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.
Whatever FORTIFY_SOURCE does, either it is poorly-constructed or the way
you're using it is.
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.
If you have a link, you should provide us with it :-) Right-click on the
frame to copy a URL.
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.
Probably you are calling different versions with different PATH
variables. Use "which" to find out.
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.
My Googling suggests -U-FORTIFY-SOURCE is the way to turn it off.
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?
This "feature" is probably a security thing to prevent malicious code
using buffer overruns to get access to do bad things. Unless you're
making GROMACS freely available to a potential hacker, if you trust the
GROMACS developers, then you don't want FORTIFY_SOURCE enabled if it
causes problems.
Mark
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
