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
