[gmx-users] Running multiple Gromacs simulations on the same node

[Wes Barnett]

On Fri, Sep 8, 2017 at 12:00 AM, MING HA <mingtha at scarletmail.rutgers.edu>
wrote:

> Hi all,
>
>
> It may seem a bit weird, but I'm trying to run multiple Gromacs simulations
> simultaneously on the same node, and I specified each Gromacs simulation
> to use only 1 MPI process and 1 OMP thread. I'm doing this because I am
> trying to check how accurate my model can predict an application using a
> single thread and process.
>
> My question is: If, for example, I am running multiple Gromacs simulations
> simultaneously, each with 1 MPI process and 1 OMP thread,  on the same
> node, does each simulation use separate MPI processes and OMP threads,
> or are they shared?
>
>
> Sincerely,
> Ming


I think that depends on how your mpi library decides to assign threads. I
know there are some switches that you can pass to mpirun that modify this
behavior. mdrun also has the "-pin on" setting that can prevent threads
from moving around. See
http://www.gromacs.org/Documentation/Acceleration_and_parallelization#Pinning_threads_to_physical_cores

You could also try using the "-multi" and "-multidir" flags provided by
mdrun to run multiple simulations at the same time with one mdrun command.

-- 
James "Wes" Barnett
Postdoctoral Research Scientist
Department of Chemical Engineering
Kumar Research Group <http://www.columbia.edu/cu/kumargroup/>
Columbia University
w.barnett at columbia.edu
http://wbarnett.us