[gmx-users] Multi-level parallelization: MPI + OpenMP
germaneau at sjtu.edu.cn
Tue Jul 23 03:25:11 CEST 2013
I'm making some tests using 2 ranks/node, what I was trying to do.
It seems working now, thank you.
On 07/19/2013 08:56 PM, Szilárd Páll wrote:
> 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
> 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
>> 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,
>> /Be the change you wish to see in the world
>> / --- Mahatma Gandhi ---
>> Éric Germaneau <http://hpc.sjtu.edu.cn/index.htm>
>> Shanghai Jiao Tong University
>> Network & Information Center
>> room 205
>> Minhang Campus
>> 800 Dongchuan Road
>> Shanghai 200240
>> View Éric Germaneau's profile on LinkedIn
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/Be the change you wish to see in the world
/ --- Mahatma Gandhi ---
Éric Germaneau <http://hpc.sjtu.edu.cn/index.htm>
Shanghai Jiao Tong University
Network & Information Center
800 Dongchuan Road
View Éric Germaneau's profile on LinkedIn
/Please, if possible, don't send me MS Word or PowerPoint attachments
Why? See: http://www.gnu.org/philosophy/no-word-attachments.html/
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