Andreas, Try removing -D_FORTIFY_SOURCE=2 as a compiler option...
PyMOL's macros sometimes choke on that. Cheers, Warren > -----Original Message----- > From: pymol-users-boun...@lists.sourceforge.net > [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf > Of Andreas Henschel > Sent: Friday, April 27, 2007 2:28 PM > To: Michael Kluge > Cc: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] PyMOL compilation from source > > Hi, > > Michael Kluge wrote: > > >Hi Andreas, > > > >gcc is not the best compiler on an IA64 machine. We always recommend > >using the Intel compilers. Would it be possible to try those? > > > > > > > I have to figure out, where to modify in the setup script/distutils. > Thanks. > > Andreas > > PS. @Michael > From Martin Hoefling: > > >i have no idea about your error but i can provide you RPMs > for Opensuse > >10.2 > >i586 and x86_64, if you need them for other SuSE > distributions, I can > >try to add them to my repository. > > > Would that be feasable? > > >Regards, Michael > > > >Andreas Henschel wrote: > > > > > >>Hi all, > >> > >>did anyone of you come across the mysterious "internal > compiler error: > >>Segmentation fault" > >>while compiling pymol from source? > >> > >>The offending lines are in contrib/champ/champ.c:2787 > >> > >> PRINTFD(FB_smiles_parsing) > >> " ChampParseBlockAtom: called.\n" > >> ENDFD; > >> > >>Can I get around it somehow? Is it a 64-bit/gcc issue? > >>Any help would be greatly appreciated. > >> > >>Some more error/system details: > >> > >> > >> > >>>python setup.py install > >>> > >>> > >>... > >>building 'chempy.champ._champ' extension gcc -pthread > >>-fno-strict-aliasing -DNDEBUG -O2 -fmessage-length=0 -Wall > >>-D_FORTIFY_SOURCE=2 -g -fPIC -Icontrib/champ > -I/usr/include/python2.4 > >>-c contrib/champ/champ.c -o > >>build/temp.linux-ia64-2.4/contrib/champ/champ.o > >>contrib/champ/champ.c: In function 'ChampParseBlockAtom': > >>contrib/champ/champ.c:2787: internal compiler error: Segmentation > >>fault Please submit a full bug report, with preprocessed source if > >>appropriate. > >>See <URL:http://www.suse.de/feedback> for instructions. > >>error: command 'gcc' failed with exit status 1 > >> > >> > >> > >>>uname -a > >>> > >>> > >>Linux mars 2.6.16.27-0.6-default #1 SMP Wed Dec 13 09:34:50 UTC 2006 > >>ia64 ia64 ia64 GNU/Linux > >> > >> > >> > >>>gcc -v > >>> > >>> > >>Using built-in specs. > >>Target: ia64-suse-linux > >>Configured with: ../configure --enable-threads=posix --prefix=/usr > >>--with-local-prefix=/usr/local --infodir=/usr/share/info > >>--mandir=/usr/share/man --libdir=/usr/lib --libexecdir=/usr/lib > >>--enable-languages=c,c++,objc,fortran,java,ada > >>--enable-checking=release > >>--with-gxx-include-dir=/usr/include/c++/4.1.0 --enable-ssp > >>--disable-libssp --enable-java-awt=gtk --enable-gtk-cairo > >>--disable-libjava-multilib --with-slibdir=/lib --with-system-zlib > >>--enable-shared --enable-__cxa_atexit > --enable-libstdcxx-allocator=new > >>--with-system-libunwind --host=ia64-suse-linux Thread > model: posix gcc > >>version 4.1.0 (SUSE Linux) > >>ia64 GNU/Linux > >> > >>Cheers, > >>Andreas > >> > >> > >> > > > > > > > > > > -- > Andreas Henschel > Bioinformatics Group > TU Dresden > Tatzberg 47-51 > 01307 Dresden, Germany > > Phone: +49 351 463 40063 > EMail: a...@biotec.tu-dresden.de > > > > -------------------------------------------------------------- > ----------- > This SF.net email is sponsored by DB2 Express Download DB2 > Express C - the FREE version of DB2 express and take control > of your XML. No limits. Just data. Click to get it now. > http://sourceforge.net/powerbar/db2/ > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
