[gmx-users] Performance issues with Gromacs 2020 on GPUs - slower than 2019.5

[Szilárd Páll]

Hi,

Can you please check the performance when running on a single GPU 2019 vs
2020 with your inputs?

Also note that you are using some peculiar settings that will have an
adverse effect on performance (like manually set rlist disallowing the dual
pair-list setup, and nstcalcenergy=1).

Cheers,

--
Szilárd


On Wed, Feb 26, 2020 at 4:11 PM Andreas Baer <andreas.baer at fau.de> wrote:

> Hello,
>
> here is a link to the logfiles.
>
> https://faubox.rrze.uni-erlangen.de/getlink/fiX8wP1LwSBkHRoykw6ksjqY/benchmarks_2019-2020
>
> If necessary, I can also provide some more log or tpr/gro/... files.
>
> Cheers,
> Andreas
>
>
> On 26.02.20 16:09, Paul bauer wrote:
> > Hello,
> >
> > you can't add attachments to the list, please upload the files
> > somewhere to share them.
> > This might be quite important to us, because the performance
> > regression is not expected by us.
> >
> > Cheers
> >
> > Paul
> >
> > On 26/02/2020 15:54, Andreas Baer wrote:
> >> Hello,
> >>
> >> from a set of benchmark tests with large systems using Gromacs
> >> versions 2019.5 and 2020, I obtained some unexpected results:
> >> With the same set of parameters and the 2020 version, I obtain a
> >> performance that is about 2/3 of the 2019.5 version. Interestingly,
> >> according to nvidia-smi, the GPU usage is about 20% higher for the
> >> 2020 version.
> >> Also from the log files it seems, that the 2020 version does the
> >> computations more efficiently, but spends so much more time waiting,
> >> that the overall performance drops.
> >>
> >> Some background info on the benchmarks:
> >> - System contains about 2.1 million atoms.
> >> - Hardware: 2x Intel Xeon Gold 6134 („Skylake“) @3.2 GHz = 16 cores +
> >> SMT; 4x NVIDIA Tesla V100
> >>   (similar results with less significant performance drop (~15%) on a
> >> different machine: 2 or 4 nodes with each [2x Intel Xeon 2660v2 („Ivy
> >> Bridge“) @ 2.2GHz = 20 cores + SMT; 2x NVIDIA Kepler K20])
> >> - Several options for -ntmpi, -ntomp, -bonded, -pme are used to find
> >> the optimal set. However the performance drop seems to be persistent
> >> for all such options.
> >>
> >> Two representative log files are attached.
> >> Does anyone have an idea, where this drop comes from, and how to
> >> choose the parameters for the 2020 version to circumvent this?
> >>
> >> Regards,
> >> Andreas
> >>
> >
>
> --
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