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Scalene error: received signal SIGSEGV #110

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shaharkadmiel opened this issue Jan 6, 2021 · 14 comments
Closed

Scalene error: received signal SIGSEGV #110

shaharkadmiel opened this issue Jan 6, 2021 · 14 comments

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@shaharkadmiel
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Getting Scalene error: received signal SIGSEGV when trying to profile a python program.

I believe one of the imports at the top of my code breaks the profiler.

test.py:

#!/usr/bin/env python
# coding: utf-8

import obspy

profiling

scalene test.py

output: Scalene error: received signal SIGSEGV

Desktop:

  • OS: macOS-10.16-x86_64
@emeryberger
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Now works fine with the latest version of Scalene; please upgrade (pip install -U scalene) and test. Thanks!

@simonw simonw mentioned this issue Feb 8, 2021
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@simonw
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simonw commented Feb 8, 2021

I got this error too in simonw/datasette#1219 - steps to reproduce:

cd /tmp
python3 -m venv v
v
source bin/activate
git clone https://github.com/simonw/datasette
cd datasette
pip install -e '.[test]'
pip install scalene
echo 'if __name__ == "__main__":\n    import sys, pytest\n    pytest.main(sys.argv)' > run_tests.py
scalene --profile-all run_tests.py -sv -x .

That produced the following output for me:

================================================================================= test session starts =================================================================================
platform darwin -- Python 3.9.1, pytest-6.2.2, py-1.10.0, pluggy-0.13.1 -- python3
cachedir: .pytest_cache
rootdir: /private/tmp/v/datasette, configfile: pytest.ini
plugins: asyncio-0.14.0, timeout-1.4.2
collecting ... Fatal Python error: Segmentation fault

Current thread 0x00000001123fedc0 (most recent call first):
  File "/private/tmp/v/datasette/datasette/utils/__init__.py", line 553 in detect_json1
  File "/private/tmp/v/datasette/datasette/filters.py", line 168 in Filters
  File "/private/tmp/v/datasette/datasette/filters.py", line 94 in <module>
  File "<frozen importlib._bootstrap>", line 228 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 790 in exec_module
  File "<frozen importlib._bootstrap>", line 680 in _load_unlocked
  File "<frozen importlib._bootstrap>", line 986 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1007 in _find_and_load
  File "/private/tmp/v/datasette/datasette/views/table.py", line 27 in <module>
  File "<frozen importlib._bootstrap>", line 228 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 790 in exec_module
  File "<frozen importlib._bootstrap>", line 680 in _load_unlocked
  File "<frozen importlib._bootstrap>", line 986 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1007 in _find_and_load
  File "/private/tmp/v/datasette/datasette/app.py", line 42 in <module>
  File "<frozen importlib._bootstrap>", line 228 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 790 in exec_module
  File "<frozen importlib._bootstrap>", line 680 in _load_unlocked
  File "<frozen importlib._bootstrap>", line 986 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1007 in _find_and_load
  File "/private/tmp/v/datasette/tests/test_api.py", line 1 in <module>
  File "/private/tmp/v/lib/python3.9/site-packages/_pytest/assertion/rewrite.py", line 170 in exec_module
  File "<frozen importlib._bootstrap>", line 680 in _load_unlocked
  File "<frozen importlib._bootstrap>", line 986 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1007 in _find_and_load
  File "<frozen importlib._bootstrap>", line 1030 in _gcd_import
  File "/usr/local/Cellar/python@3.9/3.9.1_7/Frameworks/Python.framework/Versions/3.9/lib/python3.9/importlib/__init__.py", line 127 in import_module
  File "/private/tmp/v/lib/python3.9/site-packages/_pytest/pathlib.py", line 531 in import_path
  File "/private/tmp/v/lib/python3.9/site-packages/_pytest/python.py", line 578 in _importtestmodule
  File "/private/tmp/v/lib/python3.9/site-packages/_pytest/python.py", line 500 in _getobj
  File "/private/tmp/v/lib/python3.9/site-packages/_pytest/python.py", line 291 in obj
  File "/private/tmp/v/lib/python3.9/site-packages/_pytest/python.py", line 516 in _inject_setup_module_fixture
  File "/private/tmp/v/lib/python3.9/site-packages/_pytest/python.py", line 503 in collect
  File "/private/tmp/v/lib/python3.9/site-packages/_pytest/runner.py", line 341 in <lambda>
  File "/private/tmp/v/lib/python3.9/site-packages/_pytest/runner.py", line 311 in from_call
  File "/private/tmp/v/lib/python3.9/site-packages/_pytest/runner.py", line 341 in pytest_make_collect_report
  File "/private/tmp/v/lib/python3.9/site-packages/pluggy/callers.py", line 187 in _multicall
  File "/private/tmp/v/lib/python3.9/site-packages/pluggy/manager.py", line 84 in <lambda>
  File "/private/tmp/v/lib/python3.9/site-packages/pluggy/manager.py", line 93 in _hookexec
  File "/private/tmp/v/lib/python3.9/site-packages/pluggy/hooks.py", line 286 in __call__
  File "/private/tmp/v/lib/python3.9/site-packages/_pytest/runner.py", line 458 in collect_one_node
  File "/private/tmp/v/lib/python3.9/site-packages/_pytest/main.py", line 808 in genitems
  File "/private/tmp/v/lib/python3.9/site-packages/_pytest/main.py", line 811 in genitems
  File "/private/tmp/v/lib/python3.9/site-packages/_pytest/main.py", line 634 in perform_collect
  File "/private/tmp/v/lib/python3.9/site-packages/_pytest/main.py", line 333 in pytest_collection
  File "/private/tmp/v/lib/python3.9/site-packages/pluggy/callers.py", line 187 in _multicall
  File "/private/tmp/v/lib/python3.9/site-packages/pluggy/manager.py", line 84 in <lambda>
  File "/private/tmp/v/lib/python3.9/site-packages/pluggy/manager.py", line 93 in _hookexec
  File "/private/tmp/v/lib/python3.9/site-packages/pluggy/hooks.py", line 286 in __call__
  File "/private/tmp/v/lib/python3.9/site-packages/_pytest/main.py", line 322 in _main
  File "/private/tmp/v/lib/python3.9/site-packages/_pytest/main.py", line 269 in wrap_session
  File "/private/tmp/v/lib/python3.9/site-packages/_pytest/main.py", line 316 in pytest_cmdline_main
  File "/private/tmp/v/lib/python3.9/site-packages/pluggy/callers.py", line 187 in _multicall
  File "/private/tmp/v/lib/python3.9/site-packages/pluggy/manager.py", line 84 in <lambda>
  File "/private/tmp/v/lib/python3.9/site-packages/pluggy/manager.py", line 93 in _hookexec
  File "/private/tmp/v/lib/python3.9/site-packages/pluggy/hooks.py", line 286 in __call__
  File "/private/tmp/v/lib/python3.9/site-packages/_pytest/config/__init__.py", line 162 in main
  File "run_tests.py", line 3 in <module>
  File "/private/tmp/v/lib/python3.9/site-packages/scalene/scalene_profiler.py", line 1771 in main
  File "/private/tmp/v/lib/python3.9/site-packages/scalene/__main__.py", line 7 in main
  File "/private/tmp/v/lib/python3.9/site-packages/scalene/__main__.py", line 14 in <module>
  File "/usr/local/Cellar/python@3.9/3.9.1_7/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
  File "/usr/local/Cellar/python@3.9/3.9.1_7/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main
Scalene error: received signal SIGSEGV

I'm on macOS and the system crash dialog showed up containing the following:

Process:               Python [4744]
Path:                  /usr/local/Cellar/python@3.9/3.9.1_7/Frameworks/Python.framework/Versions/3.9/Resources/Python.app/Contents/MacOS/Python
Identifier:            Python
Version:               3.9.1 (3.9.1)
Code Type:             X86-64 (Native)
Parent Process:        Python [4742]
Responsible:           Terminal [329]
User ID:               501

Date/Time:             2021-02-08 14:13:15.095 -0800
OS Version:            Mac OS X 10.15.6 (19G2021)
Report Version:        12
Bridge OS Version:     4.6 (17P6610)
Anonymous UUID:        0315A45A-F711-A259-969A-69C9E27538E8

Sleep/Wake UUID:       FC8FB062-544C-41A5-B2D3-E50364079D69

Time Awake Since Boot: 710000 seconds
Time Since Wake:       250 seconds

System Integrity Protection: enabled

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

Exception Type:        EXC_BAD_ACCESS (SIGSEGV)
Exception Codes:       KERN_INVALID_ADDRESS at 0x0000000000000000
Exception Note:        EXC_CORPSE_NOTIFY

VM Regions Near 0:
--> 
    __TEXT                 00000001049a6000-00000001049aa000 [   16K] r-x/r-x SM=COW  /usr/local/Cellar/python@3.9/3.9.1_7/Frameworks/Python.framework/Versions/3.9/Resources/Python.app/Contents/MacOS/Python

Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0   libsystem_kernel.dylib        	0x00007fff6a85133a __pthread_kill + 10
1   libsystem_pthread.dylib       	0x00007fff6a90de60 pthread_kill + 430
2   libsystem_c.dylib             	0x00007fff6a76893e raise + 26
3   libsystem_platform.dylib      	0x00007fff6a9025fd _sigtramp + 29
4   ???                           	000000000000000000 0 + 0
5   libsqlite3.0.dylib            	0x00000001064866c4 sqlite3Malloc + 230
6   libsqlite3.0.dylib            	0x000000010648a499 sqlite3MallocZero + 15
7   libsqlite3.0.dylib            	0x000000010649df6e pthreadMutexAlloc + 44
8   libsqlite3.0.dylib            	0x0000000106485e73 sqlite3_initialize + 240
9   libsqlite3.0.dylib            	0x00000001064965ba openDatabase + 50
10  _sqlite3.cpython-39-darwin.so 	0x000000010646b121 pysqlite_connection_init + 397
11  org.python.python             	0x0000000105a40227 type_call + 150
12  org.python.python             	0x00000001059fdf55 _PyObject_Call + 138
13  _sqlite3.cpython-39-darwin.so 	0x000000010646f6d9 module_connect + 211
14  org.python.python             	0x0000000105a2e42f cfunction_call + 122
15  org.python.python             	0x00000001059fdad3 _PyObject_MakeTpCall + 266
16  org.python.python             	0x0000000105aa5b57 call_function + 455
17  org.python.python             	0x0000000105aa2cb4 _PyEval_EvalFrameDefault + 27452
18  org.python.python             	0x00000001059fe178 function_code_fastcall + 97
19  org.python.python             	0x0000000105aa5b23 call_function + 403
20  org.python.python             	0x0000000105aa2d60 _PyEval_EvalFrameDefault + 27624
21  org.python.python             	0x0000000105aa666b _PyEval_EvalCode + 1998
22  org.python.python             	0x0000000105a9c123 PyEval_EvalCodeEx + 128
23  org.python.python             	0x0000000105a9832d builtin___build_class__ + 1224
24  org.python.python             	0x0000000105a2dd97 cfunction_vectorcall_FASTCALL_KEYWORDS + 124
25  org.python.python             	0x0000000105aa5b23 call_function + 403
26  org.python.python             	0x0000000105aa2d60 _PyEval_EvalFrameDefault + 27624
27  org.python.python             	0x0000000105aa666b _PyEval_EvalCode + 1998
28  org.python.python             	0x0000000105a9c09d PyEval_EvalCode + 79
29  org.python.python             	0x0000000105a993d7 builtin_exec + 581
30  org.python.python             	0x0000000105a2dceb cfunction_vectorcall_FASTCALL + 203
31  org.python.python             	0x0000000105aa30d9 _PyEval_EvalFrameDefault + 28513
32  org.python.python             	0x0000000105aa666b _PyEval_EvalCode + 1998
33  org.python.python             	0x00000001059fe108 _PyFunction_Vectorcall + 248
34  org.python.python             	0x0000000105aa5b23 call_function + 403
35  org.python.python             	0x0000000105aa2cb4 _PyEval_EvalFrameDefault + 27452
36  org.python.python             	0x00000001059fe178 function_code_fastcall + 97
37  org.python.python             	0x0000000105aa5b23 call_function + 403
38  org.python.python             	0x0000000105aa2c98 _PyEval_EvalFrameDefault + 27424
39  org.python.python             	0x00000001059fe178 function_code_fastcall + 97
40  org.python.python             	0x0000000105aa5b23 call_function + 403
41  org.python.python             	0x0000000105aa2d60 _PyEval_EvalFrameDefault + 27624
42  org.python.python             	0x00000001059fe178 function_code_fastcall + 97
43  org.python.python             	0x0000000105aa5b23 call_function + 403
44  org.python.python             	0x0000000105aa2d60 _PyEval_EvalFrameDefault + 27624
45  org.python.python             	0x00000001059fe178 function_code_fastcall + 97
46  org.python.python             	0x00000001059ff1c7 object_vacall + 402
47  org.python.python             	0x00000001059ff32e _PyObject_CallMethodIdObjArgs + 248
48  org.python.python             	0x0000000105ac1815 PyImport_ImportModuleLevelObject + 1179
49  org.python.python             	0x0000000105aa16b8 _PyEval_EvalFrameDefault + 21824
50  org.python.python             	0x0000000105aa666b _PyEval_EvalCode + 1998
51  org.python.python             	0x0000000105a9c09d PyEval_EvalCode + 79
52  org.python.python             	0x0000000105a993d7 builtin_exec + 581
53  org.python.python             	0x0000000105a2dceb cfunction_vectorcall_FASTCALL + 203
54  org.python.python             	0x0000000105aa30d9 _PyEval_EvalFrameDefault + 28513
55  org.python.python             	0x0000000105aa666b _PyEval_EvalCode + 1998
56  org.python.python             	0x00000001059fe108 _PyFunction_Vectorcall + 248
57  org.python.python             	0x0000000105aa5b23 call_function + 403
58  org.python.python             	0x0000000105aa2cb4 _PyEval_EvalFrameDefault + 27452
59  org.python.python             	0x00000001059fe178 function_code_fastcall + 97
60  org.python.python             	0x0000000105aa5b23 call_function + 403
61  org.python.python             	0x0000000105aa2c98 _PyEval_EvalFrameDefault + 27424
62  org.python.python             	0x00000001059fe178 function_code_fastcall + 97
63  org.python.python             	0x0000000105aa5b23 call_function + 403
64  org.python.python             	0x0000000105aa2d60 _PyEval_EvalFrameDefault + 27624
65  org.python.python             	0x00000001059fe178 function_code_fastcall + 97
66  org.python.python             	0x0000000105aa5b23 call_function + 403
67  org.python.python             	0x0000000105aa2d60 _PyEval_EvalFrameDefault + 27624
68  org.python.python             	0x00000001059fe178 function_code_fastcall + 97
69  org.python.python             	0x00000001059ff1c7 object_vacall + 402
70  org.python.python             	0x00000001059ff32e _PyObject_CallMethodIdObjArgs + 248
71  org.python.python             	0x0000000105ac1815 PyImport_ImportModuleLevelObject + 1179
72  org.python.python             	0x0000000105aa16b8 _PyEval_EvalFrameDefault + 21824
73  org.python.python             	0x0000000105aa666b _PyEval_EvalCode + 1998
74  org.python.python             	0x0000000105a9c09d PyEval_EvalCode + 79
75  org.python.python             	0x0000000105a993d7 builtin_exec + 581
76  org.python.python             	0x0000000105a2dceb cfunction_vectorcall_FASTCALL + 203
77  org.python.python             	0x0000000105aa30d9 _PyEval_EvalFrameDefault + 28513
78  org.python.python             	0x0000000105aa666b _PyEval_EvalCode + 1998
79  org.python.python             	0x00000001059fe108 _PyFunction_Vectorcall + 248
80  org.python.python             	0x0000000105aa5b23 call_function + 403
81  org.python.python             	0x0000000105aa2cb4 _PyEval_EvalFrameDefault + 27452
82  org.python.python             	0x00000001059fe178 function_code_fastcall + 97
83  org.python.python             	0x0000000105aa5b23 call_function + 403
84  org.python.python             	0x0000000105aa2c98 _PyEval_EvalFrameDefault + 27424
85  org.python.python             	0x00000001059fe178 function_code_fastcall + 97
86  org.python.python             	0x0000000105aa5b23 call_function + 403
87  org.python.python             	0x0000000105aa2d60 _PyEval_EvalFrameDefault + 27624
88  org.python.python             	0x00000001059fe178 function_code_fastcall + 97
89  org.python.python             	0x0000000105aa5b23 call_function + 403
90  org.python.python             	0x0000000105aa2d60 _PyEval_EvalFrameDefault + 27624
91  org.python.python             	0x00000001059fe178 function_code_fastcall + 97
92  org.python.python             	0x00000001059ff1c7 object_vacall + 402
93  org.python.python             	0x00000001059ff32e _PyObject_CallMethodIdObjArgs + 248
94  org.python.python             	0x0000000105ac1815 PyImport_ImportModuleLevelObject + 1179
95  org.python.python             	0x0000000105aa16b8 _PyEval_EvalFrameDefault + 21824
96  org.python.python             	0x0000000105aa666b _PyEval_EvalCode + 1998
97  org.python.python             	0x0000000105a9c09d PyEval_EvalCode + 79
98  org.python.python             	0x0000000105a993d7 builtin_exec + 581
99  org.python.python             	0x0000000105a2dceb cfunction_vectorcall_FASTCALL + 203
100 org.python.python             	0x0000000105aa5b23 call_function + 403
101 org.python.python             	0x0000000105aa2d60 _PyEval_EvalFrameDefault + 27624
102 org.python.python             	0x00000001059fe178 function_code_fastcall + 97
103 org.python.python             	0x0000000105aa5b23 call_function + 403
104 org.python.python             	0x0000000105aa2c98 _PyEval_EvalFrameDefault + 27424
105 org.python.python             	0x00000001059fe178 function_code_fastcall + 97
106 org.python.python             	0x0000000105aa5b23 call_function + 403
107 org.python.python             	0x0000000105aa2d60 _PyEval_EvalFrameDefault + 27624
108 org.python.python             	0x00000001059fe178 function_code_fastcall + 97
109 org.python.python             	0x0000000105aa5b23 call_function + 403
110 org.python.python             	0x0000000105aa2d60 _PyEval_EvalFrameDefault + 27624
111 org.python.python             	0x00000001059fe178 function_code_fastcall + 97
112 org.python.python             	0x0000000105aa5b23 call_function + 403
113 org.python.python             	0x0000000105aa2d60 _PyEval_EvalFrameDefault + 27624
114 org.python.python             	0x0000000105aa666b _PyEval_EvalCode + 1998
115 org.python.python             	0x00000001059fe108 _PyFunction_Vectorcall + 248
116 org.python.python             	0x0000000105aa5b23 call_function + 403
117 org.python.python             	0x0000000105aa2cb4 _PyEval_EvalFrameDefault + 27452
118 org.python.python             	0x0000000105aa666b _PyEval_EvalCode + 1998
119 org.python.python             	0x00000001059fe108 _PyFunction_Vectorcall + 248
120 org.python.python             	0x0000000105aa5b23 call_function + 403
121 org.python.python             	0x0000000105aa2cb4 _PyEval_EvalFrameDefault + 27452
122 org.python.python             	0x0000000105aa666b _PyEval_EvalCode + 1998
123 org.python.python             	0x00000001059fe108 _PyFunction_Vectorcall + 248
124 org.python.python             	0x0000000105aa5b23 call_function + 403
125 org.python.python             	0x0000000105aa2e1e _PyEval_EvalFrameDefault + 27814
126 org.python.python             	0x00000001059fe178 function_code_fastcall + 97
127 org.python.python             	0x0000000105aa5b23 call_function + 403
128 org.python.python             	0x0000000105aa2c98 _PyEval_EvalFrameDefault + 27424
129 org.python.python             	0x00000001059fe178 function_code_fastcall + 97
130 org.python.python             	0x0000000105aa5b23 call_function + 403
131 org.python.python             	0x0000000105aa2c98 _PyEval_EvalFrameDefault + 27424
132 org.python.python             	0x00000001059fe178 function_code_fastcall + 97
133 org.python.python             	0x0000000105a059f7 property_descr_get + 114
134 org.python.python             	0x0000000105a3167d _PyObject_GenericGetAttrWithDict + 177
135 org.python.python             	0x0000000105aa1117 _PyEval_EvalFrameDefault + 20383
136 org.python.python             	0x0000000105aa666b _PyEval_EvalCode + 1998
137 org.python.python             	0x00000001059fe108 _PyFunction_Vectorcall + 248
138 org.python.python             	0x0000000105aa5b23 call_function + 403
139 org.python.python             	0x0000000105aa2c98 _PyEval_EvalFrameDefault + 27424
140 org.python.python             	0x0000000105aa666b _PyEval_EvalCode + 1998
141 org.python.python             	0x00000001059fe108 _PyFunction_Vectorcall + 248
142 org.python.python             	0x0000000105aa5b23 call_function + 403
143 org.python.python             	0x0000000105aa2c98 _PyEval_EvalFrameDefault + 27424
144 org.python.python             	0x0000000105aa666b _PyEval_EvalCode + 1998
145 org.python.python             	0x00000001059fe108 _PyFunction_Vectorcall + 248
146 org.python.python             	0x0000000105aa5b23 call_function + 403
147 org.python.python             	0x0000000105aa2d60 _PyEval_EvalFrameDefault + 27624
148 org.python.python             	0x0000000105aa666b _PyEval_EvalCode + 1998
149 org.python.python             	0x00000001059fe108 _PyFunction_Vectorcall + 248
150 org.python.python             	0x00000001059ffddb method_vectorcall + 164
151 org.python.python             	0x0000000105aa5b23 call_function + 403
152 org.python.python             	0x0000000105aa2cb4 _PyEval_EvalFrameDefault + 27452
153 org.python.python             	0x0000000105aa666b _PyEval_EvalCode + 1998
154 org.python.python             	0x00000001059fe108 _PyFunction_Vectorcall + 248
155 org.python.python             	0x0000000105aa2fe4 _PyEval_EvalFrameDefault + 28268
156 org.python.python             	0x0000000105aa666b _PyEval_EvalCode + 1998
157 org.python.python             	0x00000001059fe108 _PyFunction_Vectorcall + 248
158 org.python.python             	0x0000000105aa5b23 call_function + 403
159 org.python.python             	0x0000000105aa2e1e _PyEval_EvalFrameDefault + 27814
160 org.python.python             	0x0000000105aa666b _PyEval_EvalCode + 1998
161 org.python.python             	0x00000001059fe108 _PyFunction_Vectorcall + 248
162 org.python.python             	0x0000000105aa5b23 call_function + 403
163 org.python.python             	0x0000000105aa2cb4 _PyEval_EvalFrameDefault + 27452
164 org.python.python             	0x00000001059fe178 function_code_fastcall + 97
165 org.python.python             	0x00000001059ffddb method_vectorcall + 164
166 org.python.python             	0x0000000105aa5b23 call_function + 403
167 org.python.python             	0x0000000105aa2cb4 _PyEval_EvalFrameDefault + 27452
168 org.python.python             	0x0000000105aa666b _PyEval_EvalCode + 1998
169 org.python.python             	0x00000001059fe108 _PyFunction_Vectorcall + 248
170 org.python.python             	0x00000001059fd958 _PyObject_FastCallDictTstate + 149
171 org.python.python             	0x00000001059fe3c1 _PyObject_Call_Prepend + 139
172 org.python.python             	0x0000000105a45e2b slot_tp_call + 87
173 org.python.python             	0x00000001059fdad3 _PyObject_MakeTpCall + 266
174 org.python.python             	0x0000000105aa5b57 call_function + 455
175 org.python.python             	0x0000000105aa2e1e _PyEval_EvalFrameDefault + 27814
176 org.python.python             	0x00000001059fe178 function_code_fastcall + 97
177 org.python.python             	0x0000000105aa5b23 call_function + 403
178 org.python.python             	0x0000000105aa2d60 _PyEval_EvalFrameDefault + 27624
179 org.python.python             	0x0000000105a0c05c gen_send_ex + 269
180 org.python.python             	0x0000000105a9f48c _PyEval_EvalFrameDefault + 13076
181 org.python.python             	0x0000000105a0c05c gen_send_ex + 269
182 org.python.python             	0x0000000105a15625 list_extend + 169
183 org.python.python             	0x0000000105a050ce method_vectorcall_O + 292
184 org.python.python             	0x0000000105aa5b23 call_function + 403
185 org.python.python             	0x0000000105aa2c98 _PyEval_EvalFrameDefault + 27424
186 org.python.python             	0x0000000105aa666b _PyEval_EvalCode + 1998
187 org.python.python             	0x00000001059fe108 _PyFunction_Vectorcall + 248
188 org.python.python             	0x0000000105aa5b23 call_function + 403
189 org.python.python             	0x0000000105aa2c98 _PyEval_EvalFrameDefault + 27424
190 org.python.python             	0x00000001059fe178 function_code_fastcall + 97
191 org.python.python             	0x0000000105aa2fe4 _PyEval_EvalFrameDefault + 28268
192 org.python.python             	0x0000000105aa666b _PyEval_EvalCode + 1998
193 org.python.python             	0x00000001059fe108 _PyFunction_Vectorcall + 248
194 org.python.python             	0x0000000105aa5b23 call_function + 403
195 org.python.python             	0x0000000105aa2e1e _PyEval_EvalFrameDefault + 27814
196 org.python.python             	0x0000000105aa666b _PyEval_EvalCode + 1998
197 org.python.python             	0x00000001059fe108 _PyFunction_Vectorcall + 248
198 org.python.python             	0x0000000105aa5b23 call_function + 403
199 org.python.python             	0x0000000105aa2cb4 _PyEval_EvalFrameDefault + 27452
200 org.python.python             	0x00000001059fe178 function_code_fastcall + 97
201 org.python.python             	0x00000001059ffddb method_vectorcall + 164
202 org.python.python             	0x0000000105aa5b23 call_function + 403
203 org.python.python             	0x0000000105aa2cb4 _PyEval_EvalFrameDefault + 27452
204 org.python.python             	0x0000000105aa666b _PyEval_EvalCode + 1998
205 org.python.python             	0x00000001059fe108 _PyFunction_Vectorcall + 248
206 org.python.python             	0x00000001059fd958 _PyObject_FastCallDictTstate + 149
207 org.python.python             	0x00000001059fe3c1 _PyObject_Call_Prepend + 139
208 org.python.python             	0x0000000105a45e2b slot_tp_call + 87
209 org.python.python             	0x00000001059fdad3 _PyObject_MakeTpCall + 266
210 org.python.python             	0x0000000105aa5b57 call_function + 455
211 org.python.python             	0x0000000105aa2e1e _PyEval_EvalFrameDefault + 27814
212 org.python.python             	0x00000001059fe178 function_code_fastcall + 97
213 org.python.python             	0x0000000105aa5b23 call_function + 403
214 org.python.python             	0x0000000105aa2d60 _PyEval_EvalFrameDefault + 27624
215 org.python.python             	0x00000001059fe178 function_code_fastcall + 97
216 org.python.python             	0x0000000105aa5b23 call_function + 403
217 org.python.python             	0x0000000105aa2d60 _PyEval_EvalFrameDefault + 27624
218 org.python.python             	0x00000001059fe178 function_code_fastcall + 97
219 org.python.python             	0x0000000105aa2fe4 _PyEval_EvalFrameDefault + 28268
220 org.python.python             	0x0000000105aa666b _PyEval_EvalCode + 1998
221 org.python.python             	0x00000001059fe108 _PyFunction_Vectorcall + 248
222 org.python.python             	0x0000000105aa5b23 call_function + 403
223 org.python.python             	0x0000000105aa2e1e _PyEval_EvalFrameDefault + 27814
224 org.python.python             	0x0000000105aa666b _PyEval_EvalCode + 1998
225 org.python.python             	0x00000001059fe108 _PyFunction_Vectorcall + 248
226 org.python.python             	0x0000000105aa5b23 call_function + 403
227 org.python.python             	0x0000000105aa2cb4 _PyEval_EvalFrameDefault + 27452
228 org.python.python             	0x00000001059fe178 function_code_fastcall + 97
229 org.python.python             	0x00000001059ffddb method_vectorcall + 164
230 org.python.python             	0x0000000105aa5b23 call_function + 403
231 org.python.python             	0x0000000105aa2cb4 _PyEval_EvalFrameDefault + 27452
232 org.python.python             	0x0000000105aa666b _PyEval_EvalCode + 1998
233 org.python.python             	0x00000001059fe108 _PyFunction_Vectorcall + 248
234 org.python.python             	0x00000001059fd958 _PyObject_FastCallDictTstate + 149
235 org.python.python             	0x00000001059fe3c1 _PyObject_Call_Prepend + 139
236 org.python.python             	0x0000000105a45e2b slot_tp_call + 87
237 org.python.python             	0x00000001059fdad3 _PyObject_MakeTpCall + 266
238 org.python.python             	0x0000000105aa5b57 call_function + 455
239 org.python.python             	0x0000000105aa2e1e _PyEval_EvalFrameDefault + 27814
240 org.python.python             	0x0000000105aa666b _PyEval_EvalCode + 1998
241 org.python.python             	0x00000001059fe108 _PyFunction_Vectorcall + 248
242 org.python.python             	0x0000000105aa5b23 call_function + 403
243 org.python.python             	0x0000000105aa2cb4 _PyEval_EvalFrameDefault + 27452
244 org.python.python             	0x0000000105aa666b _PyEval_EvalCode + 1998
245 org.python.python             	0x0000000105a9c09d PyEval_EvalCode + 79
246 org.python.python             	0x0000000105a993d7 builtin_exec + 581
247 org.python.python             	0x0000000105a2dceb cfunction_vectorcall_FASTCALL + 203
248 org.python.python             	0x0000000105aa5b23 call_function + 403
249 org.python.python             	0x0000000105aa2d60 _PyEval_EvalFrameDefault + 27624
250 org.python.python             	0x00000001059fe178 function_code_fastcall + 97
251 org.python.python             	0x0000000105aa5b23 call_function + 403
252 org.python.python             	0x0000000105aa2cb4 _PyEval_EvalFrameDefault + 27452
253 org.python.python             	0x00000001059fe178 function_code_fastcall + 97
254 org.python.python             	0x0000000105aa5b23 call_function + 403
255 org.python.python             	0x0000000105aa2d60 _PyEval_EvalFrameDefault + 27624
256 org.python.python             	0x0000000105aa666b _PyEval_EvalCode + 1998
257 org.python.python             	0x0000000105a9c09d PyEval_EvalCode + 79
258 org.python.python             	0x0000000105a993d7 builtin_exec + 581
259 org.python.python             	0x0000000105a2dceb cfunction_vectorcall_FASTCALL + 203
260 org.python.python             	0x0000000105aa5b23 call_function + 403
261 org.python.python             	0x0000000105aa2d60 _PyEval_EvalFrameDefault + 27624
262 org.python.python             	0x0000000105aa666b _PyEval_EvalCode + 1998
263 org.python.python             	0x00000001059fe108 _PyFunction_Vectorcall + 248
264 org.python.python             	0x0000000105aa5b23 call_function + 403
265 org.python.python             	0x0000000105aa2d60 _PyEval_EvalFrameDefault + 27624
266 org.python.python             	0x0000000105aa666b _PyEval_EvalCode + 1998
267 org.python.python             	0x00000001059fe108 _PyFunction_Vectorcall + 248
268 org.python.python             	0x0000000105aece13 pymain_run_module + 353
269 org.python.python             	0x0000000105aec638 Py_RunMain + 1199
270 org.python.python             	0x0000000105aecbf1 pymain_main + 306
271 org.python.python             	0x0000000105aecc3f Py_BytesMain + 42
272 libdyld.dylib                 	0x00007fff6a709cc9 start + 1

Thread 0 crashed with X86 Thread State (64-bit):
  rax: 0x0000000000000000  rbx: 0x00000001123fedc0  rcx: 0x00007ff24009fa58  rdx: 0x0000000000000000
  rdi: 0x0000000000000307  rsi: 0x000000000000000b  rbp: 0x00007ff24009fa80  rsp: 0x00007ff24009fa58
   r8: 0x0000000000000003   r9: 0xcccccccccccccccd  r10: 0x00000001123fedc0  r11: 0x0000000000000246
  r12: 0x0000000000000307  r13: 0x00007ff20e4f0f60  r14: 0x000000000000000b  r15: 0x0000000000000016
  rip: 0x00007fff6a85133a  rfl: 0x0000000000000246  cr2: 0x00007ff24009ff48
  
Logical CPU:     0
Error Code:      0x02000148
Trap Number:     133


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    0x7fff6a7e9000 -     0x7fff6a7f1fff  libsystem_darwin.dylib (1353.100.2) <5B12B5DB-3F30-37C1-8ECC-49A66B1F2864> /usr/lib/system/libsystem_darwin.dylib
    0x7fff6a7f2000 -     0x7fff6a7f9fff  libsystem_dnssd.dylib (1096.100.3) <EBB4C2C2-E031-3094-B40A-E67BF261D295> /usr/lib/system/libsystem_dnssd.dylib
    0x7fff6a7fa000 -     0x7fff6a7fbffb  libsystem_featureflags.dylib (17) <29FD922A-EC2C-3F25-BCCC-B58D716E60EC> /usr/lib/system/libsystem_featureflags.dylib
    0x7fff6a7fc000 -     0x7fff6a849ff7  libsystem_info.dylib (538) <8A321605-5480-330B-AF9E-64E65DE61747> /usr/lib/system/libsystem_info.dylib
    0x7fff6a84a000 -     0x7fff6a876ff7  libsystem_kernel.dylib (6153.141.1) <2B6311E6-6240-3EF7-8C87-475B66F7452C> /usr/lib/system/libsystem_kernel.dylib
    0x7fff6a877000 -     0x7fff6a8befff  libsystem_m.dylib (3178) <00F331F1-0D09-39B3-8736-1FE90E64E903> /usr/lib/system/libsystem_m.dylib
    0x7fff6a8bf000 -     0x7fff6a8e6fff  libsystem_malloc.dylib (283.100.6) <8549294E-4C53-36EB-99F3-584A7393D8D5> /usr/lib/system/libsystem_malloc.dylib
    0x7fff6a8e7000 -     0x7fff6a8f4ffb  libsystem_networkextension.dylib (1095.140.2) <F06C65C5-2CBE-313C-96E1-A09240F9FE57> /usr/lib/system/libsystem_networkextension.dylib
    0x7fff6a8f5000 -     0x7fff6a8feff7  libsystem_notify.dylib (241.100.2) <FA22F928-D91B-3AA5-96BB-3186AC0FB264> /usr/lib/system/libsystem_notify.dylib
    0x7fff6a8ff000 -     0x7fff6a907fef  libsystem_platform.dylib (220.100.1) <009A7C1F-313A-318E-B9F2-30F4C06FEA5C> /usr/lib/system/libsystem_platform.dylib
    0x7fff6a908000 -     0x7fff6a912fff  libsystem_pthread.dylib (416.100.3) <62CB1A98-0B8F-31E7-A02B-A1139927F61D> /usr/lib/system/libsystem_pthread.dylib
    0x7fff6a913000 -     0x7fff6a917ff3  libsystem_sandbox.dylib (1217.141.1) <6DE13684-5A67-3009-A53A-C9086CF241C3> /usr/lib/system/libsystem_sandbox.dylib
    0x7fff6a918000 -     0x7fff6a91afff  libsystem_secinit.dylib (62.100.2) <F80872AA-E1FD-3D7E-8729-467656EC6561> /usr/lib/system/libsystem_secinit.dylib
    0x7fff6a91b000 -     0x7fff6a922ffb  libsystem_symptoms.dylib (1238.120.1) <5820A2AF-CE72-3AB3-ABCC-273A3419FB55> /usr/lib/system/libsystem_symptoms.dylib
    0x7fff6a923000 -     0x7fff6a939ff2  libsystem_trace.dylib (1147.120) <04B47629-847B-3D74-8ABE-C05EF9DEEFE4> /usr/lib/system/libsystem_trace.dylib
    0x7fff6a93b000 -     0x7fff6a940ff7  libunwind.dylib (35.4) <42B7B509-BAFE-365B-893A-72414C92F5BF> /usr/lib/system/libunwind.dylib
    0x7fff6a941000 -     0x7fff6a976ffe  libxpc.dylib (1738.140.1) <3E243A41-030F-38E3-9FD2-7B38C66C35B1> /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: 82691702
    thread_create: 0
    thread_set_state: 0

VM Region Summary:
ReadOnly portion of Libraries: Total=466.1M resident=0K(0%) swapped_out_or_unallocated=466.1M(100%)
Writable regions: Total=1.0G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=1.0G(100%)
 
                                VIRTUAL   REGION 
REGION TYPE                        SIZE    COUNT (non-coalesced) 
===========                     =======  ======= 
Kernel Alloc Once                    8K        1 
MALLOC                           193.1M       67 
MALLOC guard page                   24K        5 
MALLOC_MEDIUM (reserved)         840.0M        7         reserved VM address space (unallocated)
Stack                             16.0M        1 
Stack Guard                          4K        1 
VM_ALLOCATE                       1028K        1 
__DATA                            22.9M      166 
__DATA_CONST                       904K       44 
__LINKEDIT                       390.7M       85 
__OBJC_RO                         32.3M        1 
__OBJC_RW                         1904K        1 
__TEXT                            75.8M      164 
__UNICODE                          564K        1 
mapped file                        1.0G        6 
shared memory                       12K        3 
===========                     =======  ======= 
TOTAL                              2.5G      554 
TOTAL, minus reserved VM space     1.7G      554 

Model: MacBookPro16,1, BootROM 1037.147.4.0.0 (iBridge: 17.16.16610.0.0,0), 6 processors, 6-Core Intel Core i7, 2.6 GHz, 32 GB, SMC 
Graphics: kHW_IntelUHDGraphics630Item, Intel UHD Graphics 630, spdisplays_builtin
Graphics: kHW_AMDRadeonPro5300MItem, AMD Radeon Pro 5300M, spdisplays_pcie_device, 4 GB
Memory Module: BANK 0/ChannelA-DIMM0, 16 GB, DDR4, 2667 MHz, SK Hynix, -
Memory Module: BANK 2/ChannelB-DIMM0, 16 GB, DDR4, 2667 MHz, SK Hynix, -
AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x7BF), wl0: Apr  7 2020 13:09:12 version 9.30.357.41.32.5.49 FWID 01-617711e7
Bluetooth: Version 7.0.6f7, 3 services, 27 devices, 1 incoming serial ports
Network Service: Wi-Fi, AirPort, en0
USB Device: USB 3.1 Bus
USB Device: Apple T2 Bus
USB Device: Composite Device
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., 55.3
Thunderbolt Bus: MacBook Pro, Apple Inc., 55.3

@simonw
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simonw commented Feb 8, 2021

My crash report starts on this line: File "/private/tmp/v/datasette/datasette/utils/__init__.py", line 553 in detect_json1

That's this code here: https://github.com/simonw/datasette/blob/aa1fe0692c2abb901216738bfb35f9fcc5090e7d/datasette/utils/__init__.py#L551-L558

def detect_json1(conn=None):
    if conn is None:
        conn = sqlite3.connect(":memory:")
    try:
        conn.execute("SELECT json('{}')")
        return True
    except Exception:
        return False

Could this be something to do with Scalene attempting to profile sqlite3, which is a C module (from the standard library)?

@emeryberger emeryberger reopened this Apr 6, 2021
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I just discovered this issue had been closed; the current version of Scalene in the repository works on the above example. Would be great if you could put it through its paces, @simonw !

python3 -m pip install -U git+https://github.com/plasma-umass/scalene.git

@emeryberger
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We just found and fixed a bug that specifically affected SQLite on Mac, so this hopefully will be fixed!

@emeryberger
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Please verify (if you don't mind), @simonw @shaharkadmiel - thanks!

@gkaissis
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gkaissis commented Apr 15, 2021 •
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I am also experiencing the same error in code which isn't importing sqlite but using PyTorch. macos 11.2.3 using the version directly from master. The SIGSEV error is preceded by a barrage of errors of type [E thread_pool.cpp:112] Exception in thread pool task: mutex lock failed: Invalid argument. Of note, PyTorch is set to run on CPU.
I tried running the torchtest.py script from the tests directory, but this also produces a barrage of mutex errors and a SIGBUS error.

@emeryberger
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I wasn't able to reproduce this, @gkaissis - if you can meet on Discord, we can try to see what's going on - https://discord.gg/6Dtaf6HW3m

@sternj
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sternj commented Apr 17, 2021

@gkaissis if possible could you provide a minimal example of this behavior?

@sternj
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sternj commented Apr 17, 2021

Replicated with python3 -m scalene test/testpyt.py on MacOS x86

@sternj
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sternj commented Apr 26, 2021

I wanted to update on this issue-- it seems like this is actually a problem in PyTorch itself and how it interacts with signals on MacOS. I think it's a good idea to keep this issue open, but I'm also going to open up an issue in PyTorch.

@emeryberger
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For reference, this issue has been posted on the PyTorch repo. As it's not a Scalene bug, I'm closing the issue here.

@emeryberger
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Note: Scalene works fine with at least one earlier version of PyTorch (1.5.1), which also does not exhibit this bug!

@emeryberger emeryberger reopened this Apr 29, 2021
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Documented in README.md with 6636d95.

@HansBambel HansBambel mentioned this issue Sep 28, 2021
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@sdbhosale sdbhosale mentioned this issue Sep 19, 2023
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@simonw @emeryberger @shaharkadmiel @sternj @gkaissis