On Wed, Apr 10, 2013 at 4:24 PM, Szilárd Páll <szilard.p...@cbr.su.se> wrote: > Hi Andrew, > > As others have said, 40x speedup with GPUs is certainly possible, but more > often than not comparisons leading to such numbers are not entirely fair - > at least from a computational perspective. The most common case is when > people compare legacy, poorly (SIMD)-optimized codes with some new GPU > accelerated code that typically somebody just spent a lot of effort on. Of > course, performance improvement for the users of any code is beneficial, but > the way such achievements are pitched (and published), is IMHO rather > questionable. > > If you look around in the computing/computational science literature and try > to find the sound comparisons of highly (or at least comparably) tuned CPU > and GPU codes, you will mostly see around 3-10x speedup reported. There are > cases when the performance difference can be much more e.g solvers, random > number generators, and in general codes that are more suitable for GPUs and > can make use of the Teraflops of raw computational horsepower. For a CPU-GPU > comparison of "basic" algorithms you can have a look at this recent report > from NVIDIA in which you'll see that even BLAS is only 2-10x faster on GPUs: > http://goo.gl/I7ADg > > When it comes to GROMACS, you can expect 2-4x performance improvement (with > PME), but the numbers will depend a *lot* on simulation settings, hardware, > as well as system size. Besides Erik Lindahl's soon to be published > web-seminar, you can also have a look at related talks from the 2012 and > 2013 GTC conference.
It's just occurred to me that our talks from this year's GTC are not online yet, but they should be available in a few weeks. You can find them by searching for "gromacs" here: http://www.gputechconf.com/gtcnew/on-demand-gtc.php -- Szilárd > > > Finally, just a note on the ~5 ns/day on 24 CPU (cores I assume). I'm not > sure what exactly are you simulating, but the numbers seem to be rather low. > With a small solvated protein system of ~7000 atoms with vsites and 5 fs > time steps, on a single 6-core Core i7-3930K CPU I get 250 ns/day and by > adding a GeForce GTX 680 GPU I get 600 ns/day. Even with accounting for the > 2-2.5x performance difference due to longer time steps, this is still more > than an order of magnitude higher than what you get. If you really need > particle decomposition, you can consider using the Verlet scheme without > domain-decomposition with OpenMP multithreading parallelization which is > roughly equivalent with PD and runs efficiently on up to 24-32 threads on > Intel. > > Cheers, > -- > Szilárd > > > On Tue, Apr 9, 2013 at 5:38 PM, Andrew DeYoung <adeyo...@andrew.cmu.edu> > wrote: >> >> Hi, >> >> For the past 2 years I have been running Gromacs on a standard Linux >> cluster >> (with nodes containing 24 CPUs). As you know, Gromacs scales excellently >> (and is super efficient), and since the CPUs are Intel Xeon 2.4 GHz >> processors, the simulations run quite fast (I can run 10 ns of ~7000 atoms >> in ~2 days on 24 CPUs). Can I expect GPUs to be any or much faster than >> these CPUs? >> >> There is a rumor in the department that GPUs can give a performance >> increase >> of 10-40 times relative to CPUs, although that group is using another MD >> package. I am curious whether this performance improvement is typical. >> (I >> would not expect it for Gromacs, though, since Gromacs is already super >> fast!) >> >> If you have time, do you know of any review or opinion papers that might >> discuss the advantages (advantages of performance or otherwise) of using >> GPUs over CPUs? >> >> Thanks for your time! >> >> Andrew DeYoung >> Carnegie Mellon University >> >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> * Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
