Fatal Python error (Python3 OpenSim import)

Provide easy-to-use, extensible software for modeling, simulating, controlling, and analyzing the neuromusculoskeletal system.
POST REPLY
User avatar
Ton Leenen
Posts: 17
Joined: Tue Apr 07, 2020 3:16 am

Fatal Python error (Python3 OpenSim import)

Post by Ton Leenen » Mon Jun 08, 2020 2:41 pm

Dear all,

Earlier this week I already posted some issues with importing the OpenSim module into the Python environment. At the moment I was able to rebuild (with Superbuild) OpenSim 4.1 with the Source Code using Python 3.8.3. I cleaned my whole Mac system by other Python version and installed Python 3.8.3. from Python.org.

Now the other issues I reported earlier are fixed, but when I import OpenSim in Python3 environment I get the following error:

Code: Select all

Fatal Python error: _PyInterpreterState_Get(): no current thread state
Python runtime state: unknown

zsh: abort      python3 -c "import opensim"
Directly after receiving this error the macOS 'Problem Report' opens with the following information.

Code: Select all

Process:               Python [59601]
Path:                  /usr/local/Cellar/python@3.8/3.8.3/Frameworks/Python.framework/Versions/3.8/Resources/Python.app/Contents/MacOS/Python
Identifier:            Python
Version:               3.8.3 (3.8.3)
Code Type:             X86-64 (Native)
Parent Process:        zsh [57548]
Responsible:           pycharm [57536]
User ID:               501

Date/Time:             2020-06-08 23:32:01.805 +0200
OS Version:            Mac OS X 10.15.5 (19F101)
Report Version:        12
Bridge OS Version:     4.5 (17P5300)
Anonymous UUID:        23F949A0-D24B-E339-1332-F83C8C0CF82A

Sleep/Wake UUID:       4B36B4A0-7363-4B57-A487-4EBE12A006CA

Time Awake Since Boot: 29000 seconds
Time Since Wake:       12000 seconds

System Integrity Protection: enabled

Crashed Thread:        0  Dispatch queue: com.apple.main-thread

Exception Type:        EXC_CRASH (SIGABRT)
Exception Codes:       0x0000000000000000, 0x0000000000000000
Exception Note:        EXC_CORPSE_NOTIFY

Application Specific Information:
abort() called

Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0   libsystem_kernel.dylib        	0x00007fff6a17233a __pthread_kill + 10
1   libsystem_pthread.dylib       	0x00007fff6a22ee60 pthread_kill + 430
2   libsystem_c.dylib             	0x00007fff6a0f9808 abort + 120
3   org.python.python             	0x000000010ca70f94 fatal_error + 788
4   org.python.python             	0x000000010ca70c76 Py_FatalError + 22
5   org.python.python             	0x000000010ca726b1 _PyInterpreterState_Get + 49
6   org.python.python             	0x000000010c99da02 PyModule_Create2 + 18
7   _simbody.so                   	0x000000010c1e5f4d PyInit__simbody + 61
8   org.python.python             	0x000000010bc4965e _PyImport_LoadDynamicModuleWithSpec + 613
9   org.python.python             	0x000000010bc48ff1 _imp_create_dynamic + 291
10  org.python.python             	0x000000010bbbc6e5 cfunction_vectorcall_FASTCALL + 169
11  org.python.python             	0x000000010bb8e23d PyVectorcall_Call + 108
12  org.python.python             	0x000000010bc2b784 _PyEval_EvalFrameDefault + 31520
13  org.python.python             	0x000000010bc2f12b _PyEval_EvalCodeWithName + 1958
14  org.python.python             	0x000000010bb8e95c _PyFunction_Vectorcall + 228
15  org.python.python             	0x000000010bc2e5fc call_function + 346
16  org.python.python             	0x000000010bc2b1e5 _PyEval_EvalFrameDefault + 30081
17  org.python.python             	0x000000010bb8e7f6 function_code_fastcall + 106
18  org.python.python             	0x000000010bc2e5fc call_function + 346
19  org.python.python             	0x000000010bc2b1c9 _PyEval_EvalFrameDefault + 30053
20  org.python.python             	0x000000010bb8e7f6 function_code_fastcall + 106
21  org.python.python             	0x000000010bc2e5fc call_function + 346
22  org.python.python             	0x000000010bc2b2a5 _PyEval_EvalFrameDefault + 30273
23  org.python.python             	0x000000010bb8e7f6 function_code_fastcall + 106
24  org.python.python             	0x000000010bc2e5fc call_function + 346
25  org.python.python             	0x000000010bc2b2a5 _PyEval_EvalFrameDefault + 30273
26  org.python.python             	0x000000010bb8e7f6 function_code_fastcall + 106
27  org.python.python             	0x000000010bc2e5fc call_function + 346
28  org.python.python             	0x000000010bc2b2a5 _PyEval_EvalFrameDefault + 30273
29  org.python.python             	0x000000010bb8e7f6 function_code_fastcall + 106
30  org.python.python             	0x000000010bc2e5fc call_function + 346
31  org.python.python             	0x000000010bc2b2a5 _PyEval_EvalFrameDefault + 30273
32  org.python.python             	0x000000010bc2f12b _PyEval_EvalCodeWithName + 1958
33  org.python.python             	0x000000010bb8e95c _PyFunction_Vectorcall + 228
34  org.python.python             	0x000000010bc2e5fc call_function + 346
35  org.python.python             	0x000000010bc2b1e5 _PyEval_EvalFrameDefault + 30081
36  org.python.python             	0x000000010bc2f12b _PyEval_EvalCodeWithName + 1958
37  org.python.python             	0x000000010bb8e95c _PyFunction_Vectorcall + 228
38  org.python.python             	0x000000010bc2e5fc call_function + 346
39  org.python.python             	0x000000010bc2b1e5 _PyEval_EvalFrameDefault + 30081
40  org.python.python             	0x000000010bb8e7f6 function_code_fastcall + 106
41  org.python.python             	0x000000010bc2e5fc call_function + 346
42  org.python.python             	0x000000010bc2b2a5 _PyEval_EvalFrameDefault + 30273
43  org.python.python             	0x000000010bc2f12b _PyEval_EvalCodeWithName + 1958
44  org.python.python             	0x000000010bc23bc1 PyEval_EvalCode + 51
45  org.python.python             	0x000000010bc2146f builtin_exec + 581
46  org.python.python             	0x000000010bbbc6e5 cfunction_vectorcall_FASTCALL + 169
47  org.python.python             	0x000000010bb8e23d PyVectorcall_Call + 108
48  org.python.python             	0x000000010bc2b784 _PyEval_EvalFrameDefault + 31520
49  org.python.python             	0x000000010bc2f12b _PyEval_EvalCodeWithName + 1958
50  org.python.python             	0x000000010bb8e95c _PyFunction_Vectorcall + 228
51  org.python.python             	0x000000010bc2e5fc call_function + 346
52  org.python.python             	0x000000010bc2b1e5 _PyEval_EvalFrameDefault + 30081
53  org.python.python             	0x000000010bb8e7f6 function_code_fastcall + 106
54  org.python.python             	0x000000010bc2e5fc call_function + 346
55  org.python.python             	0x000000010bc2b1c9 _PyEval_EvalFrameDefault + 30053
56  org.python.python             	0x000000010bb8e7f6 function_code_fastcall + 106
57  org.python.python             	0x000000010bc2e5fc call_function + 346
58  org.python.python             	0x000000010bc2b2a5 _PyEval_EvalFrameDefault + 30273
59  org.python.python             	0x000000010bb8e7f6 function_code_fastcall + 106
60  org.python.python             	0x000000010bc2e5fc call_function + 346
61  org.python.python             	0x000000010bc2b2a5 _PyEval_EvalFrameDefault + 30273
62  org.python.python             	0x000000010bb8e7f6 function_code_fastcall + 106
63  org.python.python             	0x000000010bb8fc88 object_vacall + 334
64  org.python.python             	0x000000010bb8fdcb _PyObject_CallMethodIdObjArgs + 219
65  org.python.python             	0x000000010bc48149 PyImport_ImportModuleLevelObject + 1587
66  org.python.python             	0x000000010bc2963d _PyEval_EvalFrameDefault + 23001
67  org.python.python             	0x000000010bc2f12b _PyEval_EvalCodeWithName + 1958
68  org.python.python             	0x000000010bc23bc1 PyEval_EvalCode + 51
69  org.python.python             	0x000000010bc2146f builtin_exec + 581
70  org.python.python             	0x000000010bbbc6e5 cfunction_vectorcall_FASTCALL + 169
71  org.python.python             	0x000000010bb8e23d PyVectorcall_Call + 108
72  org.python.python             	0x000000010bc2b784 _PyEval_EvalFrameDefault + 31520
73  org.python.python             	0x000000010bc2f12b _PyEval_EvalCodeWithName + 1958
74  org.python.python             	0x000000010bb8e95c _PyFunction_Vectorcall + 228
75  org.python.python             	0x000000010bc2e5fc call_function + 346
76  org.python.python             	0x000000010bc2b1e5 _PyEval_EvalFrameDefault + 30081
77  org.python.python             	0x000000010bb8e7f6 function_code_fastcall + 106
78  org.python.python             	0x000000010bc2e5fc call_function + 346
79  org.python.python             	0x000000010bc2b1c9 _PyEval_EvalFrameDefault + 30053
80  org.python.python             	0x000000010bb8e7f6 function_code_fastcall + 106
81  org.python.python             	0x000000010bc2e5fc call_function + 346
82  org.python.python             	0x000000010bc2b2a5 _PyEval_EvalFrameDefault + 30273
83  org.python.python             	0x000000010bb8e7f6 function_code_fastcall + 106
84  org.python.python             	0x000000010bc2e5fc call_function + 346
85  org.python.python             	0x000000010bc2b2a5 _PyEval_EvalFrameDefault + 30273
86  org.python.python             	0x000000010bb8e7f6 function_code_fastcall + 106
87  org.python.python             	0x000000010bb8fc88 object_vacall + 334
88  org.python.python             	0x000000010bb8fdcb _PyObject_CallMethodIdObjArgs + 219
89  org.python.python             	0x000000010bc48149 PyImport_ImportModuleLevelObject + 1587
90  org.python.python             	0x000000010bc2963d _PyEval_EvalFrameDefault + 23001
91  org.python.python             	0x000000010bc2f12b _PyEval_EvalCodeWithName + 1958
92  org.python.python             	0x000000010bc23bc1 PyEval_EvalCode + 51
93  org.python.python             	0x000000010bc5d1f9 run_eval_code_obj + 102
94  org.python.python             	0x000000010bc5c64b run_mod + 82
95  org.python.python             	0x000000010bc5b659 PyRun_StringFlags + 120
96  org.python.python             	0x000000010bc5b5a4 PyRun_SimpleStringFlags + 69
97  org.python.python             	0x000000010bc71ee3 Py_RunMain + 424
98  org.python.python             	0x000000010bc72785 pymain_main + 308
99  org.python.python             	0x000000010bc727d3 Py_BytesMain + 42
100 libdyld.dylib                 	0x00007fff6a02acc9 start + 1

Thread 0 crashed with X86 Thread State (64-bit):
  rax: 0x0000000000000000  rbx: 0x0000000117715dc0  rcx: 0x00007ffee4090318  rdx: 0x0000000000000000
  rdi: 0x0000000000000307  rsi: 0x0000000000000006  rbp: 0x00007ffee4090340  rsp: 0x00007ffee4090318
   r8: 0x00000000000130a8   r9: 0x0000000000000000  r10: 0x0000000117715dc0  r11: 0x0000000000000246
  r12: 0x0000000000000307  r13: 0x0000000000000000  r14: 0x0000000000000006  r15: 0x0000000000000016
  rip: 0x00007fff6a17233a  rfl: 0x0000000000000246  cr2: 0x000000010cae3270
  
Logical CPU:     0
Error Code:      0x02000148
Trap Number:     133


Binary Images:
       0x10bb6b000 -        0x10bb6cfff +org.python.python (3.8.3 - 3.8.3) <456BE146-C288-38A9-BE5D-B2FA2237EAF9> /usr/local/Cellar/python@3.8/3.8.3/Frameworks/Python.framework/Versions/3.8/Resources/Python.app/Contents/MacOS/Python
       0x10bb74000 -        0x10bd48ff7 +org.python.python (3.8.3, [c] 2001-2019 Python Software Foundation. - 3.8.3) <0FAC7F9B-A265-3EC4-9EF4-BD116178A70B> /usr/local/Cellar/python@3.8/3.8.3/Frameworks/Python.framework/Versions/3.8/Python
       0x10c018000 -        0x10c01bfff +_heapq.cpython-38-darwin.so (0) <9B913BAB-3B52-38CF-BB11-CE734A1239B5> /usr/local/Cellar/python@3.8/3.8.3/Frameworks/Python.framework/Versions/3.8/lib/python3.8/lib-dynload/_heapq.cpython-38-darwin.so
       0x10c1df000 -        0x10c617ffb +_simbody.so (0) <07BF2D61-512A-3B9E-A73F-9283E236E4EB> /usr/local/lib/python3.8/site-packages/opensim-4.1-py3.8.egg/opensim/_simbody.so
       0x10c79d000 -        0x10c873ffb +libosimTools.dylib (0) <D7BFAA8D-7B0C-317A-A3B8-9BDE6AEA28CC> /Users/USER/*/libosimTools.dylib
       0x10c8e0000 -        0x10c916ffb +libosimExampleComponents.dylib (0) <9902B571-DEE1-349E-8547-A800C9ECCA6C> /Users/USER/*/libosimExampleComponents.dylib
       0x10c93f000 -        0x10cb75ff7 +org.python.python (3.8.3, [c] 2001-2019 Python Software Foundation. - 3.8.3) <ABC651E1-72AF-3D91-955E-B57001D86FC2> /Library/Frameworks/Python.framework/Versions/3.8/Python
       0x10ccb7000 -        0x10cd76ff7 +libosimAnalyses.dylib (0) <2092E2BE-DC3F-3639-B7D1-969D6F1D38F8> /Users/USER/*/libosimAnalyses.dylib
       0x10cddf000 -        0x10ce86ff3 +libosimActuators.dylib (0) <88E641D7-6472-33F8-AEAA-0615E3E2A5B6> /Users/USER/*/libosimActuators.dylib
       0x10ceed000 -        0x10d20bff3 +libosimSimulation.dylib (0) <411C8974-3A67-3E26-93E4-C44665CFDABF> /Users/USER/*/libosimSimulation.dylib
       0x10d3a4000 -        0x10d57eff3 +libosimCommon.dylib (0) <2CFEC32F-E0DD-3D7E-AC99-40A3A05FA695> /Users/USER/*/libosimCommon.dylib
       0x10d666000 -        0x10d67bfff +libosimLepton.dylib (0) <FE048DA8-7459-3CFF-93B0-CB1BE8D1E4C1> /Users/USER/*/libosimLepton.dylib
       0x10d697000 -        0x10d91efff +libSimTKsimbody.3.7.dylib (0) <67120898-F5E5-3FB2-9095-71022AC5CD85> /Users/USER/*/libSimTKsimbody.3.7.dylib
       0x10db09000 -        0x10dddfff7 +libSimTKmath.3.7.dylib (0) <BDFC714F-DCD0-3A58-A066-D967BC17019C> /Users/USER/*/libSimTKmath.3.7.dylib
       0x10ded3000 -        0x10e0b3ff7 +libSimTKcommon.3.7.dylib (0) <29414EFB-ECB4-3098-AEFF-0C57B5FFF394> /Users/USER/*/libSimTKcommon.3.7.dylib
       0x11764b000 -        0x1176dceff  dyld (750.5) <E4698FBD-806A-3396-B279-E685BA37430B> /usr/lib/dyld
    0x7fff2bc37000 -     0x7fff2bc37fff  com.apple.Accelerate (1.11 - Accelerate 1.11) <56DFF715-6A4E-3231-BDCC-A348BCB05047> /System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate
    0x7fff2bc4f000 -     0x7fff2c2a5fff  com.apple.vImage (8.1 - 524.2.1) <17C93AB9-1625-3FDB-9851-C5E77BBE3428> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vImage.framework/Versions/A/vImage
    0x7fff2c2a6000 -     0x7fff2c50dff7  libBLAS.dylib (1303.60.1) <CBC28BE4-3C78-3AED-9565-0D625251D121> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
    0x7fff2c50e000 -     0x7fff2c9e1fef  libBNNS.dylib (144.100.2) <8D653678-1F9B-3670-AAE2-46DFB8D37643> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBNNS.dylib
    0x7fff2c9e2000 -     0x7fff2cd7dfff  libLAPACK.dylib (1303.60.1) <F8E9D081-7C60-32EC-A47D-2D30CAD73C5F> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib
    0x7fff2cd7e000 -     0x7fff2cd93fec  libLinearAlgebra.dylib (1303.60.1) <D2C1ACEA-2B6A-339A-9EEB-62A76CC92CBE> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLinearAlgebra.dylib
    0x7fff2cd94000 -     0x7fff2cd99ff3  libQuadrature.dylib (7) <3112C977-8306-3190-8313-01A952B7F3CF> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libQuadrature.dylib
    0x7fff2cd9a000 -     0x7fff2ce0afff  libSparse.dylib (103) <40510BF9-99A7-3155-A81D-6DE5A0C73EDC> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libSparse.dylib
    0x7fff2ce0b000 -     0x7fff2ce1dfef  libSparseBLAS.dylib (1303.60.1) <3C1066AB-20D5-38D2-B1F2-70A03DE76D0B> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libSparseBLAS.dylib
    0x7fff2ce1e000 -     0x7fff2cff5fd7  libvDSP.dylib (735.121.1) <74702E2E-ED05-3765-B18C-64BEFF62B517> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libvDSP.dylib
    0x7fff2cff6000 -     0x7fff2d0b8fef  libvMisc.dylib (735.121.1) <137558BF-503D-3A6E-96DC-A181E3FB31FF> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libvMisc.dylib
    0x7fff2d0b9000 -     0x7fff2d0b9fff  com.apple.Accelerate.vecLib (3.11 - vecLib 3.11) <D7E8E400-35C8-3174-9956-8D1B483620DA> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/vecLib
    0x7fff2ffac000 -     0x7fff3042bffb  com.apple.CoreFoundation (6.9 - 1676.105) <6AF8B3CC-BC3F-3869-B9FB-1D881422364E> /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation
    0x7fff66b3a000 -     0x7fff66b3cff7  libDiagnosticMessagesClient.dylib (112) <27220E98-6CE2-33E3-BD48-3CC3CE4AA036> /usr/lib/libDiagnosticMessagesClient.dylib
    0x7fff67010000 -     0x7fff67011fff  libSystem.B.dylib (1281.100.1) <B6FDA8A9-3D2B-3BD5-B5B0-57D311C0FF3D> /usr/lib/libSystem.B.dylib
    0x7fff672f6000 -     0x7fff67348fff  libc++.1.dylib (902.1) <AD0805FE-F98B-3E2F-B072-83782B22DAC9> /usr/lib/libc++.1.dylib
    0x7fff67349000 -     0x7fff6735effb  libc++abi.dylib (902) <771E9263-E832-3985-9477-8F1B2D73B771> /usr/lib/libc++abi.dylib
    0x7fff67372000 -     0x7fff67389fd7  libcompression.dylib (87) <21F37C2E-B9AA-38CE-9023-B763C8828AC6> /usr/lib/libcompression.dylib
    0x7fff67dc8000 -     0x7fff67dcafff  libfakelink.dylib (149.1) <122F530F-F10E-3DD5-BBEA-91796BE583F3> /usr/lib/libfakelink.dylib
    0x7fff67eda000 -     0x7fff68131fff  libicucore.A.dylib (64260.0.1) <7B9204AC-EA14-3FF3-B6B9-4C85B37EED79> /usr/lib/libicucore.A.dylib
    0x7fff6814d000 -     0x7fff68165ff3  liblzma.5.dylib (16) <4DB30730-DBD1-3503-957A-D604049B98F9> /usr/lib/liblzma.5.dylib
    0x7fff68e70000 -     0x7fff68ea3fde  libobjc.A.dylib (787.1) <CA836D3E-4595-33F1-B70C-7E39A3FBBE16> /usr/lib/libobjc.A.dylib
    0x7fff6954c000 -     0x7fff6955eff3  libz.1.dylib (76) <DB120508-3BED-37A8-B439-5235EAB4618A> /usr/lib/libz.1.dylib
    0x7fff69e0c000 -     0x7fff69e11ff3  libcache.dylib (83) <A5ECC751-A681-30D8-B33C-D192C15D25C8> /usr/lib/system/libcache.dylib
    0x7fff69e12000 -     0x7fff69e1dfff  libcommonCrypto.dylib (60165.120.1) <C321A74A-AA91-3785-BEBF-BEDC6975026C> /usr/lib/system/libcommonCrypto.dylib
    0x7fff69e1e000 -     0x7fff69e25fff  libcompiler_rt.dylib (101.2) <652A6012-7E5C-3F4F-9438-86BC094526F3> /usr/lib/system/libcompiler_rt.dylib
    0x7fff69e26000 -     0x7fff69e2fff7  libcopyfile.dylib (166.40.1) <40113A69-A81C-3397-ADC6-1D16B9A22C3E> /usr/lib/system/libcopyfile.dylib
    0x7fff69e30000 -     0x7fff69ec2fe3  libcorecrypto.dylib (866.120.3) <5E4B0E50-24DD-3E04-9374-EDA9FFD6257B> /usr/lib/system/libcorecrypto.dylib
    0x7fff69fcf000 -     0x7fff6a00fff0  libdispatch.dylib (1173.100.2) <201EDBF3-0B36-31BA-A7CB-443CE35C05D4> /usr/lib/system/libdispatch.dylib
    0x7fff6a010000 -     0x7fff6a046fff  libdyld.dylib (750.5) <7E711A46-5E4D-393C-AEA6-440E2A5CCD0C> /usr/lib/system/libdyld.dylib
    0x7fff6a047000 -     0x7fff6a047ffb  libkeymgr.dylib (30) <52662CAA-DB1F-30A3-BE13-D6274B1A6D7B> /usr/lib/system/libkeymgr.dylib
    0x7fff6a055000 -     0x7fff6a055ff7  liblaunch.dylib (1738.120.8) <07CF647B-F9DC-3907-AD98-2F85FCB34A72> /usr/lib/system/liblaunch.dylib
    0x7fff6a056000 -     0x7fff6a05bff7  libmacho.dylib (959.0.1) <D91DFF00-E22F-3796-8A1C-4C1F5F8FA03C> /usr/lib/system/libmacho.dylib
    0x7fff6a05c000 -     0x7fff6a05eff3  libquarantine.dylib (110.40.3) <D3B7D02C-7646-3FB4-8529-B36DCC2419EA> /usr/lib/system/libquarantine.dylib
    0x7fff6a05f000 -     0x7fff6a060ff7  libremovefile.dylib (48) <B5E88D9B-C2BE-3496-BBB2-C996317E18A3> /usr/lib/system/libremovefile.dylib
    0x7fff6a061000 -     0x7fff6a078ff3  libsystem_asl.dylib (377.60.2) <1170348D-2491-33F1-AA79-E2A05B4A287C> /usr/lib/system/libsystem_asl.dylib
    0x7fff6a079000 -     0x7fff6a079ff7  libsystem_blocks.dylib (74) <7AFBCAA6-81BE-36C3-8DB0-AAE0A4ACE4C5> /usr/lib/system/libsystem_blocks.dylib
    0x7fff6a07a000 -     0x7fff6a101fff  libsystem_c.dylib (1353.100.2) <935DDCE9-4ED0-3F79-A05A-A123DDE399CC> /usr/lib/system/libsystem_c.dylib
    0x7fff6a102000 -     0x7fff6a105ffb  libsystem_configuration.dylib (1061.120.2) <EA9BC2B1-5001-3463-9FAF-39FF61CAC87C> /usr/lib/system/libsystem_configuration.dylib
    0x7fff6a106000 -     0x7fff6a109fff  libsystem_coreservices.dylib (114) <3D0A3AA8-8415-37B2-AAE3-66C03BCE8B55> /usr/lib/system/libsystem_coreservices.dylib
    0x7fff6a10a000 -     0x7fff6a112fff  libsystem_darwin.dylib (1353.100.2) <6EEC9975-EE3B-3C95-AA5B-030FD10587BC> /usr/lib/system/libsystem_darwin.dylib
    0x7fff6a113000 -     0x7fff6a11afff  libsystem_dnssd.dylib (1096.100.3) <0115092A-E61B-317D-8670-41C7C34B1A82> /usr/lib/system/libsystem_dnssd.dylib
    0x7fff6a11b000 -     0x7fff6a11cffb  libsystem_featureflags.dylib (17) <AFDB5095-0472-34AC-BA7E-497921BF030A> /usr/lib/system/libsystem_featureflags.dylib
    0x7fff6a11d000 -     0x7fff6a16aff7  libsystem_info.dylib (538) <851693E9-C079-3547-AD41-353F8C248BE8> /usr/lib/system/libsystem_info.dylib
    0x7fff6a16b000 -     0x7fff6a197ff7  libsystem_kernel.dylib (6153.121.2) <9F9902C9-A46F-3CA9-B7F9-5CCFE98FBF75> /usr/lib/system/libsystem_kernel.dylib
    0x7fff6a198000 -     0x7fff6a1dffff  libsystem_m.dylib (3178) <436CFF76-6A99-36F2-A3B6-8D017396A050> /usr/lib/system/libsystem_m.dylib
    0x7fff6a1e0000 -     0x7fff6a207fff  libsystem_malloc.dylib (283.100.6) <D4BA7DF2-57AC-33B0-B948-A688EE43C799> /usr/lib/system/libsystem_malloc.dylib
    0x7fff6a208000 -     0x7fff6a215ffb  libsystem_networkextension.dylib (1095.120.6) <6DE86DB0-8CD2-361E-BD6A-A34282B47847> /usr/lib/system/libsystem_networkextension.dylib
    0x7fff6a216000 -     0x7fff6a21fff7  libsystem_notify.dylib (241.100.2) <7E9E2FC8-DF26-340C-B196-B81B11850C46> /usr/lib/system/libsystem_notify.dylib
    0x7fff6a220000 -     0x7fff6a228fef  libsystem_platform.dylib (220.100.1) <736920EA-6AE0-3B1B-BBDA-7DCDF0C229DF> /usr/lib/system/libsystem_platform.dylib
    0x7fff6a229000 -     0x7fff6a233fff  libsystem_pthread.dylib (416.100.3) <77488669-19A3-3993-AD65-CA5377E2475A> /usr/lib/system/libsystem_pthread.dylib
    0x7fff6a234000 -     0x7fff6a238ff3  libsystem_sandbox.dylib (1217.120.7) <20C93D69-6452-3C82-9521-8AE54345C66F> /usr/lib/system/libsystem_sandbox.dylib
    0x7fff6a239000 -     0x7fff6a23bfff  libsystem_secinit.dylib (62.100.2) <E851113D-D5B1-3FB0-9D29-9C7647A71961> /usr/lib/system/libsystem_secinit.dylib
    0x7fff6a23c000 -     0x7fff6a243ffb  libsystem_symptoms.dylib (1238.120.1) <25C3866B-004E-3621-9CD3-B1E9C4D887EB> /usr/lib/system/libsystem_symptoms.dylib
    0x7fff6a244000 -     0x7fff6a25aff2  libsystem_trace.dylib (1147.120) <A1ED1D3A-5FAD-3559-A1D6-1BE4E1C5756A> /usr/lib/system/libsystem_trace.dylib
    0x7fff6a25c000 -     0x7fff6a261ff7  libunwind.dylib (35.4) <253A12E2-F88F-3838-A666-C5306F833CB8> /usr/lib/system/libunwind.dylib
    0x7fff6a262000 -     0x7fff6a297ffe  libxpc.dylib (1738.120.8) <68D433B6-DCFF-385D-8620-F847FB7D4A5A> /usr/lib/system/libxpc.dylib

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: 23293
    thread_create: 0
    thread_set_state: 0

VM Region Summary:
ReadOnly portion of Libraries: Total=454.1M resident=0K(0%) swapped_out_or_unallocated=454.1M(100%)
Writable regions: Total=52.9M written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=52.9M(100%)
 
                                VIRTUAL   REGION 
REGION TYPE                        SIZE    COUNT (non-coalesced) 
===========                     =======  ======= 
Kernel Alloc Once                    8K        1 
MALLOC                            32.0M       25 
MALLOC guard page                   16K        3 
MALLOC_LARGE (reserved)            640K        1         reserved VM address space (unallocated)
STACK GUARD                          4K        1 
Stack                             16.0M        1 
VM_ALLOCATE                       3840K       15 
__DATA                            3107K       78 
__DATA_CONST                       540K       15 
__LINKEDIT                       398.9M       18 
__OBJC_RO                         32.2M        1 
__OBJC_RW                         1892K        2 
__TEXT                            55.3M       73 
__UNICODE                          564K        1 
shared memory                       12K        3 
===========                     =======  ======= 
TOTAL                            544.8M      238 
TOTAL, minus reserved VM space   544.2M      238 

Model: MacBookPro15,1, BootROM 1037.120.87.0.0 (iBridge: 17.16.15300.0.0,0), 6 processors, 6-Core Intel Core i7, 2,2 GHz, 16 GB, SMC 
Graphics: kHW_IntelUHDGraphics630Item, Intel UHD Graphics 630, spdisplays_builtin
Graphics: kHW_AMDRadeonPro555XItem, Radeon Pro 555X, spdisplays_pcie_device, 4 GB
Memory Module: BANK 0/ChannelA-DIMM0, 8 GB, DDR4, 2400 MHz, SK Hynix, -
Memory Module: BANK 2/ChannelB-DIMM0, 8 GB, DDR4, 2400 MHz, SK Hynix, -
AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x7BF), wl0: Feb 28 2020 15:24:56 version 9.30.357.35.32.5.47 FWID 01-9ce4adf3
Bluetooth: Version 7.0.5f6, 3 services, 27 devices, 1 incoming serial ports
Network Service: USB 10/100/1000 LAN 2, Ethernet, en12
Network Service: iPad, Ethernet, en10
USB Device: USB3.0 Hub
USB Device: USB3.0 Card Reader
USB Device: 4-Port USB 3.0 Hub
USB Device: USB 10/100/1000 LAN
USB Device: USB 3.1 Bus
USB Device: USB2.0 Hub
USB Device: 4-Port USB 2.0 Hub
USB Device: USB 2.0 BILLBOARD
USB Device: USB Billboard Device
USB Device: iPad
USB Device: Apple T2 Bus
USB Device: Touch Bar Backlight
USB Device: Touch Bar Display
USB Device: Apple Internal Keyboard / Trackpad
USB Device: Headset
USB Device: Ambient Light Sensor
USB Device: FaceTime HD Camera (Built-in)
USB Device: Apple T2 Controller
Thunderbolt Bus: MacBook Pro, Apple Inc., 47.4
Thunderbolt Bus: MacBook Pro, Apple Inc., 47.4
Is Python version 3.8.3. the reason for this error? Despite the fact that OpenSim is (re-)built with this version?

I hope you can help me to fix this issue! I have the feeling I am really close!

Kinds regards,

Ton Leenen

Tags:

User avatar
Christopher Dembia
Posts: 506
Joined: Fri Oct 12, 2012 4:09 pm

Re: Fatal Python error (Python3 OpenSim import)

Post by Christopher Dembia » Mon Jun 08, 2020 3:17 pm

It sounds like you have multiple Python installations on your computer: one from Homebrew, and one from Python.org. Make sure to use the same Python interpreter that OpenSim was built with.

For starters, type

Code: Select all

which python3
in your terminal.

User avatar
Ton Leenen
Posts: 17
Joined: Tue Apr 07, 2020 3:16 am

Re: Fatal Python error (Python3 OpenSim import)

Post by Ton Leenen » Tue Jun 09, 2020 5:03 am

Hi Chris,

Thanks you for you reply! This was indeed the problem! After spending 1.5 week trying to get OpenSim 4.1 up and running in Python I finally solved all the issues! I have OpenSim 4.1 with Python 3.7.7. running in a PyCharm Virtualenv environment! :D

I was able to solve the issues due to the following actions:
- All the versions of Python and the dependencies should be compatible.
- I used the 'default' version of Python 3.7.7. installed via the GUI and downloaded via Python.org.
- I installed SWIG 3.0.12 via Homebrew (brew install swig@3) and the SWIG_DIR (in my case: /usr/local/Cellar/swig@3/3.0.12/share/swig/3.0.) and SWIG_EXECUTABLE (in my case: /usr/local/bin/swig) should be checked when using the CMake (I used the 3.17.0 version).
- I installed the C3D and Numpy module to the 'default' Python 3.7.7. via pip3 in the terminal.

- The following paths should also be checked and most likely corrected in CMake:
PYTHON_EXECUTABLE = /Library/Frameworks/Python.framework/Versions/3.7/bin/python3.7m
PYTHON_INCLUDE_DIR = /Library/Frameworks/Python.framework/Versions/3.7/include/python3.7m
PYTHON_LIBRARY = /Library/Frameworks/Python.framework/Versions/3.7/lib/libpython3.7m.

In my case CMake or macOS sometimes automatically selects the paths, which were in my case not correct. The PYTHON_EXECUTABLE was set on the Python installed in the system (/user/bin/python).

Furthermore, I used the latest version of Xcode Version 11.5 (11E608c).

Chris and Ayman, thank you for your support!

Cheers,

Ton Leenen

User avatar
Christopher Dembia
Posts: 506
Joined: Fri Oct 12, 2012 4:09 pm

Re: Fatal Python error (Python3 OpenSim import)

Post by Christopher Dembia » Tue Jun 09, 2020 1:40 pm

Good to hear. We hope to make this process easier in the future by providing OpenSim through Conda.

POST REPLY