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

[Mark Abraham]

Hi,

That's the standard content of CUDA - that deliberate compiler error has to
be suppressed (per the link in the original post) if you want to use a
different compiler.

The issue here is that the version of the C standard library that ships on
the operating system has a new feature that interacts poorly with versions
of CUDA that pre-dated it. Using a compatible compiler doesn't help, if it
shares that standard library. To fix, as Szilard tried to suggest, you can
use

cmake -DCMAKE_C_FLAGS="-D_FORCE_INLINES"

which avoids the problematic code path. The irritating part about trying to
consider a workaround for GROMACS is that memcpy is supposed to be defined
by string.h, so it is somehow inconsistent that it is not defined...

Mark

On Tue, May 31, 2016 at 10:58 PM Fabricio Cannini <fcannini at gmail.com>
wrote:

> Em 31-05-2016 17:25, Szilárd Páll escreveu:
> >   Hi,
> >
> > 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.
>
> Surely the ubuntu cuda maintainers patched 'include/host_config.h'
> This is from the 7.5 nvidia packages:
>
> =====================================
> #if defined(__GNUC__)
>
> #if __GNUC__ > 4 || (__GNUC__ == 4 && __GNUC_MINOR__ > 9)
>
> #error -- unsupported GNU version! gcc versions later than 4.9 are not
> supported!
> =====================================
>
> IMHO there may be a good reason for nvidia to do it (Please correct me
> if I'm wrong) :
> https://gcc.gnu.org/onlinedocs/libstdc++/manual/using_dual_abi.html
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