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

[Jussi Lehtola]

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