gcc is not the best compiler on an IA64 machine. We always recommend using the Intel compilers. Would it be possible to try those?
Concerning compilation of the pyMol on the IA64 architecture I am using the Intel compiler with the following options/flags in setup.py file at line #90:
ext_comp_args=["-ffast-math","-funroll-loops","-O3","-ip"] ext_link_args=["-limf","-lirc","-L/local/programs/icc/9.1.045/lib"] No more changes are necessary in my case. It works fine and pretty fast. On 5/2/07, Andreas Henschel <a...@biotec.tu-dresden.de> wrote:
DeLano Scientific wrote: >Andreas, > >Try removing -D_FORTIFY_SOURCE=2 as a compiler option... > > Hi Warren, I tried running gcc without that option manually - it worked. I did not find any place in the distutils/setup.py where this option (or the compiler itself) is set. Now I get this error: > python setup.py install --prefix=$PWD running install running build running build_py running build_ext 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/feedback2.c -o build/temp.linux-ia64-2.4/contrib/champ/feedback2.o contrib/champ/feedback2.c:121:1: error: unterminated argument list invoking macro "fprintf" contrib/champ/feedback2.c: In function 'feedback_Push': contrib/champ/feedback2.c:60: warning: statement with no effect contrib/champ/feedback2.c:60: error: expected ';' at end of input error: command 'gcc' failed with exit status 1 Any idea? Thanks again, Andreas >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 >> >> > > >------------------------------------------------------------------------- >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. 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