[gmx-users] Gromacs and Gcc5.2

Barnett, James W jbarnet4 at tulane.edu
Sat Oct 3 06:13:58 CEST 2015

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]
> 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

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