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Fatal Python error (Python3 OpenSim import)

https://simtk.org/plugins/phpBB/viewtopic.php?f=91&t=12076

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Fatal Python error (Python3 OpenSim import)

Posted: Mon Jun 08, 2020 2:41 pm
by antoniusleenen
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:
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  Calls made by all processes on this machine:
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VM Region Summary:
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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) 
===========                     =======  ======= 
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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
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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

Re: Fatal Python error (Python3 OpenSim import)

Posted: Mon Jun 08, 2020 3:17 pm
by chrisdembia
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.

Re: Fatal Python error (Python3 OpenSim import)

Posted: Tue Jun 09, 2020 5:03 am
by antoniusleenen
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

Re: Fatal Python error (Python3 OpenSim import)

Posted: Tue Jun 09, 2020 1:40 pm
by chrisdembia
Good to hear. We hope to make this process easier in the future by providing OpenSim through Conda.
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