[gmx-users] RE: Looking for GPU benchmarks

[Mathieu38]

Hi,

 

Thanks for your answer.

 

The thing is that I am a benchmarker and I have no knowledge of the
physics behind GROMACS. My goal is to demonstrate the interest (or not)
in using GPUs for a customer test case.

 

So my idea would be to do one run using the CPU only version of GROMACS,
then modify the input file to add “cutoff-scheme = Verlet” and run the
GPU version.

 

I am not sure how to modify any other parameters without changing the
physics of the problem.

 

Regards,

 

 

Mathieu Dubois

 

Hardware Accelerators expert

Applications & Performances Team

tel : +33 (0)4.76.29.70.56

BULL, Architect of An Open World

http://www.bull.com

 

P Pensez à l’environnement avant d’imprimer / Before printing, think
about the environment.

 

 

 

De : Szilárd Páll [via GROMACS] <ml-node+s5086n5000577h4 at n6.nabble.com>
[mailto:Szilárd Páll [via GROMACS]
<ml-node+s5086n5000577h4 at n6.nabble.com>] 
Envoyé : lundi 27 août 2012 17:26
À : Mathieu38 <mathieu.dubois at bull.net>
Objet : Re: Looking for GPU benchmarks

 


Which system did you run? What settings? 

A few tips: 
- Use CUDA 4.2 (5.0 on Kepler); 
- Have at least 10-20k atoms/GPU (and more to get peak GPU performance);
- Use the shortest cut-off possible to allow CPU-GPU load balancing; 
- Due to initial domain-decomposition/parallelization overhead, 
scaling from one to two GPUs is affected by this overhead. 
(- If load balancing is limited, try using multiple MPI ranks per GPU.) 

-- 
Szilárd 


On Mon, Aug 27, 2012 at 1:31 PM, Mathieu38 <[hidden email]> wrote: 


> I have tried the basic approcah of taking some of the input files that
are 
> provided with the sources of Gromacs or on the website, and adding the
line 
> 
> cutoff-scheme = Verlet 
> 
> in the grompp.mdp file 
> 
> However, I have not find a case where use of GPUs (2 MPI Tasks, 4
OpenMP 
> Threads per MPI tasks, 2 GPUs) lead to a significant speed up,
comparing to 
> a CPU only version using 8 cores on a single node. 
> 
> I don't know if this is because GPU implementation is still not
performant 
> or if this is because my test cases are unappropriate. 
> 
> Any help here would be very much appreciated. 
> 
> Thx 
> 
> 
> 
> 
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