Re: [PyMOL] PyMOL compilation from source
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From: Michael Kluge <Michael.Kluge@tu...> - 2007-04-28 05:04:22
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Hi Andreas, > PS. @Michael > From Martin Hoefling: >=20 >> i have no idea about your error but i can provide you RPMs for=20 >> Opensuse 10.2 i586 and x86_64, if you need them for other SuSE=20 >> distributions, I can try to add them to my repository. >> > Would that be feasable? You could try the IA32 stuff in the Itanium. But that runs through an=20 IA32 emulation layer. Thats like running with ball and chains. For a GUI=20 is this probably OK as processor utilization is not the key, but for HPC=20 it is just slow. We have 2584 Core AMD Athlon PC Farm. Maybe you want to=20 try deimos? Michael ____________________________________________ Michael Kluge, M.Sc. Technische Universit=E4t Dresden Center for Information Services and High Performance Computing (ZIH) D-01062 Dresden Germany Contact: Room : HRSK 151 Phone: (+49) 351 463 32424 Fax : (+49) 351 463 37773 email: michael.kluge@... |
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From: Siv Midtun Hollup <sivh@ii...> - 2007-04-26 12:32:10
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Hi, I was wondering if it's possible to redefine the x, y and z axis using coordinates of your own choice. I would like to not only set origin for a coordinates system, but also where the x, y and z axes go. I know how to get coordinates and unit vectors for the new coordinate system, but I don't know where to input them to get the effect that I want in PYMOL :) Btw, thanks very much for the help with the spheres, that worked out just great :) Cheers, Siv -- Siv Midtun Hollup PhD Student Dept. of Informatics University of Bergen, Norway sivh@... (NOTE: new email adress) - Blessed are the flexible, for they can be tied into knots. - |
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From: Andreas Henschel <ah@bi...> - 2007-04-26 13:52:51
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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: ah@...
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From: Michael Kluge <Michael.Kluge@tu...> - 2007-04-26 13:58:21
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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? Regards, Michael Andreas Henschel wrote: > Hi all, >=20 > did anyone of you come across the mysterious "internal compiler error: > Segmentation fault" > while compiling pymol from source? >=20 > The offending lines are in contrib/champ/champ.c:2787 >=20 > PRINTFD(FB_smiles_parsing) > " ChampParseBlockAtom: called.\n" > ENDFD; >=20 > Can I get around it somehow? Is it a 64-bit/gcc issue? > Any help would be greatly appreciated. >=20 > Some more error/system details: >=20 >> python setup.py install > ... > building 'chempy.champ._champ' extension > gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -fmessage-length=3D0 -Wa= ll > -D_FORTIFY_SOURCE=3D2 -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 >=20 >> 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 >=20 >> gcc -v > Using built-in specs. > Target: ia64-suse-linux > Configured with: ../configure --enable-threads=3Dposix --prefix=3D/usr > --with-local-prefix=3D/usr/local --infodir=3D/usr/share/info > --mandir=3D/usr/share/man --libdir=3D/usr/lib --libexecdir=3D/usr/lib > --enable-languages=3Dc,c++,objc,fortran,java,ada --enable-checking=3Dre= lease > --with-gxx-include-dir=3D/usr/include/c++/4.1.0 --enable-ssp > --disable-libssp --enable-java-awt=3Dgtk --enable-gtk-cairo > --disable-libjava-multilib --with-slibdir=3D/lib --with-system-zlib > --enable-shared --enable-__cxa_atexit --enable-libstdcxx-allocator=3Dne= w > --with-system-libunwind --host=3Dia64-suse-linux > Thread model: posix > gcc version 4.1.0 (SUSE Linux) > ia64 GNU/Linux >=20 > Cheers, > Andreas >=20 --=20 ____________________________________________ Michael Kluge, M.Sc. Technische Universit=E4t Dresden Center for Information Services and High Performance Computing (ZIH) D-01062 Dresden Germany Contact: Willersbau, Room HRSK 151 Phone: (+49) 351 463-32424 Fax: (+49) 351 463-37773 e-mail: michael.kluge@... WWW: http://www.tu-dresden.de/zih |
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From: Andreas Henschel <ah@bi...> - 2007-04-27 21:27:37
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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: ah@... |
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From: DeLano Scientific <delsci@de...> - 2007-04-30 22:22:50
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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-bounces@... > [mailto:pymol-users-bounces@...] On Behalf > Of Andreas Henschel > Sent: Friday, April 27, 2007 2:28 PM > To: Michael Kluge > Cc: pymol-users@... > 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: ah@... > > > > -------------------------------------------------------------- > ----------- > 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@... > https://lists.sourceforge.net/lists/listinfo/pymol-users |
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From: Andreas Henschel <ah@bi...> - 2007-05-02 13:16:52
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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-bounces@... >>[mailto:pymol-users-bounces@...] On Behalf >>Of Andreas Henschel >>Sent: Friday, April 27, 2007 2:28 PM >>To: Michael Kluge >>Cc: pymol-users@... >>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: ah@... >> >> >> >>-------------------------------------------------------------- >>----------- >>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@... >>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. Click to get it now. >http://sourceforge.net/powerbar/db2/ >_______________________________________________ >PyMOL-users mailing list >PyMOL-users@... >https://lists.sourceforge.net/lists/listinfo/pymol-users > > -- Andreas Henschel Bioinformatics Group TU Dresden Tatzberg 47-51 01307 Dresden, Germany Phone: +49 351 463 40063 EMail: ah@... |
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From: Andrew Ryzhkov <redandr@gm...> - 2007-05-02 15:04:51
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>>>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 <ah@...> 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-bounces@... > >>[mailto:pymol-users-bounces@...] On Behalf > >>Of Andreas Henschel > >>Sent: Friday, April 27, 2007 2:28 PM > >>To: Michael Kluge > >>Cc: pymol-users@... > >>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: ah@... > >> > >> > >> > >>-------------------------------------------------------------- > >>----------- > >>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@... > >>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. Click to get it now. > >http://sourceforge.net/powerbar/db2/ > >_______________________________________________ > >PyMOL-users mailing list > >PyMOL-users@... > >https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > > > -- > Andreas Henschel > Bioinformatics Group > TU Dresden > Tatzberg 47-51 > 01307 Dresden, Germany > > Phone: +49 351 463 40063 > EMail: ah@... > > > > ------------------------------------------------------------------------- > 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@... > https://lists.sourceforge.net/lists/listinfo/pymol-users > -- Andrew B. Ryzhkov RedAndr@... http://www.meteo.mcgill.ca/andrew |
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From: Michael Kluge <Michael.Kluge@tu...> - 2007-04-28 05:04:22
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Hi Andreas, > PS. @Michael > From Martin Hoefling: >=20 >> i have no idea about your error but i can provide you RPMs for=20 >> Opensuse 10.2 i586 and x86_64, if you need them for other SuSE=20 >> distributions, I can try to add them to my repository. >> > Would that be feasable? You could try the IA32 stuff in the Itanium. But that runs through an=20 IA32 emulation layer. Thats like running with ball and chains. For a GUI=20 is this probably OK as processor utilization is not the key, but for HPC=20 it is just slow. We have 2584 Core AMD Athlon PC Farm. Maybe you want to=20 try deimos? Michael ____________________________________________ Michael Kluge, M.Sc. Technische Universit=E4t Dresden Center for Information Services and High Performance Computing (ZIH) D-01062 Dresden Germany Contact: Room : HRSK 151 Phone: (+49) 351 463 32424 Fax : (+49) 351 463 37773 email: michael.kluge@... |
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From: Martin <martin.hoefling@gm...> - 2007-04-28 19:55:34
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Am Samstag, 28. April 2007 schrieb Michael Kluge: > > Would that be feasable? Oh sorry, i overlooked the ia64 in your gcc line. I have no idea how much I= A64=20 SuSE, differs from the others. OpenSuSE is only provided for i586 and=20 x86_64, not Itanium. But if you want, you can either use my spec file and=20 compile yourself or I can also ask the guys here at the LRZ if they can che= ck=20 this. I am using opensuse build service to build for Opensuse 10.2 http://build.opensuse.org/project/monitor?project=3Dhome%3Amartoss > You could try the IA32 stuff in the Itanium. But that runs through an > IA32 emulation layer. Thats like running with ball and chains. For a GUI The emulation layer is really... =2E.. slow :-). Newer Itaniums don't even have hardware support for=20 this "feature" but do it entirely in SW.=20 > is this probably OK as processor utilization is not the key, but for HPC > it is just slow. We have 2584 Core AMD Athlon PC Farm. Maybe you want to > try deimos? Hmm, still did not get the point? Do you wanna run pymol on a cluster and n= ot=20 on a workstation? Most workstations are intel core or opteron/athlon64 base= d. Cheers Martin =2D-=20 Echt frustrierend, wenn man so vor seiner Hardware sitzt und den min=FCtlichen Preisverfall verfolgt... (John Gawe in de.comp misc) |