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.

Python - build application for mac with pyqt5

Welcome, I have a written program in Python with using PyQt5, a problem lies in that I want to build him to form of one file EXE for Windows which I was able to make with a help of pyinstaller and everything is working well on freshly installed system without any additional installations, but I have a problem with MacOS when I'm trying to do it with pyInstaller or py2app I'm getting errors during the opening of file .app
I've tried those commands:
PyInstaller:
pyinstaller --windowed --onefile filename.spec
(Link to file .spec is under)
When starting application (after a while) is closing without any error
Py2App:
python setup.py py2app
(Link to file setup.py is under)
During performing this command we can see that all libraries of type PyQt5 are added and application have weight of 196 MB so they're there but at startup I'm getting a error report (Link to this report under)
If I use command "python setup.py py2app -A' then application is working but it's taking only 222kb and I can assume that on this computer which an application will be running there has to be all libraries. And I want to avoid it.
I want to get one file which I'm sending to 1 person and without any installations of additional libraries application is starting up.
Setup.py:
from setuptools import setup
APP=['nazwa_pliku.py']
OPTIONS = {
'argv_emulation': True,
'includes': [
'PyQt5', 'PyQt5.QtCore', 'PyQt5.QtGui', 'PyQt5.QtWidgets',
'getmac', 'requests', 'shutil', 'zipfile', 'hashlib'
]
}
DATA_FILES = [('', ['resources'])]
setup(
app=APP,
options={'py2app': OPTIONS},
data_files=DATA_FILES,
setup_requires=['py2app']
)
PyInstaller (.spec):
# -*- mode: python ; coding: utf-8 -*-
block_cipher = None
a = Analysis(['nazwa_pliku.py'],
pathex=['PyQt5', 'PyQt5.QtCore', 'PyQt5.QtGui', 'PyQt5.QtWidgets', 'getmac', 'requests', 'shutil', 'zipfile', 'hashlib'],
binaries=[],
datas=[],
hiddenimports=[],
hookspath=[],
hooksconfig={},
runtime_hooks=[],
excludes=[],
win_no_prefer_redirects=False,
win_private_assemblies=False,
cipher=block_cipher,
noarchive=False)
pyz = PYZ(a.pure, a.zipped_data,
cipher=block_cipher)
exe = EXE(pyz,
a.scripts,
a.binaries,
a.zipfiles,
a.datas,
[],
name='nazwa_pliku',
debug=False,
bootloader_ignore_signals=False,
strip=False,
upx=True,
upx_exclude=[],
runtime_tmpdir=None,
console=False,
disable_windowed_traceback=False,
target_arch=None,
codesign_identity=None,
entitlements_file=None )
app = BUNDLE(exe,
name='nazwa_pliku.app',
icon=None,
bundle_identifier=None)
Problem report:
Process: nazwa_pliku [1657]
Path: /Users/USER/Downloads/*/nazwa_pliku.app/Contents/MacOS/nazwa_pliku
Identifier: org.pythonmac.unspecified.nazwa_pliku
Version: 0.0.0 (0.0.0)
Code Type: X86-64 (Native)
Parent Process: ??? [1]
Responsible: nazwa_pliku [1657]
User ID: 501
Date/Time: 2022-01-27 08:27:10.807 -0800
OS Version: macOS 11.0.1 (20B29)
Report Version: 12
Anonymous UUID: B619491E-F16C-B54A-87DC-CEF880698C90
Time Awake Since Boot: 1200 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 0x00007fff202f8462 __pthread_kill + 10
1 libsystem_pthread.dylib 0x00007fff20326610 pthread_kill + 263
2 libsystem_c.dylib 0x00007fff20279720 abort + 120
3 QtCore 0x0000000106d19529 qt_message_fatal(QtMsgType, QMessageLogContext const&, QString const&) + 9
4 QtCore 0x0000000106d1ac74 QMessageLogger::fatal(char const*, ...) const + 202
5 QtGui 0x00000001067273d9 QGuiApplicationPrivate::createPlatformIntegration() + 7193
6 QtGui 0x00000001067273fb QGuiApplicationPrivate::createEventDispatcher() + 27
7 QtCore 0x0000000106ef91af QCoreApplicationPrivate::init() + 1599
8 QtGui 0x0000000106721b59 QGuiApplicationPrivate::init() + 57
9 QtWidgets 0x000000010613cada QApplicationPrivate::init() + 26
10 QtWidgets.abi3.so 0x0000000105db55d8 0x105c6a000 + 1357272
11 sip.cpython-310-darwin.so 0x000000010735175b 0x10734b000 + 26459
12 org.python.python 0x0000000104e2cdf5 0x104d1b000 + 1121781
13 org.python.python 0x0000000104da1fe7 _PyObject_MakeTpCall + 135
14 org.python.python 0x0000000104ee322d 0x104d1b000 + 1868333
15 org.python.python 0x0000000104ed8635 _PyEval_EvalFrameDefault + 19717
16 org.python.python 0x0000000104ed1fe2 0x104d1b000 + 1798114
17 org.python.python 0x0000000104ee316f 0x104d1b000 + 1868143
18 org.python.python 0x0000000104ed8635 _PyEval_EvalFrameDefault + 19717
19 org.python.python 0x0000000104ed1fe2 0x104d1b000 + 1798114
20 org.python.python 0x0000000104ecc2db 0x104d1b000 + 1774299
21 org.python.python 0x0000000104e08ca6 0x104d1b000 + 973990
22 org.python.python 0x0000000104ee316f 0x104d1b000 + 1868143
23 org.python.python 0x0000000104ed8635 _PyEval_EvalFrameDefault + 19717
24 org.python.python 0x0000000104ed1fe2 0x104d1b000 + 1798114
25 org.python.python 0x0000000104ee316f 0x104d1b000 + 1868143
26 org.python.python 0x0000000104ed8635 _PyEval_EvalFrameDefault + 19717
27 org.python.python 0x0000000104ed1fe2 0x104d1b000 + 1798114
28 org.python.python 0x0000000104f4736d 0x104d1b000 + 2278253
29 org.python.python 0x0000000104f46b2d _PyRun_SimpleFileObject + 365
30 org.python.python 0x0000000104f4a5cd PyRun_SimpleFileExFlags + 109
31 org.pythonmac.unspecified.nazwa_pliku 0x0000000102fbbec5 0x102fb7000 + 20165
32 org.pythonmac.unspecified.nazwa_pliku 0x0000000102fba357 main + 257
33 libdyld.dylib 0x00007fff20341631 start + 1
Thread 1:
0 libsystem_pthread.dylib 0x00007fff20322458 start_wqthread + 0
Thread 2:
0 libsystem_pthread.dylib 0x00007fff20322458 start_wqthread + 0
Thread 3:
0 libsystem_pthread.dylib 0x00007fff20322458 start_wqthread + 0
Thread 0 crashed with X86 Thread State (64-bit):
rax: 0x0000000000000000 rbx: 0x0000000112224e00 rcx: 0x00007ffeecc45348 rdx: 0x0000000000000000
rdi: 0x0000000000000307 rsi: 0x0000000000000006 rbp: 0x00007ffeecc45370 rsp: 0x00007ffeecc45348
r8: 0x00000000000130a8 r9: 0x00007fff88a9fe68 r10: 0x0000000112224e00 r11: 0x0000000000000246
r12: 0x0000000000000307 r13: 0x0000000107283658 r14: 0x0000000000000006 r15: 0x0000000000000016
rip: 0x00007fff202f8462 rfl: 0x0000000000000246 cr2: 0x00007fc002ca6000
Logical CPU: 0
Error Code: 0x02000148
Trap Number: 133
Thread 0 instruction stream not available.
Thread 0 last branch register state not available.
Binary Images:
0x102fb7000 - 0x102fbefff +org.pythonmac.unspecified.nazwa_pliku (0.0.0 - 0.0.0) <ABECB05C-E91D-336E-81D6-4A467D071EE8> /Users/USER/Downloads/*/nazwa_pliku.app/Contents/MacOS/nazwa_pliku
0x104d1b000 - 0x105092fff +org.python.python (3.10.1, [c] 2001-2021 Python Software Foundation. - 3.10.1) <1071A8DD-3E3D-3958-95BF-BA33F1F82BE5> /Users/USER/Downloads/*/nazwa_pliku.app/Contents/Frameworks/Python.framework/Versions/3.10/Python
0x105304000 - 0x10530bfff +zlib.cpython-310-darwin.so (0) <87FA5122-1EC5-3030-B8B6-D9F6A4EE2EA8> /Users/USER/Downloads/*/nazwa_pliku.app/Contents/Resources/zlib.cpython-310-darwin.so
0x105417000 - 0x10542afff +_ctypes.so (0) <A0E1A89B-9D11-36E4-9D58-393EBF9F0D8A> /Users/USER/Downloads/*/nazwa_pliku.app/Contents/Resources/lib/python3.10/lib-dynload/_ctypes.so
0x105438000 - 0x10543ffff +_struct.so (0) <9399186E-C4E1-3BC6-9DB3-FB26E3BF1AA3> /Users/USER/Downloads/*/nazwa_pliku.app/Contents/Resources/lib/python3.10/lib-dynload/_struct.so
0x105acc000 - 0x105ae7fff +_pickle.so (0) <FDD8E805-90D8-39A2-838D-B1EFCE959BD7> /Users/USER/Downloads/*/nazwa_pliku.app/Contents/Resources/lib/python3.10/lib-dynload/_pickle.so
0x105af5000 - 0x105b04fff +_socket.so (0) <92B8B527-7B8F-318E-B2A5-7DF9472FD531> /Users/USER/Downloads/*/nazwa_pliku.app/Contents/Resources/lib/python3.10/lib-dynload/_socket.so
0x105b11000 - 0x105b1cfff +math.so (0) <66D1DAE5-3559-30ED-826D-9B2143C1BB28> /Users/USER/Downloads/*/nazwa_pliku.app/Contents/Resources/lib/python3.10/lib-dynload/math.so
0x105b28000 - 0x105b2ffff +select.so (0) <988B1C8F-D008-3880-8A84-32E5B631D225>
Thanks in advance

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.

Segmentation Violation when running MATLAB r2017a with caffe (python script)

I get the following crash when running Matlab r2017a with caffe from python script (selective_search.py from https://github.com/sergeyk/selective_search_ijcv_with_python). I run it with user root on ubuntu 17.10 and CPU mode only!. I also tried to run *.m file with matlab and it works fine. you can see below more details. also you can see below the matlab script parameters (['matlab', '-softwareopengl' atc)
root#desktop-home:/home/USERNAME/deepLearning/hed/python# python detect.py /home.USERNAME/Desktop/input.txt /home/USERNAME/Desktop/output.csv
CPU mode !!!!!!
WARNING: Logging before InitGoogleLogging() is written to STDERR
I0102 22:59:10.099709 3052 net.cpp:50] Initializing net from parameters:
name: "FCN"
input: "data"
input_dim: 1
input_dim: 3
...
...
...
I0102 22:59:10.636869 3052 upgrade_proto.cpp:620] Attempting to upgrade input file specified using deprecated V1LayerParameter: /home/USERNAME/deepLearning/hed/examples/hed/5stage-vgg.caffemodel
I0102 22:59:10.847916 3052 upgrade_proto.cpp:628] Successfully upgraded file specified using deprecated V1LayerParameter
Loading input...
selective_search_rcnn({'/home/USERNAME/Desktop/camera_500_X_500.jpg'}, '/tmp/tmphzvr5w.mat')
['matlab', '-softwareopengl', '-nojvm', '-r', "try; selective_search_rcnn({'/home/USERNAME/Desktop/camera_500_X_500.jpg'}, '/tmp/tmphzvr5w.mat'); catch; exit; end; exit"]
['matlab', '-softwareopengl', '-nojvm', '-r', "try; selective_search_rcnn({'/home/USERNAME/Desktop/camera_500_X_500.jpg'}, '/tmp/tmphzvr5w.mat'); catch; exit; end; exit"]
/home/USERNAME/deepLearning/hed/python/selective_search_ijcv_with_python
No protocol specified
------------------------------------------------------------------------
Segmentation violation detected at Tue Jan 2 22:59:13 2018
------------------------------------------------------------------------
Configuration:
Crash Decoding : Disabled - No sandbox or build area path
Crash Mode : continue (default)
Current Graphics Driver: Unknown software
Current Visual : None
Default Encoding : UTF-8
Deployed : false
GNU C Library : 2.26 stable
Host Name : USERNAME-home
MATLAB Architecture : glnxa64
MATLAB Entitlement ID: 3324953
MATLAB Root : /usr/local/MATLAB/R2017a
MATLAB Version : 9.2.0.556344 (R2017a)
OpenGL : software
Operating System : Linux 4.13.0-21-generic #24-Ubuntu SMP Mon Dec 18 17:29:16 UTC 2017 x86_64
Processor ID : x86 Family 6 Model 158 Stepping 9, GenuineIntel
Window System : No active display
Fault Count: 1
Abnormal termination:
Segmentation violation
Register State (from fault):
RAX = 00007f80b7df83d0 RBX = 0000000000000000
RCX = 0000000000000000 RDX = 00007f80b7df8600
RSP = 00007f80b7df82a0 RBP = 00007f80b7df8790
RSI = 00007f80bc3b6833 RDI = 00007f80b7df8390
R8 = 0000000000000000 R9 = 0000000000000000
R10 = 00000000000003ad R11 = 00007f80dbe55fe0
R12 = 00007f80b7df8390 R13 = 00007f80b7df8600
R14 = 00007f80b7df88a0 R15 = 00007f80dc10a7a0
RIP = 00007f80bc37c628 EFL = 0000000000010202
CS = 0033 FS = 0000 GS = 0000
Stack Trace (from fault):
[ 0] 0x00007f80bc37c628 bin/glnxa64/libmwddux_impl.so+00661032
[ 1] 0x00007f80bc356be9 bin/glnxa64/libmwddux_impl.so+00506857
[ 2] 0x00007f80bc3466b6 bin/glnxa64/libmwddux_impl.so+00439990
[ 3] 0x00007f80bc34c85a bin/glnxa64/libmwddux_impl.so+00464986
[ 4] 0x00007f80bc348370 bin/glnxa64/libmwddux_impl.so+00447344
[ 5] 0x00007f80d7cbe7d2 bin/glnxa64/libmwms.so+03168210
[ 6] 0x00007f80bc34808a bin/glnxa64/libmwddux_impl.so+00446602
[ 7] 0x00007f80da64bf65 /usr/local/MATLAB/R2017a/bin/glnxa64/libboost_thread.so.1.56.0+00073573
[ 8] 0x00007f80db6757fc /lib/x86_64-linux-gnu/libpthread.so.0+00030716
[ 9] 0x00007f80db3a2b0f /lib/x86_64-linux-gnu/libc.so.6+01133327 clone+00000063
[ 10] 0x0000000000000000 <unknown-module>+00000000
If this problem is reproducible, please submit a Service Request via:
http://www.mathworks.com/support/contact_us/
A technical support engineer might contact you with further information.
Thank you for your help.** This crash report has been saved to disk as /root/matlab_crash_dump.3072-1 **
MATLAB is exiting because of fatal error
Traceback (most recent call last):
File "detect.py", line 178, in <module>
main(sys.argv)
File "detect.py", line 149, in main
detections = detector.detect_selective_search(inputs)
File "/home/USERNAME/deepLearning/hed/python/caffe/detector.py", line 120, in detect_selective_search
cmd='selective_search_rcnn'
File "/home/USERNAME/deepLearning/hed/python/selective_search_ijcv_with_python/selective_search.py", line 51, in get_windows
raise Exception("Matlab script did not exit successfully!")
Exception: Matlab script did not exit successfully!

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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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.