[gmx-users] GPU error

Justin Lemkul jalemkul at vt.edu
Tue Mar 26 13:39:38 CET 2019

On 3/26/19 2:05 AM, RAHUL SURESH wrote:
> Hi Dr Mark
> System is pretty tiny only with 15000 atoms. 1 GpU is automatically
> selected.

You will certainly not benefit from trying to use multiple GPUs for such 
a small system.

> I get a note stating potentially sub-optimal launch configuration, gmx
> started with less pp Mpi process for node than GPUs available.
> So the use of GPU is automated depending on the size of the system?

mdrun will try to utilize everything it finds, and automatically tune 
for the best performance, but in your case you definitely only want to 
use 1 GPU.

> Also, I can find a line in the log file, "Binary not matching Hardware- you
> might be losing performance.
> Please help us understand this more.

The last message suggests you have not compiled GROMACS in the best way 
to maximize performance. At compilation, cmake will recommend what type 
of hardware optimization to use. Follow its suggestion, or simply do not 
override it with your own specification.



Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129


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