On Mon, Mar 04, 2013 at 07:59:03AM -0700, Alexander Hansen wrote: > On 3/4/13 7:39 AM, Alan wrote: > > Hi, I followed the issues with GMX 4.6 and waited. So today I gave a try > > and got this: > > > > [skip] > > make > > [ 0%] Building NVCC (Device) object > > src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_memtestG80_core.cu.o > > [ 0%] Building NVCC (Device) object > > src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_gpu_utils.cu.o > > Scanning dependencies of target gpu_utils > > [ 0%] Building CXX object > > src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/dummy.cpp.o > > Linking CXX static library libgpu_utils.a > > /usr/bin/ranlib: file: libgpu_utils.a(dummy.cpp.o) has no symbols > > /usr/bin/ranlib: file: libgpu_utils.a(dummy.cpp.o) has no symbols > > [ 0%] Built target gpu_utils > > [ 0%] Building NVCC (Device) object > > src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o > > /sw/src/fink.build/gromacs-4.6-2/gromacs-4.6/src/gmxlib/cuda_tools/pmalloc_cuda.cu > > <http://pmalloc_cuda.cu>(64): error: no instance of overloaded function > > "cudaMallocHost" matches the argument list > > argument types are: (void **, size_t, int) > > > > /sw/src/fink.build/gromacs-4.6-2/gromacs-4.6/src/gmxlib/cuda_tools/pmalloc_cuda.cu > > <http://pmalloc_cuda.cu>(87): error: no instance of overloaded function > > "cudaMallocHost" matches the argument list > > argument types are: (void **, size_t, int) > > > > 2 errors detected in the compilation of > > "/tmp/tmpxft_000029fc_00000000-4_pmalloc_cuda.cpp1.ii". > > CMake Error at cuda_tools_generated_pmalloc_cuda.cu.o.cmake:264 (message): > > Error generating file > > > > /sw/src/fink.build/gromacs-4.6-2/gromacs-4.6/build/src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o > > > > > > make[2]: *** > > [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/./cuda_tools_generated_pmalloc_cuda.cu.o] > > Error 1 > > make[1]: *** [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/all] Error 2 > > make: *** [all] Error 2 > > ### execution of /tmp/fink._AHcW failed, exit code 2 > > ### execution of /tmp/fink.9rNkw failed, exit code 2 > > Removing runtime build-lock... > > Removing build-lock package... > > /sw/bin/dpkg-lockwait -r fink-buildlock-gromacs-4.6-2 > > (Reading database ... 179750 files and directories currently installed.) > > Removing fink-buildlock-gromacs-4.6-2 ... > > Reading buildlock packages... > > /sw/bin/dpkg-lockwait -i /sw/fink/debs/gromacs_4.5.4-2_darwin-x86_64.deb > > Selecting previously deselected package gromacs. > > (Reading database ... 179749 files and directories currently installed.) > > Unpacking gromacs (from .../gromacs_4.5.4-2_darwin-x86_64.deb) ... > > Setting up gromacs (4.5.4-2) ... > > > > Updating the list of locally available binary packages. > > Failed: phase installing: gromacs-4.6-2 failed > > > > Package manager version: 0.34.5 > > Distribution version: selfupdate-rsync Mon Mar 4 13:32:14 2013, 10.8, > > x86_64 > > Trees: local/main stable/main local/injected > > Xcode.app: 4.6 > > Xcode command-line tools: 4.5.0.0.1.1249367152 > > Max. Fink build jobs: 4 > > > > > > > > -- > > Alan Wilter SOUSA da SILVA, DSc > > Bioinformatician, UniProt - PANDA, EMBL-EBI > > CB10 1SD, Hinxton, Cambridge, UK > > +44 1223 49 4588 > > > > > > > I didn't see this when I built it here. You might start by updating > your Xcode command-line tools (e.g. via the Xcode Preferences).
I believe that Alan must have some third-party CUDA devtools installed. There is no way fink can properly support that configuration so they needed to be disabled in .cshrc/.bashrc or moved aside/deinstalled first. > > -- > Alexander Hansen, Ph.D. > Fink User Liaison > My package updates: http://finkakh.wordpress.com/ ------------------------------------------------------------------------------ Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_feb _______________________________________________ Fink-users mailing list [email protected] List archive: http://news.gmane.org/gmane.os.macosx.fink.user Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-users
