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.mic...@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.mic...@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.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. -- 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.