Homebrew + Python on mac os x 10.8: Fatal Python error: PyThreadState_Get: no current thread importing mapnik
46,151
Solution 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.
Solution 2
I encountered the same problem between python27-apple and python27 (installed by Macport). I tried these steps, and it worked for me.
According to @Evert's comments of different libraries used by different python, I tried to revert the python27-apple to be "active".
sudo port select --list python
For my computer, it showed:
Available versions for python:
none
python25-apple
python26
python26-apple
python27 (active)
python27-apple
in which python27(by Macport) was currently active. Then,
sudo port select python python27-apple
to make python27-apple active as the default lib were called previously. To double check,
sudo port select --list python
It now showed:
Available versions for python:
none
python25-apple
python26
python26-apple
python27
python27-apple (active)
And the python crash had gone when I ran the scripts.
Solution 3
You can use the homebrew python like this:
/usr/bin/python2.7 yourscript.py
Solution 4
I face the similar problem in using androguard. Though it's not quite the same, it can be a reference. My crash also is Fatal Python error: PyThreadState_Get: no current thread
Abort trap: 6. Run otool -L <lib>, suggest the dylib link to the system python.
Try solution:
python-config --ldflags- Copy the output to corresponding MakeFile. For example change
LDFLAGS += -lm -lbz2 -lz -llzma -lsnappy -lmuparser -lpythontoLDFLAGS += -lm -lbz2 -lz -llzma -lsnappy -lmuparser -L/usr/local/Cellar/python/2.7.10_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/config -lpython2.7 -ldl -framework CoreFoundation. make clean, then make again.
Now the dylib is OK, and no error anymore.
Alternatively ...
... when you use otool -L <lib> to find the wrongly linked python dylib you can use install_name_tool to change the symbol like:
install_name_tool -change /System/Library/Frameworks/Python.framework/Versions/2.7/Python /usr/local/Cellar/python/2.7.6_1/Frameworks/Python.framework/Versions/2.7/lib/libpython2.7.dylib <lib>
Comments
-
otmezger about 4 years
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 enterimport mapnik, the following error comes and python exits:>>> import mapnik Fatal Python error: PyThreadState_Get: no current thread Abort trap: 6Mac 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 - 0x102961fff +org.python.python (2.7.3 - 2.7.3) <62DA7BCA-2A0C-3753-A043-7459827F56D1> /usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python 0x102964000 - 0x102a6cfff +org.python.python (2.7.3, [c] 2004-2012 Python Software Foundation. - 2.7.3) <81E6FB4A-287C-37C3-A26D-D045B604933F> /usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/Python 0x102c4c000 - 0x102c4efff +readline.so (0) <C4F1219C-CDFD-37D2-A762-22974D3F2918> /usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/readline.so 0x102c54000 - 0x102c77fff +libreadline.6.2.dylib (6.2) <2131C2A4-E75D-3680-9C8D-E42D78A5E1B9> /usr/local/opt/readline/lib/libreadline.6.2.dylib 0x102cfc000 - 0x102d01fff +itertools.so (0) <F857A819-40A9-3F72-A0B1-3E97BA5F3DAA> /usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/itertools.so 0x102d0a000 - 0x102f2cfff +_mapnik.so (0) <433DAD47-AB4D-37C5-A0EA-FE1134B63D3D> /usr/local/lib/python2.7/site-packages/mapnik/_mapnik.so 0x103603000 - 0x103978ff7 +libmapnik.dylib (0) <0E898678-9D86-35B4-A772-0248924F5BF3> /usr/local/Cellar/mapnik/2.1.0/lib/libmapnik.dylib 0x104138000 - 0x104170ff7 +libboost_python-mt.dylib (0) <9B5DD680-BEC9-3988-9F55-F59DA38CC175> /usr/local/lib/libboost_python-mt.dylib 0x1041b3000 - 0x1041c2ff7 +libboost_thread-mt.dylib (0) <24432300-9373-30B6-89F6-857CBEF9C105> /usr/local/lib/libboost_thread-mt.dylib 0x1041de000 - 0x10424dff7 +libfreetype.6.dylib (0) <490EDE42-5B78-34BA-85E7-D0547BE778E1> /usr/local/lib/libfreetype.6.dylib 0x104262000 - 0x104268fff +libltdl.7.dylib (0) <E437E59F-FC2E-3837-BDF8-301BEF13C7D6> /usr/local/lib/libltdl.7.dylib 0x10426c000 - 0x10428bff7 +libpng15.15.dylib (0) <52907DBF-A04C-325D-9E77-DF56A771026F> /usr/local/lib/libpng15.15.dylib 0x104293000 - 0x1042e6fff +libtiff.5.dylib (0) <AE85D7B1-F4E5-3B27-832D-5756EFCDE912> /usr/local/lib/libtiff.5.dylib 0x1042f2000 - 0x104326fff +libproj.0.dylib (0) <C799D9A7-0DDA-334D-9AEA-13A4AE7A67A2> /usr/local/lib/libproj.0.dylib 0x104333000 - 0x104441ff7 +libicuuc.50.1.dylib (0) <5FDBBF25-EEA6-3649-9ED6-B18CE89CE510> /usr/local/opt/icu4c/lib/libicuuc.50.1.dylib 0x1044a3000 - 0x1044b2fff +libboost_filesystem-mt.dylib (0) <B2C03485-5FA6-3744-BC99-DB4E87DA4D87> /usr/local/lib/libboost_filesystem-mt.dylib 0x1044c3000 - 0x1044c5ff7 +libboost_system-mt.dylib (0) <FE5E6E11-C7FB-3895-9976-526D22997EDC> /usr/local/lib/libboost_system-mt.dylib 0x1044ca000 - 0x104578fff +libboost_regex-mt.dylib (0) <BC1D7F46-F6AB-3964-B344-E692EFC5D3B7> /usr/local/lib/libboost_regex-mt.dylib 0x10461c000 - 0x10464bff7 +libjpeg.8.dylib (0) <9EC07360-CF18-3529-AE54-E60DBF1313DC> /usr/local/lib/libjpeg.8.dylib 0x104652000 - 0x105a24fff +libicudata.50.dylib (0) <B74D5789-7082-3084-9BF0-9A3AE6F2B046> /usr/local/opt/icu4c/lib/libicudata.50.dylib 0x105a26000 - 0x105b33fff org.python.python (2.7.2 - 2.7.2) <E7F3EED1-E55D-32AF-9649-77C814693F6A> /System/Library/Frameworks/Python.framework/Versions/2.7/Python 0x7fff62561000 - 0x7fff6259593f dyld (210.2.3) <36CAA36E-72BC-3E48-96D9-B96A2DF77730> /usr/lib/dyld 0x7fff8ae57000 - 0x7fff8ae7cff7 libc++abi.dylib (26) <D86169F3-9F31-377A-9AF3-DB17142052E4> /usr/lib/libc++abi.dylib 0x7fff8c50f000 - 0x7fff8c510ff7 libsystem_sandbox.dylib (220.2) <6838A6FD-8626-3356-BB4F-BB4787216207> /usr/lib/system/libsystem_sandbox.dylib 0x7fff8c511000 - 0x7fff8c523ff7 libz.1.dylib (43) <2A1551E8-A272-3DE5-B692-955974FE1416> /usr/lib/libz.1.dylib 0x7fff8d337000 - 0x7fff8d342fff libsystem_notify.dylib (98.5) <C49275CC-835A-3207-AFBA-8C01374927B6> /usr/lib/system/libsystem_notify.dylib 0x7fff8d9e6000 - 0x7fff8d9ebfff libcompiler_rt.dylib (30) <08F8731D-5961-39F1-AD00-4590321D24A9> /usr/lib/system/libcompiler_rt.dylib 0x7fff8dd72000 - 0x7fff8dd73fff libDiagnosticMessagesClient.dylib (8) <8548E0DC-0D2F-30B6-B045-FE8A038E76D8> /usr/lib/libDiagnosticMessagesClient.dylib 0x7fff902d7000 - 0x7fff90326ff7 libcorecrypto.dylib (106.2) <CE0C29A3-C420-339B-ADAA-52F4683233CC> /usr/lib/system/libcorecrypto.dylib 0x7fff9064f000 - 0x7fff90650fff libsystem_blocks.dylib (59) <D92DCBC3-541C-37BD-AADE-ACC75A0C59C8> /usr/lib/system/libsystem_blocks.dylib 0x7fff90a75000 - 0x7fff90a7dff7 libsystem_dnssd.dylib (379.37) <616FC901-151E-38BF-B2C4-24A351C5FAAD> /usr/lib/system/libsystem_dnssd.dylib 0x7fff914fd000 - 0x7fff9150afff libbz2.1.0.dylib (29) <CE9785E8-B535-3504-B392-82F0064D9AF2> /usr/lib/libbz2.1.0.dylib 0x7fff92899000 - 0x7fff928a7fff libcommonCrypto.dylib (60027) <BAAFE0C9-BB86-3CA7-88C0-E3CBA98DA06F> /usr/lib/system/libcommonCrypto.dylib 0x7fff92aa4000 - 0x7fff92b70ff7 libsystem_c.dylib (825.26) <4C9EB006-FE1F-3F8F-8074-DFD94CF2CE7B> /usr/lib/system/libsystem_c.dylib 0x7fff92bba000 - 0x7fff92bc0ff7 libunwind.dylib (35.1) <21703D36-2DAB-3D8B-8442-EAAB23C060D3> /usr/lib/system/libunwind.dylib 0x7fff92ed3000 - 0x7fff92f3cfff libstdc++.6.dylib (56) <EAA2B53E-EADE-39CF-A0EF-FB9D4940672A> /usr/lib/libstdc++.6.dylib 0x7fff93019000 - 0x7fff93065ff7 libauto.dylib (185.1) <73CDC482-16E3-3FC7-9BB4-FBA2DA44DBC2> /usr/lib/libauto.dylib 0x7fff930cf000 - 0x7fff930d5fff libmacho.dylib (829) <BF332AD9-E89F-387E-92A4-6E1AB74BD4D9> /usr/lib/system/libmacho.dylib 0x7fff93177000 - 0x7fff93199ff7 libxpc.dylib (140.42) <BBE558BD-5E55-35E4-89ED-1AA6B056D05A> /usr/lib/system/libxpc.dylib 0x7fff931f6000 - 0x7fff931f7ff7 libremovefile.dylib (23.2) <6763BC8E-18B8-3AD9-8FFA-B43713A7264F> /usr/lib/system/libremovefile.dylib 0x7fff931f8000 - 0x7fff93260ff7 libc++.1.dylib (65.1) <20E31B90-19B9-3C2A-A9EB-474E08F9FE05> /usr/lib/libc++.1.dylib 0x7fff9345d000 - 0x7fff9365dfff libicucore.A.dylib (491.11.2) <FD6282D8-DF3F-3842-8C2E-CF478D2B9669> /usr/lib/libicucore.A.dylib 0x7fff9365e000 - 0x7fff9365efff libkeymgr.dylib (25) <CC9E3394-BE16-397F-926B-E579B60EE429> /usr/lib/system/libkeymgr.dylib 0x7fff936d4000 - 0x7fff936dcfff liblaunch.dylib (442.26.2) <2F71CAF8-6524-329E-AC56-C506658B4C0C> /usr/lib/system/liblaunch.dylib 0x7fff9424d000 - 0x7fff9427bff7 libsystem_m.dylib (3022.6) <B434BE5C-25AB-3EBD-BAA7-5304B34E3441> /usr/lib/system/libsystem_m.dylib 0x7fff94284000 - 0x7fff94286fff libquarantine.dylib (52) <4BE2E642-A14F-340A-B482-5BD2AEFD9C24> /usr/lib/system/libquarantine.dylib 0x7fff94381000 - 0x7fff94382ff7 libdnsinfo.dylib (453.19) <14202FFB-C3CA-3FCC-94B0-14611BF8692D> /usr/lib/system/libdnsinfo.dylib 0x7fff944ef000 - 0x7fff9450aff7 libsystem_kernel.dylib (2050.22.13) <5A961E2A-CFB8-362B-BC43-122704AEB047> /usr/lib/system/libsystem_kernel.dylib 0x7fff94579000 - 0x7fff94587ff7 libsystem_network.dylib (77.10) <0D99F24E-56FE-380F-B81B-4A4C630EE587> /usr/lib/system/libsystem_network.dylib 0x7fff94821000 - 0x7fff9493992f libobjc.A.dylib (532.2) <90D31928-F48D-3E37-874F-220A51FD9E37> /usr/lib/libobjc.A.dylib 0x7fff9493a000 - 0x7fff9494fff7 libdispatch.dylib (228.23) <D26996BF-FC57-39EB-8829-F63585561E09> /usr/lib/system/libdispatch.dylib 0x7fff95c25000 - 0x7fff95d22ff7 libxml2.2.dylib (22.3) <47B09CB2-C636-3024-8B55-6040F7829B4C> /usr/lib/libxml2.2.dylib 0x7fff96350000 - 0x7fff96351ff7 libSystem.B.dylib (169.3) <9089D72D-E714-31E1-80C8-698A8E8B05AD> /usr/lib/libSystem.B.dylib 0x7fff96397000 - 0x7fff9639cfff libcache.dylib (57) <65187C6E-3FBF-3EB8-A1AA-389445E2984D> /usr/lib/system/libcache.dylib 0x7fff96646000 - 0x7fff9664dfff libcopyfile.dylib (89) <876573D0-E907-3566-A108-577EAD1B6182> /usr/lib/system/libcopyfile.dylib 0x7fff966bd000 - 0x7fff966c0ff7 libdyld.dylib (210.2.3) <F59367C9-C110-382B-A695-9035A6DD387E> /usr/lib/system/libdyld.dylib 0x7fff96961000 - 0x7fff96963ff7 libunc.dylib (25) <92805328-CD36-34FF-9436-571AB0485072> /usr/lib/system/libunc.dylib 0x7fff974ba000 - 0x7fff974f0fff libsystem_info.dylib (406.17) <4FFCA242-7F04-365F-87A6-D4EFB89503C1> /usr/lib/system/libsystem_info.dylib 0x7fff97850000 - 0x7fff97888fff libncurses.5.4.dylib (37.3) <68D5B5F5-8252-3F1E-AFF1-C6AFE145DBC1> /usr/lib/libncurses.5.4.dylib 0x7fff978d3000 - 0x7fff97abdff7 com.apple.CoreFoundation (6.8 - 744.18) <A60C3C9B-3764-3291-844C-C487ACF77C2C> /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation 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 / 3Any problems with linking my pythons? how can I fix it? thanks!