[gmx-users] Gromacs and Gcc5.2

Mark Abraham mark.j.abraham at gmail.com
Sat Oct 3 16:15:29 CEST 2015


On Fri, Oct 2, 2015 at 9:58 AM Nicolas Cheron <
nicolas.cheron.boulot at gmail.com> 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).

It satisfies the technical requirements (in the install guide), so go ahead.

Is it recommended
> or not?

It's probably best overall (which is why the install guide recommends you
get the latest version of your compiler), but the actual optimum depends on
your simulation, hardware and other infrastructure.

> Should we expect improvements?

Only minor ones. Minor regressions have been known, too.

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).

Seems normal.

> 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]
> I don't think it is relevant and I am not worried about it, but just wanted
> to check with you.

That's a known issue with older OpenMPI headers (and not a problem for
running GROMACS). It's probably fixed in the latest version of OpenMPI, as
James suggested.


Thank you.
> Nicolas
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