[gmx-users] multiple GPU on multiple nodes

[cyberjhon]

On Tue, Feb 4, 2014 at 1:51 AM, cyberjhon <cyberjhon@> wrote:
> Dear Szilárd
>
> Thanks for your answer.
>
> To submit the job I do;
>
> qsub -l nodes=2:ppn=16,walltime=12:00:00
>
> Then, to run gromacs I can do:
> aprun -n 1 mdrun_mpi -deffnm protein

>Those qsub and aprun commands are not in like with each other. Your
>submission requests 2 nodes and 16 ranks/processes per node, that this
>32 ranks in total. However, your aprun lauch requests only a single
>rank (and only two below). Please consult the machine's documentation
>on how to launch jobs correctly.

I now what you are saying, an I am agree with you. When I run gromacs using
only CPUs I do
 aprun -n 32 mdrun_mpi -deffnm protein 
And this works perfectly !!!

But when I am trying to use the GPUs in those two nodes, if I run this
command, I get the error that I told you before:

> -------------------------------------------------------
> Program mdrun_mpi, VERSION 4.6.2
> Source code file:
> /N/soft/cle4/gromacs/gromacs-4.6.2/src/gmxlib/gmx_detect_hardware.c, line:
> 356
>
> Fatal error:
> Incorrect launch configuration: mismatching number of PP MPI processes and
> GPUs per node.
> mdrun_mpi was started with 32 PP MPI processes per node, but only 1 GPU
> were
> detected.
> For more information and tips for troubleshooting, please check the
> GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ------------------------------------------------------- 

So according to this the problem is not in the aprun command, it looks like
the problem is in gromacs.
In your presentation 
http://www.gromacs.org/@api/deki/files/213/=gromacs_parallelization_acceleration.pdf
Page 49 you show that  you run gromacs in Blue waters in multiple nodes, and
base on the date you used 4.6.2, how you did that?

Thanks

John Michael

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