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

Yasuyuki Araki yasu.araki at gmail.com
Tue Sep 8 14:11:48 CEST 2009


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.

I found these two additional troubles;
3: Commands including gromacs make no problems when I appoint it by
absolute path, for example /usr/bin/grompp (in my gentoo box),
however in this case,
just typing command only "grompp" makes buffer overflow.
4: Super user has no problems to use gromacs in my gentoo box.

As it happened I re-build gromacs with the environmental variable
CFLAGS="-U_FORTIFY_SOURCE" to turn off the FORTIFY_SOURCE feature,
all problems mentioned above seem clear.

Can I ask you I should turn off the FORTIFY_SOURCE feature to build and use
gromacs with such a gcc version or I can find the other way?


Yasuyuki Araki

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