[gmx-users] Multi-level parallelization: MPI + OpenMP

[Szilárd Páll]

Depending on the level of parallelization (number of nodes and number
of particles/core) you may want to try:

- 2 ranks/node: 8 cores + 1 GPU, no separate PME (default):
  mpirun -np 2*Nnodes mdrun_mpi [-gpu_id 01 -npme 0]

- 4 ranks per node: 4 cores + 1 GPU (shared between two ranks), no separate PME
  mpirun -np 4*Nnodes mdrun_mpi -gpu_id 0011 [-npme 0]

- 4 ranks per node, 2 PP/2PME: 4 cores + 1 GPU (not shared), separate PME
  mpirun -np 4*Nnodes mdrun_mpi [-gpu_id 01] -npme 2*Nnodes

- at high parallelization you may want to try (especially with
homogeneous systems) 8 ranks per node

Cheers,
--
Szilárd


On Fri, Jul 19, 2013 at 4:35 AM, Éric Germaneau <germaneau at sjtu.edu.cn> wrote:
> Dear all,
>
> I'm note a gromacs user,  I've installed gromacs 4.6.3 on our cluster and
> making some test.
> Each node of our machine has 16 cores and 2 GPU.
> I'm trying to figure how to submit efficient multiple nodes LSF jobs using
> the maximum of resources.
> After reading the documentation
> <http://www.gromacs.org/Documentation/Acceleration_and_parallelization#Locking_threads_to_physical_cores>
> on "Acceleration and parallelization" I got confused and inquire some help.
> I'm just wondering whether someone with some experiences on this matter.
> I thank you in advance,
>
>                                                 Éric.
>
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>
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