Re: [gmx-users] Gomacs and multiple GPU

2016-12-02 Thread Alexis Michon
Hi,

Others software doesn't assist the user as gromacs, they don't use
CUDA_VISIBLE without an action by the user (with an option, or a
specific environnement variable), in case the use this variable they
wrote a bit more information, like what they detect and will be used. So
i was convince gromacs works in the same way even though you wrote in
your mail. sorry :(

Alexis

On 01/12/16 18:28, Szilárd Páll wrote:
> Hi,
>
> Welcome!
>
>> Thank for you reply. Yes, i have read them and know them. I use them
> will success with other software.
>
> BTW, what did you refer to here? It seems like you were focused on
> figuring out the detection issue and might have ignored my other
> recommendations on using multi (which incidentally would have solved
> the original issue too as well as would do correct job placement for
> you) and 2+ ranks per GPU?
> Cheers,
> --
> Szilárd
>
>
> On Thu, Dec 1, 2016 at 6:12 PM, Alexis Michon  wrote:
>> 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  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  
> 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  
>>> 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 

Re: [gmx-users] Gomacs and multiple GPU

2016-12-01 Thread Szilárd Páll
Hi,

Welcome!

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

BTW, what did you refer to here? It seems like you were focused on
figuring out the detection issue and might have ignored my other
recommendations on using multi (which incidentally would have solved
the original issue too as well as would do correct job placement for
you) and 2+ ranks per GPU?
Cheers,
--
Szilárd


On Thu, Dec 1, 2016 at 6:12 PM, Alexis Michon  wrote:
> 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  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  
 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  
>> 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.mic...@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!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://mail

Re: [gmx-users] Gomacs and multiple GPU

2016-12-01 Thread Alexis Michon
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  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  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  
> 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.mic...@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!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
 --
 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.mic...@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://ww

Re: [gmx-users] Gomacs and multiple GPU

2016-12-01 Thread Szilárd Páll
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  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  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  
 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.mic...@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!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>>> --
>>> 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.mic...@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!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send 
>>> a mail to gmx-users-requ...@gromacs.org.
>
> --
> 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,

Re: [gmx-users] Gomacs and multiple GPU

2016-12-01 Thread Alexis Michon
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  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  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.mic...@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.mic...@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.mic...@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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Re: [gmx-users] Gomacs and multiple GPU

2016-12-01 Thread 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  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  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.mic...@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!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-requ...@gromacs.org.
>
> --
> 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.mic...@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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Re: [gmx-users] Gomacs and multiple GPU

2016-12-01 Thread Alexis Michon
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  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.mic...@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!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.

-- 
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.mic...@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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Re: [gmx-users] Gomacs and multiple GPU

2016-12-01 Thread Mark Abraham
Hi,

On Wed, Nov 30, 2016 at 5:38 PM Alexis Michon  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.mic...@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!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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Re: [gmx-users] Gomacs and multiple GPU

2016-11-30 Thread Nikhil Maroli
Hi,

It would be better if you provide more details such as the mdrun command
and  log file etc.
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