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

[Andreas Baer]

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
>>
>