[gmx-users] GPU warnings

[Szilárd Páll]

Hi Thomas,

It looks like some gcc 4.7-s don't work with CUDA, although I've been using
various Ubuntu/Linaro versions, most recently 4.7.2 and had no
issues whatsoever. Some people seem to have bumped into the same problem
(see http://goo.gl/1onBz or http://goo.gl/JEnuk) and the suggested fix is
to put
#undef _GLIBCXX_ATOMIC_BUILTINS
#undef _GLIBCXX_USE_INT128
in a header and pre-include it for nvcc by calling it like this:
nvcc --pre-include undef_atomics_int128.h

Cheers,

--
Szilárd



On Sun, Dec 9, 2012 at 12:18 PM, Thomas Evangelidis <tevang3 at gmail.com>wrote:

> > > gcc 4.7.2 is not supported by any CUDA version.
> > >
> >
> > I suggest that you just fix it by editing the include/host_config.h and
> > changing the version check macro (line 82 AFAIK). I've never had real
> > problems with using new and officially not supported gcc-s, the version
> > check is more of a promise from NVIDIA that "we've tested thoroughly
> > internally and we more or less vouch for thins combination".
> >
> > Cheers,
> > --
> > Szilárd
> >
> > PS:
> > Disclamer: I don't take responsibility if your machine goes up in flames!
> > ;)
> >
> >
> Hi Szilárd,,
>
> I tried to compile gromacs-4.6beta1, is this the version you suggested? If
> not, please indicate how to download the source cause I am confused with
> all these development versions.
>
> Anyway, this is the error I get with 4.6beta1, gcc 4.7.2 and cuda 5:
>
> [  0%] Building NVCC (Device) object
>
> src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_cudautils.cu.o
>
> /usr/lib/gcc/x86_64-redhat-linux/4.7.2/../../../../include/c++/4.7.2/ext/atomicity.h(48):
> error: identifier "__atomic_fetch_add" is undefined
>
>
> /usr/lib/gcc/x86_64-redhat-linux/4.7.2/../../../../include/c++/4.7.2/ext/atomicity.h(52):
> error: identifier "__atomic_fetch_add" is undefined
>
> 2 errors detected in the compilation of
> "/tmp/tmpxft_00002394_00000000-9_cudautils.compute_30.cpp1.ii".
> CMake Error at cuda_tools_generated_cudautils.cu.o.cmake:252 (message):
>   Error generating file
>
>
> /home/thomas/Programs/gromacs-4.6-beta1_gnu_cuda5_build/src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_cudautils.cu.o
>
>
> gmake[3]: ***
>
> [src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/./cuda_tools_generated_cudautils.cu.o]
> Error 1
> gmake[2]: *** [src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/all]
> Error 2
> gmake[1]: *** [src/programs/mdrun/CMakeFiles/mdrun.dir/rule] Error 2
> gmake: *** [mdrun] Error 2
>
>
> Unless I am missing something, cuda 5 does not support gcc 4.7.2.
>
>
>  Thomas
> --
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