[gmx-users] Installation on Ubuntu 12.04LTS

Mark Abraham mark.j.abraham at gmail.com
Thu Jun 27 14:01:04 CEST 2013

On Thu, Jun 27, 2013 at 12:57 PM, Mare Libero <mareliber27 at 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

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...


> Thanks in advance for your help,
> Al
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