[gmx-developers] Running Gromacs on GPUs on multiple machines

[Mark Abraham]

On May 29, 2014 4:53 PM, "Vedran Miletić" <rivanvx at gmail.com> wrote:
>
> 2014-05-29 16:36 GMT+02:00 Anders Gabrielsson <andgab at kth.se>:
> > You'll probably have to supply -npernode/-ppn too so that your mpirun
> > doesn't put all MPI ranks on the same host.
> >
> > /Anders
> >
> > On 29 May 2014, at 13:17, Vedran Miletić <rivanvx at gmail.com> wrote:
> >
> > Fatal error:
> > Incorrect launch configuration: mismatching number of PP MPI processes
> > and GPUs per node.
> > mdrun_mpi was started with 5 PP MPI processes per node, but you
provided 1
> > GPU.
>
> Hi Anders,
>
> thanks for your response. Weirdly enough, mpirun actually doesn't run
> processes all on one node, it distributes them as equally as possible,
> going around your hostfile in a round-robin fashion. (I verified this
> by running hostname.)

What were the hostnames? There is some logic that tries to reconstruct the
nodes from hostnames as supplied by MPI, but GROMACS assumes the form

yourmachinename043

with the digits varying across nodes. So far, this has worked, since
sysadmins are orderly types... IIRC we use a hash in GROMACS 5, or at least
we talked about it!

Mark

> However, it seems that for some reason Gromacs assumes mpirun does run
> 5 processes on a single node. Regardless, i tried
>
> mpirun -np 5 -npernode 1 -hostfile ... mdrun_mpi -v -deffnm ... -gpu_id 0
>
> but it produces the same error. Anything else I could try?
>
> Regards,
> Vedran
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