Indeed. New players will benefit from http://www.hpcwire.com/hpcwire/2011-12-13/ten_ways_to_fool_the_masses_when_giving_performance_results_on_gpus.html:-)
Mark On Apr 9, 2013 5:59 PM, "Justin Lemkul" <[email protected]> wrote: > On Tue, Apr 9, 2013 at 11:38 AM, Andrew DeYoung <[email protected] > >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? > > > > > You can try it out yourself for free and see: > > http://www.nvidia.com/object/gpu-test-drive.html?cid=gputestdrive > > I would expect better CPU performance, honestly. Have you done benchmarking > on your system to see if fewer processors actually achieve better > performance by eliminating some communication overhead? Using more > processors is not necessarily better. > > > > 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!) > > > > > Relative speedup depends heavily upon what is being compared. Gromacs has a > very fast baseline, so the relative speedup may not be as high as other > codes that are not as intrinsically fast on CPU :) The GPU performance of > Gromacs, in absolute terms, is very impressive. We run simulations of > ~150,000 atoms on a single GPU card (which is somewhat outdated) and can > achieve around 10 ns/day. Newer hardware would undoubtedly perform better. > > > > 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? > > > > > Hopefully very soon, Erik's webinar from last week will be posted online ( > http://www.gputechconf.com/page/gtc-express-webinar.html). I learned a lot > from it, and I suspect others will as well. There is plenty of literature > about GPU development in MD simulations, but again, be aware of unequal > comparisons and baselines. > > -Justin > > -- > > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) > 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list [email protected] > 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 [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
