[gmx-users] Optimal hardware for running Gromacs

[Kutzner, Carsten]

Dear David,

I think you will find answers to many of your questions in the following
publication:

http://onlinelibrary.wiley.com/doi/10.1002/jcc.24030/full

Best,
  Carsten



> On 12 Mar 2016, at 02:52, David Berquist <berquist at buffalo.edu> wrote:
> 
> I'm looking into building a desktop computer for running Gromacs
> simulations.  I'd like to know how I should configure it to get the best
> performance possible for the price.
> 
> One example of something I might run on this system would be: simulate an
> ionic polymer of approximately 100k atoms for 1 millisecond.  Coarse
> grained atoms, using Martini force field.
> 
> I would be planning to spend something under $1500 on this system.
> 
> 
> 
> In regards to the graphics card, what factors are important?  I assume that
> the single precision Flop/s are a big factor, but what about memory
> bandwidth(on the card itself)?
> 
> I've noticed that Gromacs pages on GPUs tend to recommend nVidia cards,
> specifically those with CUDA Compute Capability 5.2.  But, AMD Radeon cards
> appear to offer the same processing power for far lower prices(or
> alternatively, significantly more processing power for the same price).
> 
> For example, the nVidia GTX 970 offers 3494 GFlop/s of single precision,
> and 109 GFlop/s of double precision.  It currently costs $290 at Newegg.
> On the other hand, the AMD Radeon R9 380 provides 3476.5 GFlop/s single
> precision, and 217.3 GFlop/s of double precision.  It currently costs $150
> on Newegg.
> 
> That's practically the same single precision, and nearly double the
> double-precision for around half the price.
> 
> Or, for about the same price as the nVidia GTX 970 I could get an AMD
> Radeon R9 390.  It provides 5120 GFlop/s of single precision and 640
> GFlop/s of double precision.  That costs $310 on Newegg.
> 
> That is, on paper, 46.5% more single precision performance, and 487% more
> double precision performance(nearly 5 times as much) for only a 6.9% higher
> price.
> 
> So, does Gromacs run a lot faster on nVidia GPUs?  Would the nVidia GTX 970
> provide similar or better performance than the AMD Radeon R9 390?
> 
> One more GPU Question; does Gromacs scale linearly across multiple graphics
> cards?   So, if I have two identical cards which offer 2000 GFlop/s
> performance each, would they both together perform about the same as a
> more-expensive single card which provides 4000GFlop/s(provided you have a
> fast enough CPU, of course)?
> 
> 
> 
> Now, how about the CPU performance?  Would it be better to spend a lot of
> my budget on a high-end GPU, and then go for a low cost CPU?  Something
> like an  AMD Athlon X4 860K Kaveri Quad-Core 3.7 GHz CPU?  Or would
> something like that bottleneck the performance of an nVidia GTX 970 or GTX
> 980?  Maybe a AMD FX-6300 Vishera 6-Core 3.5 GHz?  AMD FX-8300 Vishera
> 8-Core 3.3GHz?
> Does Intel vs AMD make any significant difference?  When running Gromacs on
> a system with GPU compute turned on, what sort of computing load does
> Gromacs put on the CPU?  Is there any commonly used CPU benchmark that can
> be used to approximate relative Gromacs performance between CPUs?
> 
> 
> 
> How important is the system RAM speed?  Should I spend more of my budget
> building a DDR4 system(more expensive CPU, motherboard, and RAM modules),
> or would that not make a significant difference over DDR3?
> 
> Would you happen to know what quantity of memory should be sufficient for
> common Gromacs simulation runs, or runs such as the example I included
> above?
> 
> 
> Finally, does the speed of the hard drive impact Gromacs performance?  The
> options are a cheap spinning-platter hard drive(100-200MB/s sequential
> write), a low-cost SSD(400-500MB/s sequential write), or a high-speed PCI-E
> SSD(1000-1500MB/s sequential write).  Would writing out the data(.xtc,
> .trr, .edr) to a slower hard drive(100-200MB/s sequential write speed)
> cause the Gromacs simulation to slow down?
> I don't see any reason that a cheap spinning platter hard drive would slow
> Gromacs simulations down, but I want to make sure I'm not missing
> anything.
> 
> Thank you for your time.  I'd be very grateful for any information you can
> give me, or direct me to.
> 
> David Berquist
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