Hi Szilard Thanks for this tip; it was extremely useful. The problem was indeed the incompatibility between the installed NVIDIA driver and the CUDA 5.0 runtime library. Installation of an older driver solved the problem. The programs devideQuery etc can now detect the GPU.
GROMACS can also detect now the card but unfortunately aborts with the following error Fatal error: Incorrect launch configuration: mismatching number of PP MPI processes and GPUs per node. mdrun_mpi was started with 12 PP MPI processes per node, but only 1 GPU were detected. Here is my command line mpirun -np 12 mdrun_mpi -s test.tpr -deffnm test_out -nb gpu What can be the problem? Thanks again > Hi George, > As I said before, that just means that most probably the GPU driver is not > compatible with the CUDA runtime (libcudart) that you installed with the CUDA toolkit. I've no clue about the Mac OS installers and releases, you'll > have to do the research on that. Let us know if you have further (GROMACS-related) issues. > Cheers, > -- > Szil?rd > On Fri, Mar 1, 2013 at 2:48 PM, George Patargias <g...@bioacademy.gr> wrote: >> Hi Szilαrd >> Thanks for your reply. I have run the deviceQuery utility and what I got >> back is >> /deviceQuery Starting... >> CUDA Device Query (Runtime API) version (CUDART static linking) >> cudaGetDeviceCount returned 38 >> -> no CUDA-capable device is detected >> Should I understand from this that the CUDA driver was not installed from >> the MAC OS X CUDA 5.0 Production Release? >> George >> > HI, >> > That looks like the driver does not work or is incompatible with the runtime. Please get the SDK, compile a simple program, e.g. >> deviceQuery >> > and >> > see if that works (I suspect that it won't). >> > Regarding your machines, just FYI, the Quadro 4000 is a pretty slow >> card >> > (somewhat slower than a GTX 460) so you'll hava a quite strong >> resource >> > imbalance: a lot of CPU compute power (2x Xeon 5xxx, right?) and >> little >> > GPU >> > compute power which will lead to the CPU idling while waiting for the >> GPU. >> > Cheers, >> > -- >> > Szilαrd >> > On Thu, Feb 28, 2013 at 4:52 PM, George Patargias >> > <g...@bioacademy.gr>wrote: >> >> Hello >> >> We are trying to install the GPU version of GROMACS 4.6 on our own MacOS cluster. So for the cluster nodes that have the NVIDIA Quadro >> 4000 >> >> cards: >> >> - We have downloaded and install the MAC OS X CUDA 5.0 Production Release >> >> from here: https://developer.nvidia.com/cuda-downloads >> >> placing the libraries contained in this download in >> /usr/local/cuda/lib >> >> - We have managed to compile GROMACS 4.6 linking it statically with these >> >> CUDA libraries and the MPI libraries (with BUILD_SHARED_LIBS=OFF and GMX_PREFER_STATIC_LIBS=ON) >> >> Unfortunately, when we tried to run a test job with the generated mdrun_mpi, GROMACS reported that it cannot detect any CUDA-enabled devices. It also reports 0.0 version for CUDA driver and runtime. Is the actual CUDA driver missing from the MAC OS X CUDA 5.0 >> Production >> >> Release that we installed? Do we need to install it from here: http://www.nvidia.com/object/cuda-mac-driver.html >> >> Or is something else that we need to do? >> >> Many thanks in advance. >> >> George >> >> 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 >> 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 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
