[gmx-users] multiple GPU on multiple nodes

cyberjhon cyberjhon at hotmail.com
Tue Feb 4 16:10:44 CET 2014

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
> 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 
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?


John Michael

View this message in context: http://gromacs.5086.x6.nabble.com/multiple-GPU-on-multiple-nodes-tp5014085p5014279.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.

More information about the gromacs.org_gmx-users mailing list