[gmx-users] Computer processor and graphics card choice
Guillem Prats Ejarque
Guillem.Prats.Ejarque at uab.cat
Sat Dec 3 02:13:00 CET 2016
> Hi Guillem,
> I can answer your last question - the 10xx series does indeed work well
> with GROMACS (currently running GROMACS 2016 with a GTX1070), although I
> would be inclined to get the GTX1070 if your budget can stretch to it.
>> 80k atom MEM Benchmark System - 2fs time step - gmx2016.B2
>> GTX1070 - i7 6700k 4.00 GHz - 4 core - 42 ns/day - net cost per node (pc
>> chassis) ~ 950 EUR
>> GTX1070 - Xeon E5 2630v4 2.20 - 10 core - 58 ns/day - net cost per node (19"
>> rack) ~ 1600 EUR
>> GTX1080 will give you about the same performance but it is much more expensive, GTX1060 (6GB) is about 10% slower
> Note that this does not apply in general; here it is (most likely) the
> case because this specific simulation (with the GROMACS version used)
> is CPU-bound already with the 1070. If the GPU is "fast enough" for
> the workload, it does not help usign a faster GPU. Take another system
> (e.g. a CHARMM setup) and you might see significant speedup with the
> The 1060 being only marginally slower is also specific to the load
> balance in the MEM benchmark! With some other workload that's more
> GPU-bound on the 1060 + whichever CPU you were referring to, the 1070
> will give much larger simulation speedup.
> Certainly, if ns/day/buck is a major consideration (rather than high
> perf per node), the 1060 or 1070 are better value for the money!
> CPU-wise, I think the 6700k, 6800k or 6850K would be better options.
> If you plan to have a second GPU, the 6700k and 6800k will not be
> ideal (too few PCI-E lanes to run both GPUs at full speed unless you
> get a special mobo). While the 2620v4 has 8 cores, it also has a low
> TDP, so it's unlikely those will run anything more than 2.5 GHz which
> won't be faster than six i7 cores at 3.3-3.5 GHz.
> If you don't need to buy right away, you might also consider the
> upcoming AMD CPUs which will be announced soon. Performance could end
> up being pretty good.
> The GTX 10xx series GPUs indeed work very well. Given the high clock
> the 1060 will certainly be faster than the 970. Andrew is right, the
> 1070 will give a further, significant bump in speed (>1.4x).
> (Note that these performance comparisons refer to the
> GPU-only/nonbonded kernel performance!)
> Hi Guille,
> I'm not an expert on this, but it'll also depend on what kind of MD
> simulations you want to run. Coarse-grained forcefields, for example,
> don't benefit much from a GPU.
> So what kind of simulations do you have in mind? Atomistic? QM/MM? How
> many particles? ...?
Thank you all for your valuable comments. Looking at that, the Xeon one really does not seem to be worth it. Regarding the other processors that you suggest, i7-6800K seems interesting to me. I do not plan to use more than one GPU. About the graphic card, probably I will choose the GTX1060(6GB), because GTX1070 is getting out of my budget.
Mostly, what I want to simulate is a protein-ligand complex on an AMBER forcefield, and also some QM/MM simulations. My system is small, between 30 to 50 thousand atoms. I don't know if it is more CPU or GPU-bound.
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