PM, Gloria Saracino <glosara at yahoo.it> wrote:
>> Hallo,
>> we are evaluating the possibility of expanding our cluster with hybrid
>> CPU/GPU node. Which could be the better proportion CPUcores/GPU on the same
>> nodeto obtain the best performance of Gromacs 4.6?
>> Thank you in advance,
>> Gloria Saracino
>> --
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