[gmx-users] Gromacs 2018 and GPU

[Justin Lemkul]

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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-- 
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Justin A. Lemkul, Ph.D.
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Virginia Tech Department of Biochemistry

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