Python Abort trap: 6 using nupic

Question

I have problems using python and want to figure out if I'm using a wrong version of it.

I'm trying to work with nupic-stuido (https://github.com/nupic-community/nupic.studio/wiki/Installing-and-Building)

The installation works fine but when I try to run it, I get

$ python program.py
Fatal Python error: PyThreadState_Get: no current thread
Abort trap: 6

I found a similar problem here Homebrew + Python on mac os x 10.8: Fatal Python error: PyThreadState_Get: no current thread importing mapnik

but I the solutions doesn't work or I don't understand them correctly.

Mac os x also shows an error window, with the following content (I put only the first half because I don't know how to make this post longer then 30000 sign):

Process:               Python [524]
Path:                  /Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python
Identifier:            Python
Version:               2.7.10 (2.7.10)
Code Type:             X86-64 (Native)
Parent Process:        bash [310]
Responsible:           Terminal [233]
User ID:               501

Date/Time:             2015-12-07 13:20:55.133 +0100
OS Version:            Mac OS X 10.11 (15A284)
Report Version:        11
Anonymous UUID:        C6665704-A59C-4BB9-3694-A149FF9BCD29

Sleep/Wake UUID:       6DE48D71-EFF8-4C4C-A0B0-53BBBED062A5

Time Awake Since Boot: 3500 seconds
Time Since Wake:       2200 seconds

System Integrity Protection: enabled

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          0x00007fff94bec0ae __pthread_kill + 10
1   libsystem_pthread.dylib         0x00007fff9614e500 pthread_kill + 90
2   libsystem_c.dylib               0x00007fff9b6be37b abort + 129
3   org.python.python               0x000000010865fce2 Py_FatalError + 49
4   org.python.python               0x000000010865f1f0 PyThreadState_Get + 28
5   org.python.python               0x000000010865c03a Py_InitModule4_64 + 62
6   _math.so                        0x0000000109012fb0 init_math + 864 (math_wrap.cxx:140036)
7   org.python.python               0x00000001000deba1 _PyImport_LoadDynamicModule + 177
8   org.python.python               0x00000001000dcc58 imp_load_module + 184
9   org.python.python               0x00000001000c357d PyEval_EvalFrameEx + 24829
10  org.python.python               0x00000001000c467e PyEval_EvalFrameEx + 29182
11  org.python.python               0x00000001000c58e3 PyEval_EvalCodeEx + 2115
12  org.python.python               0x00000001000c5a06 PyEval_EvalCode + 54
13  org.python.python               0x00000001000da0a0 PyImport_ExecCodeModuleEx + 208
14  org.python.python               0x00000001000db2a2 load_source_module + 626
15  org.python.python               0x00000001000dd28b import_submodule + 315
16  org.python.python               0x00000001000dd73a load_next + 234
17  org.python.python               0x00000001000dda7c PyImport_ImportModuleLevel + 412
18  org.python.python               0x00000001000bafe3 builtin___import__ + 131
19  org.python.python               0x000000010000c612 PyObject_Call + 98
20  org.python.python               0x00000001000bc1c7 PyEval_CallObjectWithKeywords + 87
21  org.python.python               0x00000001000c0432 PyEval_EvalFrameEx + 12210
22  org.python.python               0x00000001000c58e3 PyEval_EvalCodeEx + 2115
23  org.python.python               0x00000001000c5a06 PyEval_EvalCode + 54
24  org.python.python               0x00000001000da0a0 PyImport_ExecCodeModuleEx + 208
25  org.python.python               0x00000001000db2a2 load_source_module + 626
26  org.python.python               0x00000001000dd28b import_submodule + 315
27  org.python.python               0x00000001000dd73a load_next + 234
28  org.python.python               0x00000001000dda7c PyImport_ImportModuleLevel + 412
29  org.python.python               0x00000001000bafe3 builtin___import__ + 131
30  org.python.python               0x000000010000c612 PyObject_Call + 98
31  org.python.python               0x00000001000bc1c7 PyEval_CallObjectWithKeywords + 87
32  org.python.python               0x00000001000c0432 PyEval_EvalFrameEx + 12210
33  org.python.python               0x00000001000c58e3 PyEval_EvalCodeEx + 2115
34  org.python.python               0x00000001000c5a06 PyEval_EvalCode + 54
35  org.python.python               0x00000001000da0a0 PyImport_ExecCodeModuleEx + 208
36  org.python.python               0x00000001000db2a2 load_source_module + 626
37  org.python.python               0x00000001000dd28b import_submodule + 315
38  org.python.python               0x00000001000dd73a load_next + 234
39  org.python.python               0x00000001000dda7c PyImport_ImportModuleLevel + 412
40  org.python.python               0x00000001000bafe3 builtin___import__ + 131
41  org.python.python               0x000000010000c612 PyObject_Call + 98
42  org.python.python               0x00000001000bc1c7 PyEval_CallObjectWithKeywords + 87
43  org.python.python               0x00000001000c0432 PyEval_EvalFrameEx + 12210
44  org.python.python               0x00000001000c58e3 PyEval_EvalCodeEx + 2115
45  org.python.python               0x00000001000c5a06 PyEval_EvalCode + 54
46  org.python.python               0x00000001000da0a0 PyImport_ExecCodeModuleEx + 208
47  org.python.python               0x00000001000db2a2 load_source_module + 626
48  org.python.python               0x00000001000dd28b import_submodule + 315
49  org.python.python               0x00000001000dd73a load_next + 234
50  org.python.python               0x00000001000dda7c PyImport_ImportModuleLevel + 412
51  org.python.python               0x00000001000bafe3 builtin___import__ + 131
52  org.python.python               0x000000010000c612 PyObject_Call + 98
53  org.python.python               0x00000001000bc1c7 PyEval_CallObjectWithKeywords + 87
54  org.python.python               0x00000001000c0432 PyEval_EvalFrameEx + 12210
55  org.python.python               0x00000001000c58e3 PyEval_EvalCodeEx + 2115
56  org.python.python               0x00000001000c5a06 PyEval_EvalCode + 54
57  org.python.python               0x00000001000ea41e PyRun_FileExFlags + 174
58  org.python.python               0x00000001000ea6ba PyRun_SimpleFileExFlags + 458
59  org.python.python               0x000000010010187d Py_Main + 3101
60  org.python.python               0x0000000100000f14 0x100000000 + 3860

Thread 0 crashed with X86 Thread State (64-bit):
  rax: 0x0000000000000000  rbx: 0x0000000000000006  rcx: 0x00007fff5fbfd288  rdx: 0x0000000000000000
  rdi: 0x0000000000000a0b  rsi: 0x0000000000000006  rbp: 0x00007fff5fbfd2b0  rsp: 0x00007fff5fbfd288
   r8: 0x0000000000000040   r9: 0x00007fff7d52f1e0  r10: 0x0000000008000000  r11: 0x0000000000000206
  r12: 0x0000000000000000  r13: 0x0000000109294edd  r14: 0x00007fff7c919000  r15: 0x0000000108595ec4
  rip: 0x00007fff94bec0ae  rfl: 0x0000000000000206  cr2: 0x00007fff7d52d038

Logical CPU:     0
Error Code:      0x02000148
Trap Number:     133


Binary Images:
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If I use otool -L on .dylib files, what can I do then? For example:

$ otool -L /usr/lib/system/libsystem_kernel.dylib
/usr/lib/system/libsystem_kernel.dylib:
    /usr/lib/system/libsystem_kernel.dylib (compatibility version 1.0.0, current version 3247.1.106)

What do I do now with install_name_tool?

I also tried it with

port select python

and get an error:

aps-MacBook-Pro:bin ap$ port select python
Warning: Unable to get active selected version: The specified group 'python' does not exist.
Error: The 'list' command failed: The specified group 'python' does not exist.

Also "sudo port select --list python" and "sudo port select python" doesn't work.

I use python2.7

$ which python
/Library/Frameworks/Python.framework/Versions/2.7/bin/python

Somebody has an idea?

Answer 1

After trying many solution symlink, tkinter and all. This was related to pyopenssl using old dependencies in my case. You can fix it by removing the cryptography package and upgrading it.

pip3 install --upgrade cryptography

Answer 2

We are aware of this issue, see: https://github.com/numenta/nupic/issues/1813. The only workaround at this point is to compile from source code.