[gmx-users] Gromacs 2018 and GPU

[paul buscemi]

thank you for the prompt response.  I will check out the link.  Regarding 2)  One can immediately determine if the GPU is/is  running since Gromacs tells you at the beginning - in my case - that the CPU’s being used and linux system monitor tells you that all CPU’s are running, - not to mention the fan speed, and nvidia-smi registers no GPU running

What I was asking was for the proper format for invoking the GPU .  I used 
gmx mdrun -deffnm md_0_1 -nb gpu     ##   this is from the lysozyme tutorial MD page
but this starts Gromacs using the CPU’s and was asking if this is a proper format for a single GPU.

thanks
Paul

> On 4,May 2018, at 11:57 AM, Mark Abraham <mark.j.abraham at gmail.com> wrote:
> 
> Hi,
> 
> On Fri, May 4, 2018 at 6:43 PM paul buscemi <pbuscemi at q.com <mailto: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
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/08_MD.html <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/08_MD.html>
> 
> 
>> 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.
> 
> Mark
> 
> 
>> 
>> Regards
>> Paul
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