[gmx-users] Installation on Ubuntu 12.04LTS

Mare Libero mareliber27 at yahoo.com
Thu Jun 27 12:57:57 CEST 2013

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

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

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

Thanks in advance for your help,


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