[gmx-users] Gromacs 2018 and GPU

[paul buscemi]

Thank you Justin. 

Not at the linux system at the moment, but is there anything in particular I should look for in the log file ?

Paul

> On 4,May 2018, at 12:55 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 
> 
> 
> On 5/4/18 1:48 PM, paul buscemi wrote:
>> 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.
> 
> With version 2018, you don't even need to use "-nb gpu," mdrun will automatically run on the GPU if it is detected properly. As Mark said, check your .log file for a full breakdown of how mdrun configured the simulation using the available hardware.
> 
> -Justin
> 
>> 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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