[gmx-users] Gromacs and Gcc5.2

[Barnett, James W]

On Fri, 2015-10-02 at 09:57 +0200, Nicolas Cheron wrote:
> Dear all,
> 
> I am wondering if there is an official statement regarding compiling
> Gromacs with gcc5.2.0 (or any gcc from the 5.x branch). Is it recommended
> or not? Should we expect improvements? 

I don't think there is an official statement other than that versions 4.7 and
above are required. I use 5.2.0 on several systems without any problems. I know
that more recent gcc versions have better SIMD support, so if you're upgrading
from 4.8 series you should see improvements.


> I have tried quickly some small
> benchmarks (with Gromacs 4.6.3 and Gromacs 5.1) and found improvement on
> ns/day between 1 and 3% (with respect to gcc4.8.5).
> 
> Also, during compilation I get several warnings such as:
> 
> In file included from /usr/local/openmpi-gnu/include/mpi.h:253:0,
>                  from
> /home2/ncheron/Programs/gromacs-5.1/src/gromacs/utility/gmxmpi.h:59,
>                  from
> /home2/ncheron/Programs/gromacs
> -5.1/src/gromacs/legacyheaders/types/commrec.h:45,
>                  from
> /home2/ncheron/Programs/gromacs-5.1/src/gromacs/legacyheaders/gmx_ga2la.h:40,
>                  from
> /home2/ncheron/Programs/gromacs
> -5.1/src/gromacs/domdec/domdec_constraints.cpp:55:
> /usr/local/openmpi-gnu/include/mpi_portable_platform.h:374:34: warning:
> invalid suffix on literal; C++11 requires a space between literal and
> string macro [-Wliteral-suffix]
> 
> _STRINGIFY(__GNUC__)"."_STRINGIFY(__GNUC_MINOR__)"."_STRINGIFY(__GNUC_PATCHLEV
> EL__)
> 
> I don't think it is relevant and I am not worried about it, but just wanted
> to check with you.

It looks like to me the warning is generated from your OpenMPI library that
GROMACS links to and not GROMACS itself. I suggest updating OpenMPI to the
latest version and compiling with GCC 5.2 as well.

-- 
James “Wes” Barnett, Ph.D. Candidate
Louisiana Board of Regents Fellow

Chemical and Biomolecular Engineering
Tulane University
341-B Lindy Boggs Center for Energy and Biotechnology
6823 St. Charles Ave
New Orleans, Louisiana 70118-5674
jbarnet4 at tulane.ed