[gmx-users] Gomacs and multiple GPU

Alexis Michon alexis.michon at ibcp.fr
Thu Dec 1 17:16:57 CET 2016


Hi,

Thank for you reply. Yes, i have read them and know them. I use them
will success with other software.

My first and main problem is mdrun doesn't see the second GPU on the
system. And i try to find the root cause of and the remediation.

Hardware is a bi xeon with 2 Titan-xp GPU,  so my goal is to run 2
differentes simulations with two mdrun process each with one dedicated GPU.

Do you have any idea ?

Cheers
Alexis

On 01/12/16 16:38, Szilárd Páll wrote:
> 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/
>>>> Empreinte : C9:45:2D:7C:79:7F:0B:79:CA:C8:0B:68:41:A2:8C:EE:EA:72:82:34
>>>>
>>>>
>>>> --
>>>> Gromacs Users mailing list
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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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-- 
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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