[gmx-users] Error while re-compiling Gromacs 5.1.2 with GPU and gcc 5.3.1

Szilárd Páll pall.szilard at gmail.com
Tue May 31 22:25:22 CEST 2016


Just because gcc 5.3 and CUDA/nvcc 7.5 are in some Ubuntu repos (partner
AFAIR), it does not mean they're automatically compatible. The NVIDIA
documentation clearly indicates they're not.

However, this typically means that minor issue can prevent building. In
this case, it looks like a glibc/string.h issue (bug?) that was introduced
recently [1]. The solution seems to be as simple as adding -D-D*FORCE*INLINES
to the CUDA*NVCC*FLAGS flags (credit [2]).

[1] https://fossies.org/diffs/glibc/2.22*vs*2.23/string/string.h-diff.html
[2] https://github.com/BVLC/caffe/issues/4046


On Tue, May 31, 2016 at 7:42 PM, Diogo Martins de Sá <sadiogo at mol.bio.br>

> Hi Nikhil,
> You can get CUDA toolkit 7.5 using apt-get install nvidia-cuda-dev
> nvidia-cuda-toolkit. Also, if you open the link I've sent, you`ll see the
> step on how to install directly from provider. NAMD ran with CUDA this way.
> So it is supported. Installing directly with apt-get gives the same result
> as the one I posted.
> I just need some guidance as to what the error points to.
> Regards,
> Diogo
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