[gmx-users] Performance of GPU Workstation (GPU selection)

Szilárd Páll pall.szilard at gmail.com
Fri Dec 5 15:20:06 CET 2014

On Thu, Dec 4, 2014 at 10:35 PM,  <mail at 2718-mail.de> wrote:
> Zitat von Carsten Kutzner <ckutzne at gwdg.de>:
>> Are you planning to run a single copy of that MD system across the 4 GPUs?
>> I am not
>> sure that this will scale well.
>> I have benchmarked a ~80000 atom test system on a dual processor E5-2670v2
>> (altogether
>> 20 physical cores on a node @ 2.5 GHz) with 4x GTX 780Ti, which is
>> slightly faster than
>> the GTX 780. Even with this larger system I get 21, 46, 57, 61, 64 ns/day
>> using
>> 0, 1, 2, 3, 4 of the GPUs (at a 2 fs time step). So more than 2 GPUs does
>> not really
>> make sense here I would say.
> Well, probably 1 System per CPU for the small ones. The larger systems run
> here (~130k atoms (40000 water Molecules) get 38ns/day on 4 16 core nodes.
> Would the same performance be in reach with a 2 or 4 GPU node?

To "drive" four GPUs, be it 780 Ti or 980, you'll need a high-end pair
of Xeons rather than mid-range ones, e.g. at least something like E5
268x, preferably 269x v3, but v2 can be a good option too.

If you plan to do mostly GPUs accelerated runs, I suggest you to
consider Ivy Bridge (v2) Xeons, you may be able to find the 269x
models for a good price. These can actually give more ns/day/Eur
because Haswell Xeons throttle when running any AVX code, e.g. the E5
2898 with 2.3 GHz base clock will have only 1.9 GHz base clock when
running AVX code.

> If we decide to use just two GPUs, would it be better to upgrade to 2 GTX
> 980, or use stronger CPUs?

If you care about power consumption, go with the 980's, those consume
up to 33% less power. Otherwise, the 980 is 15-20% faster than the 780
Ti, which is quite reasonable for the extra ~20% cost (100 EUR or so)
- at the high end you often pay more for better performance. At the
same time, the CPU and GPU upgrade are not very comparable. Upgrading
to the CPU for the same amount of money (if it's even enough for a
2650v3) will bring you quite little performance benefit. However,
note, that if your runs are CPU bound, every bit of extra CPU
performance will translate to ns/day while a faster GPU may not have
much impact in these runs (hopefully this will change soon, perhaps
already in GROMACS 5.1).


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