[gmx-users] problems for GPU simulations

Szilárd Páll szilard.pall at cbr.su.se
Thu Feb 7 13:34:32 CET 2013

On Thu, Feb 7, 2013 at 10:16 AM, Albert <mailmd2011 at gmail.com> wrote:

> Hello:
>  I got a workstation with two GTX590 which have two core for each GPU. I
> can submit gromacs GPU jobs with command:
> mpirun  -np 4 mdrun .....
> with such running, I can get 26ns/day for Gromacs-4.6 beta version.
> However, I found that for Gromacs-4.6 final version (which is the latest
> one), it claimed that I only have two GPU, it asked me to adjust -np to 2.

Please make sure that nvididia-smi or the deviceQuery SDK tool show all
four GPUs. If that is the case and mdrun still shows only two, please file
a bug report with you OS info and a log file attached.


> so I submit the jobs with command:
> mpirun -np 2 mdrun...
> for the same system with the same paramters (of course the tpr file must
> be regenerated). I found that I can get only half of the speed, something
> around 10 ns/day.
> So I am just wondering what's happening?
> thank you very much
> best
> Albert
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