What Geoff said. Look at the output of "grep -i python CMakeCache.txt". I think you will find that bits of several different Pythons have been involved. To fix, specify the correct Python locations when configuring CMake.
- Noel On 27 February 2015 at 23:53, Geoffrey Hutchison <geoff.hutchi...@gmail.com> wrote: > I *strongly* recommend contacting the openbabel mailing list rather than me > personally. My e-mail box is horrendous. > > In this case, I suspect you either have multiple versions of Python > installed, or the active python is not able to load the _openbabel.so > correctly. > > I usually see this sort of error when you run one Python binary, but > _openbabel.so is linked against a different libpython. > > Others may have other suggestions. > > Hope that helps, > -Geoff > > > On Feb 26, 2015, at 12:10 PM, Damir Herman <damir.her...@gmail.com> wrote: > > Geoff, > > I saw you are an active contributor to openbabel so I wanted to ask you a > question about installation and running of python openbabel bindings on a > mac. > <Screen Shot 2015-02-26 at 9.08.01 AM.png> > I pulled openbabel from repo (details below). When I start python, here is > what I run into. I googled around, but noone reported this issue so far. Do > you think you can have a look? > > Thanks, > > --Damir > > Python 2.7.9 (default, Jan 7 2015, 11:49:12) > [GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.56)] on darwin > Type "help", "copyright", "credits" or "license" for more information. >>>> import openbabel > Traceback (most recent call last): > File "<stdin>", line 1, in <module> > File "/usr/local/lib/python2.7/site-packages/openbabel.py", line 1727 > def OBPlugin_List(PluginID, param=None, os): > SyntaxError: non-default argument follows default argument >>>> > > In /usr/local/lib/python2.7/site-packages/openbabel.py, line 1727 I have > > 1726 > 1727 def OBPlugin_List(PluginID, param=None, os): > 1728 return _openbabel.OBPlugin_List(PluginID, param, os) > 1729 OBPlugin_List = _openbabel.OBPlugin_List > 1730 > > If I replace the line 1727 with > > def OBPlugin_List(PluginID, os, param=None): > > when I import openbabel I get: > >>>> import openbabel > Fatal Python error: PyThreadState_Get: no current thread > Abort trap: 6 > > > ================= > tl;dr > > > cd var > git clone https://github.com/openbabel/openbabel.git > mkdir build > cd build > cmake -DBUILD_GUI=ON -DPYTHON_BINDINGS=ON -DRUN_SWIG=ON ../openbabel > output of cmake in cmake.out > make -j8 > make.out and make.err attached > sudo make install > install.out attached > > Openbabel command line utilities installed: > > obabel -V > Open Babel 2.3.90 -- Feb 26 2015 -- 08:58:33 > > > <cmake.out><make.out><make.err><install.out> > > > > ------------------------------------------------------------------------------ > Dive into the World of Parallel Programming The Go Parallel Website, > sponsored > by Intel and developed in partnership with Slashdot Media, is your hub for > all > things parallel software development, from weekly thought leadership blogs > to > news, videos, case studies, tutorials and more. Take a look and join the > conversation now. http://goparallel.sourceforge.net/ > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > ------------------------------------------------------------------------------ Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
