Thanks Noel, Should I use sudo instead of root?
Some more info: 'env | grep PYTHION' gives: PYTHONPATH=/usr/people/douglas/programs/mgltools_i86Linux2_1.5.4/MGLToolsPckgs PYTHONHOME=/usr/people/douglas/programs/mgltools_i86Linux2_1.5.4 This comes from this line in my .cshrc: source /usr/people/douglas/programs/mgltools_i86Linux2_1.5.4/bin/mglenv.csh 'grep PYTHON /usr/people/douglas/programs/mgltools_i86Linux2_1.5.4/bin/mglenv.csh' gives: unset PYTHONHOME setenv PYTHONHOME $MGL_ROOT setenv PYTHONPATH $MGL_ROOT/MGLToolsPckgs I know that if I don't run mglenv.csh each login AutoDockTools breaks. I have tried both this: '~douglas/programs/cmake-2.8.7/bin/cmake ~/openbabel-2.3.2 -DPYTHON_BINDINGS=ON -DPYTHON_INCLUDE_DIR=/usr/people/douglas/programs/mgltools_i86Linux2_1.5.4/include/python2.5/ -DPYTHON_LIBRARY=/usr/people/douglas/programs/mgltools_i86Linux2_1.5.4/lib/python2.5/ -DPYTHON_EXECUTABLE=/usr/people/douglas/programs/mgltools_i86Linux2_1.5.4/bin/python' and this: '~douglas/programs/cmake-2.8.7/bin/cmake ~/openbabel-2.3.2 -DPYTHON_BINDINGS=ON -DPYTHON_INCLUDE_DIR=/usr/local/include/python2.7 -DPYTHON_LIBRARY=/usr/local/lib/libpython2.7.a -DPYTHON_EXECUTABLE=/usr/local/bin/python2.7' The former fails with: [100%] Built target test_tetranonplanar [100%] Built target test_tetraplanar [100%] [100%] Built target test_unitcell Linking CXX shared module ../lib/_openbabel.so CMakeFiles/bindings_python.dir/python/openbabel-python.cpp.o: In function `SWIG_Python_ErrorType': /root/openbabel-2.3.2/scripts/python/openbabel-python.cpp:1010: undefined reference to `PyExc_RuntimeError' /root/openbabel-2.3.2/scripts/python/openbabel-python.cpp:977: undefined reference to `PyExc_MemoryError' /root/openbabel-2.3.2/scripts/python/openbabel-python.cpp:1007: undefined reference to `PyExc_AttributeError' /root/openbabel-2.3.2/scripts/python/openbabel-python.cpp:1004: undefined reference to `PyExc_SystemError' ... CMakeFiles/bindings_python.dir/python/openbabel-python.cpp.o: In function `assign<swig::SwigPySequence_Cont<OpenBabel::OBRing>, std::vector<OpenBabel::OBRing, std::allocator<Op enBabel::OBRing> > >': /root/openbabel-2.3.2/scripts/python/openbabel-python.cpp:4553: undefined reference to `PyErr_Occurred' CMakeFiles/bindings_python.dir/python/openbabel-python.cpp.o: In function `swig::traits_from_stdseq<std::vector<OpenBabel::vector3, std::allocator<OpenBabel::vector3> >, OpenBa bel::vector3>::from(std::vector<OpenBabel::vector3, std::allocator<OpenBabel::vector3> > const&)': /root/openbabel-2.3.2/scripts/python/openbabel-python.cpp:4886: undefined reference to `PyTuple_New' /root/openbabel-2.3.2/scripts/python/openbabel-python.cpp:4890: undefined reference to `PyTuple_SetItem' /root/openbabel-2.3.2/scripts/python/openbabel-python.cpp:4894: undefined reference to `PyExc_OverflowError' /root/openbabel-2.3.2/scripts/python/openbabel-python.cpp:4894: undefined reference to `PyErr_SetString' CMakeFiles/bindings_python.dir/python/openbabel-python.cpp.o:(.data.rel.ro+0x48): undefined reference to `PyObject_GenericGetAttr' CMakeFiles/bindings_python.dir/python/openbabel-python.cpp.o:(.data.rel.ro+0x108): undefined reference to `PyObject_GenericGetAttr' collect2: ld returned 1 exit status make[2]: *** [lib/_openbabel.so] Error 1 make[1]: *** [scripts/CMakeFiles/bindings_python.dir/all] Error 2 make: *** [all] Error 2 The latter fails with: [100%] Built target test_unitcell Linking CXX shared module ../lib/_openbabel.so /usr/local/lib/libpython2.7.a(thread.o): In function `_pythread_pthread_set_stacksize': /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:497: undefined reference to `pthread_attr_setstacksize' /usr/local/lib/libpython2.7.a(thread.o): In function `PyThread_release_lock': /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:350: undefined reference to `sem_post' /usr/local/lib/libpython2.7.a(thread.o): In function `PyThread_free_lock': /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:294: undefined reference to `sem_destroy' /usr/local/lib/libpython2.7.a(thread.o): In function `PyThread_allocate_lock': /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:269: undefined reference to `sem_init' /usr/local/lib/libpython2.7.a(thread.o): In function `PyThread_acquire_lock': /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:326: undefined reference to `sem_trywait' /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:324: undefined reference to `sem_wait' /usr/local/lib/libpython2.7.a(thread.o): In function `PyThread_start_new_thread': /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:184: undefined reference to `pthread_attr_setstacksize' /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:194: undefined reference to `pthread_create' /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:210: undefined reference to `pthread_detach' /usr/local/lib/libpython2.7.a(thread.o): In function `PyThread_release_lock': /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:350: undefined reference to `sem_post' /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:350: undefined reference to `sem_post' /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:350: undefined reference to `sem_post' /usr/local/lib/libpython2.7.a(thread.o): In function `PyThread_allocate_lock': /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:269: undefined reference to `sem_init' /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:269: undefined reference to `sem_init' /usr/local/lib/libpython2.7.a(posixmodule.o): In function `posix_forkpty': /usr/bin/tmp/Python-2.7.6/./Modules/posixmodule.c:3958: undefined reference to `forkpty' /usr/local/lib/libpython2.7.a(posixmodule.o): In function `posix_openpty': /usr/bin/tmp/Python-2.7.6/./Modules/posixmodule.c:3898: undefined reference to `openpty' collect2: ld returned 1 exit status make[2]: *** [lib/_openbabel.so] Error 1 make[1]: *** [scripts/CMakeFiles/bindings_python.dir/all] Error 2 make: *** [all] Error 2 In the latter case the errors mention /usr/bin/tmp/Python-2.7.6/ ... but I have not specified any location with 'tmp' in the path ... ? The output from 'grep PYTHON CMakeCache.txt' (below) also does not mention any pathname with 'tmp' in it ... so where is this coming from? PYTHON_BINDINGS:BOOL=ON PYTHON_EXECUTABLE:FILEPATH=/usr/local/bin/python2.7 PYTHON_INCLUDE_DIR:PATH=/usr/local/include/python2.7 PYTHON_LIBRARY:FILEPATH=/usr/local/lib/libpython2.7.a //ADVANCED property for variable: PYTHON_EXECUTABLE PYTHON_EXECUTABLE-ADVANCED:INTERNAL=1 //ADVANCED property for variable: PYTHON_INCLUDE_DIR PYTHON_INCLUDE_DIR-ADVANCED:INTERNAL=1 PYTHON_INCLUDE_PATH:INTERNAL=/usr/local/include/python2.7 //ADVANCED property for variable: PYTHON_LIBRARY PYTHON_LIBRARY-ADVANCED:INTERNAL=1 cheers, Doug Quoting Noel O'Boyle <baoille...@gmail.com> on Fri, 14 Nov 2014 13:05:04 +0000: > Hi Douglas, > > Your system appears to have at least two, and possibly more, competing > installations of Python. Is the Python 2.7 in /usr/local the same as > the one in /usr/bin/tmp? Either way you need to pick a Python > installation and stick with it - I would try the system Python first > of all, which appears to be Python 2.5 in your case. Does your PyMol > use a specific Python installation? - if so, try that one next. > > If you "grep PYTHON CMakeCache.txt" you will see which Python has been > found and what the variable names are. Something like "cmake .. > -DPYTHON_INCLUDE_DIR=whatever -DPYTHON_LIBRARY=whatever > -DPYTHON_EXECUTABLE=whatever" (check the variable names) will cover > all of the bases. If this is not clear, let us know. > > And as I always say on this list, as a general rule you should not > compile anything as root. This may lead to permissions problems down > the line which will be difficult to diagnose. > > Regards, > Noel > > On 14 November 2014 10:05, Douglas Houston > <dhous...@staffmail.ed.ac.uk> wrote: >> Hi all, >> >> I am trying to install a Pymol plugin and it requires my Open Babel to >> be re-installed, this time including the Python bindings: >> >> Python 2.5.1 (r251:54863, Sep 21 2007, 11:20:07) >> [GCC 3.2.3 20030502 (Red Hat Linux 3.2.3-56)] on linux2 >> Type "help", "copyright", "credits" or "license" for more information. >> import openbabel >> Traceback (most recent call last): File "<stdin>", line 1, in <module> >> ImportError: No module named openbabel >> >> >> I have tried recompiling Open Babel as root with the Python bindings using: >> >> tar -xvf openbabel-2.3.2.tar.gz >> cd openbabel-2.3.2 >> mkdir build >> cd build/ >> ~douglas/programs/cmake-2.8.7/bin/cmake ~/openbabel-2.3.2 >> -DPYTHON_BINDINGS=ON >> make -j2 >> >> >> but it fails with the following errors; can anyone help?: >> >> >> [100%] Building CXX object >> scripts/CMakeFiles/bindings_python.dir/python/openbabel-python.cpp.o >> Linking CXX executable ../bin/test_unitcell >> [100%] Built target test_unitcell >> Linking CXX shared module ../lib/_openbabel.so >> /usr/local/lib/libpython2.7.a(thread.o): In function >> `_pythread_pthread_set_stacksize': >> /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:497: undefined >> reference to `pthread_attr_setstacksize' >> /usr/local/lib/libpython2.7.a(thread.o): In function >> `PyThread_release_lock': >> /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:350: undefined >> reference to `sem_post' >> /usr/local/lib/libpython2.7.a(thread.o): In function `PyThread_free_lock': >> /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:294: undefined >> reference to `sem_destroy' >> /usr/local/lib/libpython2.7.a(thread.o): In function >> `PyThread_allocate_lock': >> /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:269: undefined >> reference to `sem_init' >> /usr/local/lib/libpython2.7.a(thread.o): In function >> `PyThread_acquire_lock': >> /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:326: undefined >> reference to `sem_trywait' >> /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:324: undefined >> reference to `sem_wait' >> /usr/local/lib/libpython2.7.a(thread.o): In function >> `PyThread_start_new_thread': >> /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:184: undefined >> reference to `pthread_attr_setstacksize' >> /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:194: undefined >> reference to `pthread_create' >> /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:210: undefined >> reference to `pthread_detach' >> /usr/local/lib/libpython2.7.a(thread.o): In function >> `PyThread_release_lock': >> /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:350: undefined >> reference to `sem_post' >> /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:350: undefined >> reference to `sem_post' >> /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:350: undefined >> reference to `sem_post' >> /usr/local/lib/libpython2.7.a(thread.o): In function >> `PyThread_allocate_lock': >> /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:269: undefined >> reference to `sem_init' >> /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:269: undefined >> reference to `sem_init' >> /usr/local/lib/libpython2.7.a(posixmodule.o): In function `posix_forkpty': >> /usr/bin/tmp/Python-2.7.6/./Modules/posixmodule.c:3958: undefined >> reference to `forkpty' >> /usr/local/lib/libpython2.7.a(posixmodule.o): In function `posix_openpty': >> /usr/bin/tmp/Python-2.7.6/./Modules/posixmodule.c:3898: undefined >> reference to `openpty' >> collect2: ld returned 1 exit status >> make[2]: *** [lib/_openbabel.so] Error 1 >> make[1]: *** [scripts/CMakeFiles/bindings_python.dir/all] Error 2 >> make: *** [all] Error 2 >> >> >> >> -- >> The University of Edinburgh is a charitable body, registered in >> Scotland, with registration number SC005336. >> >> >> >> ------------------------------------------------------------------------------ >> Comprehensive Server Monitoring with Site24x7. >> Monitor 10 servers for $9/Month. >> Get alerted through email, SMS, voice calls or mobile push notifications. >> Take corrective actions from your mobile device. >> http://pubads.g.doubleclick.net/gampad/clk?id=154624111&iu=/4140/ostg.clktrk >> _______________________________________________ >> OpenBabel-discuss mailing list >> OpenBabel-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ------------------------------------------------------------------------------ Comprehensive Server Monitoring with Site24x7. Monitor 10 servers for $9/Month. Get alerted through email, SMS, voice calls or mobile push notifications. Take corrective actions from your mobile device. http://pubads.g.doubleclick.net/gampad/clk?id=154624111&iu=/4140/ostg.clktrk _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
