Hi, Thanks for the reply, >> 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 guess it's depend on my lack of knowledge about gcc. > If you have a link, you should provide us with it :-) Right-click on the > frame to copy a URL. This topic was in the thread followed by this reoprt; http://lists.gromacs.org/pipermail/gmx-users/2009-July/043177.html >> 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. It is not the point. I am installing gromacs with the package manager available in gentoo linux, so only one version of gromacs (4.0.5) exists 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. > > My Googling suggests -U-FORTIFY-SOURCE is the way to turn it off. Yes, so I guess this buffer overflow have triggered by FORTIFY_SOURCE feature. >> 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. OK, I just turn off FORTIFY_SOURCE feature when I build gromacs. Thanks, Yasuyuki Araki _______________________________________________ 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
