Hi Doug, Sudo is nicer to use than root, but it's the same problem. You should only use root if/when you need it, like for "make install" if the install target is /usr/local. This is general Unix advice which you can google up if interested.
Regarding the Python install, don't worry about PYTHONPATH (this is used by Python to find packages for import) or PYTHONHOME (not used by Python itself). You have correctly configured the build to use the Python 2.7 install - there's just something wrong with that version of Python (or at least, that is who I read it - I'm not interested in debugging the various ways it is possible to misconfigure a Python installation for linking against). As I said in my previous email, just try the system Python. The parts will be in /usr/include and /usr/lib (or /usr/lib64). The issue with the usr/bin/tmp must be a symlink. You have an interestingly configured system there. - Noel On 14 November 2014 16:00, Douglas Houston <dhous...@staffmail.ed.ac.uk> wrote: > 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 ------------------------------------------------------------------------------ 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
