[gmx-users] Launching MPI/OpenMP hybrid run

Alexander Björling alex.bjorling at gmail.com
Tue Mar 4 13:08:12 CET 2014

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.

Any hints would be most appreciated,

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