[gmx-users] Using gromacs 4.0.5 built with FORTIFY_SOURCE feature

Jussi Lehtola jussi.lehtola at helsinki.fi
Tue Sep 8 20:32:16 CEST 2009

On Tue, 2009-09-08 at 21:11 +0900, Yasuyuki Araki wrote:
> hi,
> I now use gentoo linux with gcc 4.3.4, which has FORTIFY_SOURCE feature.
> When I built gromacs 4.0.5 with this gcc, every command, like grompp, pdb2gmx
> and so on, makes buffer overflow and stoppes immediately.
> I saw the archives of this mailing list and found this situation was
> quite similar to
>  the report by Adam on July 6, 2009.
> Simply summarized like;
> 1: In some case, commands including gromacs make buffer overflow on Fedora 10.
> 2: Even in such a case, commands running on gdb seems no problems on Fedora 10.

The Fedora packages of GROMACS have been compiled with the default
Fedora build flags which include -Wp,-D_FORTIFY_SOURCE=2 and no such
problems have been encountered. This is both in Fedora 10 and 11, and in
RHEL 4 and 5.

Maybe your Gentoo is just broken?
Jussi Lehtola, FM, Tohtorikoulutettava
Fysiikan laitos, Helsingin Yliopisto
jussi.lehtola at helsinki.fi, p. 191 50632
Mr. Jussi Lehtola, M. Sc., Doctoral Student
Department of Physics, University of Helsinki, Finland
jussi.lehtola at helsinki.fi

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