[gmx-users] GROMACS-4.6.3 CUDA version on multiple nodes each having 2 GPUs

[Carsten Kutzner]

Hi,

if you run on a single node with 2 GPUs, this command line should work:

> mpirun -np 2  mdrun -v -deffnm $configfile

If you run on two nodes, try this:
mpirun -np 4 mdrun

Choosing -np equal to the total number of GPUs should work (although it might
not be the best option performance-wise).

For a better performance you can try
mpirun -np 4 mdrun -gpu_id 0011    on a single node
or
mpirun -np 8 mdrun -gpu_id 0011    on two nodes

Carsten


On Nov 13, 2013, at 7:55 PM, "Prajapati, Jigneshkumar Dahyabhai" <j.prajapati at jacobs-university.de> wrote:

> Hello,
> 
> I am trying to run MPI, OpenMP and CUDA enable GROMACS 4.6.3 on nodes having 12 cores (2 CPUs) and 2 GPUs (Tesla M2090) each. The problem is when I launch job GROMCAS is using only GPUs on first node come across and failing to use GPUs on other nodes.
> 
> The command I used for two gpu enable nodes was,
> 
> mpirun -np 2  mdrun -v -deffnm $configfile
> 
> I tried with many other options but none of them worked. The one thing needs to remember here is that on all the nodes, GPUs got id 0 and 1 so -gpu_id option also didn't work.
> 
> This old thread gave me some idea but I didn't understand it completely.
> http://lists.gromacs.org/pipermail/gmx-users/2013-March/079802.html
> 
> Please suggests me the possible solutions for this issue.
> 
> Thank you
> --Jignesh
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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