[gmx-users] General conceptual question about advantage of GPUs

[Mark Abraham]

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" <jalemkul at vt.edu> wrote:

> On Tue, Apr 9, 2013 at 11:38 AM, Andrew DeYoung <adeyoung at 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?
> >
> >
> 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 ~150,000 atoms on a single GPU card (which is somewhat outdated) and can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
>
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