[gmx-users] Job Submission script for Multiple nodes GPUs calculation

[Carsten Kutzner]

Hi,

On 22 Aug 2014, at 01:38, Xingcheng Lin <linxingcheng50311 at gmail.com> wrote:

> Good afternoon,
> 
> I am trying to use multiple nodes to do GPU simulation, each node has two
> GPUs and 12 CPUs mounted. Is there any submission script for doing that?
> 
> For single node I used:
> 
> mpiexec -np 2 mdrun_mpi -s run.tpr -cpi state.cpt -cpo state.cpt -noappend
> -gpu_id 01 -nb gpu -ntomp 6
> 
> For 2 nodes I cannot use the script like
> 
> mpiexec -np 4 mdrun_mpi -s run.tpr -cpi state.cpt -cpo state.cpt -noappend
> -gpu_id 0123 -nb gpu -ntomp 6
The -gpu_id string refers to the GPU id’s _per node_, so you should also
use -gpu_id 01 on two and more of these nodes.

Best,
  Carsten



> 
> Any suggestion about what I should do?
> 
> Thank you,
> 
> Arrow
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--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/grubmueller/kutzner
http://www.mpibpc.mpg.de/grubmueller/sppexa