On Thu, Nov 29, 2012 at 9:20 PM, 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 > > 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 > This is not a warning just a note. Is this confusing? > -- Found CUDA: /cm/shared/apps/cuda40/toolkit/4.0.17 (found suitable > version > "4.0", minimum required is "3.2") > ... > > 2. It says FFTW isn't detected, but it actually is: > > ... > -- checking for module 'fftw3f' > -- package 'fftw3f' not found > It checks several ways. The first (pgkconfig) din't work. Again just a note. > -- 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 > > 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. > Could be this cmake bug: http://www.gccxml.org/Bug/view.php?id=13674 Could you try whether any other cmake version (e.g. 2.8.9) works? Roland > > -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 > > ======================================== > -- > 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 > > > > > -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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
