Develop Reference

Mac m1 pyodbc.connect causes zsh: abort

When I run pyodbc.connect(...) my python crashes and I get zsh: abort error in terminal.
Running:
Mac M1 Pro Monterey
Python 3.8.9
Installed MS ODBC drivers (tried 17 and 18).
Tried running in base Python and virtual environments.
In base python, I get the following system error:
Translated Report (Full Report Below)
Process: Python [1869]
Path: /Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.8/Resources/Python.app/Contents/MacOS/Python
Identifier: com.apple.python3
Version: 3.8.9 (3.8.9)
Build Info: python3-103000000000000~1538
Code Type: ARM-64 (Native)
Parent Process: zsh [611]
Responsible: Terminal [80951]
User ID: 501
Date/Time: 2022-03-08 17:42:55.3063 +0200
OS Version: macOS 12.2.1 (21D62)
Report Version: 12
Anonymous UUID: 919246FC-3C09-6151-CCAB-05C65A4A9B63
Sleep/Wake UUID: 4CFF985F-843A-4C63-ABC8-97435300AADE
Time Awake Since Boot: 370000 seconds
Time Since Wake: 2014 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:
stack buffer overflow
Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0 libsystem_kernel.dylib 0x18ff659b8 __pthread_kill + 8
1 libsystem_pthread.dylib 0x18ff98eb0 pthread_kill + 288
2 libsystem_c.dylib 0x18fed63a0 __abort + 128
3 libsystem_c.dylib 0x18fec818c __stack_chk_fail + 96
4 pyodbc.cpython-38-darwin.so 0x102c4f5d4 GetErrorFromHandle(Connection*, char const*, void*, void*) + 1024
5 pyodbc.cpython-38-darwin.so 0x102c4f188 RaiseErrorFromHandle(Connection*, char const*, void*, void*) + 16
6 pyodbc.cpython-38-darwin.so 0x102c48cf0 Connection_New(_object*, bool, bool, long, bool, _object*, Object&) + 1324
7 pyodbc.cpython-38-darwin.so 0x102c54b34 mod_connect(_object*, _object*, _object*) + 1468
8 Python3 0x103185968 cfunction_call_varargs + 140
9 Python3 0x103185368 _PyObject_MakeTpCall + 372
10 Python3 0x1032523fc call_function + 448
11 Python3 0x10324f800 _PyEval_EvalFrameDefault + 23692
12 Python3 0x1032532e4 _PyEval_EvalCodeWithName + 3048
13 Python3 0x103249ae0 PyEval_EvalCode + 60
14 Python3 0x10328f384 PyRun_InteractiveOneObjectEx + 712
15 Python3 0x10328e92c PyRun_InteractiveLoopFlags + 156
16 Python3 0x10328e84c PyRun_AnyFileExFlags + 72
17 Python3 0x1032ac808 Py_RunMain + 2120
18 Python3 0x1032acb1c pymain_main + 340
19 Python3 0x1032acb98 Py_BytesMain + 40
20 dyld 0x1029ed0f4 start + 520
(this is just a small extract of the report because I can't figure out how to "embed" the full report in a scrollable object in my post)
I have tried zsh: abort python error when I try to run the app in venv
Any help is appreciated.

py2app build errors Terminating app due to uncaught exception 'NSInvalidArgumentException'

I am new to building standalone files using py2app for MacOS. I am getting the following error when I launch the app after the build
Terminating app due to uncaught exception 'NSInvalidArgumentException' reason: '-[__NSCFString count]: unrecognized selector sent to instance 0x6000026004e0'
I would highly appreciate if someone points me how to resolve this issue.
Below is my setup file
from setuptools import setup
APP = ['jarvis_starter.py']
DATA_FILES = ['Template2.pptx']
OPTIONS = {'iconfile':'jarvislogo.icns',
'argv_emulation': True,
'packages': 'certifi',
'plist': {
'PyRuntimeLocations':'/Library/Frameworks/Python.framework/Versions/3.7/lib/libpython3.7.dylib',
'LSPrefersPPC':True,
}
}
setup(
app=APP,
data_files=DATA_FILES,
options={'py2app': OPTIONS},
setup_requires=['py2app'],
)
I am posting error log below
Path: /Users/USER/Documents/*/jarvis_starter.app/Contents/MacOS/jarvis_starter
Identifier: org.pythonmac.unspecified.jarvis_starter
Version: 0.0.0 (0.0.0)
Code Type: X86-64 (Native)
Parent Process: ??? [1]
Responsible: jarvis_starter [64308]
User ID: 501
Date/Time: 2020-01-26 17:59:07.513 -0800
OS Version: Mac OS X 10.15.2 (19C57)
Report Version: 12
Bridge OS Version: 3.0 (14Y908)
Anonymous UUID: 0333FAC2-3E0F-7B44-E2C1-9EEFF2508FB0
Sleep/Wake UUID: E6B1DB47-C4DB-424F-834B-90F142B2FBF5
Time Awake Since Boot: 390000 seconds
Time Since Wake: 700 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:
*** Terminating app due to uncaught exception 'NSInvalidArgumentException', reason: '-[__NSCFString count]: unrecognized selector sent to instance 0x6000026004e0'
abort() called
terminating with uncaught exception of type NSException
Application Specific Backtrace 1:
0 CoreFoundation 0x00007fff2bfd48ab __exceptionPreprocess + 250
1 libobjc.A.dylib 0x00007fff62245805 objc_exception_throw + 48
2 CoreFoundation 0x00007fff2c053b61 -[NSObject(NSObject) __retain_OA] + 0
3 CoreFoundation 0x00007fff2bf38adf ___forwarding___ + 1427
4 CoreFoundation 0x00007fff2bf384b8 _CF_forwarding_prep_0 + 120
5 jarvis_starter 0x0000000100001674 py2app_main + 372
6 jarvis_starter 0x0000000100000f48 main + 344
7 jarvis_starter 0x0000000100000dc4 start + 52
8 ??? 0x0000000000000001 0x0 + 1
Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0 libsystem_kernel.dylib 0x00007fff636fa7fa __pthread_kill + 10
1 libsystem_pthread.dylib 0x00007fff637b7bc1 pthread_kill + 432
2 libsystem_c.dylib 0x00007fff63681a1c abort + 120
3 libc++abi.dylib 0x00007fff6071fbe8 abort_message + 231
4 libc++abi.dylib 0x00007fff6071fd9c demangling_terminate_handler() + 262
5 libobjc.A.dylib 0x00007fff6224778a _objc_terminate() + 96
6 libc++abi.dylib 0x00007fff6072cdc7 std::__terminate(void (*)()) + 8
7 libc++abi.dylib 0x00007fff6072cb6c __cxxabiv1::failed_throw(__cxxabiv1::__cxa_exception*) + 27
8 libc++abi.dylib 0x00007fff6071e45d __cxa_throw + 113
9 libobjc.A.dylib 0x00007fff62245933 objc_exception_throw + 350
10 com.apple.CoreFoundation 0x00007fff2c053b61 -[NSObject(NSObject) doesNotRecognizeSelector:] + 132
11 com.apple.CoreFoundation 0x00007fff2bf38adf ___forwarding___ + 1427
12 com.apple.CoreFoundation 0x00007fff2bf384b8 _CF_forwarding_prep_0 + 120
13 org.pythonmac.unspecified.jarvis_starter 0x0000000100001674 py2app_main + 372
14 org.pythonmac.unspecified.jarvis_starter 0x0000000100000f48 main + 344
15 org.pythonmac.unspecified.jarvis_starter 0x0000000100000dc4 start + 52
Thread 1:
0 libsystem_pthread.dylib 0x00007fff637b3818 start_wqthread + 0
Thread 2:
0 libsystem_pthread.dylib 0x00007fff637b3818 start_wqthread + 0
Thread 3:
0 libsystem_pthread.dylib 0x00007fff637b3818 start_wqthread + 0
Thread 0 crashed with X86 Thread State (64-bit):
rax: 0x0000000000000000 rbx: 0x0000000109351dc0 rcx: 0x00007ffeefbfbfe8 rdx: 0x0000000000000000
rdi: 0x0000000000000307 rsi: 0x0000000000000006 rbp: 0x00007ffeefbfc010 rsp: 0x00007ffeefbfbfe8
r8: 0x00007ffeefbfbeb0 r9: 0x00007ffeefbfc080 r10: 0x0000000109351dc0 r11: 0x0000000000000246
r12: 0x0000000000000307 r13: 0x0000003000000008 r14: 0x0000000000000006 r15: 0x0000000000000016
rip: 0x00007fff636fa7fa rfl: 0x0000000000000246 cr2: 0x0000000000000000
Logical CPU: 0
Error Code: 0x00000000
Trap Number: 0
Binary Images:
0x100000000 - 0x100005fff +org.pythonmac.unspecified.jarvis_starter (0.0.0 - 0.0.0) <E4EAF2F4-CF49-3C47-B544-F79C80860A1D> /Users/USER/Documents/*/jarvis_starter.app/Contents/MacOS/jarvis_starter
0x109288000 - 0x109318cb7 dyld (733.8) <EEA931D0-403E-3BC8-862A-CBA037DE4A74> /usr/lib/dyld
0x7fff27c7d000 - 0x7fff27c7dfff com.apple.Accelerate (1.11 - Accelerate 1.11) <EEBE6680-1AAB-3192-AA7C-450537B07F27> /System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate
0x7fff27c95000 - 0x7fff28300fef com.apple.vImage (8.1 - 524.2) <2BDE5231-B5ED-313E-918A-876ACE1C0FCF> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vImage.framework/Versions/A/vImage
0x7fff28301000 - 0x7fff2856afff libBLAS.dylib (1303.60.1) <94F6B3C0-5039-3F66-8B2E-98791287E459> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
0x7fff2856b000 - 0x7fff2885aff7 libBNNS.dylib (144.40.3) <F15D7D9E-0B9F-34FF-B144-DCA264614C54> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBNNS.dylib
0x7fff2885c000 - 0x7fff28c01fff libLAPACK.dylib (1303.60.1) <DCC36295-FF39-35A1-8DF1-1E8A714E2265> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib
0x7fff28c02000 - 0x7fff28c17ff8 libLinearAlgebra.dylib (1303.60.1) <E3C0CC64-906B-3B44-B8AA-3075BA20E161> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLinearAlgebra.dylib
0x7fff28c18000 - 0x7fff28c1dff3 libQuadrature.dylib (7) <17EC31E3-3D77-3B5A-8ADD-6A3DBC1531E7> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libQuadrature.dylib
0x7fff28c1e000 - 0x7fff28c8efff libSparse.dylib (103) <350DAE1C-C990-343F-A98A-1B4317EAA869> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libSparse.dylib
0x7fff28c8f000 - 0x7fff28ca1fef libSparseBLAS.dylib (1303.60.1) <8C0C7291-AC3A-3808-9D45-E359A5E03F0E> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libSparseBLAS.dylib
0x7fff28ca2000 - 0x7fff28e7bffb libvDSP.dylib (735.40.1) <BD49856D-39CE-397F-A069-

High Sierra + Python + Postgresql error: Illegal instruction: 4

I can connect to Postgres via the command line no problem, however if I try to connect via Python using the psycopg2 module I get the error below. Interestingly I have just tried connecting with PSeqal.app and it crashes with the same error.
Environment:
MacOS: 10.13.3
Xcode 9.2
Python: 3.6.4
Connection module: psycopg2
Postgresql: 10.3
Script:
Here is my simple connection script which is trying to connect via Python to Postgresql:
def connect(self, params):
""" Connect to the PostgreSQL database server """
conn = None
try:
# connect to the PostgreSQL server
logging.info('Connecting to the PostgreSQL database...')
conn = psycopg2.connect(**params)
# create a cursor
self.cursor = conn.cursor()
except (Exception, psycopg2.DatabaseError) as error:
print(error)
finally:
if conn is not None:
conn.close()
logging.warning('Database connection closed.')
Error:
Script output:
$ python3 testdb.py
Illegal instruction: 4
Apple error (partial):
Process: Python [79534]
Path: /usr/local/Cellar/python3/3.6.4_2/Frameworks/Python.framework/Versions/3.6/Resources/Python.app/Contents/MacOS/Python
Identifier: Python
Version: 3.6.4 (3.6.4)
Code Type: X86-64 (Native)
Parent Process: bash [657]
Responsible: Python [79534]
User ID: 501
Date/Time: 2018-03-02 15:30:27.642 +1300
OS Version: Mac OS X 10.13.3 (17D102)
Report Version: 12
Anonymous UUID: xx
Time Awake Since Boot: 21000 seconds
System Integrity Protection: disabled
Crashed Thread: 0 Dispatch queue: com.apple.main-thread
Exception Type: EXC_BAD_INSTRUCTION (SIGILL)
Exception Codes: 0x0000000000000001, 0x0000000000000000
Exception Note: EXC_CORPSE_NOTIFY
Termination Signal: Illegal instruction: 4
Termination Reason: Namespace SIGNAL, Code 0x4
Terminating Process: exc handler [0]
Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0 libpq.5.10.dylib 0x00000001118e8d27 initPQExpBuffer + 32
1 libpq.5.10.dylib 0x00000001118dba93 PQconninfoParse + 43
2 _psycopg.cpython-36m-darwin.so 0x0000000111897cf1 psyco_parse_dsn + 113
3 org.python.python 0x000000010fd4681a _PyCFunction_FastCallDict + 463
4 org.python.python 0x000000010fdaad8e call_function + 489
5 org.python.python 0x000000010fda3c43 _PyEval_EvalFrameDefault + 4811
6 org.python.python 0x000000010fdab4f0 _PyEval_EvalCodeWithName + 1719
7 org.python.python 0x000000010fda293d PyEval_EvalCodeEx + 57
8 org.python.python 0x000000010fd2ec76 function_call + 339
9 org.python.python 0x000000010fd0e9f2 PyObject_Call + 101
10 org.python.python 0x000000010fda3eac _PyEval_EvalFrameDefault + 5428
11 org.python.python 0x000000010fdab4f0 _PyEval_EvalCodeWithName + 1719
12 org.python.python 0x000000010fda293d PyEval_EvalCodeEx + 57
13 org.python.python 0x000000010fd2ec76 function_call + 339
14 org.python.python 0x000000010fd0e9f2 PyObject_Call + 101
15 org.python.python 0x000000010fda3eac _PyEval_EvalFrameDefault + 5428
16 org.python.python 0x000000010fdabe93 _PyFunction_FastCall + 121
17 org.python.python 0x000000010fdaad65 call_function + 448
18 org.python.python 0x000000010fda3c43 _PyEval_EvalFrameDefault + 4811
19 org.python.python 0x000000010fdabe93 _PyFunction_FastCall + 121
20 org.python.python 0x000000010fd0eb71 _PyObject_FastCallDict + 196
21 org.python.python 0x000000010fd0ec94 _PyObject_Call_Prepend + 156
22 org.python.python 0x000000010fd0e9f2 PyObject_Call + 101
23 org.python.python 0x000000010fd598ae slot_tp_init + 57
24 org.python.python 0x000000010fd5683c type_call + 184
25 org.python.python 0x000000010fd0eb3c _PyObject_FastCallDict + 143
26 org.python.python 0x000000010fdaad5e call_function + 441
27 org.python.python 0x000000010fda3c43 _PyEval_EvalFrameDefault + 4811
28 org.python.python 0x000000010fdabe93 _PyFunction_FastCall + 121
29 org.python.python 0x000000010fd0eb71 _PyObject_FastCallDict + 196
30 org.python.python 0x000000010fd0ec94 _PyObject_Call_Prepend + 156
31 org.python.python 0x000000010fd0e9f2 PyObject_Call + 101
32 org.python.python 0x000000010fd598ae slot_tp_init + 57
33 org.python.python 0x000000010fd5683c type_call + 184
34 org.python.python 0x000000010fd0eb3c _PyObject_FastCallDict + 143
35 org.python.python 0x000000010fdaad5e call_function + 441
36 org.python.python 0x000000010fda3c43 _PyEval_EvalFrameDefault + 4811
37 org.python.python 0x000000010fdab4f0 _PyEval_EvalCodeWithName + 1719
38 org.python.python 0x000000010fda28fe PyEval_EvalCode + 42
39 org.python.python 0x000000010fdcb24e run_mod + 54
40 org.python.python 0x000000010fdca26f PyRun_FileExFlags + 160
41 org.python.python 0x000000010fdc994c PyRun_SimpleFileExFlags + 285
42 org.python.python 0x000000010fddd770 Py_Main + 3484
43 org.python.python 0x000000010fd01e1d 0x10fd00000 + 7709
44 libdyld.dylib 0x00007fff6c260115 start + 1
Thread 0 crashed with X86 Thread State (64-bit):
rax: 0x00007f86c3db9200 rbx: 0x00007ffedfefe3a0 rcx: 0x0000000000000100 rdx: 0x0000000000010000
rdi: 0x0000000000000b93 rsi: 0x00000000ffff0001 rbp: 0x00007ffedfefe390 rsp: 0x00007ffedfefe380
r8: 0x000000006c3db930 r9: 0x000000000000000f r10: 0x00000000ffff0000 r11: 0x00007f86c3d00000
r12: 0x0000000110665738 r13: 0x0000000111c68510 r14: 0x0000000111cb80b0 r15: 0x00007ffedfefe3a0
rip: 0x00000001118e8d27 rfl: 0x0000000000010206 cr2: 0x00000001118ef90e
Logical CPU: 2
Error Code: 0x00000000
Trap Number: 6
What I have tried so far:
Upgraded Python to 3.6.4 from 3.5.1
Rebuilt all dependent libraries including psycopg2 to make sure they are High Sierra compatible (I hope)
Reinstalled Postgres from scratch
Upgraded Xcode + tools
So I'm at a bit of a loss as to what to try next? Has anyone else run into this? Any pointers to where to look? Anything that helps me get this working would be greatly appreciated thanks!

So it looked like the psycopg2 library was the culprit and this fixed it for me:
$pip3 uninstall psycopg2
...
Successfully uninstalled psycopg2-binary-2.7.4
$pip3 install psycopg2-binary --no-binary :all:
Collecting psycopg2-binary
Downloading psycopg2-binary-2.7.4.tar.gz (426kB)
100% |---| 430kB 649kB/s
Skipping bdist_wheel for psycopg2-binary, due to binaries being disabled for it.
Installing collected packages: psycopg2-binary
Running setup.py install for psycopg2-binary ... done
Successfully installed psycopg2-binary-2.7.4
$python3 test.py
Connecting to the PostgreSQL database...
All good.
Database connection closed.
The reason I believe is something to do with the fact I was trying to build psycopg2 on a 2010 era MBP specifically and it has a compatibility issue with the hardware - probably the 2.66 GHz Intel Core i7 processor this machine has.
Thank you #Laurenz Albe and #joop for quick replies, pointers and insights, you helped narrow me down to this answer which I hope will stay stable for the duration of this job ;) Cheers!

According to the stack trace, that error occurs in the PostgreSQL client, in this harmless piece of code:
/*
* initPQExpBuffer
*
* Initialize a PQExpBufferData struct (with previously undefined contents)
* to describe an empty string.
*/
void
initPQExpBuffer(PQExpBuffer str)
{
str->data = (char *) malloc(INITIAL_EXPBUFFER_SIZE);
if (str->data == NULL)
{
str->data = (char *) oom_buffer; /* see comment above */
str->maxlen = 0;
str->len = 0;
}
else
{
str->maxlen = INITIAL_EXPBUFFER_SIZE;
str->len = 0;
str->data[0] = '\0';
}
}
I found this and this question dealing with similar problems.
Illegal instruction should mean that execution encountered an instruction code that does not exist, which is either a compiler bug or means that the code was built for a processor with a different instruction set.
The problem is likely somewhere in the procedure with which PostgreSQL was built. You should bring this complaint to the packagers who built the binaries you are using.

osx 10.10.5 Python 2.7 "Fatal Python error: PyThreadState_Get: no current thread Abort trap: 6" error

I am using homebrew python 2.7 and I installed nupic
$ pip install nupic
Then I get error when i try to import nupic
$ python
Python 2.7.11 (default, Jan 22 2016, 08:28:37)
[GCC 4.2.1 Compatible Apple LLVM 7.0.2 (clang-700.1.81)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> from nupic.bindings.algorithms import SpatialPooler as SP
Fatal Python error: PyThreadState_Get: no current thread
Abort trap: 6
$
After I get the error:
Fatal Python error: PyThreadState_Get: no current thread
Abort trap: 6
Python exits and it asks if i want to report it to apple.
Here is the report.
Process: Python [72449]
Path: /usr/local/Cellar/python/2.7.11/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python
Identifier: Python
Version: 2.7.11 (2.7.11)
Code Type: X86-64 (Native)
Parent Process: bash [93469]
Responsible: Terminal [93466]
User ID: 501
Date/Time: 2016-02-06 17:30:50.442 +0900
OS Version: Mac OS X 10.10.5 (14F1021)
Report Version: 11
Anonymous UUID: 855D5299-1DD9-879D-F358-9483D5CA0033
Sleep/Wake UUID: A2948A3A-B3AB-4F3C-8214-250AAC8AB13F
Time Awake Since Boot: 75000 seconds
Time Since Wake: 7800 seconds
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 0x00007fff85532286 __pthread_kill + 10
1 libsystem_c.dylib 0x00007fff932e79b3 abort + 129
2 org.python.python 0x000000010a8fa2a3 Py_FatalError + 49
3 org.python.python 0x000000010a8f9785 PyThreadState_Get + 28
4 org.python.python 0x000000010a8f6522 Py_InitModule4_64 + 62
5 _algorithms.so 0x000000010a0d7c7c init_algorithms + 796
6 org.python.python 0x0000000108fdb98b _PyImport_LoadDynamicModule + 140
7 org.python.python 0x0000000108fdb422 imp_load_module + 243
8 org.python.python 0x0000000108fc5be5 PyEval_EvalFrameEx + 26858
9 org.python.python 0x0000000108fc9745 fast_function + 264
10 org.python.python 0x0000000108fc5b0b PyEval_EvalFrameEx + 26640
11 org.python.python 0x0000000108fbf109 PyEval_EvalCodeEx + 1583
12 org.python.python 0x0000000108fbead4 PyEval_EvalCode + 54
13 org.python.python 0x0000000108fd7f0f PyImport_ExecCodeModuleEx + 241
14 org.python.python 0x0000000108fdac27 load_source_module + 1089
15 org.python.python 0x0000000108fda689 import_submodule + 267
16 org.python.python 0x0000000108fda24f load_next + 284
17 org.python.python 0x0000000108fd946b PyImport_ImportModuleLevel + 1195
18 org.python.python 0x0000000108fba70a builtin___import__ + 135
19 org.python.python 0x0000000108f45ef0 PyObject_Call + 99
20 org.python.python 0x0000000108fc9087 PyEval_CallObjectWithKeywords + 165
21 org.python.python 0x0000000108fc438a PyEval_EvalFrameEx + 20623
22 org.python.python 0x0000000108fbf109 PyEval_EvalCodeEx + 1583
23 org.python.python 0x0000000108fbead4 PyEval_EvalCode + 54
24 org.python.python 0x0000000108fe2eb9 run_mod + 53
25 org.python.python 0x0000000108fe2f5c PyRun_FileExFlags + 133
26 org.python.python 0x0000000108fe2aab PyRun_SimpleFileExFlags + 698
27 org.python.python 0x0000000108ff445d Py_Main + 3137
28 libdyld.dylib 0x00007fff9331a5c9 start + 1
Thread 0 crashed with X86 Thread State (64-bit):
rax: 0x0000000000000000 rbx: 0x0000000000000006 rcx: 0x00007fff56ccd9f8 rdx: 0x0000000000000000
rdi: 0x0000000000000713 rsi: 0x0000000000000006 rbp: 0x00007fff56ccda20 rsp: 0x00007fff56ccd9f8
r8: 0x00007fff56ccda10 r9: 0x00007fff75557300 r10: 0x0000000008000000 r11: 0x0000000000000206
r12: 0x0000000109d92e94 r13: 0x000000010a4a9010 r14: 0x00007fff75557300 r15: 0x000000010906c310
rip: 0x00007fff85532286 rfl: 0x0000000000000206 cr2: 0x00007fff75ea9fd8
Logical CPU: 0
Error Code: 0x02000148
Trap Number: 133
Binary Images:
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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: 73166
thread_create: 0
thread_set_state: 0
VM Region Summary:
ReadOnly portion of Libraries: Total=109.5M resident=95.1M(87%) swapped_out_or_unallocated=14.4M(13%)
Writable regions: Total=53.9M written=13.3M(25%) resident=15.8M(29%) swapped_out=0K(0%) unallocated=38.1M(71%)
REGION TYPE VIRTUAL
=========== =======
Kernel Alloc Once 4K
MALLOC 44.8M
MALLOC (admin) 16K
STACK GUARD 56.0M
Stack 8192K
VM_ALLOCATE 16K
__DATA 2940K
__LINKEDIT 75.9M
__TEXT 33.6M
__UNICODE 552K
shared memory 4K
=========== =======
TOTAL 221.8M
Model: MacBookPro12,1, BootROM MBP121.0167.B14, 2 processors, Intel Core i5, 2.7 GHz, 8 GB, SMC 2.28f7
Graphics: Intel Iris Graphics 6100, Intel Iris Graphics 6100, Built-In
Memory Module: BANK 0/DIMM0, 4 GB, DDR3, 1867 MHz, 0x80AD, 0x483943434E4E4E424C54414C41522D4E5544
Memory Module: BANK 1/DIMM0, 4 GB, DDR3, 1867 MHz, 0x80AD, 0x483943434E4E4E424C54414C41522D4E5544
AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x133), Broadcom BCM43xx 1.0 (7.15.166.24.3)
Bluetooth: Version 4.3.6f3 16238, 3 services, 27 devices, 1 incoming serial ports
Network Service: Wi-Fi, AirPort, en0
Serial ATA Device: APPLE SSD SM0256G, 251 GB
USB Device: Internal Memory Card Reader
USB Device: Bluetooth USB Host Controller
Thunderbolt Bus: MacBook Pro, Apple Inc., 27.1
The problem does not happen if I run the native python installed on my mac. The following works just fine.
$ /usr/bin/python
Python 2.7.10 (default, Jul 14 2015, 19:46:27)
[GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.39)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> from nupic.bindings.algorithms import SpatialPooler as SP
>>>
Any help would be greatly appreciated.

malloc error when extending Python to call C++ function

I am trying to wrap a C++ function to call from Python.
My C++ code compiles and runs successfully, but when I call it from python I get the following error:
python(6805,0x7fff78401300) malloc: *** mach_vm_map(size=8245930807582093312) failed (error code=3)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
libc++abi.dylib: terminating with uncaught exception of type std::bad_alloc: std::bad_alloc
zsh: abort python
Here is my C++ function, which crawls my filesystem:
const char * crawlDirectory(const string directory)
{
std::vector<std::string> filesVector;
std::vector<std::string> dirsVector;
dirsVector.push_back(directory);
int currDirectoryIndex = 0;
while (currDirectoryIndex < dirsVector.size()) {
GetFilesInDirectory(filesVector, dirsVector, dirsVector[currDirectoryIndex].c_str());
currDirectoryIndex++;
}
std::string filesListString = "";
for (int i=0; i<filesVector.size()-1; i++) {
filesListString += filesVector[i].c_str() + SEPARATOR;
}
//add the last file path without the separator -- faster than a conditional for every iteration
filesListString += filesVector[filesVector.size()-1].c_str();
const char * retString = filesListString.c_str();
return retString;
}
I don't think the problem is in 'GetFilesInDirectory()', but I will post it if necessary.
Here is the extern block, which helps me wrap the function:
extern "C" {
Crawler* Crawler_new(){ return new Crawler(); }
const char * Crawler_crawlDirectory(Crawler* crawler, const string directory){ return(crawler->crawlDirectory(directory)); }
}
Here is the python file that defines the Crawler class:
from ctypes import cdll
from ctypes import *
lib = cdll.LoadLibrary('./libcrawler.so')
lib.Crawler_crawlDirectory.restype = c_char_p
lib.Crawler_crawlDirectory.argtypes = [c_void_p, c_char_p]
lib.Crawler_new.restype = c_void_p
class Crawler(object):
def __init__(self):
self.obj = lib.Crawler_new()
def crawlDirectory(self, path):
return lib.Crawler_crawlDirectory(self.obj, path)
I am positive that my C++ code is being compiled correctly (with g++ as a dylib), because I have tested the wrapper with other functions that return simple things like char*s and integers, and they work correctly.
Here is how I am calling the function from python:
>>> from wrapper import *
>>> c = Crawler()
>>> files = c.crawlDirectory('/Users/whatever/desktop')
Can anyone give insight about solving this issue?
Edit: here is the problem report:
Process: Python [7057]
Path: /System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python
Identifier: Python
Version: 2.7.6 (2.7.6)
Code Type: X86-64 (Native)
Parent Process: zsh [390]
Responsible: Terminal [285]
User ID: 501
PlugIn Path: /Users/USER/Documents/*/libcrawler.so
PlugIn Identifier: libcrawler.so
PlugIn Version: ??? (0)
Date/Time: 2014-06-08 16:36:24.623 -0700
OS Version: Mac OS X 10.10 (14A238x)
Report Version: 11
Anonymous UUID: F5B91E6D-C318-117A-A457-522AB46FF6DC
Sleep/Wake UUID: E228A7B4-D89E-4DBF-ABF3-510F4CF0EC3B
Time Awake Since Boot: 29000 seconds
Time Since Wake: 8000 seconds
Crashed Thread: 0 Dispatch queue: com.apple.main-thread
Exception Type: EXC_CRASH (SIGABRT)
Exception Codes: 0x0000000000000000, 0x0000000000000000
Application Specific Information:
abort() called
terminating with uncaught exception of type std::bad_alloc: std::bad_alloc
Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0 libsystem_kernel.dylib 0x00007fff90f5637a __pthread_kill + 10
1 libsystem_c.dylib 0x00007fff88fcc5ff abort + 129
2 libc++abi.dylib 0x00007fff8b95fb31 abort_message + 257
3 libc++abi.dylib 0x00007fff8b9879b9 default_terminate_handler() + 243
4 libobjc.A.dylib 0x00007fff8849c522 _objc_terminate() + 124
5 libc++abi.dylib 0x00007fff8b9850a1 std::__terminate(void (*)()) + 8
6 libc++abi.dylib 0x00007fff8b984b2c __cxa_throw + 121
7 libc++abi.dylib 0x00007fff8b98527a operator new(unsigned long) + 90
8 libc++.1.dylib 0x00007fff94fd1f05 std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >::__init(char const*, unsigned long) + 59
9 libcrawler.so 0x000000010747cce0 Crawler_crawlDirectory + 32
10 libffi.dylib 0x00007fff90eaaf44 ffi_call_unix64 + 76
11 libffi.dylib 0x00007fff90eab781 ffi_call + 853
12 _ctypes.so 0x0000000106d3c76e _ctypes_callproc + 874
13 _ctypes.so 0x0000000106d36bb9 PyCData_set + 2386
14 org.python.python 0x00000001069f03b8 PyObject_Call + 99
15 org.python.python 0x0000000106a6cc23 PyEval_EvalFrameEx + 11365
16 org.python.python 0x0000000106a7062a 0x1069e6000 + 566826
17 org.python.python 0x0000000106a6d406 PyEval_EvalFrameEx + 13384
18 org.python.python 0x0000000106a69d8a PyEval_EvalCodeEx + 1413
19 org.python.python 0x0000000106a697ff PyEval_EvalCode + 54
20 org.python.python 0x0000000106a897d1 0x1069e6000 + 669649
21 org.python.python 0x0000000106a895ed PyRun_InteractiveOneFlags + 353
22 org.python.python 0x0000000106a890fc PyRun_InteractiveLoopFlags + 192
23 org.python.python 0x0000000106a88fa6 PyRun_AnyFileExFlags + 60
24 org.python.python 0x0000000106a9ab0f Py_Main + 3051
25 libdyld.dylib 0x00007fff8a5575c9 start + 1
Thread 0 crashed with X86 Thread State (64-bit):
rax: 0x0000000000000000 rbx: 0x0000000000000006 rcx: 0x00007fff59221af8 rdx: 0x0000000000000000
rdi: 0x0000000000000d0f rsi: 0x0000000000000006 rbp: 0x00007fff59221b20 rsp: 0x00007fff59221af8
r8: 0x0000000000000000 r9: 0x00007fff88ff6e80 r10: 0x0000000008000000 r11: 0x0000000000000206
r12: 0x00007fff59221c80 r13: 0x00007fff592222e0 r14: 0x00007fff78401300 r15: 0x00007fff59221b60
rip: 0x00007fff90f5637a rfl: 0x0000000000000206 cr2: 0x00007fff785f2fc8
Logical CPU: 0
Error Code: 0x02000148
Trap Number: 133
Binary Images:
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0x7fff902c1000 - 0x7fff902d4ff7 libLinearAlgebra.dylib (1119) <F6A6D050-E257-3427-A05D-A46D2F4B57AB> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLinearAlgebra.dylib
0x7fff90eaa000 - 0x7fff90eabfff libffi.dylib (18.1) <BE2846BF-C1BA-3136-903F-A914CDBC7328> /usr/lib/libffi.dylib
0x7fff90f40000 - 0x7fff90f5dfff libsystem_kernel.dylib (2738.0.0.0.5) <07664A85-DF08-3113-8817-B726F7774B14> /usr/lib/system/libsystem_kernel.dylib
0x7fff9106e000 - 0x7fff910e3fff libcorecrypto.dylib (211.0.0.0.1) <6D9E2007-EF3B-3665-AA15-A356090540B6> /usr/lib/system/libcorecrypto.dylib
0x7fff9162d000 - 0x7fff91632fff libsystem_networkextension.dylib (112) <4C3B20D2-18FB-35BE-A695-8E56BAC1D3A8> /usr/lib/system/libsystem_networkextension.dylib
0x7fff91638000 - 0x7fff91638fff com.apple.Accelerate.vecLib (3.10 - vecLib 3.10) <1AEEC774-2F65-3763-B52E-C04C0DD05F63> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/vecLib
0x7fff918e2000 - 0x7fff918e7ff7 libunwind.dylib (35.3) <4BD86D0A-A203-3FEB-BFED-5668B180AB49> /usr/lib/system/libunwind.dylib
0x7fff93093000 - 0x7fff93099fff libsystem_trace.dylib (47.0.0.0.2) <3496EA08-6D61-37F0-A557-8AD734F0480E> /usr/lib/system/libsystem_trace.dylib
0x7fff93945000 - 0x7fff93946fff libunc.dylib (28) <43600429-64D7-3578-ACCE-7642190EE835> /usr/lib/system/libunc.dylib
0x7fff93947000 - 0x7fff9394ffff libsystem_platform.dylib (61) <90DD0380-D3ED-346A-B4A8-1F1D11D42032> /usr/lib/system/libsystem_platform.dylib
0x7fff93952000 - 0x7fff9395bffb libsystem_notify.dylib (129) <7F8F5086-AD7A-3C80-BBCB-AD54EA44376B> /usr/lib/system/libsystem_notify.dylib
0x7fff94168000 - 0x7fff945bafef com.apple.vImage (8.0 - 8.0) <ACD86E88-A9F7-3E95-BA51-4208E2D879B8> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vImage.framework/Versions/A/vImage
0x7fff9469e000 - 0x7fff946a0ff7 libquarantine.dylib (73) <EE50CAE5-1596-3344-8760-579EFAF176F2> /usr/lib/system/libquarantine.dylib
0x7fff94f92000 - 0x7fff94fe6fff libc++.1.dylib (120) <C6EFD658-B948-36F4-905D-A9780797D0D1> /usr/lib/libc++.1.dylib
0x7fff9556f000 - 0x7fff95580fff libsystem_coretls.dylib (29) <B95FEAC8-6C16-382A-BE5C-5B34F6A4E8FD> /usr/lib/system/libsystem_coretls.dylib
0x7fff9574c000 - 0x7fff958d9fff libBLAS.dylib (1119) <93F54197-FEA7-31A1-B960-CCD78F87702E> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
0x7fff95ce4000 - 0x7fff95ce4ff7 liblaunch.dylib (496.0.0.0.4) <25D0EE80-85D2-379D-BF76-09B417C0FD19> /usr/lib/system/liblaunch.dylib
0x7fff95d83000 - 0x7fff95d88ff7 libmacho.dylib (861) <BF14A7C8-2711-38E7-B05E-6AE66D5323CA> /usr/lib/system/libmacho.dylib
0x7fff961f6000 - 0x7fff96207ff7 libz.1.dylib (55) <68DE8C8A-0320-3269-AABF-D26D73F50001> /usr/lib/libz.1.dylib
0x7fff96564000 - 0x7fff96565fff libDiagnosticMessagesClient.dylib (100) <9F8277CE-07E0-39CD-A2EE-581D02EBE58B> /usr/lib/libDiagnosticMessagesClient.dylib
0x7fff96672000 - 0x7fff9669aff3 libsystem_info.dylib (456) <E997A3CF-82FE-36F5-B246-3E73C98BEE02> /usr/lib/system/libsystem_info.dylib
0x7fff96a65000 - 0x7fff96a66fff libsystem_secinit.dylib (16) <F2CA96CB-D627-3407-830C-E2E1D48E457B> /usr/lib/system/libsystem_secinit.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: 203216
thread_create: 0
thread_set_state: 493
VM Region Summary:
ReadOnly portion of Libraries: Total=100.7M resident=15.8M(16%) swapped_out_or_unallocated=85.0M(84%)
Writable regions: Total=31.9M written=8868K(27%) resident=11.9M(37%) swapped_out=0K(0%) unallocated=20.0M(63%)
REGION TYPE VIRTUAL
=========== =======
Kernel Alloc Once 4K
MALLOC 23.3M
MALLOC (admin) 16K
STACK GUARD 56.0M
Stack 8192K
VM_ALLOCATE 16K
__DATA 2080K
__LINKEDIT 74.3M
__TEXT 26.4M
__UNICODE 544K
shared memory 4K
=========== =======
TOTAL 190.7M
Model: MacBookPro5,4, BootROM MBP53.00AC.B03, 2 processors, Intel Core 2 Duo, 2.53 GHz, 8 GB, SMC 1.49f2
Graphics: NVIDIA GeForce 9400M, NVIDIA GeForce 9400M, PCI, 256 MB
Memory Module: BANK 0/DIMM0, 4 GB, DDR3, 1067 MHz, 0x857F, 0x483634353155363446373036364700000000
Memory Module: BANK 1/DIMM0, 4 GB, DDR3, 1067 MHz, 0x857F, 0x483634353155363446373036364700000000
AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x8D), Broadcom BCM43xx 1.0 (5.106.98.100.24)
Bluetooth: Version 4.3.0d49 14130, 3 services, 24 devices, 1 incoming serial ports
Network Service: AirPort, AirPort, en1
Serial ATA Device: Samsung SSD 840 EVO 750GB, 750.16 GB
Serial ATA Device: MATSHITADVD-R UJ-868
USB Device: Built-in iSight
USB Device: Internal Memory Card Reader
USB Device: Apple Internal Keyboard / Trackpad
USB Device: IR Receiver
USB Device: BRCM2046 Hub
USB Device: Bluetooth USB Host Controller
Thunderbolt Bus:
Edit: Stack trace from gdb:
http://pastebin.com/ncx5fTRg
(reached SO question size limit).
Thanks.