Homebrew + Python on mac os x 10.8: Fatal Python error: PyThreadState_Get: no current thread importing mapnik

Question

I have 2 pythons on my mac (10.8.3): The default, and 2.7 version from homebrew.

So far, I could install modules and use them with my brew python. I installed mapnik with brew install mapnik (mapnik-2.1.0) and it compiled correctly. But, if I open python and enter import mapnik, the following error comes and python exits:

>>> import mapnik Fatal Python error: PyThreadState_Get: no current thread Abort trap: 6 

Mac os x also shows an error window, with the following content:

Process:         Python [60666] Path:            /usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python Identifier:      Python Version:         2.7.3 (2.7.3) Code Type:       X86-64 (Native) Parent Process:  bash [60454] User ID:         501  Date/Time:       2013-03-28 10:21:08.535 +0100 OS Version:      Mac OS X 10.8.3 (12D78) Report Version:  10  Interval Since Last Report:          128837 sec Crashes Since Last Report:           5 Per-App Crashes Since Last Report:   4 Anonymous UUID:                      567121E6-7BAC-335F-E3B0-DD24D1F9E6BA  Crashed Thread:  0  Dispatch queue: com.apple.main-thread  Exception Type:  EXC_CRASH (SIGABRT) Exception Codes: 0x0000000000000000, 0x0000000000000000  Application Specific Information: abort() called  Thread 0 Crashed:: Dispatch queue: com.apple.main-thread 0   libsystem_kernel.dylib          0x00007fff94500d46 __kill + 10 1   libsystem_c.dylib               0x00007fff92afddf0 abort + 177 2   org.python.python               0x0000000105a77eaa Py_FatalError + 49 3   org.python.python               0x0000000105a76370 PyThreadState_Get + 28 4   org.python.python               0x0000000105a71f16 Py_InitModule4_64 + 58 5   libboost_python-mt.dylib        0x0000000104153288 boost::python::detail::init_module(char const*, void (*)()) + 40 6   org.python.python               0x00000001029fa716 _PyImport_LoadDynamicModule + 150 7   org.python.python               0x00000001029fa428 import_submodule + 296 8   org.python.python               0x00000001029f9ff1 load_next + 268 9   org.python.python               0x00000001029f80fb PyImport_ImportModuleLevel + 794 10  org.python.python               0x00000001029de9d3 builtin___import__ + 132 11  org.python.python               0x000000010296e335 PyObject_Call + 101 12  org.python.python               0x00000001029e8e10 PyEval_CallObjectWithKeywords + 93 13  org.python.python               0x00000001029e61b6 PyEval_EvalFrameEx + 11727 14  org.python.python               0x00000001029e32bd PyEval_EvalCodeEx + 1638 15  org.python.python               0x00000001029e2c51 PyEval_EvalCode + 54 16  org.python.python               0x00000001029f6e58 PyImport_ExecCodeModuleEx + 247 17  org.python.python               0x00000001029f99bf load_source_module + 1053 18  org.python.python               0x00000001029f9c7e load_package + 334 19  org.python.python               0x00000001029fa428 import_submodule + 296 20  org.python.python               0x00000001029f9ff1 load_next + 268 21  org.python.python               0x00000001029f80fb PyImport_ImportModuleLevel + 794 22  org.python.python               0x00000001029de9d3 builtin___import__ + 132 23  org.python.python               0x000000010296e335 PyObject_Call + 101 24  org.python.python               0x00000001029e8e10 PyEval_CallObjectWithKeywords + 93 25  org.python.python               0x00000001029e61b6 PyEval_EvalFrameEx + 11727 26  org.python.python               0x00000001029e32bd PyEval_EvalCodeEx + 1638 27  org.python.python               0x00000001029e2c51 PyEval_EvalCode + 54 28  org.python.python               0x0000000102a01a2b run_mod + 53 29  org.python.python               0x0000000102a0184d PyRun_InteractiveOneFlags + 365 30  org.python.python               0x0000000102a01367 PyRun_InteractiveLoopFlags + 188 31  org.python.python               0x0000000102a01218 PyRun_AnyFileExFlags + 60 32  org.python.python               0x0000000102a120b2 Py_Main + 3210 33  libdyld.dylib                   0x00007fff966bf7e1 start + 1  Thread 0 crashed with X86 Thread State (64-bit):   rax: 0x0000000000000000  rbx: 0x00007fff5d29c2b0  rcx: 0x00007fff5d29c298  rdx: 0x0000000000000000   rdi: 0x000000000000ecfa  rsi: 0x0000000000000006  rbp: 0x00007fff5d29c2c0  rsp: 0x00007fff5d29c298    r8: 0x00000000000003f5   r9: 0x00007fff5d29c270  r10: 0x00007fff94502342  r11: 0x0000000000000206   r12: 0x00007fff5d29cb00  r13: 0x0000000102e9b656  r14: 0x00000000000003f5  r15: 0x0000000000000000   rip: 0x00007fff94500d46  rfl: 0x0000000000000206  cr2: 0x00007fff7bff7ff0 Logical CPU: 0  Binary Images:        0x102961000 - 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Any problems with linking my pythons? how can I fix it? thanks!

Answer 1

It looks like you are running the homebrew python but either boost python or mapnik's python bindings ended up linking against the system python provided by apple. If a full clean and reinstall of boost and Mapnik does not fix this then I recommend stopping by #mapnik irc on freenode for help debugging. Generally to fix you need to call otool -L on boost_python.dylib and or on site_packages/mapnik/_mapnik.so to see which ended up with a linkage to the system python. Then you can fix by using install_name_tool.