[gmx-users] AMD 32 core TR

[Tamas Hegedus]

Please provide more information.

If you use gmx 2018 then I think that gmx limits the gcc version to 6 
and not cuda 10.

You did not specify what type of and how many GPUs you use.

In addition, the choice of gmx for distributing computation could be 
also informative - you find this info in the log file.

It is also not clear what do you mean of 10% improvement: 8ns/day to 
26ns/day are the only numbers but it corresponds to 3x faster 
simulations and not 1.1x

In addition, I think if you have 49.5 ns/day for 137K atoms than 
26ns/day seems to be ok for 300K.

Bests, Tamas


On 1/3/19 6:11 PM, pbuscemi at q.com wrote:
> Dear users,
>
>   
>
> I had trouble getting suitable performance from an AMD 32 core TR.  By
> updating  all the cuda drivers and runtime to v10  and using gcc,g++ -6 from
> v5  -- I did try gcc-7 but Cuda 10 did not appreciate the attempt  --  and
> in particular removing  CUDA v7 runtime.), I was able to improve a 300k atom
> nvt run from 8 ns/day to 26 ns/day .  I replicated  as far as possible the
> Gromacs ADH benchmark with 137000 atoms-spc/e.  I could achieve an md of
> 49.5 ns/day. I do not have a firm grasp if this is respectable or not (
> comments ? )  but appears at least ok.   The input command was simply mdrun
> ADH.md   -nb gpu  -pme gp   ( and not using -ntomp or ntmpi which in my
> hands degraded performance ) .   To run the ADH  I replaced the two ZN ions
> in  ADH file from PDB ( 2ieh.pdb ) with CA ions  since ZN was not found in
> the OPLS data base in using pdb2gmx.
>
>   
>
> The points being ( 1) Gromacs appears reasonably happy with  the 8 core and
> 32 core Ryzen although ( again in my hands ) for these  smallish systems
> there is only about a 10% improvement between the two, and  (2) , as often
> suggested in the Gromacs literature, use the latest drivers possible
>
>   
>
>   
>
-- 
Tamas Hegedus, PhD
Senior Research Fellow
MTA-SE Molecular Biophysics Research Group
Hungarian Academy of Sciences  | phone: (36) 1-459 1500/60233
Semmelweis University          | fax:   (36) 1-266 6656
Tuzolto utca 37-47             | mailto:tamas at hegelab.org
Budapest, 1094, Hungary        | http://www.hegelab.org