[gmx-users] Gomacs and multiple GPU

[Szilárd Páll]

Alexis,

What is the problem? Have you read the relevant docs of what
CUDA_VISIBLE_DEVICES does?
https://docs.nvidia.com/cuda/cuda-c-programming-guide/#env-vars


BTW,  you can use, but you *do not need* CUDA_VISIBLE devices to
control the mapping of GPU(s) to mdrun process, the -gpu_id variable
(or equivalent env var) alone is enough.

To run multiple processes per node, do consider:
- using mdrun -multi
- using 2 or more mdrun runs per GPU

You can find the reason, motivating performance examples, and sample
commands here (in particular Fig 5 and related section):
dx.doi.org/10.1002/jcc.24030

Cheers,
--
Szilárd


On Thu, Dec 1, 2016 at 3:38 PM, Alexis Michon <alexis.michon at ibcp.fr> wrote:
> Hi,
>
> thank you for your answer
>
> the Cmdline is:
> gmx mdrun  -deffnm nvt
>
> I played a bit with option -gpu_id, use $CUDA_VISIBLE_DEVICES  and read
> the page http://www.gromacs.org/GPU_acceleration without any succes. One
> output is in nvt.log.11,
>
> nvidia-smi returs is in  nvidia-smi.log
>
> Nvidia-smi detect 2 GPUs, but not mdrun.
>
> nvidia-smi.log : https://icloud.ibcp.fr/index.php/s/08jqFsZpWNlSUGh
> nvt.log : https://icloud.ibcp.fr/index.php/s/vC5UxCCAhyw9FuC
>
> Alexis
>
>
>
> On 01/12/16 11:34, Mark Abraham wrote:
>> Hi,
>>
>> On Wed, Nov 30, 2016 at 5:38 PM Alexis Michon <alexis.michon at ibcp.fr> wrote:
>>
>>> Hello,
>>>
>>> We have build gromacs 2016.1 from source with "DMX_GPU=on" on a bi
>>> processor bi GPU machine, mdrun detect and run fine on only 1 GPU. How
>>> could we force mdrun to detect the second GPU ?
>>>
>> If it's compatible, powered and supported by your driver, then mdrun will
>> find it. Presumably nvidia-smi tool will help you work out what's going on.
>>
>> We would like to run 2 mdrun instances on a machine equiped with 2 GPUs,
>>> each mdrun will use 1GPU. How could we tell  mdrun to use a specific GPU ?
>>>
>> Guidance is here
>> http://manual.gromacs.org/documentation/2016.1/user-guide/mdrun-performance.html#examples-for-mdrun-on-one-node
>>
>> Mark
>>
>>
>>> Cheers,
>>> Alexis
>>>
>>> --
>>> Citation : "It’s not enough to be busy; so are the ants. The question is:
>>> what are we busy about?" - Henry David Thoreau
>>> Alexis MICHON, responsable informatique
>>> CNRS IBCP, 7 passage du vercors, 69007 LYON, France
>>> Mail : alexis.michon at ibcp.fr  Tel : 04.72.72.26.03 - 06.27.56.34.80
>>> CNRS IBCP - UMS 5760 - http://www.ibcp.fr/
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>>>
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> --
> Citation : "It’s not enough to be busy; so are the ants. The question is: what are we busy about?" - Henry David Thoreau
> Alexis MICHON, responsable informatique
> CNRS IBCP, 7 passage du vercors, 69007 LYON, France
> Mail : alexis.michon at ibcp.fr  Tel : 04.72.72.26.03 - 06.27.56.34.80
> CNRS IBCP - UMS 5760 - http://www.ibcp.fr/
> Empreinte : C9:45:2D:7C:79:7F:0B:79:CA:C8:0B:68:41:A2:8C:EE:EA:72:82:34
>
>
>
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