On Thu, Jun 27, 2013 at 12:57 PM, Mare Libero <marelibe...@yahoo.com> wrote: > Hello everybody, > > Does anyone have any recommendation regarding the installation of gromacs 4.6 > on Ubuntu 12.04? I have the nvidia-cuda-toolkit that comes in synaptic > (4.0.17-3ubuntu0.1 installed in /usr/lib/nvidia-cuda-toolkit) and the drivers > 304.88. > Apparently, this is not compatible with gcc-4.5 and higher. When I issue: > > > $ cmake .. -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/lib/nvidia-cuda-toolkit > -DGMX_BUILD_OWN_FFTW=ON > $ make > > the compilation ends with: > > In file included from > /usr/lib/nvidia-cuda-toolkit/include/cuda_runtime.h:59:0, > from <command-line>:0: > /usr/include/host_config.h:82:2: error: #error -- unsupported GNU version! > gcc 4.5 and up are not supported! > > If I downgrade to gcc-4.4 this error disappears, but gromacs compilation > fails with a different error: > > cc1plus: error: unrecognized command line option "-fexcess-precision=fast" > CMake Error at cuda_tools_generated_pmalloc_cuda.cu.o.cmake:198 (message): > Error generating > > /home/me/Downloads/gromacs-4.6.2/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
I guess what happens is that you are using gcc 4.5 for the CPU code and gcc 4.4 as the nvcc host compiler. However, the compiler options used for gcc (CMAKE_CXX_FLAGS) get propagated to nvcc; -fexcess-precision=fast is supported by gcc 4.5, but not by 4.4, hence the error when compiling CUDA code. > > Also, I tried the Intel compilers that comes with the non-commercial Intel > c++ composer XE (which I believe are recommended). The compilation produces a > number of warnings, and then dies with the following error: > > > $ CC=/opt/intel/bin/icc cmake .. -DGMX_GPU=ON > -DCUDA_TOOLKIT_ROOT_DIR=/usr/lib/nvidia-cuda-toolkit -DGMX_BUILD_OWN_FFTW=ON > > [ 63%] Building C object share/template/CMakeFiles/template.dir/template.c.o > make[2]: *** No rule to make target `src/gmxlib/libgmx.so.8', needed by > `share/template/template'. Stop. > make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2 > make: *** [all] Error 2 This should work, but CUDA 4.0 is ancient surely does not support icc 13. I suggest that you get CUDA 5.0 and use gcc 4.7 (or a new icc). If you really want to stick to CUDA 4.0, try using gcc 4.4 as the general C++ compiler (CMAKE_CXX_COMPILER) which should avoid the above error. > Thanks in advance for your help, > > Al > > -- > 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
