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
