[gmx-users] Gromacs 2018 and GPU

Mark Abraham mark.j.abraham at gmail.com
Fri May 4 18:58:04 CEST 2018


On Fri, May 4, 2018 at 6:43 PM paul buscemi <pbuscemi at q.com> wrote:

> I’ve been struggling for a for several days to get Gromacs-2018 to use my
> GPU.  I followed the INSTALL instructions ( several times ! ) that are
> provided in the 2018 tarball
> I know that the GPU ( GTX1080)  is installed properly in that it works
> with Schrodinger and the Nvidia self tests.  Gromacs runs the  MD from the
> University of Baltimore  lysozyme  example normally
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/
> <
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/>
> but only on the 8 threads of the  CPU

The tutorial explicitly addresses this. See

> Make test  indicates that it sees the GPU, but
> 1)  is there a way to definitively determine if the make commands were run
> properly or that Gromacs was installed properly with the GPU

To know that a simulation ran on the GPU, you must inspect the log file
that it wrote.

> 2) for a linux desktop system with one GPU,  a/the  proper command to run
> the lysozyme .  I ask since there is indication that with one GPU  (0) it
> will be dedicated to graphics.

If the display is sharing the GPU, then it shares the GPU (and performance
of either the display or the simulation might be affected). With only one
GPU, there's no option (unless your motherboard has a built-in GPU that
you'd prefer to use for the display).

> 3) is there an up to data set of install instructions for  Gromacs 2018
> and Nvidia 9.1 toolkit,  384.11 drivers ?

No, there's nothing unusual about that, so the generic instructions apply.


> Regards
> Paul
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