[gmx-users] Launching MPI/OpenMP hybrid run

[Mark Abraham]

On Tue, Mar 4, 2014 at 1:08 PM, Alexander Björling
<alex.bjorling at gmail.com>wrote:

> Dear users,
>
> I'm trying to run simulations on a cluster of nodes, each sporting two AMD
> Opteron 8-core CPU:s. I would like to have one MPI process on each CPU,
> with OpenMP threads on the 8 cores of each. I've compiled gromacs 5.0 with
> intel MPI and OpenMP enabled.
>
> To get it running I'm just using two nodes, so 4 MPI processes. I've been
> using various combinations of the type:
>
> mpirun -np 4 -perhost 2 gmx_mpi mdrun -ntomp 8 ...,
>
> but I never manage to get the MPI process spread out on the two nodes.
> Rather, in the example above, 4 MPI processes with 4 OpenMP threads each
> runs on the first node, and the second node does nothing.
>

mdrun will just work with whatever the MPI environment says exists, so I
would look to your mpirun docs to find out what you should do.

Mark


>
> Any hints would be most appreciated,
> Cheers,
> Alex
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