[gmx-users] Gromacs 2018 and GPU

Fri May 4 20:12:20 CEST 2018

On 5/4/18 2:11 PM, paul buscemi wrote:
> 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 ?

Just look for "GPU" and you'll find it.

-Justin

> 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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>> -- 
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>>
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu <mailto:jalemkul at vt.edu> | (540) 231-3129
>> http://www.thelemkullab.com <http://www.thelemkullab.com/>
>>
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-- 
==================================================

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

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================