[gmx-users] GPU/CPU perfomance loss

[Mark Abraham]

Hi,

And it's very CPU bound because the processor is fairly antiquated and the
GPU fairly recent. Current versions of GROMACS can't work very well in that
situation.

Mark

On Tue, 10 May 2016 20:18 Szilárd Páll <pall.szilard at gmail.com> wrote:

> Hi Justin,
>
> Your run is simply *very* CPU-bound. Your GPU is so much faster than the
> CPU that even after increasing the cut-off to 2 nm to shift PME load away
> from the CPU, there is still a lot of GPU idling.
>
> For details, please have a look at on of our recent papers, e.g.
>
> http://arxiv.org/abs/1506.00716
>
> http://arxiv.org/abs/1507.00898
>
> Cheers,
>
> --
> Szilárd
>
> On Mon, May 9, 2016 at 7:00 PM, Van Zyl, J, Mnr <justinvz at sun.ac.za> <
> justinvz at sun.ac.za> wrote:
>
> > Good day,
> >
> >
> > I am running simulations from a workstation and keep getting a gromacs
> > note at the end of the run saying "The GPU has >25% less load than the
> CPU.
> > This imbalance causes performance loss."
> >
> >
> > I have read a previous post pertaining to this problem but the only thing
> > that seems to increase performance is by changing nstlist from 150 to 20
> > however the gromacs note still shows. I will post the log file of that
> run
> > soon however below is the log file of the first run:
> >
> > http://pastebin.com/3CUDh960
> >
> >
> > Is there anything I can do to increase perfomance or is this simply as
> > good as it will get for my system (22467 atoms)?
> >
> >
> > Thanks for the help,
> >
> > Regards,
> >
> > Justin van Zyl
> >
> > [http://pastebin.com/i/facebook.png]<http://pastebin.com/3CUDh960>
> >
> > md_1.log - Pastebin.com<http://pastebin.com/3CUDh960>
> > pastebin.com
> >
> >
> >
> >
> > Justin van Zyl
> > MSc. Candidate
> > Department of Chemistry and Polymer Science,
> > Stellenbosch University, Private Bag X1 Matieland,
> > 7602, South Africa
> > Cell: +27 72 9372 755
> > justinvz at sun.ac.za<mailto:rueben at sun.ac.za>
> > http://www.klumperman-group.net/
> >
> > --
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