[gmx-users] Running job on GPUs

[Mark Abraham]

On Fri, Jul 11, 2014 at 12:18 PM, Nidhi Katyal <nidhikatyal1989 at gmail.com>
wrote:

> Hello all
>
> I am trying to run my job on 2 nodes by utilizing all available cores. On
> each node of the cluster, we have two GPUs and two sockets with 8 cores
> each.
> Every time I am submitting the job, we find that it is running on one node.
> How to make use of the other node?
>
> Till now, I have used following trial commands as suggested in
> http://www.gromacs.org/Documentation/Acceleration_and_parallelization
>
> 1)  mpirun -n 2 mdrun_mpi -v -deffnm nvt -ntomp 16
>
> output:
>
> Using 2 MPI processes
> Using 16 OpenMP threads per MPI process
>
> WARNING: Oversubscribing the available 16 logical CPU cores with 32
> threads.
>          This will cause considerable performance loss!
>
> 2)  mpirun -n 4 mdrun_mpi -v -deffnm nvt -ntomp 8
>
> output:
>
> Incorrect launch configuration: mismatching number of PP MPI processes and
> GPUs per node.
> mdrun_mpi was started with 4 PP MPI processes per node, but only 2 GPUs
> were detected.
>
> I understand that the above error comes when number of MPI ranks is not a
> multiple of number of GPUs intended to be used. But in my case 4 is a
> multiple of 2.
>
> 3) mpirun -n 4 -npernode 2 mdrun_mpi -v -deffnm nvt
>
> The job still runs on 1 node.
>

That can only be because your options to mpirun and local settings specify
that. mdrun_mpi uses all of whatever mpirun has given it. Consult the
mpirun docs for -n and -npernode and seek alternatives.

Mark


>
> How can I run my job on 2 nodes utilizing all cores and GPUs?
>
> Thanks
> Nidhi
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