[gmx-users] Running job on GPUs
mark.j.abraham at gmail.com
Fri Jul 11 16:43:53 CEST 2014
On Fri, Jul 11, 2014 at 12:18 PM, Nidhi Katyal <nidhikatyal1989 at gmail.com>
> 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
> 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
> 1) mpirun -n 2 mdrun_mpi -v -deffnm nvt -ntomp 16
> Using 2 MPI processes
> Using 16 OpenMP threads per MPI process
> WARNING: Oversubscribing the available 16 logical CPU cores with 32
> This will cause considerable performance loss!
> 2) mpirun -n 4 mdrun_mpi -v -deffnm nvt -ntomp 8
> 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.
> How can I run my job on 2 nodes utilizing all cores and GPUs?
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