[gmx-users] Gomacs and multiple GPU
Alexis Michon
alexis.michon at ibcp.fr
Thu Dec 1 18:13:26 CET 2016
Hi,
You solve my problem, Thank you.
The variable CUDA_VISIBLE_DEVICES is set up by the scheduler at the
running time of my job. So after adding commandline "unset
$CUDA_VISIBLE_DEVICES" in my script, mdrun detect and use both GPUs.
Thank you for your patience.
Cheers,
Alexis
On 01/12/16 17:53, Szilárd Páll wrote:
> Hi,
>
> Do any other programs, e.g. CUDA SDK samples (like deviceQuery) detect
> both GPUs?
> I find it *very-very* unlikely that only mdrun would not be able
> detect both GPUs.
>
> Again, are you sure it's not the use of CUDA_VISIBLE_DEVICES that
> creates the confusion? Please share your full command line (with env
> vars an all) and resulting log output?
>
> Cheers,
> --
> Szilárd
>
>
> On Thu, Dec 1, 2016 at 5:10 PM, Alexis Michon <alexis.michon at ibcp.fr> wrote:
>> 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
>>>>>>
>>>>>>
>>>>>> --
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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
>>
>>
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>>
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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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