[Insight-users] Installing python ITK Mac
Bradley Lowekamp
blowekamp at mail.nih.gov
Thu Jun 13 21:36:29 EDT 2013
Thanks for including that extra bit of information!
This is not a system python. It looks like you might have an Enthought distribution.
What is the output of: "which python" and "python --version".
The current mountian lion system python version is 2.7.2. And it located here: /System/Library/Frameworks/Python.framework/Versions/2.7/
It also looks like you have some libraries from the system and others from the Enthought distribution. It likely is not stable in and of it's self. You should check you python related environment variable to ensure things are consistent.
If you wish to use SimpleITK in your custom python you will need to build it yourself[[1], and ensure that the cmake configuration points to the correct headers, libraries and executables for said python distribution.
Brad
[1] http://www.itk.org/Wiki/SimpleITK/GettingStarted#Build_It_Yourself
On Jun 13, 2013, at 9:00 PM, marvey99 <m.doyley at rochester.edu> wrote:
> /Library/Frameworks/Python.framework/Versions/7.3/Resources/Python.app/Contents/MacOS/Python
On Jun 13, 2013, at 9:00 PM, marvey99 <m.doyley at rochester.edu> wrote:
> Hi there,
>
> I get the following error message
> Fatal Python error: PyThreadState_Get: no current thread
>
> tanks
> M
>
> PS
>
> Here is the problem details and system configuration
>
> Process: Python [25953]
> Path:
> /Library/Frameworks/Python.framework/Versions/7.3/Resources/Python.app/Contents/MacOS/Python
> Identifier: Python
> Version: 2.7.3 (2.7.3)
> Code Type: X86 (Native)
> Parent Process: zsh [24886]
> User ID: 501
>
> Date/Time: 2013-06-13 20:56:14.902 -0400
> OS Version: Mac OS X 10.8.4 (12E55)
> Report Version: 10
>
> Interval Since Last Report: 722 sec
> Crashes Since Last Report: 1
> Per-App Crashes Since Last Report: 1
> Anonymous UUID: D2249165-2EA6-8258-4636-429BDF19B97D
>
> 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 0x97125a6a __pthread_kill + 10
> 1 libsystem_c.dylib 0x971b5b2f pthread_kill + 101
> 2 libsystem_c.dylib 0x971ec4ec abort + 168
> 3 org.python.python 0x0a5782d2 Py_FatalError + 61
> 4 org.python.python 0x0a5776d6 PyThreadState_Get + 35
> 5 org.python.python 0x0a56fc80 Py_InitModule4 + 40
> 6 _SimpleITK.so 0x02e56ca3 init_SimpleITK + 611
> 7 org.python.python 0x000e76d7 _PyImport_LoadDynamicModule +
> 167
> 8 org.python.python 0x000e5063 load_module + 227
> 9 org.python.python 0x000e6fef imp_load_module + 207
> 10 org.python.python 0x000cb2d1 PyEval_EvalFrameEx + 21649
> 11 org.python.python 0x000cc053 PyEval_EvalFrameEx + 25107
> 12 org.python.python 0x000cd02a PyEval_EvalCodeEx + 2042
> 13 org.python.python 0x000cd1b7 PyEval_EvalCode + 87
> 14 org.python.python 0x000e3ccc PyImport_ExecCodeModuleEx +
> 188
> 15 org.python.python 0x000e496c load_source_module + 540
> 16 org.python.python 0x000e558d import_submodule + 301
> 17 org.python.python 0x000e57e9 load_next + 201
> 18 org.python.python 0x000e6198 PyImport_ImportModuleLevel +
> 344
> 19 org.python.python 0x000bf38f builtin___import__ + 159
> 20 org.python.python 0x0000f635 PyObject_Call + 85
> 21 org.python.python 0x000c4eae PyEval_CallObjectWithKeywords
> + 78
> 22 org.python.python 0x000c7512 PyEval_EvalFrameEx + 5842
> 23 org.python.python 0x000cd02a PyEval_EvalCodeEx + 2042
> 24 org.python.python 0x000cb9db PyEval_EvalFrameEx + 23451
> 25 org.python.python 0x000cd02a PyEval_EvalCodeEx + 2042
> 26 org.python.python 0x000cb253 PyEval_EvalFrameEx + 21523
> 27 org.python.python 0x000cd02a PyEval_EvalCodeEx + 2042
> 28 org.python.python 0x000cb253 PyEval_EvalFrameEx + 21523
> 29 org.python.python 0x000cd02a PyEval_EvalCodeEx + 2042
> 30 org.python.python 0x000cb253 PyEval_EvalFrameEx + 21523
> 31 org.python.python 0x000cd02a PyEval_EvalCodeEx + 2042
> 32 org.python.python 0x000cb253 PyEval_EvalFrameEx + 21523
> 33 org.python.python 0x000cd02a PyEval_EvalCodeEx + 2042
> 34 org.python.python 0x000cb253 PyEval_EvalFrameEx + 21523
> 35 org.python.python 0x000cd02a PyEval_EvalCodeEx + 2042
> 36 org.python.python 0x000cb253 PyEval_EvalFrameEx + 21523
> 37 org.python.python 0x000cd02a PyEval_EvalCodeEx + 2042
> 38 org.python.python 0x000cb253 PyEval_EvalFrameEx + 21523
> 39 org.python.python 0x000cd02a PyEval_EvalCodeEx + 2042
> 40 org.python.python 0x000cd1b7 PyEval_EvalCode + 87
> 41 org.python.python 0x000f1898 PyRun_FileExFlags + 168
> 42 org.python.python 0x000f27c3 PyRun_SimpleFileExFlags + 867
> 43 org.python.python 0x0010ba58 Py_Main + 3560
> 44 org.python.python 0x00001fb6 0x1000 + 4022
>
> Thread 1:
> 0 libsystem_kernel.dylib 0x971258e2 __psynch_cvwait + 10
> 1 libsystem_c.dylib 0x971b9280 _pthread_cond_wait + 833
> 2 libsystem_c.dylib 0x9723f095 pthread_cond_wait$UNIX2003 +
> 71
> 3 org.python.python 0x0010882c PyThread_acquire_lock + 172
> 4 org.python.python 0x000c4b73 PyEval_RestoreThread + 67
> 5 org.python.python 0x0010d7ee lock_PyThread_acquire_lock +
> 94
> 6 org.python.python 0x000cb2d1 PyEval_EvalFrameEx + 21649
> 7 org.python.python 0x000cd02a PyEval_EvalCodeEx + 2042
> 8 org.python.python 0x000cb253 PyEval_EvalFrameEx + 21523
> 9 org.python.python 0x000cd02a PyEval_EvalCodeEx + 2042
> 10 org.python.python 0x000cb253 PyEval_EvalFrameEx + 21523
> 11 org.python.python 0x000cd02a PyEval_EvalCodeEx + 2042
> 12 org.python.python 0x00042282 function_call + 162
> 13 org.python.python 0x0000f635 PyObject_Call + 85
> 14 org.python.python 0x000c889b PyEval_EvalFrameEx + 10843
> 15 org.python.python 0x000cd02a PyEval_EvalCodeEx + 2042
> 16 org.python.python 0x000cb253 PyEval_EvalFrameEx + 21523
> 17 org.python.python 0x000cc053 PyEval_EvalFrameEx + 25107
> 18 org.python.python 0x000cc053 PyEval_EvalFrameEx + 25107
> 19 org.python.python 0x000cd02a PyEval_EvalCodeEx + 2042
> 20 org.python.python 0x00042282 function_call + 162
> 21 org.python.python 0x0000f635 PyObject_Call + 85
> 22 org.python.python 0x00021fe6 instancemethod_call + 422
> 23 org.python.python 0x0000f635 PyObject_Call + 85
> 24 org.python.python 0x000c4eae PyEval_CallObjectWithKeywords
> + 78
> 25 org.python.python 0x0010e18c t_bootstrap + 76
> 26 libsystem_c.dylib 0x971b45b7 _pthread_start + 344
> 27 libsystem_c.dylib 0x9719ed4e thread_start + 34
>
> Thread 0 crashed with X86 Thread State (32-bit):
> eax: 0x00000000 ebx: 0x000e7641 ecx: 0xbfffc3ac edx: 0x97125a6a
> edi: 0xac982a28 esi: 0x00000006 ebp: 0xbfffc3c8 esp: 0xbfffc3ac
> ss: 0x00000023 efl: 0x00000206 eip: 0x97125a6a cs: 0x0000000b
> ds: 0x00000023 es: 0x00000023 fs: 0x00000000 gs: 0x0000000f
> cr2: 0x971ec444
> Logical CPU: 0
>
> Binary Images:
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> 0x180c000 - 0x1843ffe umath.so (27.4)
> <F31C1D02-F34A-36F5-847C-16CB5DC6610A>
> /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/umath.so
> 0x184f000 - 0x1860ff7 _sort.so (27.4)
> <36D7E10C-CC33-3A4A-9717-29F165644354>
> /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/_sort.so
> 0x1865000 - 0x1868fff lapack_lite.so (27.4)
> <5F19143C-5AA0-36F7-AA00-8E265424BDBB>
> /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/linalg/lapack_lite.so
> 0x18cc000 - 0x18e6ff0 scalarmath.so (27.4)
> <078B9F29-CD28-3635-BCBC-4CFC6B392BEA>
> /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/scalarmath.so
> 0x18eb000 - 0x18f2ff7 fftpack_lite.so (27.4)
> <A7DDC6B2-A865-32DC-BC62-131527F45C56>
> /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/fft/fftpack_lite.so
> 0x18f6000 - 0x1926ff3 mtrand.so (27.4)
> <A1DCD33B-924B-3F27-A49F-E5EEC203416D>
> /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/random/mtrand.so
> 0x195f000 - 0x1960fff +_lsprof.so (???)
> <852839FB-C3ED-1669-65D0-6657C5739861>
> /Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/lib-dynload/_lsprof.so
> 0x1a6c000 - 0x1b0dff9 multiarray.so (27.4)
> <3A9DA8B8-2C58-3FB0-B491-968A52101BA4>
> /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/multiarray.so
> 0x1ba1000 - 0x1bd4ff8 +readline.so (???)
> <684DA6D4-53DD-392D-B546-6D5F233C0B33>
> /Library/Python/2.7/site-packages/readline-6.2.2-py2.7-macosx-10.7-intel.egg/readline.so
> 0x2b00000 - 0x835bfef +_SimpleITK.so (???)
> <FB2AC7F6-776D-3FF8-9298-B7B7E83ED74B>
> /Library/Python/2.7/site-packages/SimpleITK-0.6.1-py2.7-macosx-10.7-intel.egg/_SimpleITK.so
> 0xa551000 - 0xa639fff org.python.python (2.7.2 - 2.7.2)
> <75ACA258-5309-329E-9D4E-EADA3FBD8406>
> /System/Library/Frameworks/Python.framework/Versions/2.7/Python
> 0x8fec7000 - 0x8fef9e57 dyld (210.2.3)
> <23516BE4-29BE-350C-91C9-F36E7999F0F1> /usr/lib/dyld
> 0x90007000 - 0x90007fff libsystem_blocks.dylib (59)
> <3A743C5D-CFA5-37D8-80A8-B6795A9DB04F>
> /usr/lib/system/libsystem_blocks.dylib
> 0x90008000 - 0x90016ff3 libsystem_network.dylib (77.10)
> <7FBF5A15-97BA-3721-943E-E77F0C40DBE1>
> /usr/lib/system/libsystem_network.dylib
> 0x90140000 - 0x902fcffd libicucore.A.dylib (491.11.3)
> <FF55E176-7D66-3DBB-AF86-84744C47A02C> /usr/lib/libicucore.A.dylib
> 0x90f52000 - 0x90f59fff libsystem_dnssd.dylib (379.38.1)
> <4F164CA8-4A4F-3B27-B88A-0926E2FEB7D4> /usr/lib/system/libsystem_dnssd.dylib
> 0x911c8000 - 0x911c8fff com.apple.Accelerate.vecLib (3.8 - vecLib 3.8)
> <908B8D40-3FB5-3047-B482-3DF95025ECFC>
> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/vecLib
> 0x9133a000 - 0x9139cfff libc++.1.dylib (65.1)
> <C0CFF9FF-5D52-3EAE-B921-6AE1DA00A135> /usr/lib/libc++.1.dylib
> 0x927eb000 - 0x927ecfff libremovefile.dylib (23.2)
> <9813B2DB-2374-3AA2-99B6-AA2E9897B249> /usr/lib/system/libremovefile.dylib
> 0x927f7000 - 0x92809ff7 libdispatch.dylib (228.23)
> <86EF7D45-2D97-3465-A449-95038AE5DABA> /usr/lib/system/libdispatch.dylib
> 0x9280a000 - 0x9280bfff libsystem_sandbox.dylib (220.3)
> <C532F6A6-7E85-38F3-8660-EC1066DF67BE>
> /usr/lib/system/libsystem_sandbox.dylib
> 0x92cb6000 - 0x92d1efe7 libvDSP.dylib (380.6)
> <55780308-4DCA-3B10-9703-EAFC3E13A3FA>
> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libvDSP.dylib
> 0x92d97000 - 0x92dc4ffe libsystem_m.dylib (3022.6)
> <9975D9C3-3B71-38E3-AA21-C5C5F9D9C431> /usr/lib/system/libsystem_m.dylib
> 0x92dc5000 - 0x92dccfff liblaunch.dylib (442.26.2)
> <310C99F8-0811-314D-9BB9-D0ED6DFA024B> /usr/lib/system/liblaunch.dylib
> 0x930a6000 - 0x930c3fff libxpc.dylib (140.43)
> <C628073D-51A0-3541-A665-1121520508C6> /usr/lib/system/libxpc.dylib
> 0x931d6000 - 0x931d7fff libDiagnosticMessagesClient.dylib (8)
> <39B3D25A-148A-3936-B800-0D393A00E64F>
> /usr/lib/libDiagnosticMessagesClient.dylib
> 0x931d8000 - 0x931e3fff libcommonCrypto.dylib (60027)
> <8EE30FA5-AA8D-3FA6-AB0F-05DA8B0425D9> /usr/lib/system/libcommonCrypto.dylib
> 0x938ac000 - 0x938d8ff7 libsystem_info.dylib (406.17)
> <AA5611DB-A944-3072-B6BE-ACAB08689547> /usr/lib/system/libsystem_info.dylib
> 0x93968000 - 0x9396bff7 libcompiler_rt.dylib (30)
> <CE5DBDB4-0124-3E2B-9105-989DF98DD108> /usr/lib/system/libcompiler_rt.dylib
> 0x93da7000 - 0x93df5ff3 com.apple.SystemConfiguration (1.12.2 - 1.12.2)
> <6E858B9F-337A-314E-88B7-24A274ACE568>
> /System/Library/Frameworks/SystemConfiguration.framework/Versions/A/SystemConfiguration
> 0x93e20000 - 0x93f5bff7 libBLAS.dylib (1073.4)
> <FF74A147-05E1-37C4-BC10-7DEB57FE5326>
> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
> 0x940c6000 - 0x94112fff libcorecrypto.dylib (106.2)
> <20EBADBA-D6D6-36F0-AE80-168E9AF13DB6> /usr/lib/system/libcorecrypto.dylib
> 0x94113000 - 0x94155fff libauto.dylib (185.4)
> <3098A75E-438E-3F18-BAAC-CD8F1CC7C2F7> /usr/lib/libauto.dylib
> 0x94a2d000 - 0x94a2dfff com.apple.Accelerate (1.8 - Accelerate 1.8)
> <4EC0548E-3A3F-310D-A366-47B51D5B6398>
> /System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate
> 0x94a2e000 - 0x94a36fff libcopyfile.dylib (89)
> <4963541B-0254-371B-B29A-B6806888949B> /usr/lib/system/libcopyfile.dylib
> 0x953e0000 - 0x953e1fff libdnsinfo.dylib (453.19)
> <3B523729-84A8-3D0B-B58C-3FC185060E67> /usr/lib/system/libdnsinfo.dylib
> 0x9541b000 - 0x95422ffb libunwind.dylib (35.1)
> <E1E8D8B3-3C78-3AB1-B398-C180DC6DCF05> /usr/lib/system/libunwind.dylib
> 0x956ed000 - 0x956eefff libquarantine.dylib (52.1)
> <094A1501-373E-3397-B632-8F7C5AC8EFD5> /usr/lib/system/libquarantine.dylib
> 0x956ef000 - 0x956f9fff libsystem_notify.dylib (98.5)
> <7EEE9475-18F8-3099-B0ED-23A3E528ABE0>
> /usr/lib/system/libsystem_notify.dylib
> 0x9571e000 - 0x9582b057 libobjc.A.dylib (532.2)
> <FA455371-7395-3D58-A89B-D1520612D1BC> /usr/lib/libobjc.A.dylib
> 0x95837000 - 0x9583bffe libcache.dylib (57)
> <834FDCA7-FE3B-33CC-A12A-E11E202477EC> /usr/lib/system/libcache.dylib
> 0x9583c000 - 0x95a24ffb com.apple.CoreFoundation (6.8 - 744.19)
> <DDD3AA21-5B5F-3D8F-B137-AD95FCA89064>
> /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation
> 0x969f8000 - 0x969f8fff libkeymgr.dylib (25)
> <D5E93F7F-9315-3AD6-92C7-941F7B54C490> /usr/lib/system/libkeymgr.dylib
> 0x969f9000 - 0x96a8bffb libvMisc.dylib (380.6)
> <6DA3A03F-20BE-300D-A664-B50A7B4E4B1A>
> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libvMisc.dylib
> 0x96ad3000 - 0x96b03fff libncurses.5.4.dylib (37.3)
> <30D8B67F-5447-34AB-900F-2D623CD4F117> /usr/lib/libncurses.5.4.dylib
> 0x96b9d000 - 0x96d26ff7 com.apple.vImage (6.0 - 6.0)
> <1D1F67FE-4F75-3689-BEF6-4A46C8039E70>
> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vImage.framework/Versions/A/vImage
> 0x96d6a000 - 0x96d6afff libSystem.B.dylib (169.3)
> <81C58EAB-0E76-3EAB-BDFD-C5A6FE95536F> /usr/lib/libSystem.B.dylib
> 0x96ea7000 - 0x96ea9fff libdyld.dylib (210.2.3)
> <05D6FF2A-F09B-309D-95F7-7AF10259C707> /usr/lib/system/libdyld.dylib
> 0x96fa8000 - 0x9700cff3 libstdc++.6.dylib (56)
> <F8FA490A-8F3C-3645-ABF5-78926CE9C62C> /usr/lib/libstdc++.6.dylib
> 0x97111000 - 0x9712bffc libsystem_kernel.dylib (2050.24.15)
> <9E58DCC0-D5FF-37E1-AA7F-F2206719E138>
> /usr/lib/system/libsystem_kernel.dylib
> 0x9717b000 - 0x9719dfff libc++abi.dylib (26)
> <3AAA8D55-F5F6-362B-BA3C-CCAF0D3C8E27> /usr/lib/libc++abi.dylib
> 0x9719e000 - 0x9725bfeb libsystem_c.dylib (825.26)
> <6E35A83F-1A5B-3AF9-8C6D-D7B57B25FB63> /usr/lib/system/libsystem_c.dylib
> 0x9726d000 - 0x9726effd libunc.dylib (25)
> <58599CBF-E262-3CEA-AFE1-35560E0177DC> /usr/lib/system/libunc.dylib
> 0x972ab000 - 0x972b9ff7 libz.1.dylib (43)
> <245F1B61-2276-3BBB-9891-99934116D833> /usr/lib/libz.1.dylib
> 0x972ba000 - 0x972beff7 libmacho.dylib (829)
> <5280A013-4F74-3F74-BE0C-7F612C49F1DC> /usr/lib/system/libmacho.dylib
> 0x99a8d000 - 0x99e45ffa libLAPACK.dylib (1073.4)
> <9A6E5EAD-F2F2-3D5C-B655-2B536DB477F2>
> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib
>
> External Modification Summary:
> Calls made by other processes targeting this process:
> task_for_pid: 39
> 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: 968298
> thread_create: 1
> thread_set_state: 0
>
> VM Region Summary:
> ReadOnly portion of Libraries: Total=171.6M resident=77.8M(45%)
> swapped_out_or_unallocated=93.8M(55%)
> Writable regions: Total=55.3M written=19.5M(35%) resident=28.5M(52%)
> swapped_out=0K(0%) unallocated=26.8M(48%)
>
> REGION TYPE VIRTUAL
> =========== =======
> MALLOC 37.2M
> MALLOC guard page 32K
> Memory tag=35 9584K
> Stack 68.0M
> VM_ALLOCATE 8K
> __DATA 7248K
> __DATA/__OBJC 52K
> __IMPORT 180K
> __LINKEDIT 60.7M
> __PAGEZERO 4K
> __TEXT 110.9M
> __UNICODE 544K
> mapped file 154.9M
> shared memory 12K
> =========== =======
> TOTAL 448.9M
>
> Model: MacBookAir3,2, BootROM MBA31.0061.B07, 2 processors, Intel Core 2
> Duo, 1.86 GHz, 4 GB, SMC 1.66f61
> Graphics: NVIDIA GeForce 320M, NVIDIA GeForce 320M, PCI, 256 MB
> Memory Module: BANK 0/DIMM0, 2 GB, DDR3, 1067 MHz, 0x80CE,
> 0x4D34373142353237334348302D5946382020
> Memory Module: BANK 1/DIMM0, 2 GB, DDR3, 1067 MHz, 0x80CE,
> 0x4D34373142353237334348302D5946382020
> AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0xD1),
> Broadcom BCM43xx 1.0 (5.106.98.100.17)
> Bluetooth: Version 4.1.4f2 12041, 2 service, 18 devices, 1 incoming serial
> ports
> Network Service: AirPort, AirPort, en0
> Serial ATA Device: OWC Mercury Aura Pro Express SSD, 240.06 GB
> USB Device: FaceTime Camera (Built-in), apple_vendor_id, 0x850a, 0x24600000
> / 2
> USB Device: Internal Memory Card Reader, apple_vendor_id, 0x8403, 0x26100000
> / 2
> USB Device: BRCM2070 Hub, 0x0a5c (Broadcom Corp.), 0x4500, 0x04500000 / 3
> USB Device: Bluetooth USB Host Controller, apple_vendor_id, 0x821b,
> 0x04530000 / 4
> USB Device: Apple Internal Keyboard / Trackpad, apple_vendor_id, 0x023f,
> 0x04300000 / 2
>
>
>
>
> --
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