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 <[email protected]> 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 > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to [email protected]. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
