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 >
CUDA 4.0 is two years old, so I would(did) get the latest package from Nvidia rather than rely on synaptic to be up to date with emerging technologies. And use a more recent gcc! > 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: Yeah CUDA's wrapper compiler does not play perfectly with non-gcc, but the result should be OK. We have filed bug reports with CUDA. > $ 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 On the other hand, FFTW development is nearly stopped, so libfftw3-dev from synaptic is fine, and I suspect the origin of this issue is either a race condition in the internal FFTW build (which will go away if you make again), or perhaps icc being evil and conveniently wrapping an FFTW interface over its MKL. We believe we've fixed the latter, but there are too many moving targets... Mark > 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
