Hi, I'm glad that it got figured out. For all those who might be wondering what exactly are you referring to here is a quick summary.
The NVIDIA driver needs /dev entries to be present for the GPU devices in use and these entries need the right permissions in order to allow user-space programs to access the devices (and the lack of permission was causing trouble in the above case). These entries are automatically created by the X server and the driver kernel module is also loaded when X starts. However, when using a headless (i.e server/without X) installation, what's otherwise automatically done by when X starts needs to be done manually. It is easiest to do it using an init script (or equivalent). For an example here's the init script I use on Ubuntu machines: http://pastebin.com/zs9Ve9qP. It works for me well, but use it at your own risk ;) Cheers, -- Szilárd On Thu, Mar 28, 2013 at 12:03 PM, Chandan Choudhury <iitd...@gmail.com>wrote: > Hi !! > > I problem with the permission of /dev/nvidia* > > changed it to 0666 /dev/nvidia* > > Everything resolved. mdrun can be executed as normal user. > > Thanks everyone. > > Chandan > > > > > -- > Chandan kumar Choudhury > NCL, Pune > INDIA > > > On Thu, Mar 28, 2013 at 4:26 PM, Chandan Choudhury <iitd...@gmail.com > >wrote: > > > > > On Thu, Mar 28, 2013 at 4:09 PM, Szilárd Páll <szilard.p...@cbr.su.se > >wrote: > > > >> Hi, > >> > >> If mdrun says that it could not detect GPUs it simply means that the GPU > >> enumeration found no GPUs, otherwise it would have printed what was > found. > >> This is rather strange because mdrun uses the same mechanism the > >> deviceQuery SDK example. I really don't have a good idea what could be > the > >> issue, but you could try recompiling or compiling with CUDA 4.2 to see > if > >> any of that makes a difference. > >> > >> Let us know if you figured out something. > >> > >> Cheers, > >> > > > > Thanks Szilárd for the eye opening comment. > > > > I just tried running gromacs as root. I recalled I had executed > > deviceQuery as root. While executing as user it produces the same error : > > > > */root/NVIDIA_CUDA-5.0_Samples/1_Utilities/deviceQuery/deviceQuery > > Starting... > > > > CUDA Device Query (Runtime API) version (CUDART static linking) > > > > cudaGetDeviceCount returned 38 > > -> no CUDA-capable device is detected* > > > > Now, running gromacs as root, it is running successfully (I suppose). > > > > Output of nvidia-smi > > > > > > +------------------------------------------------------+ > > > > | NVIDIA-SMI 4.310.40 Driver Version: 310.40 > > | > > > > > |-------------------------------+----------------------+----------------------+ > > | GPU Name | Bus-Id Disp. | Volatile Uncorr. > > ECC | > > | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util > Compute > > M. | > > > > > |===============================+======================+======================| > > | 0 NVS 300 | 0000:03:00.0 N/A | > > N/A | > > | N/A 48C N/A N/A / N/A | 3% 17MB / 511MB | N/A > > Default | > > > > > > > +-------------------------------+----------------------+----------------------+ > > | 1 Tesla K20c | 0000:04:00.0 Off | > > Off | > > | 50% 62C P0 106W / 225W | 2% 87MB / 5119MB | 76% > > Default | > > > > > > > +-------------------------------+----------------------+----------------------+ > > > > > > > > > +-----------------------------------------------------------------------------+ > > | Compute processes: GPU > > Memory | > > | GPU PID Process name > > Usage | > > > > > |=============================================================================| > > | 0 Not > > Supported | > > | 1 9127 mdrun_461 > > 72MB | > > > > > +-----------------------------------------------------------------------------+ > > > > Output of md.log > > > > 2 GPUs detected: > > #0: NVIDIA Tesla K20c, compute cap.: 3.5, ECC: no, stat: compatible > > #1: NVIDIA NVS 300, compute cap.: 1.2, ECC: no, stat: incompatible > > > > 1 GPU auto-selected for this run: #0 > > > > > > I think there is something relate to permissions. Though nvcc has 755 > > permission, something else might require additional permissions. > > > > Chandan > > > > > >> -- > >> Szilárd > >> > >> > >> On Thu, Mar 28, 2013 at 2:39 AM, Berk Hess <g...@hotmail.com> wrote: > >> > >> > > >> > Hi, > >> > > >> > I am not the expert on GPU detection, so we'll need to wait until an > >> > expert replies. > >> > Maybe GPU 0 is ignored and the GPUs are renumbered, could you try: > >> > mdrun -ntmpi 1 -gpu_id 0 > >> > > >> > Also your tpr file is from an older version. It will not run on a GPU. > >> > You need to set the mdp option: > >> > cutoff-scheme = Verlet > >> > and run grompp to get a new tpr file. > >> > > >> > Cheers, > >> > > >> > Berk > >> > > >> > > From: iitd...@gmail.com > >> > > Date: Thu, 28 Mar 2013 14:57:16 +0530 > >> > > Subject: Re: [gmx-users] no CUDA-capable device is detected > >> > > To: gmx-users@gromacs.org > >> > > > >> > > On Thu, Mar 28, 2013 at 2:41 PM, Berk Hess <g...@hotmail.com> > wrote: > >> > > > >> > > > > >> > > > Hi, > >> > > > > >> > > > The code compiled, so the compiler is not the issue. > >> > > > > >> > > > I guess mdrun picked up GPU 0, which it should have ignored. You > >> only > >> > want > >> > > > to use GPU 1. > >> > > > > >> > > > Could you try running: > >> > > > mdrun -ntmpi 1 -gpu_id 1 > >> > > > > >> > > > >> > > $mdrun_461 -ntmpi 1 -gpu_id 1 -s md0-25.tpr > >> > > Note: file tpx version 73, software tpx version 83 > >> > > > >> > > NOTE: Error occurred during GPU detection: > >> > > no CUDA-capable device is detected > >> > > Can not use GPU acceleration, will fall back to CPU kernels. > >> > > > >> > > > >> > > No GPUs detected > >> > > > >> > > > >> > > ------------------------------------------------------- > >> > > Program mdrun_461, VERSION 4.6.1 > >> > > Source code file: > >> > > /home/sudip/RPMs/gromacs-4.6.1/src/gmxlib/gmx_detect_hardware.c, > line: > >> > 580 > >> > > > >> > > Fatal error: > >> > > Some of the requested GPUs do not exist, behave strangely, or are > not > >> > > compatible: > >> > > GPU #1: inexistent > >> > > > >> > > > > >> > > > Cheers, > >> > > > > >> > > > berk > >> > > > > >> > > > > Date: Thu, 28 Mar 2013 10:51:58 +0200 > >> > > > > Subject: Re: [gmx-users] no CUDA-capable device is detected > >> > > > > From: g...@bioacademy.gr > >> > > > > To: gmx-users@gromacs.org > >> > > > > > >> > > > > Hi Chandan > >> > > > > > >> > > > > Are you using the same version of GCC compiler that you used to > >> > compile > >> > > > > CUDA 5.0? In my hands, gcc 4.7.2 could not compile CUDA 5.0 (I > >> think > >> > > > there > >> > > > > was some kind of incompatibility between the two). > >> > > > > >> > > > >> > > There is an work around with gcc 4.7.2. Please see > >> > > > >> > > >> > http://svshift.blogspot.in/2013/03/running-nvidai-cuda-sdk-50-on-opensuse.html > >> > > > >> > > > > >> > > > > Can you try compiling both CUDA 5.0 and GROMACS with gcc 4.6.1? > >> This > >> > > > > worked in my system (MacOS/Darwin). > >> > > > > > >> > > > > Just make sure to set the variables CC and CXX to point to the > >> right > >> > > > > compiler version when you run cmake. > >> > > > > > >> > > > > George > >> > > > > > >> > > > > > >> > > > > > Dear GMX Users, > >> > > > > > > >> > > > > > I am trying to execute Gromacs 4.6.1 on one of the GPU server: > >> > > > > > *OS*: OpenSuse 12.3 x86_64 3.7.10-1.1-desktop (Kernel Release) > >> > > > > > *gcc*: 4.7.2 > >> > > > > > > >> > > > > > CUDA Library paths > >> > > > > > #CUDA-5.0 > >> > > > > > export CUDA_HOME=/usr/local/cuda-5.0 > >> > > > > > export PATH=$CUDA_HOME/bin:$PATH > >> > > > > > export LD_LIBRARY_PATH=$CUDA_HOME/lib64:/lib:$LD_LIBRARY_PATH > >> > > > > > > >> > > > > > The gromacs has been compiled with > >> > > > > > > >> > > > > > > >> CMAKE_PREFIX_PATH=/opt/apps/fftw-3.3.3/single:/usr/local/cuda-5.0 > >> > > > cmake .. > >> > > > > > -DGMX_GPU=ON > -DCMAKE_INSTALL_PREFIX=/opt/apps/gromacs/461/single > >> > > > > > -DGMX_DEFAULT_SUFFIX=OFF -DGMX_BINARY_SUFFIX=_461 > >> > > > -DGMX_LIBS_SUFFIX=_461 > >> > > > > > -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda > >> > > > > > > >> > > > > > *Error on executing mdrun > >> > > > > > * > >> > > > > > * > >> > > > > > * > >> > > > > > *NOTE: Error occurred during GPU detection: > >> > > > > > no CUDA-capable device is detected > >> > > > > > Can not use GPU acceleration, will fall back to CPU kernels. > >> > > > > > > >> > > > > > > >> > > > > > Will use 24 particle-particle and 8 PME only nodes > >> > > > > > This is a guess, check the performance at the end of the log > >> file > >> > > > > > Using 32 MPI threads > >> > > > > > > >> > > > > > No GPUs detected > >> > > > > > > >> > > > > > *I checked my cuda installation. I am able to compile and > >> execute > >> > the > >> > > > > > sample programmes e.g., deviceQuery. > >> > > > > > > >> > > > > > Also executed *nvidia-smi *: > >> > > > > > +------------------------------------------------------+ > >> > > > > > | NVIDIA-SMI 4.310.40 Driver Version: 310.40 | > >> > > > > > > >> > > > > >> > > >> > |-------------------------------+----------------------+----------------------+ > >> > > > > > | GPU Name | Bus-Id Disp. | Volatile Uncorr. ECC | > >> > > > > > | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute > >> M. | > >> > > > > > > >> > > > > >> > > >> > |===============================+======================+======================| > >> > > > > > | 0 NVS 300 | 0000:03:00.0 N/A | N/A | > >> > > > > > | N/A 49C N/A N/A / N/A | 3% 16MB / 511MB | N/A Default | > >> > > > > > > >> > > > > >> > > >> > +-------------------------------+----------------------+----------------------+ > >> > > > > > | 1 Tesla K20c | 0000:04:00.0 Off | Off | > >> > > > > > | 30% 38C P8 16W / 225W | 0% 13MB / 5119MB | 0% Default | > >> > > > > > > >> > > > > >> > > >> > +-------------------------------+----------------------+----------------------+ > >> > > > > > > >> > > > > > > >> > > > > >> > > >> > +-----------------------------------------------------------------------------+ > >> > > > > > | Compute processes: GPU Memory | > >> > > > > > | GPU PID Process name Usage | > >> > > > > > > >> > > > > >> > > >> > |=============================================================================| > >> > > > > > | 0 Not Supported | > >> > > > > > > >> > > > > >> > > >> > +-----------------------------------------------------------------------------+ > >> > > > > > > >> > > > > > What am I missing that Gromacs is not detecting the GPUs. > >> > > > > > > >> > > > > > Chandan > >> > > > > > > >> > > > > > -- > >> > > > > > Chandan kumar Choudhury > >> > > > > > NCL, Pune > >> > > > > > INDIA > >> > > > > > -- > >> > > > > > gmx-users mailing list gmx-users@gromacs.org > >> > > > > > http://lists.gromacs.org/mailman/listinfo/gmx-users > >> > > > > > * Please search the archive at > >> > > > > > http://www.gromacs.org/Support/Mailing_Lists/Search before > >> > posting! > >> > > > > > * Please don't post (un)subscribe requests to the list. Use > the > >> > > > > > www interface or send it to gmx-users-requ...@gromacs.org. > >> > > > > > * Can't post? Read > http://www.gromacs.org/Support/Mailing_Lists > >> > > > > > > >> > > > > > >> > > > > > >> > > > > Dr. George Patargias > >> > > > > Postdoctoral Researcher > >> > > > > Biomedical Research Foundation > >> > > > > Academy of Athens > >> > > > > 4, Soranou Ephessiou > >> > > > > 115 27 > >> > > > > Athens > >> > > > > Greece > >> > > > > > >> > > > > Office: +302106597568 > >> > > > > > >> > > > > -- > >> > > > > gmx-users mailing list gmx-users@gromacs.org > >> > > > > http://lists.gromacs.org/mailman/listinfo/gmx-users > >> > > > > * Please search the archive at > >> > > > http://www.gromacs.org/Support/Mailing_Lists/Search before > posting! > >> > > > > * Please don't post (un)subscribe requests to the list. Use the > >> > > > > www interface or send it to gmx-users-requ...@gromacs.org. > >> > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > > > -- > >> > > > gmx-users mailing list gmx-users@gromacs.org > >> > > > http://lists.gromacs.org/mailman/listinfo/gmx-users > >> > > > * Please search the archive at > >> > > > http://www.gromacs.org/Support/Mailing_Lists/Search before > posting! > >> > > > * Please don't post (un)subscribe requests to the list. Use the > >> > > > www interface or send it to gmx-users-requ...@gromacs.org. > >> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > > > > >> > > > >> > > > >> > > > >> > > -- > >> > > Chandan kumar Choudhury > >> > > NCL, Pune > >> > > INDIA > >> > > -- > >> > > gmx-users mailing list gmx-users@gromacs.org > >> > > http://lists.gromacs.org/mailman/listinfo/gmx-users > >> > > * Please search the archive at > >> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > >> > > * Please don't post (un)subscribe requests to the list. Use the > >> > > www interface or send it to gmx-users-requ...@gromacs.org. > >> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > -- > >> > gmx-users mailing list gmx-users@gromacs.org > >> > http://lists.gromacs.org/mailman/listinfo/gmx-users > >> > * Please search the archive at > >> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > >> > * Please don't post (un)subscribe requests to the list. Use the > >> > www interface or send it to gmx-users-requ...@gromacs.org. > >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > > >> -- > >> gmx-users mailing list gmx-users@gromacs.org > >> http://lists.gromacs.org/mailman/listinfo/gmx-users > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > >> * Please don't post (un)subscribe requests to the list. Use the > >> www interface or send it to gmx-users-requ...@gromacs.org. > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > > > > > > -- > > Chandan kumar Choudhury > > NCL, Pune > > INDIA > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists