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#4667 closed defect (can't reproduce)
Crash during garbage collection
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | chimera-programmers | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.15.7-x86_64-i386-64bit
ChimeraX Version: 1.2 (2021-04-27 05:33:30 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x0000000108419dc0 (most recent call first):
File "/Applications/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/atomic/molarray.py", line 150 in
File "/Applications/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/atomic/molarray.py", line 150 in __iter__
File "/Applications/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/morph/util.py", line 69 in copyMolecule
File "/Applications/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/morph/motion.py", line 79 in __init__
File "/Applications/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/morph/motion.py", line 17 in compute_morph
File "/Applications/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/morph/morph.py", line 73 in morph
File "/Applications/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/commands/cli.py", line 2852 in run
File "/Applications/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/cmd_line/tool.py", line 275 in execute
File "/Applications/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/cmd_line/tool.py", line 112 in keyPressEvent
File "/Applications/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/ui/gui.py", line 293 in event_loop
File "/Applications/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/ChimeraX_main.py", line 866 in init
File "/Applications/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/ChimeraX_main.py", line 1015 in
File "/Applications/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/runpy.py", line 194 in _run_module_as_main
Process: ChimeraX [34337]
Path: /Applications/ChimeraX-1.2.app/Contents/MacOS/ChimeraX
Identifier: ChimeraX
Version: 1.2.0 (1.2.0.0)
Code Type: X86-64 (Native)
Parent Process: ??? [1]
Responsible: ChimeraX [34337]
User ID: 501
Date/Time: 2021-05-18 23:31:53.935 -0700
OS Version: Mac OS X 10.15.7 (19H524)
Report Version: 12
Bridge OS Version: 5.2 (18P4347)
Anonymous UUID: 70A1F055-CC14-7C36-F8C5-A5248F526FFC
Sleep/Wake UUID: 614F5721-5F28-416D-8F07-03A0BBBA5693
Time Awake Since Boot: 190000 seconds
Time Since Wake: 3100 seconds
System Integrity Protection: enabled
Crashed Thread: 0 CrBrowserMain Dispatch queue: com.apple.main-thread
Exception Type: EXC_BAD_ACCESS (SIGSEGV)
Exception Codes: KERN_INVALID_ADDRESS at 0x00000000000000a9
Exception Note: EXC_CORPSE_NOTIFY
VM Regions Near 0xa9:
-->
__TEXT 0000000100a62000-0000000100a63000 [ 4K] r-x/r-x SM=COW /Applications/ChimeraX-1.2.app/Contents/MacOS/ChimeraX
Thread 0 Crashed:: CrBrowserMain Dispatch queue: com.apple.main-thread
0 libsystem_kernel.dylib 0x00007fff6e22033a __pthread_kill + 10
1 libsystem_pthread.dylib 0x00007fff6e2dce60 pthread_kill + 430
2 libsystem_c.dylib 0x00007fff6e13793e raise + 26
3 libsystem_platform.dylib 0x00007fff6e2d15fd _sigtramp + 29
4 ??? 000000000000000000 0 + 0
5 org.python.python 0x0000000100abe411 dict_traverse + 241
6 org.python.python 0x0000000100bbf7d4 collect + 692
7 org.python.python 0x0000000100bc0744 _PyObject_GC_Alloc + 324
8 org.python.python 0x0000000100bc07b5 _PyObject_GC_New + 21
9 org.python.python 0x0000000100ab9747 PyDict_New + 87
10 cymol.cpython-38-darwin.so 0x0000000124743a6b __pyx_tp_new_8chimerax_6atomic_5cymol_CyAtom(_typeobject*, _object*, _object*) + 75
11 org.python.python 0x0000000100adf702 type_call + 50
12 org.python.python 0x0000000100a8ca85 _PyObject_MakeTpCall + 373
13 org.python.python 0x0000000100a8ec52 object_vacall + 418
14 org.python.python 0x0000000100a8ee8c PyObject_CallFunctionObjArgs + 156
15 libatomstruct.dylib 0x00000001244fbcc8 pyinstance::PythonInstance::py_instance(bool) const + 152
16 cymol.cpython-38-darwin.so 0x000000012474d693 __pyx_pw_8chimerax_6atomic_5cymol_6CyAtom_52c_ptr_to_py_inst(_object*, _object*, _object*) + 99
17 org.python.python 0x0000000100a8d018 cfunction_call_varargs + 120
18 org.python.python 0x0000000100a8ca85 _PyObject_MakeTpCall + 373
19 org.python.python 0x0000000100b5b665 call_function + 533
20 org.python.python 0x0000000100b5846e _PyEval_EvalFrameDefault + 25678
21 org.python.python 0x0000000100b5c454 _PyEval_EvalCodeWithName + 2804
22 org.python.python 0x0000000100a8d56e _PyFunction_Vectorcall + 270
23 org.python.python 0x0000000100b5b60c call_function + 444
24 org.python.python 0x0000000100b58505 _PyEval_EvalFrameDefault + 25829
25 org.python.python 0x0000000100b5c454 _PyEval_EvalCodeWithName + 2804
26 org.python.python 0x0000000100a8d56e _PyFunction_Vectorcall + 270
27 org.python.python 0x0000000100ae3b41 slot_tp_iter + 401
28 org.python.python 0x0000000100a770b9 PyObject_GetIter + 25
29 org.python.python 0x0000000100b4d4ea zip_new + 122
30 org.python.python 0x0000000100adf702 type_call + 50
31 org.python.python 0x0000000100a8ca85 _PyObject_MakeTpCall + 373
32 org.python.python 0x0000000100b5b665 call_function + 533
33 org.python.python 0x0000000100b58505 _PyEval_EvalFrameDefault + 25829
34 org.python.python 0x0000000100a8d3d0 function_code_fastcall + 128
35 org.python.python 0x0000000100b5b60c call_function + 444
36 org.python.python 0x0000000100b58505 _PyEval_EvalFrameDefault + 25829
37 org.python.python 0x0000000100b5c454 _PyEval_EvalCodeWithName + 2804
38 org.python.python 0x0000000100a8d56e _PyFunction_Vectorcall + 270
39 org.python.python 0x0000000100a8c865 _PyObject_FastCallDict + 133
40 org.python.python 0x0000000100a8dedf _PyObject_Call_Prepend + 143
41 org.python.python 0x0000000100ae4301 slot_tp_init + 145
42 org.python.python 0x0000000100adf7f9 type_call + 297
43 org.python.python 0x0000000100a8ca85 _PyObject_MakeTpCall + 373
44 org.python.python 0x0000000100b5b665 call_function + 533
45 org.python.python 0x0000000100b58598 _PyEval_EvalFrameDefault + 25976
46 org.python.python 0x0000000100b5c454 _PyEval_EvalCodeWithName + 2804
47 org.python.python 0x0000000100a8d56e _PyFunction_Vectorcall + 270
48 org.python.python 0x0000000100b5b60c call_function + 444
49 org.python.python 0x0000000100b58598 _PyEval_EvalFrameDefault + 25976
50 org.python.python 0x0000000100b5c454 _PyEval_EvalCodeWithName + 2804
51 org.python.python 0x0000000100a8d56e _PyFunction_Vectorcall + 270
52 org.python.python 0x0000000100a8cdad PyVectorcall_Call + 109
53 org.python.python 0x0000000100b58978 _PyEval_EvalFrameDefault + 26968
54 org.python.python 0x0000000100b5c454 _PyEval_EvalCodeWithName + 2804
55 org.python.python 0x0000000100a8d56e _PyFunction_Vectorcall + 270
56 org.python.python 0x0000000100b5b60c call_function + 444
57 org.python.python 0x0000000100b5844a _PyEval_EvalFrameDefault + 25642
58 org.python.python 0x0000000100b5c454 _PyEval_EvalCodeWithName + 2804
59 org.python.python 0x0000000100a8d56e _PyFunction_Vectorcall + 270
60 org.python.python 0x0000000100a8fadb method_vectorcall + 235
61 org.python.python 0x0000000100a8cdad PyVectorcall_Call + 109
62 QtCore.abi3.so 0x0000000107d76957 PyQtSlot::call(_object*, _object*) const + 39
63 QtCore.abi3.so 0x0000000107d76866 PyQtSlot::invoke(void**, _object*, void*, bool) const + 374
64 QtCore.abi3.so 0x0000000107d77455 PyQtSlotProxy::unislot(void**) + 85
65 QtCore.abi3.so 0x0000000107d773ca PyQtSlotProxy::qt_metacall(QMetaObject::Call, int, void**) + 58
66 QtCore 0x000000011267ff6e void doActivate(QObject*, int, void**) + 1118
67 QtCore 0x00000001126800d5 void doActivate(QObject*, int, void**) + 1477
68 QtWidgets 0x0000000114d44b14 QWidgetLineControl::processKeyEvent(QKeyEvent*) + 548
69 QtWidgets 0x0000000114d3b732 QLineEdit::keyPressEvent(QKeyEvent*) + 34
70 QtWidgets 0x0000000114c33e4f QWidget::event(QEvent*) + 527
71 QtWidgets 0x0000000114d3aae7 QLineEdit::event(QEvent*) + 727
72 QtWidgets 0x0000000114cfecd0 QComboBox::keyPressEvent(QKeyEvent*) + 784
73 QtWidgets.abi3.so 0x0000000114890e5b meth_QComboBox_keyPressEvent(_object*, _object*) + 139
74 org.python.python 0x0000000100a8d0c2 cfunction_call_varargs + 290
75 org.python.python 0x0000000100a8ca85 _PyObject_MakeTpCall + 373
76 org.python.python 0x0000000100b5b665 call_function + 533
77 org.python.python 0x0000000100b5846e _PyEval_EvalFrameDefault + 25678
78 org.python.python 0x0000000100b5c454 _PyEval_EvalCodeWithName + 2804
79 org.python.python 0x0000000100a8d56e _PyFunction_Vectorcall + 270
80 org.python.python 0x0000000100a8fb7c method_vectorcall + 396
81 org.python.python 0x0000000100a8cdad PyVectorcall_Call + 109
82 sip.cpython-38-darwin.so 0x0000000107f869d7 sip_api_call_procedure_method + 199
83 QtWidgets.abi3.so 0x0000000114791f18 sipQComboBox::keyPressEvent(QKeyEvent*) + 104
84 QtWidgets 0x0000000114c33e4f QWidget::event(QEvent*) + 527
85 QtWidgets 0x0000000114cfe634 QComboBox::event(QEvent*) + 372
86 QtWidgets.abi3.so 0x000000011479141f sipQComboBox::event(QEvent*) + 191
87 QtWidgets 0x0000000114bf99ea QApplicationPrivate::notify_helper(QObject*, QEvent*) + 266
88 QtWidgets 0x0000000114bfafd3 QApplication::notify(QObject*, QEvent*) + 947
89 QtWidgets.abi3.so 0x00000001147acdb9 sipQApplication::notify(QObject*, QEvent*) + 233
90 QtCore 0x000000011264ca34 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 212
91 QtWidgets 0x0000000114c52351 QWidgetWindow::handleKeyEvent(QKeyEvent*) + 145
92 QtWidgets 0x0000000114c51727 QWidgetWindow::event(QEvent*) + 295
93 QtWidgets 0x0000000114bf99ea QApplicationPrivate::notify_helper(QObject*, QEvent*) + 266
94 QtWidgets 0x0000000114bfae11 QApplication::notify(QObject*, QEvent*) + 497
95 QtWidgets.abi3.so 0x00000001147acdb9 sipQApplication::notify(QObject*, QEvent*) + 233
96 QtCore 0x000000011264ca34 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 212
97 QtGui 0x00000001152679c8 QGuiApplicationPrivate::processKeyEvent(QWindowSystemInterfacePrivate::KeyEvent*) + 152
98 QtGui 0x000000011524bd7b QWindowSystemInterface::sendWindowSystemEvents(QFlags) + 219
99 QtGui 0x0000000115246b72 QWindowSystemInterface::flushWindowSystemEvents(QFlags) + 594
100 libqcocoa.dylib 0x0000000122c23848 -[QNSView(Keys) handleKeyEvent:eventType:] + 1144
101 libqcocoa.dylib 0x0000000122c23a18 -[QNSView(Keys) keyDown:] + 88
102 com.apple.AppKit 0x00007fff31408d5d -[NSWindow(NSEventRouting) _reallySendEvent:isDelayedEvent:] + 6512
103 com.apple.AppKit 0x00007fff314071c9 -[NSWindow(NSEventRouting) sendEvent:] + 349
104 libqcocoa.dylib 0x0000000122c26dd5 -[QNSWindow sendEvent:] + 549
105 com.apple.AppKit 0x00007fff31405efe -[NSApplication(NSEvent) sendEvent:] + 2826
106 libqcocoa.dylib 0x0000000122c2e12a -[QNSApplication sendEvent:] + 74
107 com.apple.AppKit 0x00007fff312525bf -[NSApplication run] + 707
108 libqcocoa.dylib 0x0000000122c2a62f QCocoaEventDispatcher::processEvents(QFlags) + 2495
109 QtCore 0x0000000112648acf QEventLoop::exec(QFlags) + 431
110 QtCore 0x000000011264d042 QCoreApplication::exec() + 130
111 QtWidgets.abi3.so 0x000000011489e702 meth_QApplication_exec_(_object*, _object*) + 82
112 org.python.python 0x0000000100a8d0c2 cfunction_call_varargs + 290
113 org.python.python 0x0000000100a8ca85 _PyObject_MakeTpCall + 373
114 org.python.python 0x0000000100b5b665 call_function + 533
115 org.python.python 0x0000000100b5846e _PyEval_EvalFrameDefault + 25678
116 org.python.python 0x0000000100a8d3d0 function_code_fastcall + 128
117 org.python.python 0x0000000100a8fa9a method_vectorcall + 170
118 org.python.python 0x0000000100b5b60c call_function + 444
119 org.python.python 0x0000000100b5846e _PyEval_EvalFrameDefault + 25678
120 org.python.python 0x0000000100b5c454 _PyEval_EvalCodeWithName + 2804
121 org.python.python 0x0000000100a8d56e _PyFunction_Vectorcall + 270
122 org.python.python 0x0000000100b5b60c call_function + 444
123 org.python.python 0x0000000100b58505 _PyEval_EvalFrameDefault + 25829
124 org.python.python 0x0000000100b5c454 _PyEval_EvalCodeWithName + 2804
125 org.python.python 0x0000000100b51f44 PyEval_EvalCode + 100
126 org.python.python 0x0000000100b4f332 builtin_exec + 626
127 org.python.python 0x0000000100ac95ff cfunction_vectorcall_FASTCALL + 175
128 org.python.python 0x0000000100b5b60c call_function + 444
129 org.python.python 0x0000000100b58505 _PyEval_EvalFrameDefault + 25829
130 org.python.python 0x0000000100b5c454 _PyEval_EvalCodeWithName + 2804
131 org.python.python 0x0000000100a8d56e _PyFunction_Vectorcall + 270
132 org.python.python 0x0000000100b5b60c call_function + 444
133 org.python.python 0x0000000100b58505 _PyEval_EvalFrameDefault + 25829
134 org.python.python 0x0000000100b5c454 _PyEval_EvalCodeWithName + 2804
135 org.python.python 0x0000000100a8d56e _PyFunction_Vectorcall + 270
136 org.python.python 0x0000000100a8cdad PyVectorcall_Call + 109
137 org.python.python 0x0000000100bbeeb3 pymain_run_module + 195
138 org.python.python 0x0000000100bbe585 Py_RunMain + 1413
139 org.python.python 0x0000000100bbebdf pymain_main + 223
140 org.python.python 0x0000000100bbeaeb Py_Main + 43
141 edu.ucsf.cgl.ChimeraX 0x0000000100a62dc8 main + 120
142 libdyld.dylib 0x00007fff6e0d8cc9 start + 1
Thread 1:
0 libsystem_kernel.dylib 0x00007fff6e21c882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6e2dd425 _pthread_cond_wait + 698
2 libopenblas.0.dylib 0x0000000101b8627b blas_thread_server + 507
3 libsystem_pthread.dylib 0x00007fff6e2dd109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6e2d8b8b thread_start + 15
Thread 2:
0 libsystem_kernel.dylib 0x00007fff6e21c882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6e2dd425 _pthread_cond_wait + 698
2 libopenblas.0.dylib 0x0000000101b8627b blas_thread_server + 507
3 libsystem_pthread.dylib 0x00007fff6e2dd109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6e2d8b8b thread_start + 15
Thread 3:
0 libsystem_kernel.dylib 0x00007fff6e21c882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6e2dd425 _pthread_cond_wait + 698
2 libopenblas.0.dylib 0x0000000101b8627b blas_thread_server + 507
3 libsystem_pthread.dylib 0x00007fff6e2dd109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6e2d8b8b thread_start + 15
Thread 4:
0 libsystem_kernel.dylib 0x00007fff6e21c882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6e2dd425 _pthread_cond_wait + 698
2 libopenblas.0.dylib 0x0000000101b8627b blas_thread_server + 507
3 libsystem_pthread.dylib 0x00007fff6e2dd109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6e2d8b8b thread_start + 15
Thread 5:
0 libsystem_kernel.dylib 0x00007fff6e21c882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6e2dd425 _pthread_cond_wait + 698
2 libopenblas.0.dylib 0x0000000101b8627b blas_thread_server + 507
3 libsystem_pthread.dylib 0x00007fff6e2dd109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6e2d8b8b thread_start + 15
Thread 6:: ThreadPoolServiceThread
0 libsystem_kernel.dylib 0x00007fff6e222b96 kevent64 + 10
1 QtWebEngineCore 0x000000011844fe6a base::MessagePumpKqueue::DoInternalWork(base::MessagePump::Delegate::NextWorkInfo*) + 330
2 QtWebEngineCore 0x000000011844fcc7 base::MessagePumpKqueue::Run(base::MessagePump::Delegate*) + 167
3 QtWebEngineCore 0x00000001183d862b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
4 QtWebEngineCore 0x000000011839c7cb base::RunLoop::Run() + 395
5 QtWebEngineCore 0x00000001183e3a94 base::internal::ServiceThread::Run(base::RunLoop*) + 20
6 QtWebEngineCore 0x00000001183f7a7d base::Thread::ThreadMain() + 413
7 QtWebEngineCore 0x0000000118440e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
8 libsystem_pthread.dylib 0x00007fff6e2dd109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff6e2d8b8b thread_start + 15
Thread 7:: ThreadPoolBackgroundWorker
0 libsystem_kernel.dylib 0x00007fff6e219dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6e21a170 mach_msg + 60
2 QtWebEngineCore 0x0000000118445492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x00000001183ed778 base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*) + 56
4 QtWebEngineCore 0x00000001183ee150 base::internal::WorkerThread::RunWorker() + 1024
5 QtWebEngineCore 0x00000001183edc44 base::internal::WorkerThread::RunBackgroundPooledWorker() + 20
6 QtWebEngineCore 0x0000000118440e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
7 libsystem_pthread.dylib 0x00007fff6e2dd109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff6e2d8b8b thread_start + 15
Thread 8:: Chrome_IOThread
0 libsystem_kernel.dylib 0x00007fff6e222b96 kevent64 + 10
1 QtWebEngineCore 0x000000011844fe6a base::MessagePumpKqueue::DoInternalWork(base::MessagePump::Delegate::NextWorkInfo*) + 330
2 QtWebEngineCore 0x000000011844fcc7 base::MessagePumpKqueue::Run(base::MessagePump::Delegate*) + 167
3 QtWebEngineCore 0x00000001183d862b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
4 QtWebEngineCore 0x000000011839c7cb base::RunLoop::Run() + 395
5 QtWebEngineCore 0x000000011c31cf06 content::BrowserProcessSubThread::IOThreadRun(base::RunLoop*) + 102
6 QtWebEngineCore 0x00000001183f7a7d base::Thread::ThreadMain() + 413
7 QtWebEngineCore 0x0000000118440e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
8 libsystem_pthread.dylib 0x00007fff6e2dd109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff6e2d8b8b thread_start + 15
Thread 9:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff6e219dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6e21a170 mach_msg + 60
2 QtWebEngineCore 0x0000000118445492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x00000001184452cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x000000011836d1db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171
5 QtWebEngineCore 0x00000001183d862b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
6 QtWebEngineCore 0x000000011839c7cb base::RunLoop::Run() + 395
7 QtWebEngineCore 0x00000001183f7a7d base::Thread::ThreadMain() + 413
8 QtWebEngineCore 0x0000000118440e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
9 libsystem_pthread.dylib 0x00007fff6e2dd109 _pthread_start + 148
10 libsystem_pthread.dylib 0x00007fff6e2d8b8b thread_start + 15
Thread 10:: CompositorTileWorker1
0 libsystem_kernel.dylib 0x00007fff6e21c882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6e2dd425 _pthread_cond_wait + 698
2 QtWebEngineCore 0x000000011843ce18 base::ConditionVariable::Wait() + 104
3 QtWebEngineCore 0x00000001196f45f8 non-virtual thunk to cc::SingleThreadTaskGraphRunner::Run() + 56
4 QtWebEngineCore 0x0000000118440e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
5 libsystem_pthread.dylib 0x00007fff6e2dd109 _pthread_start + 148
6 libsystem_pthread.dylib 0x00007fff6e2d8b8b thread_start + 15
Thread 11:: Chrome_InProcGpuThread
0 libsystem_kernel.dylib 0x00007fff6e219dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6e21a170 mach_msg + 60
2 QtWebEngineCore 0x0000000118445492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x000000011836d20f base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 223
4 QtWebEngineCore 0x00000001183d862b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
5 QtWebEngineCore 0x000000011839c7cb base::RunLoop::Run() + 395
6 QtWebEngineCore 0x00000001183f7a7d base::Thread::ThreadMain() + 413
7 QtWebEngineCore 0x0000000118440e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
8 libsystem_pthread.dylib 0x00007fff6e2dd109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff6e2d8b8b thread_start + 15
Thread 12:: Chrome_ChildIOThread
0 libsystem_kernel.dylib 0x00007fff6e222b96 kevent64 + 10
1 QtWebEngineCore 0x000000011844fe6a base::MessagePumpKqueue::DoInternalWork(base::MessagePump::Delegate::NextWorkInfo*) + 330
2 QtWebEngineCore 0x000000011844fcc7 base::MessagePumpKqueue::Run(base::MessagePump::Delegate*) + 167
3 QtWebEngineCore 0x00000001183d862b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
4 QtWebEngineCore 0x000000011839c7cb base::RunLoop::Run() + 395
5 QtWebEngineCore 0x00000001183f7a7d base::Thread::ThreadMain() + 413
6 QtWebEngineCore 0x0000000118440e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
7 libsystem_pthread.dylib 0x00007fff6e2dd109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff6e2d8b8b thread_start + 15
Thread 13:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff6e219dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6e21a170 mach_msg + 60
2 QtWebEngineCore 0x0000000118445492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x00000001184452cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x000000011836d1db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171
5 QtWebEngineCore 0x00000001183d862b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
6 QtWebEngineCore 0x000000011839c7cb base::RunLoop::Run() + 395
7 QtWebEngineCore 0x00000001183f7a7d base::Thread::ThreadMain() + 413
8 QtWebEngineCore 0x0000000118440e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
9 libsystem_pthread.dylib 0x00007fff6e2dd109 _pthread_start + 148
10 libsystem_pthread.dylib 0x00007fff6e2d8b8b thread_start + 15
Thread 14:: VizCompositorThread
0 libsystem_kernel.dylib 0x00007fff6e219dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6e21a170 mach_msg + 60
2 QtWebEngineCore 0x0000000118445492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x00000001184452cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x000000011836d1db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171
5 QtWebEngineCore 0x00000001183d862b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
6 QtWebEngineCore 0x000000011839c7cb base::RunLoop::Run() + 395
7 QtWebEngineCore 0x00000001183f7a7d base::Thread::ThreadMain() + 413
8 QtWebEngineCore 0x0000000118440e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
9 libsystem_pthread.dylib 0x00007fff6e2dd109 _pthread_start + 148
10 libsystem_pthread.dylib 0x00007fff6e2d8b8b thread_start + 15
Thread 15:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff6e219dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6e21a170 mach_msg + 60
2 QtWebEngineCore 0x0000000118445492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x00000001184452cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x000000011836d1db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171
5 QtWebEngineCore 0x00000001183d862b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
6 QtWebEngineCore 0x000000011839c7cb base::RunLoop::Run() + 395
7 QtWebEngineCore 0x00000001183f7a7d base::Thread::ThreadMain() + 413
8 QtWebEngineCore 0x0000000118440e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
9 libsystem_pthread.dylib 0x00007fff6e2dd109 _pthread_start + 148
10 libsystem_pthread.dylib 0x00007fff6e2d8b8b thread_start + 15
Thread 16:: ThreadPoolSingleThreadForegroundBlocking0
0 libsystem_kernel.dylib 0x00007fff6e219dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6e21a170 mach_msg + 60
2 QtWebEngineCore 0x0000000118445492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x00000001184452cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x00000001183ed76a base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*) + 42
5 QtWebEngineCore 0x00000001183ee150 base::internal::WorkerThread::RunWorker() + 1024
6 QtWebEngineCore 0x00000001183edd34 base::internal::WorkerThread::RunDedicatedWorker() + 20
7 QtWebEngineCore 0x0000000118440e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
8 libsystem_pthread.dylib 0x00007fff6e2dd109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff6e2d8b8b thread_start + 15
Thread 17:: MemoryInfra
0 libsystem_kernel.dylib 0x00007fff6e219dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6e21a170 mach_msg + 60
2 QtWebEngineCore 0x0000000118445492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x00000001184452cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x000000011836d1db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171
5 QtWebEngineCore 0x00000001183d862b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
6 QtWebEngineCore 0x000000011839c7cb base::RunLoop::Run() + 395
7 QtWebEngineCore 0x00000001183f7a7d base::Thread::ThreadMain() + 413
8 QtWebEngineCore 0x0000000118440e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
9 libsystem_pthread.dylib 0x00007fff6e2dd109 _pthread_start + 148
10 libsystem_pthread.dylib 0x00007fff6e2d8b8b thread_start + 15
Thread 18:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff6e219dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6e21a170 mach_msg + 60
2 QtWebEngineCore 0x0000000118445492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x00000001184452cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x000000011836d1db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171
5 QtWebEngineCore 0x00000001183d862b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
6 QtWebEngineCore 0x000000011839c7cb base::RunLoop::Run() + 395
7 QtWebEngineCore 0x00000001183f7a7d base::Thread::ThreadMain() + 413
8 QtWebEngineCore 0x0000000118440e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
9 libsystem_pthread.dylib 0x00007fff6e2dd109 _pthread_start + 148
10 libsystem_pthread.dylib 0x00007fff6e2d8b8b thread_start + 15
Thread 19:: com.apple.NSEventThread
0 libsystem_kernel.dylib 0x00007fff6e219dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6e21a170 mach_msg + 60
2 com.apple.CoreFoundation 0x00007fff33ff1ef5 __CFRunLoopServiceMachPort + 247
3 com.apple.CoreFoundation 0x00007fff33ff09c2 __CFRunLoopRun + 1319
4 com.apple.CoreFoundation 0x00007fff33fefe3e CFRunLoopRunSpecific + 462
5 com.apple.AppKit 0x00007fff31403954 _NSEventThread + 132
6 libsystem_pthread.dylib 0x00007fff6e2dd109 _pthread_start + 148
7 libsystem_pthread.dylib 0x00007fff6e2d8b8b thread_start + 15
Thread 20:: ThreadPoolSingleThreadSharedBackgroundBlocking1
0 libsystem_kernel.dylib 0x00007fff6e219dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6e21a170 mach_msg + 60
2 QtWebEngineCore 0x0000000118445492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x00000001184452cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x00000001183ed76a base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*) + 42
5 QtWebEngineCore 0x00000001183ede3d base::internal::WorkerThread::RunWorker() + 237
6 QtWebEngineCore 0x00000001183edc74 base::internal::WorkerThread::RunBackgroundSharedWorker() + 20
7 QtWebEngineCore 0x0000000118440e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
8 libsystem_pthread.dylib 0x00007fff6e2dd109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff6e2d8b8b thread_start + 15
Thread 21:: ThreadPoolForegroundWorker
0 libsystem_kernel.dylib 0x00007fff6e219dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6e21a170 mach_msg + 60
2 QtWebEngineCore 0x0000000118445492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x00000001183ed778 base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*) + 56
4 QtWebEngineCore 0x00000001183ee150 base::internal::WorkerThread::RunWorker() + 1024
5 QtWebEngineCore 0x00000001183edcd4 base::internal::WorkerThread::RunPooledWorker() + 20
6 QtWebEngineCore 0x0000000118440e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
7 libsystem_pthread.dylib 0x00007fff6e2dd109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff6e2d8b8b thread_start + 15
Thread 22:
0 libsystem_pthread.dylib 0x00007fff6e2d8b68 start_wqthread + 0
Thread 23:: ThreadPoolForegroundWorker
0 libsystem_kernel.dylib 0x00007fff6e219dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff6e21a170 mach_msg + 60
2 QtWebEngineCore 0x0000000118445492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x00000001183ed778 base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*) + 56
4 QtWebEngineCore 0x00000001183ee150 base::internal::WorkerThread::RunWorker() + 1024
5 QtWebEngineCore 0x00000001183edcd4 base::internal::WorkerThread::RunPooledWorker() + 20
6 QtWebEngineCore 0x0000000118440e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
7 libsystem_pthread.dylib 0x00007fff6e2dd109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff6e2d8b8b thread_start + 15
Thread 24:
0 libsystem_pthread.dylib 0x00007fff6e2d8b68 start_wqthread + 0
Thread 0 crashed with X86 Thread State (64-bit):
rax: 0x0000000000000000 rbx: 0x0000000108419dc0 rcx: 0x00007fa5d5f55a58 rdx: 0x0000000000000000
rdi: 0x0000000000000307 rsi: 0x000000000000000b rbp: 0x00007fa5d5f55a80 rsp: 0x00007fa5d5f55a58
r8: 0x00007fa5d5f55f48 r9: 0x58b07e81a6a031a0 r10: 0x0000000108419dc0 r11: 0x0000000000000246
r12: 0x0000000000000307 r13: 0x0000000000000003 r14: 0x000000000000000b r15: 0x0000000000000016
rip: 0x00007fff6e22033a rfl: 0x0000000000000246 cr2: 0x00007fa5d5f55f48
Logical CPU: 0
Error Code: 0x02000148
Trap Number: 133
Binary Images:
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0x101253000 - 0x101257fff +binascii.cpython-38-darwin.so (0) /Applications/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/lib-dynload/binascii.cpython-38-darwin.so
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0x101327000 - 0x101350fff +pyexpat.cpython-38-darwin.so (0) /Applications/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/lib-dynload/pyexpat.cpython-38-darwin.so
0x101369000 - 0x10136afff +_queue.cpython-38-darwin.so (0) /Applications/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/lib-dynload/_queue.cpython-38-darwin.so
0x101373000 - 0x101389ff7 +_pickle.cpython-38-darwin.so (0) /Applications/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/lib-dynload/_pickle.cpython-38-darwin.so
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0x10571e000 - 0x105754fff +libquadmath.0.dylib (0) /Applications/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/numpy/.dylibs/libquadmath.0.dylib
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0x1077d8000 - 0x1077d9ffb +lapack_lite.cpython-38-darwin.so (0) /Applications/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/numpy/linalg/lapack_lite.cpython-38-darwin.so
0x1077e1000 - 0x1077faffb +_umath_linalg.cpython-38-darwin.so (0) /Applications/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/numpy/linalg/_umath_linalg.cpython-38-darwin.so
0x10780e000 - 0x10781ffff +_pocketfft_internal.cpython-38-darwin.so (0) /Applications/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/numpy/fft/_pocketfft_internal.cpython-38-darwin.so
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0x1078ee000 - 0x10790cff3 +bit_generator.cpython-38-darwin.so (0) /Applications/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/numpy/random/bit_generator.cpython-38-darwin.so
0x10792d000 - 0x10795fff3 +_common.cpython-38-darwin.so (0) /Applications/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/numpy/random/_common.cpython-38-darwin.so
0x10797c000 - 0x1079cbff3 +_bounded_integers.cpython-38-darwin.so (0) /Applications/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/numpy/random/_bounded_integers.cpython-38-darwin.so
0x1079f2000 - 0x107a00ff3 +_mt19937.cpython-38-darwin.so (0) /Applications/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/numpy/random/_mt19937.cpython-38-darwin.so
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0x107a59000 - 0x107adaffb +_generator.cpython-38-darwin.so (0) /Applications/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/numpy/random/_generator.cpython-38-darwin.so
0x107b3a000 - 0x107b3afff +_arrays.cpython-38-darwin.so (0) /Applications/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/arrays/_arrays.cpython-38-darwin.so
0x107b41000 - 0x107be2ff7 +libarrays.dylib (0) /Applications/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/arrays/lib/libarrays.dylib
0x107c06000 - 0x107c24ff3 +_geometry.cpython-38-darwin.so (0) /Applications/ChimeraX-1.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/geometry/_geometry.cpython-38-darwin.so
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0x7fff5ed8e000 - 0x7fff5edbeff7 com.apple.pluginkit.framework (1.0 - 1) /System/Library/PrivateFrameworks/PlugInKit.framework/Versions/A/PlugInKit
0x7fff5ede9000 - 0x7fff5edfcffc com.apple.PowerLog (1.0 - 1) /System/Library/PrivateFrameworks/PowerLog.framework/Versions/A/PowerLog
0x7fff5fc78000 - 0x7fff5fcd2ff6 com.apple.ProtectedCloudStorage (1.0 - 1) /System/Library/PrivateFrameworks/ProtectedCloudStorage.framework/Versions/A/ProtectedCloudStorage
0x7fff5fcd3000 - 0x7fff5fcecffb com.apple.ProtocolBuffer (1 - 274.24.9.16.3) /System/Library/PrivateFrameworks/ProtocolBuffer.framework/Versions/A/ProtocolBuffer
0x7fff5fdfe000 - 0x7fff5fe01ff4 com.apple.QuickLookNonBaseSystem (1.0 - 1) /System/Library/PrivateFrameworks/QuickLookNonBaseSystem.framework/Versions/A/QuickLookNonBaseSystem
0x7fff5fe02000 - 0x7fff5fe25ff0 com.apple.quicklook.QuickLookSupport (1.0 - 1) /System/Library/PrivateFrameworks/QuickLookSupport.framework/Versions/A/QuickLookSupport
0x7fff5fe6c000 - 0x7fff5fee5ff3 com.apple.Rapport (1.9.5 - 195.2) /System/Library/PrivateFrameworks/Rapport.framework/Versions/A/Rapport
0x7fff6014c000 - 0x7fff60175ff1 com.apple.RemoteViewServices (2.0 - 148) /System/Library/PrivateFrameworks/RemoteViewServices.framework/Versions/A/RemoteViewServices
0x7fff602da000 - 0x7fff60315ff0 com.apple.RunningBoardServices (1.0 - 223.140.2) /System/Library/PrivateFrameworks/RunningBoardServices.framework/Versions/A/RunningBoardServices
0x7fff61bf6000 - 0x7fff61bf9ff5 com.apple.SecCodeWrapper (4.0 - 448.100.6) /System/Library/PrivateFrameworks/SecCodeWrapper.framework/Versions/A/SecCodeWrapper
0x7fff61d6c000 - 0x7fff61e93fff com.apple.Sharing (1526.37 - 1526.37) /System/Library/PrivateFrameworks/Sharing.framework/Versions/A/Sharing
0x7fff61eec000 - 0x7fff61f0aff2 com.apple.shortcut (2.16 - 106) /System/Library/PrivateFrameworks/Shortcut.framework/Versions/A/Shortcut
0x7fff61f0b000 - 0x7fff61f2bff5 com.apple.sidecar-core (1.0 - 209.40.4) /System/Library/PrivateFrameworks/SidecarCore.framework/Versions/A/SidecarCore
0x7fff61f2c000 - 0x7fff61f3eff0 com.apple.sidecar-ui (1.0 - 209.40.4) /System/Library/PrivateFrameworks/SidecarUI.framework/Versions/A/SidecarUI
0x7fff632a8000 - 0x7fff6359eff7 com.apple.SkyLight (1.600.0 - 451.4) /System/Library/PrivateFrameworks/SkyLight.framework/Versions/A/SkyLight
0x7fff63deb000 - 0x7fff63df9ffb com.apple.SpeechRecognitionCore (6.0.91.2 - 6.0.91.2) /System/Library/PrivateFrameworks/SpeechRecognitionCore.framework/Versions/A/SpeechRecognitionCore
0x7fff644d5000 - 0x7fff64516ff9 com.apple.StreamingZip (1.0 - 1) /System/Library/PrivateFrameworks/StreamingZip.framework/Versions/A/StreamingZip
0x7fff6462d000 - 0x7fff64636ff7 com.apple.SymptomDiagnosticReporter (1.0 - 1238.120.2) /System/Library/PrivateFrameworks/SymptomDiagnosticReporter.framework/Versions/A/SymptomDiagnosticReporter
0x7fff646a7000 - 0x7fff646d1ffe com.apple.framework.SystemAdministration (1.0 - 1.0) /System/Library/PrivateFrameworks/SystemAdministration.framework/Versions/A/SystemAdministration
0x7fff648ed000 - 0x7fff648fdff3 com.apple.TCC (1.0 - 1) /System/Library/PrivateFrameworks/TCC.framework/Versions/A/TCC
0x7fff64e22000 - 0x7fff64ee8ff0 com.apple.TextureIO (3.10.9 - 3.10.9) /System/Library/PrivateFrameworks/TextureIO.framework/Versions/A/TextureIO
0x7fff6507f000 - 0x7fff65080fff com.apple.TrustEvaluationAgent (2.0 - 33) /System/Library/PrivateFrameworks/TrustEvaluationAgent.framework/Versions/A/TrustEvaluationAgent
0x7fff650b8000 - 0x7fff65310ff0 com.apple.UIFoundation (1.0 - 662) /System/Library/PrivateFrameworks/UIFoundation.framework/Versions/A/UIFoundation
0x7fff653a7000 - 0x7fff653adffe com.apple.URLFormatting (119 - 119.18) /System/Library/PrivateFrameworks/URLFormatting.framework/Versions/A/URLFormatting
0x7fff65f9f000 - 0x7fff65fbfffc com.apple.UserManagement (1.0 - 1) /System/Library/PrivateFrameworks/UserManagement.framework/Versions/A/UserManagement
0x7fff66d6b000 - 0x7fff66e56ff2 com.apple.ViewBridge (467 - 467) /System/Library/PrivateFrameworks/ViewBridge.framework/Versions/A/ViewBridge
0x7fff66ffc000 - 0x7fff66ffdfff com.apple.WatchdogClient.framework (1.0 - 67.120.2) /System/Library/PrivateFrameworks/WatchdogClient.framework/Versions/A/WatchdogClient
0x7fff67c2d000 - 0x7fff67c30ffa com.apple.dt.XCTTargetBootstrap (1.0 - 16091) /System/Library/PrivateFrameworks/XCTTargetBootstrap.framework/Versions/A/XCTTargetBootstrap
0x7fff67caa000 - 0x7fff67cb8ff5 com.apple.audio.caulk (1.0 - 32.3) /System/Library/PrivateFrameworks/caulk.framework/Versions/A/caulk
0x7fff67ffa000 - 0x7fff67ffcff3 com.apple.loginsupport (1.0 - 1) /System/Library/PrivateFrameworks/login.framework/Versions/A/Frameworks/loginsupport.framework/Versions/A/loginsupport
0x7fff67ffd000 - 0x7fff68010ffd com.apple.login (3.0 - 3.0) /System/Library/PrivateFrameworks/login.framework/Versions/A/login
0x7fff68042000 - 0x7fff6804effd com.apple.perfdata (1.0 - 51.100.6) /System/Library/PrivateFrameworks/perfdata.framework/Versions/A/perfdata
0x7fff6aad3000 - 0x7fff6aadfff9 libAudioStatistics.dylib (1104.96) /usr/lib/libAudioStatistics.dylib
0x7fff6aae0000 - 0x7fff6ab13ffa libAudioToolboxUtility.dylib (1104.96) /usr/lib/libAudioToolboxUtility.dylib
0x7fff6ab1a000 - 0x7fff6ab4efff libCRFSuite.dylib (48) /usr/lib/libCRFSuite.dylib
0x7fff6ab51000 - 0x7fff6ab5bfff libChineseTokenizer.dylib (34) /usr/lib/libChineseTokenizer.dylib
0x7fff6ab5c000 - 0x7fff6abe4fff libCoreStorage.dylib (551) /usr/lib/libCoreStorage.dylib
0x7fff6abe7000 - 0x7fff6abe9ff7 libDiagnosticMessagesClient.dylib (112) /usr/lib/libDiagnosticMessagesClient.dylib
0x7fff6ac2f000 - 0x7fff6ade6ffb libFosl_dynamic.dylib (100.4) /usr/lib/libFosl_dynamic.dylib
0x7fff6ae0d000 - 0x7fff6ae13ff3 libIOReport.dylib (54) /usr/lib/libIOReport.dylib
0x7fff6aef5000 - 0x7fff6aefcfff libMatch.1.dylib (36) /usr/lib/libMatch.1.dylib
0x7fff6af2b000 - 0x7fff6af4bff7 libMobileGestalt.dylib (826.140.5) /usr/lib/libMobileGestalt.dylib
0x7fff6afcb000 - 0x7fff6b0a8ff7 libSMC.dylib (20) /usr/lib/libSMC.dylib
0x7fff6b0bd000 - 0x7fff6b0befff libSystem.B.dylib (1281.100.1) /usr/lib/libSystem.B.dylib
0x7fff6b0bf000 - 0x7fff6b14aff7 libTelephonyUtilDynamic.dylib (5017.1) /usr/lib/libTelephonyUtilDynamic.dylib
0x7fff6b14b000 - 0x7fff6b14cfff libThaiTokenizer.dylib (3) /usr/lib/libThaiTokenizer.dylib
0x7fff6b164000 - 0x7fff6b17afff libapple_nghttp2.dylib (1.39.2) /usr/lib/libapple_nghttp2.dylib
0x7fff6b1af000 - 0x7fff6b221ff7 libarchive.2.dylib (72.140.2) /usr/lib/libarchive.2.dylib
0x7fff6b222000 - 0x7fff6b2bbfe5 libate.dylib (3.0.1) /usr/lib/libate.dylib
0x7fff6b2bf000 - 0x7fff6b2bfff3 libauto.dylib (187) /usr/lib/libauto.dylib
0x7fff6b2c0000 - 0x7fff6b384ffe libboringssl.dylib (283.120.1) /usr/lib/libboringssl.dylib
0x7fff6b385000 - 0x7fff6b395ffb libbsm.0.dylib (60.100.1) /usr/lib/libbsm.0.dylib
0x7fff6b396000 - 0x7fff6b3a2fff libbz2.1.0.dylib (44) /usr/lib/libbz2.1.0.dylib
0x7fff6b3a3000 - 0x7fff6b3f5fff libc++.1.dylib (902.1) /usr/lib/libc++.1.dylib
0x7fff6b3f6000 - 0x7fff6b40bffb libc++abi.dylib (902) /usr/lib/libc++abi.dylib
0x7fff6b40c000 - 0x7fff6b40cfff libcharset.1.dylib (59) /usr/lib/libcharset.1.dylib
0x7fff6b40d000 - 0x7fff6b41efff libcmph.dylib (8) /usr/lib/libcmph.dylib
0x7fff6b41f000 - 0x7fff6b436fd7 libcompression.dylib (87) /usr/lib/libcompression.dylib
0x7fff6b710000 - 0x7fff6b726ff7 libcoretls.dylib (167) /usr/lib/libcoretls.dylib
0x7fff6b727000 - 0x7fff6b728fff libcoretls_cfhelpers.dylib (167) /usr/lib/libcoretls_cfhelpers.dylib
0x7fff6bbcb000 - 0x7fff6bccffef libcrypto.44.dylib (47.140.1) /usr/lib/libcrypto.44.dylib
0x7fff6bcd2000 - 0x7fff6bcddfff libcsfde.dylib (551) /usr/lib/libcsfde.dylib
0x7fff6bce5000 - 0x7fff6bd44ff7 libcups.2.dylib (483.7) /usr/lib/libcups.2.dylib
0x7fff6bd46000 - 0x7fff6bdabff7 libcurl.4.dylib (118.120.2) /usr/lib/libcurl.4.dylib
0x7fff6be4e000 - 0x7fff6be4efff libenergytrace.dylib (21) /usr/lib/libenergytrace.dylib
0x7fff6be4f000 - 0x7fff6be67fff libexpat.1.dylib (19.60.2) /usr/lib/libexpat.1.dylib
0x7fff6be75000 - 0x7fff6be77fff libfakelink.dylib (149.1) /usr/lib/libfakelink.dylib
0x7fff6be86000 - 0x7fff6be8bfff libgermantok.dylib (24) /usr/lib/libgermantok.dylib
0x7fff6be8c000 - 0x7fff6be95ff7 libheimdal-asn1.dylib (564.140.1) /usr/lib/libheimdal-asn1.dylib
0x7fff6be96000 - 0x7fff6bf86fff libiconv.2.dylib (59) /usr/lib/libiconv.2.dylib
0x7fff6bf87000 - 0x7fff6c1defff libicucore.A.dylib (64260.0.1) /usr/lib/libicucore.A.dylib
0x7fff6c1f8000 - 0x7fff6c1f9fff liblangid.dylib (133) /usr/lib/liblangid.dylib
0x7fff6c1fa000 - 0x7fff6c212ff3 liblzma.5.dylib (16) /usr/lib/liblzma.5.dylib
0x7fff6c22a000 - 0x7fff6c2d1ff7 libmecab.dylib (883.11) /usr/lib/libmecab.dylib
0x7fff6c2d2000 - 0x7fff6c534ff1 libmecabra.dylib (883.11) /usr/lib/libmecabra.dylib
0x7fff6c8a1000 - 0x7fff6c8d0fff libncurses.5.4.dylib (57) /usr/lib/libncurses.5.4.dylib
0x7fff6ca00000 - 0x7fff6ce7cff5 libnetwork.dylib (1880.120.4) /usr/lib/libnetwork.dylib
0x7fff6ce7d000 - 0x7fff6ce94fff libnetworkextension.dylib (1095.140.2) /usr/lib/libnetworkextension.dylib
0x7fff6cf1d000 - 0x7fff6cf50fde libobjc.A.dylib (787.1) /usr/lib/libobjc.A.dylib
0x7fff6cf51000 - 0x7fff6cf52ff7 libodfde.dylib (26) /usr/lib/libodfde.dylib
0x7fff6cf63000 - 0x7fff6cf67fff libpam.2.dylib (25.100.1) /usr/lib/libpam.2.dylib
0x7fff6cf6a000 - 0x7fff6cfa0ff7 libpcap.A.dylib (89.120.1) /usr/lib/libpcap.A.dylib
0x7fff6cfe0000 - 0x7fff6cfeeff9 libperfcheck.dylib (37.100.2) /usr/lib/libperfcheck.dylib
0x7fff6cfef000 - 0x7fff6cff2ff3 libpmenergy.dylib (214.120.1) /usr/lib/libpmenergy.dylib
0x7fff6cff3000 - 0x7fff6cff5fff libpmsample.dylib (214.120.1) /usr/lib/libpmsample.dylib
0x7fff6d024000 - 0x7fff6d03cfff libresolv.9.dylib (67.40.1) /usr/lib/libresolv.9.dylib
0x7fff6d03e000 - 0x7fff6d082ff7 libsandbox.1.dylib (1217.141.2) /usr/lib/libsandbox.1.dylib
0x7fff6d083000 - 0x7fff6d095ff7 libsasl2.2.dylib (213.120.1) /usr/lib/libsasl2.2.dylib
0x7fff6d096000 - 0x7fff6d097ff7 libspindump.dylib (281.3) /usr/lib/libspindump.dylib
0x7fff6d098000 - 0x7fff6d282ff7 libsqlite3.dylib (308.6) /usr/lib/libsqlite3.dylib
0x7fff6d376000 - 0x7fff6d3a3ffb libssl.46.dylib (47.140.1) /usr/lib/libssl.46.dylib
0x7fff6d478000 - 0x7fff6d4d2ff8 libusrtcp.dylib (1880.120.4) /usr/lib/libusrtcp.dylib
0x7fff6d4d3000 - 0x7fff6d4d6ffb libutil.dylib (57) /usr/lib/libutil.dylib
0x7fff6d4d7000 - 0x7fff6d4e4ff7 libxar.1.dylib (425.2) /usr/lib/libxar.1.dylib
0x7fff6d4ea000 - 0x7fff6d5ccfff libxml2.2.dylib (33.8) /usr/lib/libxml2.2.dylib
0x7fff6d5d0000 - 0x7fff6d5f8fff libxslt.1.dylib (16.10) /usr/lib/libxslt.1.dylib
0x7fff6d5f9000 - 0x7fff6d60bff3 libz.1.dylib (76) /usr/lib/libz.1.dylib
0x7fff6deba000 - 0x7fff6debfff3 libcache.dylib (83) /usr/lib/system/libcache.dylib
0x7fff6dec0000 - 0x7fff6decbfff libcommonCrypto.dylib (60165.120.1) /usr/lib/system/libcommonCrypto.dylib
0x7fff6decc000 - 0x7fff6ded3fff libcompiler_rt.dylib (101.2) /usr/lib/system/libcompiler_rt.dylib
0x7fff6ded4000 - 0x7fff6deddff7 libcopyfile.dylib (166.40.1) /usr/lib/system/libcopyfile.dylib
0x7fff6dede000 - 0x7fff6df70fdb libcorecrypto.dylib (866.140.1) /usr/lib/system/libcorecrypto.dylib
0x7fff6e07d000 - 0x7fff6e0bdff0 libdispatch.dylib (1173.100.2) /usr/lib/system/libdispatch.dylib
0x7fff6e0be000 - 0x7fff6e0f4fff libdyld.dylib (750.6) /usr/lib/system/libdyld.dylib
0x7fff6e0f5000 - 0x7fff6e0f5ffb libkeymgr.dylib (30) /usr/lib/system/libkeymgr.dylib
0x7fff6e0f6000 - 0x7fff6e102ff3 libkxld.dylib (6153.141.16) /usr/lib/system/libkxld.dylib
0x7fff6e103000 - 0x7fff6e103ff7 liblaunch.dylib (1738.140.2) /usr/lib/system/liblaunch.dylib
0x7fff6e104000 - 0x7fff6e109ff7 libmacho.dylib (959.0.1) /usr/lib/system/libmacho.dylib
0x7fff6e10a000 - 0x7fff6e10cff3 libquarantine.dylib (110.40.3) /usr/lib/system/libquarantine.dylib
0x7fff6e10d000 - 0x7fff6e10eff7 libremovefile.dylib (48) /usr/lib/system/libremovefile.dylib
0x7fff6e10f000 - 0x7fff6e126ff3 libsystem_asl.dylib (377.60.2) /usr/lib/system/libsystem_asl.dylib
0x7fff6e127000 - 0x7fff6e127ff7 libsystem_blocks.dylib (74) /usr/lib/system/libsystem_blocks.dylib
0x7fff6e128000 - 0x7fff6e1affff libsystem_c.dylib (1353.100.2) /usr/lib/system/libsystem_c.dylib
0x7fff6e1b0000 - 0x7fff6e1b3ffb libsystem_configuration.dylib (1061.141.1) /usr/lib/system/libsystem_configuration.dylib
0x7fff6e1b4000 - 0x7fff6e1b7fff libsystem_coreservices.dylib (114) /usr/lib/system/libsystem_coreservices.dylib
0x7fff6e1b8000 - 0x7fff6e1c0fff libsystem_darwin.dylib (1353.100.2) /usr/lib/system/libsystem_darwin.dylib
0x7fff6e1c1000 - 0x7fff6e1c8fff libsystem_dnssd.dylib (1096.100.3) /usr/lib/system/libsystem_dnssd.dylib
0x7fff6e1c9000 - 0x7fff6e1caffb libsystem_featureflags.dylib (17) /usr/lib/system/libsystem_featureflags.dylib
0x7fff6e1cb000 - 0x7fff6e218ff7 libsystem_info.dylib (538) /usr/lib/system/libsystem_info.dylib
0x7fff6e219000 - 0x7fff6e245ff7 libsystem_kernel.dylib (6153.141.16) /usr/lib/system/libsystem_kernel.dylib
0x7fff6e246000 - 0x7fff6e28dfff libsystem_m.dylib (3178) /usr/lib/system/libsystem_m.dylib
0x7fff6e28e000 - 0x7fff6e2b5fff libsystem_malloc.dylib (283.100.6) /usr/lib/system/libsystem_malloc.dylib
0x7fff6e2b6000 - 0x7fff6e2c3ffb libsystem_networkextension.dylib (1095.140.2) /usr/lib/system/libsystem_networkextension.dylib
0x7fff6e2c4000 - 0x7fff6e2cdff7 libsystem_notify.dylib (241.100.2) /usr/lib/system/libsystem_notify.dylib
0x7fff6e2ce000 - 0x7fff6e2d6fef libsystem_platform.dylib (220.100.1) /usr/lib/system/libsystem_platform.dylib
0x7fff6e2d7000 - 0x7fff6e2e1fff libsystem_pthread.dylib (416.100.3) /usr/lib/system/libsystem_pthread.dylib
0x7fff6e2e2000 - 0x7fff6e2e6ff3 libsystem_sandbox.dylib (1217.141.2) /usr/lib/system/libsystem_sandbox.dylib
0x7fff6e2e7000 - 0x7fff6e2e9fff libsystem_secinit.dylib (62.100.2) /usr/lib/system/libsystem_secinit.dylib
0x7fff6e2ea000 - 0x7fff6e2f1ffb libsystem_symptoms.dylib (1238.120.2) /usr/lib/system/libsystem_symptoms.dylib
0x7fff6e2f2000 - 0x7fff6e308ff2 libsystem_trace.dylib (1147.120.1) /usr/lib/system/libsystem_trace.dylib
0x7fff6e30a000 - 0x7fff6e30fff7 libunwind.dylib (35.4) /usr/lib/system/libunwind.dylib
0x7fff6e310000 - 0x7fff6e345ffe libxpc.dylib (1738.140.2) /usr/lib/system/libxpc.dylib
External Modification Summary:
Calls made by other processes targeting this process:
task_for_pid: 198
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: 291898
thread_create: 0
thread_set_state: 0
VM Region Summary:
ReadOnly portion of Libraries: Total=1.0G resident=0K(0%) swapped_out_or_unallocated=1.0G(100%)
Writable regions: Total=2.5G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=2.5G(100%)
VIRTUAL REGION
REGION TYPE SIZE COUNT (non-coalesced)
=========== ======= =======
Accelerate framework 512K 4
Activity Tracing 256K 1
CG backing stores 1160K 2
CG image 468K 27
CoreAnimation 896K 64
CoreGraphics 8K 1
CoreImage 40K 4
CoreUI image data 4052K 36
Foundation 28K 2
Kernel Alloc Once 1036K 2
MALLOC 2.1G 1430
MALLOC guard page 32K 8
MALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated)
Mach message 24K 3
OpenGL GLSL 384K 5
STACK GUARD 96K 24
Stack 140.2M 25
Stack Guard 56.0M 1
VM_ALLOCATE 331.5M 305
__DATA 66.5M 569
__DATA_CONST 128K 6
__FONT_DATA 4K 1
__GLSLBUILTINS 5176K 1
__LINKEDIT 481.5M 152
__OBJC_RO 32.3M 1
__OBJC_RW 1908K 2
__TEXT 572.6M 532
__UNICODE 564K 1
mapped file 394.4M 55
shared memory 2840K 24
=========== ======= =======
TOTAL 4.1G 3289
TOTAL, minus reserved VM space 4.1G 3289
System Profile:
Network Service: Wi-Fi, AirPort, en0
bridge_os_version: Bridge OS 5.2 (18P4347)
Boot Volume File System Type: apfs
bridge_model: iBridge2,3
Memory Module: BANK 0/ChannelA-DIMM0, 8 GB, DDR4, 2400 MHz, Micron, 8ATF1G64HZ-2G6E1
Memory Module: BANK 2/ChannelB-DIMM0, 8 GB, DDR4, 2400 MHz, Micron, 8ATF1G64HZ-2G6E1
USB Device: USB3.0 Hub
USB Device: USB 10/100/1000 LAN
USB Device: Mass Storage Device
USB Device: USB3.0 Hub
USB Device: USB3.0 Hub
USB Device: USB 3.1 Bus
USB Device: USB2.0 Hub
USB Device: USB 2.0 BILLBOARD
USB Device: USB2.0 Hub
USB Device: Varmilo
USB Device: G PRO Gaming Mouse
USB Device: USB2.0 Hub
USB Device: Apple T2 Bus
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., 47.4
Thunderbolt Bus: MacBook Pro, Apple Inc., 47.4
Model: MacBookPro15,1, BootROM 1554.80.3.0.0 (iBridge: 18.16.14347.0.0,0), 6 processors, 6-Core Intel Core i7, 2.6 GHz, 16 GB, SMC
Graphics: kHW_IntelUHDGraphics630Item, Intel UHD Graphics 630, spdisplays_builtin
Graphics: kHW_AMDRadeonPro560XItem, Radeon Pro 560X, spdisplays_pcie_device, 4 GB
AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x7BF), wl0: Oct 28 2020 13:06:41 version 9.30.357.42.32.5.48 FWID 01-4f9e2d7c
Bluetooth: Version 7.0.6f8, 3 services, 27 devices, 1 incoming serial ports
Log:
UCSF ChimeraX version: 1.2 (2021-04-27)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 ATI-3.10.19
OpenGL renderer: AMD Radeon Pro 560X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro15,1
Processor Name: 6-Core Intel Core i7
Processor Speed: 2.6 GHz
Number of Processors: 1
Total Number of Cores: 6
L2 Cache (per Core): 256 KB
L3 Cache: 9 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
Boot ROM Version: 1554.80.3.0.0 (iBridge: 18.16.14347.0.0,0)
Software:
System Software Overview:
System Version: macOS 10.15.7 (19H524)
Kernel Version: Darwin 19.6.0
Time since boot: 6 days 21:05
Graphics/Displays:
Intel UHD Graphics 630:
Chipset Model: Intel UHD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3e9b
Revision ID: 0x0000
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal: Supported, feature set macOS GPUFamily2 v1
Radeon Pro 560X:
Chipset Model: Radeon Pro 560X
Type: GPU
Bus: PCIe
PCIe Lane Width: x8
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x67ef
Revision ID: 0x00c2
ROM Revision: 113-C980AL-075
VBIOS Version: 113-C97501U-005
EFI Driver Version: 01.A1.075
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal: Supported, feature set macOS GPUFamily2 v1
Displays:
G237HL:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60 Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: T0MAA0012400
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: No
Connection Type: DVI or HDMI
Adapter Firmware Version: 7.55
Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.2
Babel: 2.9.0
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.12.5
cftime: 1.4.1
chardet: 3.0.4
ChimeraX-AddCharge: 1.0
ChimeraX-AddH: 2.1.6
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.13.3
ChimeraX-AtomicLibrary: 3.1.2
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.5.2
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.1
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.2.1
ChimeraX-CommandLine: 1.1.3
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.2
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.1.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.1
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.1
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.0
ChimeraX-Hbonds: 2.1
ChimeraX-Help: 1.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.1
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-Label: 1.0
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.0.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.0
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 1.2
ChimeraX-MDcrds: 2.2
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.3
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.0.1
ChimeraX-ModelPanel: 1.0.1
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.1
ChimeraX-OpenCommand: 1.5
ChimeraX-PDB: 2.4.1
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.0.1
ChimeraX-ReadPbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.4
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.0
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.0.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.3.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.0.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.7.3
ChimeraX-uniprot: 2.1
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.3
comtypes: 1.1.7
cxservices: 1.0
cycler: 0.10.0
Cython: 0.29.21
decorator: 5.0.7
distlib: 0.3.1
docutils: 0.16
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 2.10.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.17
imagecodecs: 2020.5.30
imagesize: 1.2.0
ipykernel: 5.3.4
ipython: 7.18.1
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.7
jupyter-core: 4.7.1
kiwisolver: 1.3.1
line-profiler: 2.1.2
lxml: 4.6.2
lz4: 3.1.0
MarkupSafe: 1.1.1
matplotlib: 3.3.2
msgpack: 1.0.0
netCDF4: 1.5.4
networkx: 2.5
numexpr: 2.7.3
numpy: 1.19.2
numpydoc: 1.1.0
openvr: 1.14.1501
packaging: 20.9
ParmEd: 3.2.0
parso: 0.7.1
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 7.2.0
pip: 21.0.1
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.18
psutil: 5.7.2
ptyprocess: 0.7.0
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.7.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.1
pytz: 2021.1
pyzmq: 22.0.3
qtconsole: 4.7.7
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.5.2
setuptools: 50.3.2
sfftk-rw: 0.6.7.dev1
six: 1.15.0
snowballstemmer: 2.1.0
sortedcontainers: 2.2.2
Sphinx: 3.2.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 1.0.3
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.4
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2020.9.3
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.0.5
urllib3: 1.25.11
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.36.0
wheel-filename: 1.3.0
Change History (17)
comment:1 by , 4 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash during garbage collection |
comment:3 by , 4 years ago
I studied the stack trace. I don't understand your explanation of the crash. The atom map dictionary being constructed should be completely safe during garbage collection. My interpretation is that it was creating a Python Atom instance
6 org.python.python 0x0000000100bbf7d4 collect + 692
7 org.python.python 0x0000000100bc0744 _PyObject_GC_Alloc + 324
8 org.python.python 0x0000000100bc07b5 _PyObject_GC_New + 21
9 org.python.python 0x0000000100ab9747 PyDict_New + 87
10 cymol.cpython-38-darwin.so 0x0000000124743a6b pyx_tp_new_8chimerax_6atomic_5cymol_CyAtom(_typeobject*, _object*, _object*) + 75
and creating the instance tried to create a new dictionary (maybe the instance dictionary) trigger garbage collection. Then dict_traverse() crashes during the garbage collection, but what dictionary was it traversing? It could be any dictionary. I don't see any clues that point to what dictionary was in an inconsistent state. I would guess a dictionary key or value C object had been deleted due to a reference count error.
comment:4 by , 4 years ago
We don't have any other bug reports containing dict_traverse. All our other garbage collection crashes (20 reported) were in tupletraverse(). Maybe this bug report is caused by the asme problem. But I have no clue where that problem is other than it is a bad (probably deleted) Python object in a tuple or in a dictionary.
comment:5 by , 4 years ago
It getting the values/keys for the dictionary via the iter method of Collection when this crash happens. Unless the dictionary hasn't even been started at this point (which I don't think is true, but not 100% sure) then it's going to be in an inconsistent state.
The exact same thing could happen while populating a tuple/list.
comment:6 by , 4 years ago
Looking at the stacks for a handful of other reports of this, you are right that my analysis of this crash does not apply to them since there is no c_ptr_to_py_inst call in those traces. Doesn't mean my analysis here is wrong, but it could be, and the solution I propose doesn't seem like it would help in those other cases.
follow-up: 7 comment:7 by , 4 years ago
Not sure which dictionary you think would be in an inconsistent state. If you mean the one from the Python morph copyMolecule code
atomMap = {a:ca for a,ca in zip(m.atoms, c.atoms)}
I don't think that could possibly be in an inconsistent state. I would guess it creates an empty dictionary and then adds elements one by one to it, so the dictionary is always consistent. Otherwise any iterator in this kind of dictionary comprehension that triggers garbage collection would lead to crashes -- that can't be, all kinds of Python code would be crashing.
It is an interesting idea that this dictionary is the cause of the crash though. Seems unlikely, but could our Python Atom construction or pointer to Python instance code be failing to do a needed incref?
comment:8 by , 4 years ago
Yeah, you're probably right about that particular dictionary not being the culprit -- certainly a dictionary comprehension could involve constructors directly (rather than indirectly as is the case here).
It's conceivable that the problematic object (if that's the cause) is only in an unreachable cycle, or has no true references despite having a non-zero reference count. If so, then this crash would *only* occur in garbage collection.
follow-up: 9 comment:9 by , 4 years ago
My guess is that some object has reference count one too low due to a bug where an incref was not done. Its refcount drops to zero and is deleted by Python even though it still belongs to a tuple or dictionary. Then garbage collection happens and it hits the freed object and kaboom. I bet our code is making the incref mistake. But I spent several hours surveying our code and its current increfs several months ago and did not see anything amiss.
comment:10 by , 4 years ago
So, looking at the code for zip_new() in Python/bltinmodule.c I see that it does a PyTuple_New of the tuple size and then fills in the tuple with iterators. The iterator for Collections, unlike most iterators, calls constructors that in turn can kick off garbage collection. Garbage collection checking of that partially filled in tuple will undoubtedly cause a crash.
So I guess I'm again asserting that the solution is to turn off garbage collection in c_ptr_to_py_inst.
comment:11 by , 4 years ago
Really Collection.__iter__ would need to be overhauled to only construct objects during the actual iteration.
follow-up: 13 comment:13 by , 4 years ago
Interesting, but really hard to believe. It would mean that zip(x,y) should be prone to crashing whenever getting the iterator for x triggers garbage collection. That seems like a pretty serious bug in Python. Should be trivial to make a standalone test case, just make x an instance whose __iter__() directly calls garbage collection.
comment:14 by , 4 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
Yep, tried various monkeyshines with iterators and bupkis.
follow-up: 15 comment:15 by , 4 years ago
I have an idea about how to get more clues on this garbage collection crash and many other crashes. Log every command (but not command output) to a temp file and include the command list with crash reports. This will help us narrow down what kind of data and operations lead to the crash. I think it will be extremely low overhead, since writing a line to a file is just going to go to the OS cache, but on crash should get flushed to disk.
follow-up: 17 comment:17 by , 4 years ago
I was just going to add it if I have time, or make a ticket for it if I don't. Does not seem controversial. Our non-crash bug reports already normally contain the full log. Needs testing to see if the buffered written commands actually get to the log during a crash.
Note:
See TracTickets
for help on using tickets.
With the new more complete stack information, I _think_ I know what's going on. Morph is forming a dictionary by zipping together two Atoms collections. The Atoms
__iter__method is using the C++ pointer to get a Python instance via Atom.c_ptr_to_py_inst. That eventually calls back to the Atom constructor. Itsnewmethod performs garbage collection during the memory allocation. Part of the collection does a dictionary traversal on the in-progress dictionary construction and crashes.I lean to putting in a call to temporarily disable garbage collection in c_ptr_to_py_inst, but am open to better solutions.