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

[Mark Abraham]

Either approach can work, but you could have tried your command before
emailing :-)

Mark

On Wed, 1 Jun 2016 00:35 Diogo Martins de Sá <sadiogo at mol.bio.br> wrote:

> Hi Mark and Szilard,
>
> Thanks for all the help. Just to make sure I understood, I should run
> cmake like this:
>
> cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=on
> -DGPU_DEPLOYMENT_KIT_ROOT_DIR=/usr/local/cuda-7.5
> -DCMAKE_C_FLAGS="-D_FORCE_INLINES"
>
> or should I try to modify a CMakefile.txt or Makefile? If so, which? I've
> been looking around but can't seem to find the correct file to modify.
>
> Best regards,
> Diogo
>
>
> From: Mark Abraham <mark.j.abraham at ...
> <http://gmane.org/get-address.php?address=mark.j.abraham%2dRe5JQEeQqe8AvxtiuMwx3w%40public.gmane.org>
> >
>
> Subject: Re: [gmx-users] Error while re-compiling Gromacs 5.1.2 with GPU
> and gcc 5.3.1
> <http://news.gmane.org/find-root.php?message_id=CAMNuMAR25zQe6exe%2bn4NL%2dPkm%3dxcmQn%5fSuv0fS4LncdPEGyP%2bQ%40mail.gmail.com>
> Newsgroups: gmane.science.biology.gromacs.user
> <http://news.gmane.org/gmane.science.biology.gromacs.user>
> Date: 2016-05-31 21:16:07 GMT (41 minutes ago)
>
> 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
>
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