On Fri, Nov 30, 2012 at 3:20 AM, Justin Lemkul <jalem...@vt.edu> wrote:
> > Hooray for being the first to report a problem with the beta :) > > We have a cluster at our university that provides us with access to some > CPU-only nodes and some CPU-GPU nodes. I'm having problems with getting > 4.6beta1 to build, and I suspect the issue is related to GPU detection. > > Here are some specifics: > > FFTW 3.3.3 > CMake 2.8.10 > gcc 4.3.4 > CUDA 4.0 > 64-bit Linux on AMD hardware > GPU nodes have Tesla C2050 cards > Note that on AMD you might have to use less threads per process than the default and therefore more than one process per GPU: set -gpu_id=00 for two processes in a node to both use the first GPU. Additionally, you might want to use a newer gcc and CUDA, both will provide performance improvements. > > Commands: > > cmake ../gromacs-4.6-beta1 -DCMAKE_INSTALL_PREFIX=/home/** > jalemkul/software/gromacs-**46beta1 -DGMX_X11=OFF -DGMX_GPU=ON > -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DCMAKE_PREFIX_PATH=/home/ > **jalemkul/software/fftw-3.3.3/ > > The first step runs alright, but two things to note: > > 1. It doesn't detect any GPU, which is correct because I'm on a head node > and not a compute node: > > ...-- Looking for NVIDIA GPUs present in the system > -- Could not detect NVIDIA GPUs > -- Found CUDA: /cm/shared/apps/cuda40/**toolkit/4.0.17 (found suitable > version "4.0", minimum required is "3.2") > ... > That is just an informative message. We try to detect GPUs on the build machine to suggest users compiling with GPU acceleration enabled. > > 2. It says FFTW isn't detected, but it actually is: > > ... > -- checking for module 'fftw3f' > -- package 'fftw3f' not found > -- Looking for fftwf_plan_r2r_1d in /home/jalemkul/ATHENA/** > software/fftw-3.3.3/lib/**libfftw3f.so > -- Looking for fftwf_plan_r2r_1d in /home/jalemkul/ATHENA/** > software/fftw-3.3.3/lib/**libfftw3f.so - found > -- Looking for fftwf_have_simd_avx in /home/jalemkul/ATHENA/** > software/fftw-3.3.3/lib/**libfftw3f.so > -- Looking for fftwf_have_simd_avx in /home/jalemkul/ATHENA/** > software/fftw-3.3.3/lib/**libfftw3f.so - not found > -- Looking for fftwf_have_simd_sse2 in /home/jalemkul/ATHENA/** > software/fftw-3.3.3/lib/**libfftw3f.so > -- Looking for fftwf_have_simd_sse2 in /home/jalemkul/ATHENA/** > software/fftw-3.3.3/lib/**libfftw3f.so - found > ... > > Upon running "make," I get an immediate failure: > > [ 0%] Building NVCC (Device) object src/gmxlib/gpu_utils/** > CMakeFiles/gpu_utils.dir//./**gpu_utils_generated_gpu_utils.**cu.o > nvcc fatal : redefinition of argument 'compiler-bindir' > CMake Error at gpu_utils_generated_gpu_utils.**cu.o.cmake:206 (message): > Error generating > > /home/jalemkul/gmxbuild/src/**gmxlib/gpu_utils/CMakeFiles/** > gpu_utils.dir//./gpu_utils_**generated_gpu_utils.cu.o > > > make[2]: *** [src/gmxlib/gpu_utils/**CMakeFiles/gpu_utils.dir/./** > gpu_utils_generated_gpu_utils.**cu.o] Error 1 > make[1]: *** [src/gmxlib/gpu_utils/**CMakeFiles/gpu_utils.dir/all] Error 2 > make: *** [all] Error 2 > That's bad and I don't exactly know why does it happen, it looks like the nvcc host compiler gets double-set. Could you put your CMakeCache.txt of this configuration into pastbin and link it (attachments are blocked, I think)? One option to get it work is to remove the "-ccbin=/path/to/your/gcc" form the CUDA_NVCC_FLAGS cache variable and re-configure. -- Szilárd > > Any ideas? I'm guessing it's related to the GPU detection failing, > because I can build on a workstation in our lab that has a C2075 card. > > -Justin > > -- > ==============================**========== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<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
