Homebrew + Python on mac os x 10.8: Fatal Python error: PyThreadState_Get: no current thread importing mapnik
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:
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External Modification Summary:
Calls made by other processes targeting this process:
task_for_pid: 0
thread_create: 0
thread_set_state: 0
Calls made by this process:
task_for_pid: 0
thread_create: 0
thread_set_state: 0
Calls made by all processes on this machine:
task_for_pid: 18730
thread_create: 2
thread_set_state: 0
VM Region Summary:
ReadOnly portion of Libraries: Total=109.5M resident=53.3M(49%) swapped_out_or_unallocated=56.2M(51%)
Writable regions: Total=20.6M written=2644K(13%) resident=3256K(15%) swapped_out=0K(0%) unallocated=17.5M(85%)
REGION TYPE VIRTUAL
=========== =======
MALLOC 11.8M
MALLOC guard page 32K
STACK GUARD 56.0M
Stack 8192K
__DATA 2356K
__LINKEDIT 68.3M
__TEXT 41.2M
__UNICODE 544K
shared memory 12K
=========== =======
TOTAL 188.2M
Model: MacBookPro8,2, BootROM MBP81.0047.B27, 4 processors, Intel Core i7, 2 GHz, 8 GB, SMC 1.69f4
Graphics: Intel HD Graphics 3000, Intel HD Graphics 3000, Built-In, 512 MB
Graphics: AMD Radeon HD 6490M, AMD Radeon HD 6490M, PCIe, 256 MB
Memory Module: BANK 0/DIMM0, 4 GB, DDR3, 1333 MHz, 0x80CE, 0x4D34373142353237334348302D4348392020
Memory Module: BANK 1/DIMM0, 4 GB, DDR3, 1333 MHz, 0x80CE, 0x4D34373142353237334348302D4348392020
AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0xD6), Broadcom BCM43xx 1.0 (5.106.98.100.16)
Bluetooth: Version 4.1.3f3 11349, 2 service, 11 devices, 1 incoming serial ports
Network Service: Wi-Fi, AirPort, en1
Serial ATA Device: ST9500420AS, 500.11 GB
Serial ATA Device: MATSHITADVD-R UJ-898
USB Device: FaceTime HD Camera (Built-in), apple_vendor_id, 0x8509, 0xfa200000 / 3
USB Device: hub_device, 0x0424 (SMSC), 0x2513, 0xfa100000 / 2
USB Device: Apple Internal Keyboard / Trackpad, apple_vendor_id, 0x0246, 0xfa120000 / 5
USB Device: BRCM2070 Hub, 0x0a5c (Broadcom Corp.), 0x4500, 0xfa110000 / 4
USB Device: Bluetooth USB Host Controller, apple_vendor_id, 0x821a, 0xfa113000 / 8
USB Device: hub_device, 0x0424 (SMSC), 0x2513, 0xfd100000 / 2
USB Device: IR Receiver, apple_vendor_id, 0x8242, 0xfd110000 / 3
Any problems with linking my pythons? how can I fix it? thanks!
Answer
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.