[gmx-users] Best step to run simulation over GPU?

Kutzner, Carsten ckutzne at gwdg.de
Fri Jul 24 10:35:58 CEST 2015


> On 24 Jul 2015, at 08:48, RJ <rajiv at kaist.ac.kr> wrote:
> Dear gmx,
> I have a single PC contains 24 threads with GTX 980Ti.
> I would like to know how do i run the 3 or 2 simulation in same time with above mentioned PC would have similar speed.
Simply try it out :)

It could be beneficial to use the -multi options of gmx mdrun
to start the multiple simulations. This way GROMACS would automatically
take care of proper process placement and pinning.

You could make a quick check with, e.g., mdrun -nsteps 5000 -resethway -multi …
to get a performance estimate for 2 and for 3 simulations.

There is more information about this on page 7 of


> I also read about -pin options but couldnt understand well. Moreover i run in default i get this error "The GPU has >25% less load than the CPU. This imbalance causes performance loss".
> Its much appreciated if you could provide some info about multi simulation. Thanks.
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Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302

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