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Opened 3 years ago
Closed 3 years ago
#8457 closed defect (fixed)
Crash clearing aniso_u6
| Reported by: | Owned by: | Tristan Croll | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Editing | Version: | |
| Keywords: | Cc: | Eric Pettersen, Tom Goddard, Zach Pearson | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-11.5.1-arm64-arm-64bit
ChimeraX Version: 1.5 (2022-11-24 00:03:27 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 0x0000000102627d40 (most recent call first):
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/atomic/molarray.py", line 846 in _set_aniso_u6
File "/Users/seiyahirai/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/clipper/sanity_check.py", line 12 in remove_invalid_anisou
File "/Users/seiyahirai/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/clipper/symmetry.py", line 667 in _anisou_sanity_check
File "/Users/seiyahirai/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/clipper/symmetry.py", line 636 in add_model
File "/Users/seiyahirai/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/clipper/symmetry.py", line 594 in __init__
File "/Users/seiyahirai/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/clipper/symmetry.py", line 170 in _get_symmetry_handler
File "/Users/seiyahirai/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/clipper/symmetry.py", line 159 in get_symmetry_handler
File "/Users/seiyahirai/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/isolde/isolde.py", line 814 in _change_selected_model
File "/Users/seiyahirai/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/isolde/isolde.py", line 771 in change_selected_model
File "/Users/seiyahirai/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/isolde/isolde.py", line 433 in selected_model
File "/Users/seiyahirai/Library/Application Support/ChimeraX/1.5/site-packages/chimerax/isolde/ui/main_win.py", line 157 in _set_selected_model
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 283 in event_loop
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 884 in init
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1035 in
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main
Process: ChimeraX [12742]
Path: /Applications/ChimeraX-1.5.app/Contents/MacOS/ChimeraX
Identifier: edu.ucsf.cgl.ChimeraX
Version: 1.5.0 (1.5.0.0)
Code Type: ARM-64 (Native)
Parent Process: ??? [1]
Responsible: ChimeraX [12742]
User ID: 501
Date/Time: 2023-02-08 16:33:23.933 +0900
OS Version: macOS 11.5.1 (20G80)
Report Version: 12
Anonymous UUID: A143588D-7754-31A9-9C73-363555E3C01C
Sleep/Wake UUID: 2C05A555-40F5-4714-BF9C-55BC4FBFE11D
Time Awake Since Boot: 21000 seconds
Time Since Wake: 2200 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 0x0000000000000008
Exception Note: EXC_CORPSE_NOTIFY
VM Regions Near 0x8:
-->
__TEXT 102198000-10219c000 [ 16K] r-x/r-x SM=COW /Applications/ChimeraX-1.5.app/Contents/MacOS/ChimeraX
Thread 0 Crashed:: CrBrowserMain Dispatch queue: com.apple.main-thread
0 libsystem_kernel.dylib 0x000000018e814e68 __pthread_kill + 8
1 libsystem_pthread.dylib 0x000000018e84743c pthread_kill + 292
2 libsystem_c.dylib 0x000000018e726e10 raise + 32
3 libsystem_platform.dylib 0x000000018e892c44 _sigtramp + 56
4 libmolc.dylib 0x0000000170de3054 clear_atom_aniso_u6 + 32
5 libmolc.dylib 0x0000000170de3054 clear_atom_aniso_u6 + 32
6 libffi.dylib 0x000000019b70c050 ffi_call_SYSV + 80
7 libffi.dylib 0x000000019b7149e4 ffi_call_int + 948
8 _ctypes.cpython-39-darwin.so 0x000000010fb16944 _ctypes_callproc + 1404
9 _ctypes.cpython-39-darwin.so 0x000000010fb0fc10 PyCFuncPtr_call + 1168
10 org.python.python 0x00000001021f8870 _PyObject_MakeTpCall + 360
11 org.python.python 0x00000001022cebc8 call_function + 512
12 org.python.python 0x00000001022cc284 _PyEval_EvalFrameDefault + 23232
13 org.python.python 0x00000001021f8ffc function_code_fastcall + 112
14 org.python.python 0x00000001021f9f84 object_vacall + 256
15 org.python.python 0x00000001021fa1ac PyObject_CallFunctionObjArgs + 48
16 org.python.python 0x00000001022022ec property_descr_set + 80
17 org.python.python 0x000000010223ffa4 _PyObject_GenericSetAttrWithDict + 184
18 org.python.python 0x000000010223f384 PyObject_SetAttr + 132
19 org.python.python 0x00000001022c9650 _PyEval_EvalFrameDefault + 11916
20 org.python.python 0x00000001021f8ffc function_code_fastcall + 112
21 org.python.python 0x00000001022ceb68 call_function + 416
22 org.python.python 0x00000001022cc284 _PyEval_EvalFrameDefault + 23232
23 org.python.python 0x00000001021f8ffc function_code_fastcall + 112
24 org.python.python 0x00000001022ceb68 call_function + 416
25 org.python.python 0x00000001022cc1e4 _PyEval_EvalFrameDefault + 23072
26 org.python.python 0x00000001022cfa90 _PyEval_EvalCode + 2988
27 org.python.python 0x00000001021f8f80 _PyFunction_Vectorcall + 256
28 org.python.python 0x00000001021faf60 method_vectorcall + 168
29 org.python.python 0x00000001022ceb68 call_function + 416
30 org.python.python 0x00000001022cc300 _PyEval_EvalFrameDefault + 23356
31 org.python.python 0x00000001022cfa90 _PyEval_EvalCode + 2988
32 org.python.python 0x00000001021f8f80 _PyFunction_Vectorcall + 256
33 org.python.python 0x00000001021f8614 _PyObject_FastCallDictTstate + 140
34 org.python.python 0x00000001021f9304 _PyObject_Call_Prepend + 148
35 org.python.python 0x000000010225b828 slot_tp_init + 216
36 org.python.python 0x0000000102252898 type_call + 352
37 org.python.python 0x00000001021f8870 _PyObject_MakeTpCall + 360
38 org.python.python 0x00000001022cebc8 call_function + 512
39 org.python.python 0x00000001022cc300 _PyEval_EvalFrameDefault + 23356
40 org.python.python 0x00000001022cfa90 _PyEval_EvalCode + 2988
41 org.python.python 0x00000001021f8f80 _PyFunction_Vectorcall + 256
42 org.python.python 0x00000001022ceb68 call_function + 416
43 org.python.python 0x00000001022cc284 _PyEval_EvalFrameDefault + 23232
44 org.python.python 0x00000001022cfa90 _PyEval_EvalCode + 2988
45 org.python.python 0x00000001021f8f80 _PyFunction_Vectorcall + 256
46 org.python.python 0x00000001022ceb68 call_function + 416
47 org.python.python 0x00000001022cc300 _PyEval_EvalFrameDefault + 23356
48 org.python.python 0x00000001022cfa90 _PyEval_EvalCode + 2988
49 org.python.python 0x00000001021f8f80 _PyFunction_Vectorcall + 256
50 org.python.python 0x00000001021faf60 method_vectorcall + 168
51 org.python.python 0x00000001022ceb68 call_function + 416
52 org.python.python 0x00000001022cc300 _PyEval_EvalFrameDefault + 23356
53 org.python.python 0x00000001021f8ffc function_code_fastcall + 112
54 org.python.python 0x00000001022ceb68 call_function + 416
55 org.python.python 0x00000001022cc1e4 _PyEval_EvalFrameDefault + 23072
56 org.python.python 0x00000001021f8ffc function_code_fastcall + 112
57 org.python.python 0x00000001021f9f84 object_vacall + 256
58 org.python.python 0x00000001021fa1ac PyObject_CallFunctionObjArgs + 48
59 org.python.python 0x00000001022022ec property_descr_set + 80
60 org.python.python 0x000000010223ffa4 _PyObject_GenericSetAttrWithDict + 184
61 org.python.python 0x000000010223f384 PyObject_SetAttr + 132
62 org.python.python 0x00000001022c9650 _PyEval_EvalFrameDefault + 11916
63 org.python.python 0x00000001022cfa90 _PyEval_EvalCode + 2988
64 org.python.python 0x00000001021f8f80 _PyFunction_Vectorcall + 256
65 QtCore.abi3.so 0x000000011f4a65b8 PyQtSlot::call(_object*, _object*) const + 68
66 QtCore.abi3.so 0x000000011f4a6440 PyQtSlot::invoke(void**, _object*, void*, bool) const + 292
67 QtCore.abi3.so 0x000000011f4a736c PyQtSlotProxy::unislot(void**) + 92
68 QtCore.abi3.so 0x000000011f4a72dc PyQtSlotProxy::qt_metacall(QMetaObject::Call, int, void**) + 68
69 QtCore 0x000000011f7ae5dc 0x11f700000 + 714204
70 QtGui 0x0000000125e3be3c QAction::activate(QAction::ActionEvent) + 368
71 QtWidgets 0x00000001256dbc00 0x12553c000 + 1702912
72 QtWidgets 0x00000001256d97b4 0x12553c000 + 1693620
73 QtWidgets 0x00000001256e0410 QMenu::mouseReleaseEvent(QMouseEvent*) + 492
74 QtWidgets.abi3.so 0x0000000124f8f888 sipQMenu::mouseReleaseEvent(QMouseEvent*) + 148
75 QtWidgets 0x00000001255935d0 QWidget::event(QEvent*) + 132
76 QtWidgets 0x00000001256e0ab8 QMenu::event(QEvent*) + 1232
77 QtWidgets.abi3.so 0x0000000124f8eea0 sipQMenu::event(QEvent*) + 224
78 QtWidgets 0x0000000125549c90 QApplicationPrivate::notify_helper(QObject*, QEvent*) + 272
79 QtWidgets 0x000000012554bea8 QApplication::notify(QObject*, QEvent*) + 5040
80 QtWidgets.abi3.so 0x000000012504ce04 sipQApplication::notify(QObject*, QEvent*) + 248
81 QtCore 0x000000011f765d40 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 208
82 QtWidgets 0x000000012554a3c8 QApplicationPrivate::sendMouseEvent(QWidget*, QMouseEvent*, QWidget*, QWidget*, QWidget**, QPointer&, bool, bool) + 908
83 QtWidgets 0x00000001255a76ac 0x12553c000 + 439980
84 QtWidgets 0x00000001255a64e4 0x12553c000 + 435428
85 QtWidgets 0x0000000125549c90 QApplicationPrivate::notify_helper(QObject*, QEvent*) + 272
86 QtWidgets 0x000000012554acf8 QApplication::notify(QObject*, QEvent*) + 512
87 QtWidgets.abi3.so 0x000000012504ce04 sipQApplication::notify(QObject*, QEvent*) + 248
88 QtCore 0x000000011f765d40 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 208
89 QtGui 0x0000000125b5cd98 QGuiApplicationPrivate::processMouseEvent(QWindowSystemInterfacePrivate::MouseEvent*) + 1820
90 QtGui 0x0000000125bb02d0 QWindowSystemInterface::sendWindowSystemEvents(QFlags) + 444
91 libqcocoa.dylib 0x00000001277dc344 0x1277c4000 + 99140
92 com.apple.CoreFoundation 0x000000018e946a84 __CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE0_PERFORM_FUNCTION__ + 28
93 com.apple.CoreFoundation 0x000000018e9469d0 __CFRunLoopDoSource0 + 208
94 com.apple.CoreFoundation 0x000000018e9466bc __CFRunLoopDoSources0 + 268
95 com.apple.CoreFoundation 0x000000018e945044 __CFRunLoopRun + 820
96 com.apple.CoreFoundation 0x000000018e944598 CFRunLoopRunSpecific + 600
97 com.apple.HIToolbox 0x0000000196867280 RunCurrentEventLoopInMode + 292
98 com.apple.HIToolbox 0x0000000196866f0c ReceiveNextEventCommon + 320
99 com.apple.HIToolbox 0x0000000196866db4 _BlockUntilNextEventMatchingListInModeWithFilter + 72
100 com.apple.AppKit 0x0000000191135a64 _DPSNextEvent + 836
101 com.apple.AppKit 0x0000000191134404 -[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 1292
102 com.apple.AppKit 0x0000000191126290 -[NSApplication run] + 596
103 libqcocoa.dylib 0x00000001277db22c 0x1277c4000 + 94764
104 QtCore 0x000000011f76f39c QEventLoop::exec(QFlags) + 544
105 QtWidgets 0x00000001256df088 0x12553c000 + 1716360
106 QtWidgets 0x00000001256def2c QMenu::exec(QPoint const&, QAction*) + 52
107 QtWidgets 0x00000001256ef760 0x12553c000 + 1783648
108 QtCore 0x000000011f7ae86c 0x11f700000 + 714860
109 QtWidgets 0x0000000125644768 0x12553c000 + 1083240
110 QtWidgets 0x00000001256452dc QAbstractButton::mousePressEvent(QMouseEvent*) + 232
111 QtWidgets.abi3.so 0x000000012502b620 sipQPushButton::mousePressEvent(QMouseEvent*) + 148
112 QtWidgets 0x00000001255935d0 QWidget::event(QEvent*) + 132
113 QtWidgets.abi3.so 0x000000012502bfa8 sipQPushButton::event(QEvent*) + 224
114 QtWidgets 0x0000000125549c90 QApplicationPrivate::notify_helper(QObject*, QEvent*) + 272
115 QtWidgets 0x000000012554bea8 QApplication::notify(QObject*, QEvent*) + 5040
116 QtWidgets.abi3.so 0x000000012504ce04 sipQApplication::notify(QObject*, QEvent*) + 248
117 QtCore 0x000000011f765d40 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 208
118 QtWidgets 0x000000012554a3c8 QApplicationPrivate::sendMouseEvent(QWidget*, QMouseEvent*, QWidget*, QWidget*, QWidget**, QPointer&, bool, bool) + 908
119 QtWidgets 0x00000001255a7214 0x12553c000 + 438804
120 QtWidgets 0x00000001255a64e4 0x12553c000 + 435428
121 QtWidgets 0x0000000125549c90 QApplicationPrivate::notify_helper(QObject*, QEvent*) + 272
122 QtWidgets 0x000000012554acf8 QApplication::notify(QObject*, QEvent*) + 512
123 QtWidgets.abi3.so 0x000000012504ce04 sipQApplication::notify(QObject*, QEvent*) + 248
124 QtCore 0x000000011f765d40 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 208
125 QtGui 0x0000000125b5cd98 QGuiApplicationPrivate::processMouseEvent(QWindowSystemInterfacePrivate::MouseEvent*) + 1820
126 QtGui 0x0000000125bb02d0 QWindowSystemInterface::sendWindowSystemEvents(QFlags) + 444
127 libqcocoa.dylib 0x00000001277dc344 0x1277c4000 + 99140
128 com.apple.CoreFoundation 0x000000018e946a84 __CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE0_PERFORM_FUNCTION__ + 28
129 com.apple.CoreFoundation 0x000000018e9469d0 __CFRunLoopDoSource0 + 208
130 com.apple.CoreFoundation 0x000000018e9466bc __CFRunLoopDoSources0 + 268
131 com.apple.CoreFoundation 0x000000018e945044 __CFRunLoopRun + 820
132 com.apple.CoreFoundation 0x000000018e944598 CFRunLoopRunSpecific + 600
133 com.apple.HIToolbox 0x0000000196867280 RunCurrentEventLoopInMode + 292
134 com.apple.HIToolbox 0x0000000196866f0c ReceiveNextEventCommon + 320
135 com.apple.HIToolbox 0x0000000196866db4 _BlockUntilNextEventMatchingListInModeWithFilter + 72
136 com.apple.AppKit 0x0000000191135a64 _DPSNextEvent + 836
137 com.apple.AppKit 0x0000000191134404 -[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 1292
138 com.apple.AppKit 0x0000000191126290 -[NSApplication run] + 596
139 libqcocoa.dylib 0x00000001277db22c 0x1277c4000 + 94764
140 QtCore 0x000000011f76f39c QEventLoop::exec(QFlags) + 544
141 QtCore 0x000000011f7663f4 QCoreApplication::exec() + 128
142 QtWidgets.abi3.so 0x00000001251522b4 meth_QApplication_exec(_object*, _object*) + 96
143 org.python.python 0x000000010223b1dc cfunction_call + 172
144 org.python.python 0x00000001021f8870 _PyObject_MakeTpCall + 360
145 org.python.python 0x00000001022cebc8 call_function + 512
146 org.python.python 0x00000001022cc208 _PyEval_EvalFrameDefault + 23108
147 org.python.python 0x00000001021f8ffc function_code_fastcall + 112
148 org.python.python 0x00000001021faf60 method_vectorcall + 168
149 org.python.python 0x00000001022ceb68 call_function + 416
150 org.python.python 0x00000001022cc208 _PyEval_EvalFrameDefault + 23108
151 org.python.python 0x00000001022cfa90 _PyEval_EvalCode + 2988
152 org.python.python 0x00000001021f8f80 _PyFunction_Vectorcall + 256
153 org.python.python 0x00000001022ceb68 call_function + 416
154 org.python.python 0x00000001022cc284 _PyEval_EvalFrameDefault + 23232
155 org.python.python 0x00000001022cfa90 _PyEval_EvalCode + 2988
156 org.python.python 0x00000001022c66fc PyEval_EvalCode + 80
157 org.python.python 0x00000001022c34a4 builtin_exec + 672
158 org.python.python 0x000000010223a98c cfunction_vectorcall_FASTCALL + 232
159 org.python.python 0x00000001022ceb68 call_function + 416
160 org.python.python 0x00000001022cc284 _PyEval_EvalFrameDefault + 23232
161 org.python.python 0x00000001022cfa90 _PyEval_EvalCode + 2988
162 org.python.python 0x00000001021f8f80 _PyFunction_Vectorcall + 256
163 org.python.python 0x00000001022ceb68 call_function + 416
164 org.python.python 0x00000001022cc284 _PyEval_EvalFrameDefault + 23232
165 org.python.python 0x00000001022cfa90 _PyEval_EvalCode + 2988
166 org.python.python 0x00000001021f8f80 _PyFunction_Vectorcall + 256
167 org.python.python 0x0000000102329ea4 pymain_run_module + 200
168 org.python.python 0x00000001023294e8 Py_RunMain + 764
169 org.python.python 0x0000000102329d54 pymain_main + 340
170 org.python.python 0x0000000102329bf4 Py_Main + 36
171 edu.ucsf.cgl.ChimeraX 0x000000010219bd54 main + 128
172 libdyld.dylib 0x000000018e865430 start + 4
Thread 1:
0 libsystem_pthread.dylib 0x000000018e8425cc start_wqthread + 0
Thread 2:
0 libsystem_pthread.dylib 0x000000018e8425cc start_wqthread + 0
Thread 3:
0 libsystem_pthread.dylib 0x000000018e8425cc start_wqthread + 0
Thread 4:: ThreadPoolServiceThread
0 libsystem_kernel.dylib 0x000000018e817ee8 kevent64 + 8
1 QtWebEngineCore 0x00000001636197c8 0x160000000 + 56727496
2 QtWebEngineCore 0x00000001636196f8 0x160000000 + 56727288
3 QtWebEngineCore 0x00000001635a0f6c 0x160000000 + 56233836
4 QtWebEngineCore 0x00000001635644bc 0x160000000 + 55985340
5 QtWebEngineCore 0x00000001635c0d88 0x160000000 + 56364424
6 QtWebEngineCore 0x00000001635aa1a8 0x160000000 + 56271272
7 QtWebEngineCore 0x00000001635c0f10 0x160000000 + 56364816
8 QtWebEngineCore 0x00000001635e6be4 0x160000000 + 56519652
9 libsystem_pthread.dylib 0x000000018e847878 _pthread_start + 320
10 libsystem_pthread.dylib 0x000000018e8425e0 thread_start + 8
Thread 5:: ThreadPoolForegroundWorker
0 libsystem_kernel.dylib 0x000000018e80cdd4 mach_msg_trap + 8
1 libsystem_kernel.dylib 0x000000018e80d184 mach_msg + 76
2 QtWebEngineCore 0x00000001635ed5e4 0x160000000 + 56546788
3 QtWebEngineCore 0x00000001635b566c 0x160000000 + 56317548
4 QtWebEngineCore 0x00000001635b60f4 0x160000000 + 56320244
5 QtWebEngineCore 0x00000001635b5d20 0x160000000 + 56319264
6 QtWebEngineCore 0x00000001635e6be4 0x160000000 + 56519652
7 libsystem_pthread.dylib 0x000000018e847878 _pthread_start + 320
8 libsystem_pthread.dylib 0x000000018e8425e0 thread_start + 8
Thread 6:: ThreadPoolBackgroundWorker
0 libsystem_kernel.dylib 0x000000018e80cdd4 mach_msg_trap + 8
1 libsystem_kernel.dylib 0x000000018e80d184 mach_msg + 76
2 QtWebEngineCore 0x00000001635ed5e4 0x160000000 + 56546788
3 QtWebEngineCore 0x00000001635b566c 0x160000000 + 56317548
4 QtWebEngineCore 0x00000001635b60f4 0x160000000 + 56320244
5 QtWebEngineCore 0x00000001635b5c9c 0x160000000 + 56319132
6 QtWebEngineCore 0x00000001635e6be4 0x160000000 + 56519652
7 libsystem_pthread.dylib 0x000000018e847878 _pthread_start + 320
8 libsystem_pthread.dylib 0x000000018e8425e0 thread_start + 8
Thread 7:: Chrome_IOThread
0 libsystem_kernel.dylib 0x000000018e817ee8 kevent64 + 8
1 QtWebEngineCore 0x00000001636197c8 0x160000000 + 56727496
2 QtWebEngineCore 0x00000001636196f8 0x160000000 + 56727288
3 QtWebEngineCore 0x00000001635a0f6c 0x160000000 + 56233836
4 QtWebEngineCore 0x00000001635644bc 0x160000000 + 55985340
5 QtWebEngineCore 0x00000001635c0d88 0x160000000 + 56364424
6 QtWebEngineCore 0x00000001626b5c04 0x160000000 + 40590340
7 QtWebEngineCore 0x00000001635c0f10 0x160000000 + 56364816
8 QtWebEngineCore 0x00000001635e6be4 0x160000000 + 56519652
9 libsystem_pthread.dylib 0x000000018e847878 _pthread_start + 320
10 libsystem_pthread.dylib 0x000000018e8425e0 thread_start + 8
Thread 8:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x000000018e80cdd4 mach_msg_trap + 8
1 libsystem_kernel.dylib 0x000000018e80d184 mach_msg + 76
2 QtWebEngineCore 0x00000001635ed5e4 0x160000000 + 56546788
3 QtWebEngineCore 0x00000001635ed3b0 0x160000000 + 56546224
4 QtWebEngineCore 0x00000001635375a0 0x160000000 + 55801248
5 QtWebEngineCore 0x00000001635a0f6c 0x160000000 + 56233836
6 QtWebEngineCore 0x00000001635644bc 0x160000000 + 55985340
7 QtWebEngineCore 0x00000001635c0d88 0x160000000 + 56364424
8 QtWebEngineCore 0x00000001635c0f10 0x160000000 + 56364816
9 QtWebEngineCore 0x00000001635e6be4 0x160000000 + 56519652
10 libsystem_pthread.dylib 0x000000018e847878 _pthread_start + 320
11 libsystem_pthread.dylib 0x000000018e8425e0 thread_start + 8
Thread 9:: ThreadPoolForegroundWorker
0 libsystem_kernel.dylib 0x000000018e80cdd4 mach_msg_trap + 8
1 libsystem_kernel.dylib 0x000000018e80d184 mach_msg + 76
2 QtWebEngineCore 0x00000001635ed5e4 0x160000000 + 56546788
3 QtWebEngineCore 0x00000001635b566c 0x160000000 + 56317548
4 QtWebEngineCore 0x00000001635b60f4 0x160000000 + 56320244
5 QtWebEngineCore 0x00000001635b5d20 0x160000000 + 56319264
6 QtWebEngineCore 0x00000001635e6be4 0x160000000 + 56519652
7 libsystem_pthread.dylib 0x000000018e847878 _pthread_start + 320
8 libsystem_pthread.dylib 0x000000018e8425e0 thread_start + 8
Thread 10:: ThreadPoolForegroundWorker
0 libsystem_kernel.dylib 0x000000018e80cdd4 mach_msg_trap + 8
1 libsystem_kernel.dylib 0x000000018e80d184 mach_msg + 76
2 QtWebEngineCore 0x00000001635ed5e4 0x160000000 + 56546788
3 QtWebEngineCore 0x00000001635b566c 0x160000000 + 56317548
4 QtWebEngineCore 0x00000001635b60f4 0x160000000 + 56320244
5 QtWebEngineCore 0x00000001635b5d20 0x160000000 + 56319264
6 QtWebEngineCore 0x00000001635e6be4 0x160000000 + 56519652
7 libsystem_pthread.dylib 0x000000018e847878 _pthread_start + 320
8 libsystem_pthread.dylib 0x000000018e8425e0 thread_start + 8
Thread 11:: ThreadPoolForegroundWorker
0 libsystem_kernel.dylib 0x000000018e80cdd4 mach_msg_trap + 8
1 libsystem_kernel.dylib 0x000000018e80d184 mach_msg + 76
2 QtWebEngineCore 0x00000001635ed5e4 0x160000000 + 56546788
3 QtWebEngineCore 0x00000001635b566c 0x160000000 + 56317548
4 QtWebEngineCore 0x00000001635b60f4 0x160000000 + 56320244
5 QtWebEngineCore 0x00000001635b5d20 0x160000000 + 56319264
6 QtWebEngineCore 0x00000001635e6be4 0x160000000 + 56519652
7 libsystem_pthread.dylib 0x000000018e847878 _pthread_start + 320
8 libsystem_pthread.dylib 0x000000018e8425e0 thread_start + 8
Thread 12:: CompositorTileWorker1
0 libsystem_kernel.dylib 0x000000018e810548 __psynch_cvwait + 8
1 libsystem_pthread.dylib 0x000000018e847dac _pthread_cond_wait + 1248
2 QtWebEngineCore 0x00000001635e6048 0x160000000 + 56516680
3 QtWebEngineCore 0x000000016519afe4 0x160000000 + 85569508
4 QtWebEngineCore 0x00000001635e6be4 0x160000000 + 56519652
5 libsystem_pthread.dylib 0x000000018e847878 _pthread_start + 320
6 libsystem_pthread.dylib 0x000000018e8425e0 thread_start + 8
Thread 13:: Chrome_InProcGpuThread
0 libsystem_kernel.dylib 0x000000018e80cdd4 mach_msg_trap + 8
1 libsystem_kernel.dylib 0x000000018e80d184 mach_msg + 76
2 QtWebEngineCore 0x00000001635ed5e4 0x160000000 + 56546788
3 QtWebEngineCore 0x000000016353753c 0x160000000 + 55801148
4 QtWebEngineCore 0x00000001635a0f6c 0x160000000 + 56233836
5 QtWebEngineCore 0x00000001635644bc 0x160000000 + 55985340
6 QtWebEngineCore 0x00000001635c0d88 0x160000000 + 56364424
7 QtWebEngineCore 0x00000001635c0f10 0x160000000 + 56364816
8 QtWebEngineCore 0x00000001635e6be4 0x160000000 + 56519652
9 libsystem_pthread.dylib 0x000000018e847878 _pthread_start + 320
10 libsystem_pthread.dylib 0x000000018e8425e0 thread_start + 8
Thread 14:: Chrome_ChildIOThread
0 libsystem_kernel.dylib 0x000000018e817ee8 kevent64 + 8
1 QtWebEngineCore 0x00000001636197c8 0x160000000 + 56727496
2 QtWebEngineCore 0x00000001636196f8 0x160000000 + 56727288
3 QtWebEngineCore 0x00000001635a0f6c 0x160000000 + 56233836
4 QtWebEngineCore 0x00000001635644bc 0x160000000 + 55985340
5 QtWebEngineCore 0x00000001635c0d88 0x160000000 + 56364424
6 QtWebEngineCore 0x00000001635c0f10 0x160000000 + 56364816
7 QtWebEngineCore 0x00000001635e6be4 0x160000000 + 56519652
8 libsystem_pthread.dylib 0x000000018e847878 _pthread_start + 320
9 libsystem_pthread.dylib 0x000000018e8425e0 thread_start + 8
Thread 15:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x000000018e80cdd4 mach_msg_trap + 8
1 libsystem_kernel.dylib 0x000000018e80d184 mach_msg + 76
2 QtWebEngineCore 0x00000001635ed5e4 0x160000000 + 56546788
3 QtWebEngineCore 0x00000001635ed3b0 0x160000000 + 56546224
4 QtWebEngineCore 0x00000001635375a0 0x160000000 + 55801248
5 QtWebEngineCore 0x00000001635a0f6c 0x160000000 + 56233836
6 QtWebEngineCore 0x00000001635644bc 0x160000000 + 55985340
7 QtWebEngineCore 0x00000001635c0d88 0x160000000 + 56364424
8 QtWebEngineCore 0x00000001635c0f10 0x160000000 + 56364816
9 QtWebEngineCore 0x00000001635e6be4 0x160000000 + 56519652
10 libsystem_pthread.dylib 0x000000018e847878 _pthread_start + 320
11 libsystem_pthread.dylib 0x000000018e8425e0 thread_start + 8
Thread 16:: VizCompositorThread
0 libsystem_kernel.dylib 0x000000018e80cdd4 mach_msg_trap + 8
1 libsystem_kernel.dylib 0x000000018e80d184 mach_msg + 76
2 QtWebEngineCore 0x00000001635ed5e4 0x160000000 + 56546788
3 QtWebEngineCore 0x000000016353753c 0x160000000 + 55801148
4 QtWebEngineCore 0x00000001635a0f6c 0x160000000 + 56233836
5 QtWebEngineCore 0x00000001635644bc 0x160000000 + 55985340
6 QtWebEngineCore 0x00000001635c0d88 0x160000000 + 56364424
7 QtWebEngineCore 0x00000001635c0f10 0x160000000 + 56364816
8 QtWebEngineCore 0x00000001635e6be4 0x160000000 + 56519652
9 libsystem_pthread.dylib 0x000000018e847878 _pthread_start + 320
10 libsystem_pthread.dylib 0x000000018e8425e0 thread_start + 8
Thread 17:: NetworkService
0 libsystem_kernel.dylib 0x000000018e817ee8 kevent64 + 8
1 QtWebEngineCore 0x00000001636197c8 0x160000000 + 56727496
2 QtWebEngineCore 0x00000001636196f8 0x160000000 + 56727288
3 QtWebEngineCore 0x00000001635a0f6c 0x160000000 + 56233836
4 QtWebEngineCore 0x00000001635644bc 0x160000000 + 55985340
5 QtWebEngineCore 0x00000001635c0d88 0x160000000 + 56364424
6 QtWebEngineCore 0x00000001635c0f10 0x160000000 + 56364816
7 QtWebEngineCore 0x00000001635e6be4 0x160000000 + 56519652
8 libsystem_pthread.dylib 0x000000018e847878 _pthread_start + 320
9 libsystem_pthread.dylib 0x000000018e8425e0 thread_start + 8
Thread 18:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x000000018e80cdd4 mach_msg_trap + 8
1 libsystem_kernel.dylib 0x000000018e80d184 mach_msg + 76
2 QtWebEngineCore 0x00000001635ed5e4 0x160000000 + 56546788
3 QtWebEngineCore 0x00000001635ed3b0 0x160000000 + 56546224
4 QtWebEngineCore 0x00000001635375a0 0x160000000 + 55801248
5 QtWebEngineCore 0x00000001635a0f6c 0x160000000 + 56233836
6 QtWebEngineCore 0x00000001635644bc 0x160000000 + 55985340
7 QtWebEngineCore 0x00000001635c0d88 0x160000000 + 56364424
8 QtWebEngineCore 0x00000001635c0f10 0x160000000 + 56364816
9 QtWebEngineCore 0x00000001635e6be4 0x160000000 + 56519652
10 libsystem_pthread.dylib 0x000000018e847878 _pthread_start + 320
11 libsystem_pthread.dylib 0x000000018e8425e0 thread_start + 8
Thread 19:: ThreadPoolSingleThreadForegroundBlocking0
0 libsystem_kernel.dylib 0x000000018e80cdd4 mach_msg_trap + 8
1 libsystem_kernel.dylib 0x000000018e80d184 mach_msg + 76
2 QtWebEngineCore 0x00000001635ed5e4 0x160000000 + 56546788
3 QtWebEngineCore 0x00000001635b566c 0x160000000 + 56317548
4 QtWebEngineCore 0x00000001635b60f4 0x160000000 + 56320244
5 QtWebEngineCore 0x00000001635b5d78 0x160000000 + 56319352
6 QtWebEngineCore 0x00000001635e6be4 0x160000000 + 56519652
7 libsystem_pthread.dylib 0x000000018e847878 _pthread_start + 320
8 libsystem_pthread.dylib 0x000000018e8425e0 thread_start + 8
Thread 20:: Thread (pooled)
0 libsystem_kernel.dylib 0x000000018e810548 __psynch_cvwait + 8
1 libsystem_pthread.dylib 0x000000018e847dac _pthread_cond_wait + 1248
2 QtCore 0x000000011f8cf6fc 0x11f700000 + 1898236
3 QtCore 0x000000011f8cf3b4 0x11f700000 + 1897396
4 QtCore 0x000000011f8cf2f4 QWaitCondition::wait(QMutex*, QDeadlineTimer) + 108
5 QtCore 0x000000011f8c9bfc 0x11f700000 + 1874940
6 QtCore 0x000000011f8c5b8c 0x11f700000 + 1858444
7 libsystem_pthread.dylib 0x000000018e847878 _pthread_start + 320
8 libsystem_pthread.dylib 0x000000018e8425e0 thread_start + 8
Thread 21:: Thread (pooled)
0 libsystem_kernel.dylib 0x000000018e810548 __psynch_cvwait + 8
1 libsystem_pthread.dylib 0x000000018e847dac _pthread_cond_wait + 1248
2 QtCore 0x000000011f8cf6fc 0x11f700000 + 1898236
3 QtCore 0x000000011f8cf3b4 0x11f700000 + 1897396
4 QtCore 0x000000011f8cf2f4 QWaitCondition::wait(QMutex*, QDeadlineTimer) + 108
5 QtCore 0x000000011f8c9bfc 0x11f700000 + 1874940
6 QtCore 0x000000011f8c5b8c 0x11f700000 + 1858444
7 libsystem_pthread.dylib 0x000000018e847878 _pthread_start + 320
8 libsystem_pthread.dylib 0x000000018e8425e0 thread_start + 8
Thread 22:: Thread (pooled)
0 libsystem_kernel.dylib 0x000000018e810548 __psynch_cvwait + 8
1 libsystem_pthread.dylib 0x000000018e847dac _pthread_cond_wait + 1248
2 QtCore 0x000000011f8cf6fc 0x11f700000 + 1898236
3 QtCore 0x000000011f8cf3b4 0x11f700000 + 1897396
4 QtCore 0x000000011f8cf2f4 QWaitCondition::wait(QMutex*, QDeadlineTimer) + 108
5 QtCore 0x000000011f8c9bfc 0x11f700000 + 1874940
6 QtCore 0x000000011f8c5b8c 0x11f700000 + 1858444
7 libsystem_pthread.dylib 0x000000018e847878 _pthread_start + 320
8 libsystem_pthread.dylib 0x000000018e8425e0 thread_start + 8
Thread 23:: Thread (pooled)
0 libsystem_kernel.dylib 0x000000018e810548 __psynch_cvwait + 8
1 libsystem_pthread.dylib 0x000000018e847dac _pthread_cond_wait + 1248
2 QtCore 0x000000011f8cf6fc 0x11f700000 + 1898236
3 QtCore 0x000000011f8cf3b4 0x11f700000 + 1897396
4 QtCore 0x000000011f8cf2f4 QWaitCondition::wait(QMutex*, QDeadlineTimer) + 108
5 QtCore 0x000000011f8c9bfc 0x11f700000 + 1874940
6 QtCore 0x000000011f8c5b8c 0x11f700000 + 1858444
7 libsystem_pthread.dylib 0x000000018e847878 _pthread_start + 320
8 libsystem_pthread.dylib 0x000000018e8425e0 thread_start + 8
Thread 24:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x000000018e80cdd4 mach_msg_trap + 8
1 libsystem_kernel.dylib 0x000000018e80d184 mach_msg + 76
2 QtWebEngineCore 0x00000001635ed5e4 0x160000000 + 56546788
3 QtWebEngineCore 0x00000001635ed3b0 0x160000000 + 56546224
4 QtWebEngineCore 0x00000001635375a0 0x160000000 + 55801248
5 QtWebEngineCore 0x00000001635a0f6c 0x160000000 + 56233836
6 QtWebEngineCore 0x00000001635644bc 0x160000000 + 55985340
7 QtWebEngineCore 0x00000001635c0d88 0x160000000 + 56364424
8 QtWebEngineCore 0x00000001635c0f10 0x160000000 + 56364816
9 QtWebEngineCore 0x00000001635e6be4 0x160000000 + 56519652
10 libsystem_pthread.dylib 0x000000018e847878 _pthread_start + 320
11 libsystem_pthread.dylib 0x000000018e8425e0 thread_start + 8
Thread 25:
0 libsystem_pthread.dylib 0x000000018e8425cc start_wqthread + 0
Thread 26:
0 libsystem_pthread.dylib 0x000000018e8425cc start_wqthread + 0
Thread 27:: ThreadPoolBackgroundWorker
0 libsystem_kernel.dylib 0x000000018e80cdd4 mach_msg_trap + 8
1 libsystem_kernel.dylib 0x000000018e80d184 mach_msg + 76
2 QtWebEngineCore 0x00000001635ed5e4 0x160000000 + 56546788
3 QtWebEngineCore 0x00000001635b566c 0x160000000 + 56317548
4 QtWebEngineCore 0x00000001635b5e84 0x160000000 + 56319620
5 QtWebEngineCore 0x00000001635b5c9c 0x160000000 + 56319132
6 QtWebEngineCore 0x00000001635e6be4 0x160000000 + 56519652
7 libsystem_pthread.dylib 0x000000018e847878 _pthread_start + 320
8 libsystem_pthread.dylib 0x000000018e8425e0 thread_start + 8
Thread 28:: ThreadPoolForegroundWorker
0 libsystem_kernel.dylib 0x000000018e80cdd4 mach_msg_trap + 8
1 libsystem_kernel.dylib 0x000000018e80d184 mach_msg + 76
2 QtWebEngineCore 0x00000001635ed5e4 0x160000000 + 56546788
3 QtWebEngineCore 0x00000001635b566c 0x160000000 + 56317548
4 QtWebEngineCore 0x00000001635b5e84 0x160000000 + 56319620
5 QtWebEngineCore 0x00000001635b5d20 0x160000000 + 56319264
6 QtWebEngineCore 0x00000001635e6be4 0x160000000 + 56519652
7 libsystem_pthread.dylib 0x000000018e847878 _pthread_start + 320
8 libsystem_pthread.dylib 0x000000018e8425e0 thread_start + 8
Thread 29:: com.apple.NSEventThread
0 libsystem_kernel.dylib 0x000000018e80cdd4 mach_msg_trap + 8
1 libsystem_kernel.dylib 0x000000018e80d184 mach_msg + 76
2 com.apple.CoreFoundation 0x000000018e946d00 __CFRunLoopServiceMachPort + 372
3 com.apple.CoreFoundation 0x000000018e9451cc __CFRunLoopRun + 1212
4 com.apple.CoreFoundation 0x000000018e944598 CFRunLoopRunSpecific + 600
5 com.apple.AppKit 0x00000001912b4738 _NSEventThread + 196
6 libsystem_pthread.dylib 0x000000018e847878 _pthread_start + 320
7 libsystem_pthread.dylib 0x000000018e8425e0 thread_start + 8
Thread 30:: MemoryInfra
0 libsystem_kernel.dylib 0x000000018e80cdd4 mach_msg_trap + 8
1 libsystem_kernel.dylib 0x000000018e80d184 mach_msg + 76
2 QtWebEngineCore 0x00000001635ed5e4 0x160000000 + 56546788
3 QtWebEngineCore 0x00000001635ed3b0 0x160000000 + 56546224
4 QtWebEngineCore 0x00000001635375a0 0x160000000 + 55801248
5 QtWebEngineCore 0x00000001635a0f6c 0x160000000 + 56233836
6 QtWebEngineCore 0x00000001635644bc 0x160000000 + 55985340
7 QtWebEngineCore 0x00000001635c0d88 0x160000000 + 56364424
8 QtWebEngineCore 0x00000001635c0f10 0x160000000 + 56364816
9 QtWebEngineCore 0x00000001635e6be4 0x160000000 + 56519652
10 libsystem_pthread.dylib 0x000000018e847878 _pthread_start + 320
11 libsystem_pthread.dylib 0x000000018e8425e0 thread_start + 8
Thread 31:: ThreadPoolSingleThreadSharedBackgroundBlocking1
0 libsystem_kernel.dylib 0x000000018e80cdd4 mach_msg_trap + 8
1 libsystem_kernel.dylib 0x000000018e80d184 mach_msg + 76
2 QtWebEngineCore 0x00000001635ed5e4 0x160000000 + 56546788
3 QtWebEngineCore 0x00000001635b566c 0x160000000 + 56317548
4 QtWebEngineCore 0x00000001635b5e84 0x160000000 + 56319620
5 QtWebEngineCore 0x00000001635b5cc8 0x160000000 + 56319176
6 QtWebEngineCore 0x00000001635e6be4 0x160000000 + 56519652
7 libsystem_pthread.dylib 0x000000018e847878 _pthread_start + 320
8 libsystem_pthread.dylib 0x000000018e8425e0 thread_start + 8
Thread 32:
0 libsystem_kernel.dylib 0x000000018e810548 __psynch_cvwait + 8
1 libsystem_pthread.dylib 0x000000018e847dac _pthread_cond_wait + 1248
2 libopenblas64_.0.dylib 0x0000000106169b60 blas_thread_server + 360
3 libsystem_pthread.dylib 0x000000018e847878 _pthread_start + 320
4 libsystem_pthread.dylib 0x000000018e8425e0 thread_start + 8
Thread 33:
0 libsystem_kernel.dylib 0x000000018e810548 __psynch_cvwait + 8
1 libsystem_pthread.dylib 0x000000018e847dac _pthread_cond_wait + 1248
2 libopenblas64_.0.dylib 0x0000000106169b60 blas_thread_server + 360
3 libsystem_pthread.dylib 0x000000018e847878 _pthread_start + 320
4 libsystem_pthread.dylib 0x000000018e8425e0 thread_start + 8
Thread 34:
0 libsystem_kernel.dylib 0x000000018e810548 __psynch_cvwait + 8
1 libsystem_pthread.dylib 0x000000018e847dac _pthread_cond_wait + 1248
2 libopenblas64_.0.dylib 0x0000000106169b60 blas_thread_server + 360
3 libsystem_pthread.dylib 0x000000018e847878 _pthread_start + 320
4 libsystem_pthread.dylib 0x000000018e8425e0 thread_start + 8
Thread 35:
0 libsystem_kernel.dylib 0x000000018e810548 __psynch_cvwait + 8
1 libsystem_pthread.dylib 0x000000018e847dac _pthread_cond_wait + 1248
2 libopenblas64_.0.dylib 0x0000000106169b60 blas_thread_server + 360
3 libsystem_pthread.dylib 0x000000018e847878 _pthread_start + 320
4 libsystem_pthread.dylib 0x000000018e8425e0 thread_start + 8
Thread 36:
0 libsystem_kernel.dylib 0x000000018e810548 __psynch_cvwait + 8
1 libsystem_pthread.dylib 0x000000018e847dac _pthread_cond_wait + 1248
2 libopenblas64_.0.dylib 0x0000000106169b60 blas_thread_server + 360
3 libsystem_pthread.dylib 0x000000018e847878 _pthread_start + 320
4 libsystem_pthread.dylib 0x000000018e8425e0 thread_start + 8
Thread 37:
0 libsystem_kernel.dylib 0x000000018e810548 __psynch_cvwait + 8
1 libsystem_pthread.dylib 0x000000018e847dac _pthread_cond_wait + 1248
2 libopenblas64_.0.dylib 0x0000000106169b60 blas_thread_server + 360
3 libsystem_pthread.dylib 0x000000018e847878 _pthread_start + 320
4 libsystem_pthread.dylib 0x000000018e8425e0 thread_start + 8
Thread 38:
0 libsystem_kernel.dylib 0x000000018e810548 __psynch_cvwait + 8
1 libsystem_pthread.dylib 0x000000018e847dac _pthread_cond_wait + 1248
2 libopenblas64_.0.dylib 0x0000000106169b60 blas_thread_server + 360
3 libsystem_pthread.dylib 0x000000018e847878 _pthread_start + 320
4 libsystem_pthread.dylib 0x000000018e8425e0 thread_start + 8
Thread 39:: Thread (pooled)
0 libsystem_kernel.dylib 0x000000018e810548 __psynch_cvwait + 8
1 libsystem_pthread.dylib 0x000000018e847dac _pthread_cond_wait + 1248
2 QtCore 0x000000011f8cf6fc 0x11f700000 + 1898236
3 QtCore 0x000000011f8cf3b4 0x11f700000 + 1897396
4 QtCore 0x000000011f8cf2f4 QWaitCondition::wait(QMutex*, QDeadlineTimer) + 108
5 QtCore 0x000000011f8c9bfc 0x11f700000 + 1874940
6 QtCore 0x000000011f8c5b8c 0x11f700000 + 1858444
7 libsystem_pthread.dylib 0x000000018e847878 _pthread_start + 320
8 libsystem_pthread.dylib 0x000000018e8425e0 thread_start + 8
Thread 40:: Thread (pooled)
0 libsystem_kernel.dylib 0x000000018e810548 __psynch_cvwait + 8
1 libsystem_pthread.dylib 0x000000018e847dac _pthread_cond_wait + 1248
2 QtCore 0x000000011f8cf6fc 0x11f700000 + 1898236
3 QtCore 0x000000011f8cf3b4 0x11f700000 + 1897396
4 QtCore 0x000000011f8cf2f4 QWaitCondition::wait(QMutex*, QDeadlineTimer) + 108
5 QtCore 0x000000011f8c9bfc 0x11f700000 + 1874940
6 QtCore 0x000000011f8c5b8c 0x11f700000 + 1858444
7 libsystem_pthread.dylib 0x000000018e847878 _pthread_start + 320
8 libsystem_pthread.dylib 0x000000018e8425e0 thread_start + 8
Thread 41:: Dispatch queue: com.apple.root.user-interactive-qos
0 libsystem_kernel.dylib 0x000000018e80ce28 semaphore_timedwait_trap + 8
1 libdispatch.dylib 0x000000018e6984a4 _dispatch_sema4_timedwait + 64
2 libdispatch.dylib 0x000000018e698ab4 _dispatch_semaphore_wait_slow + 76
3 com.apple.AppKit 0x0000000191a276e0 __22-[NSCGSLocalFence set]_block_invoke_2 + 164
4 com.apple.QuartzCore 0x0000000194be4578 CA::Transaction::run_commit_handlers(CATransactionPhase) + 120
5 com.apple.QuartzCore 0x0000000194d2d86c CA::Context::commit_transaction(CA::Transaction*, double, double*) + 740
6 com.apple.QuartzCore 0x0000000194be36dc CA::Transaction::commit() + 684
7 com.apple.AppKit 0x000000019118910c NSPerformVisuallyAtomicChange + 160
8 com.apple.AppKit 0x00000001913ae5cc __42-[NSAnimation(NSInternal) _runInNewThread]_block_invoke + 116
9 libdispatch.dylib 0x000000018e696128 _dispatch_call_block_and_release + 32
10 libdispatch.dylib 0x000000018e697ec0 _dispatch_client_callout + 20
11 libdispatch.dylib 0x000000018e6a97b0 _dispatch_root_queue_drain + 688
12 libdispatch.dylib 0x000000018e6a9e90 _dispatch_worker_thread2 + 112
13 libsystem_pthread.dylib 0x000000018e843860 _pthread_wqthread + 216
14 libsystem_pthread.dylib 0x000000018e8425d4 start_wqthread + 8
Thread 42:
0 libsystem_pthread.dylib 0x000000018e8425cc start_wqthread + 0
Thread 43:
0 libsystem_pthread.dylib 0x000000018e8425cc start_wqthread + 0
Thread 0 crashed with ARM Thread State (64-bit):
x0: 0x0000000000000000 x1: 0x0000000000000000 x2: 0x0000000000000001 x3: 0x000000018e88fead
x4: 0x0000000128047c18 x5: 0x68430aff5cbb020d x6: 0x000000016dc5ec10 x7: 0x000000010fe047b0
x8: 0x11e015912671960a x9: 0x11e015902413eb4a x10: 0x0000000000001bba x11: 0x0000000205797b5e
x12: 0x0000000205797b5e x13: 0x0000000000000004 x14: 0x0000000000000881 x15: 0x000000008000001f
x16: 0x0000000000000148 x17: 0x00000001fd2c6e90 x18: 0x0000000138953940 x19: 0x000000000000000b
x20: 0x0000000102627d40 x21: 0x0000000000000103 x22: 0x0000000102627e20 x23: 0x000000016dc5ed50
x24: 0x0000000000000002 x25: 0x0000000000000008 x26: 0x0000000000000008 x27: 0x0000000000000002
x28: 0x000000016dc5ed08 fp: 0x0000000128047b50 lr: 0x000000018e84743c
sp: 0x0000000128047b30 pc: 0x000000018e814e68 cpsr: 0x40000000
far: 0x0000000128047bb0 esr: 0x56000080
Binary Images:
0x102198000 - 0x10219bfff +edu.ucsf.cgl.ChimeraX (1.5.0 - 1.5.0.0) /Applications/ChimeraX-1.5.app/Contents/MacOS/ChimeraX
0x1021b4000 - 0x102423fff +org.python.python (3.9.11, [c] 2001-2021 Python Software Foundation. - 3.9.11) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/Python
0x10256c000 - 0x1025ebfff dyld (852.2) /usr/lib/dyld
0x1028c0000 - 0x1028c3fff +_heapq.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/_heapq.cpython-39-darwin.so
0x1028d4000 - 0x1028dbfff +binascii.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/binascii.cpython-39-darwin.so
0x1028ec000 - 0x1028effff +_bz2.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/_bz2.cpython-39-darwin.so
0x102f00000 - 0x102f07fff +zlib.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/zlib.cpython-39-darwin.so
0x102f18000 - 0x102f47fff +_lzma.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/_lzma.cpython-39-darwin.so
0x102f5c000 - 0x102f5ffff +grp.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/grp.cpython-39-darwin.so
0x102fb0000 - 0x102fb7fff +_struct.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/lib-dynload/_struct.cpython-39-darwin.so
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0x1a3ce0000 - 0x1a3d00fff com.apple.MarkupUI (1.0 - 383.6) /System/Library/PrivateFrameworks/MarkupUI.framework/Versions/A/MarkupUI
0x1a3d01000 - 0x1a3d16fff com.apple.Engram (1.0 - 1) /System/Library/PrivateFrameworks/Engram.framework/Versions/A/Engram
0x1a3d17000 - 0x1a3d3efff com.apple.openscripting (1.7 - 190) /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/OpenScripting.framework/Versions/A/OpenScripting
0x1a3d3f000 - 0x1a3d42fff com.apple.securityhi (9.0 - 55008) /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/SecurityHI.framework/Versions/A/SecurityHI
0x1a3d43000 - 0x1a3d46fff com.apple.ink.framework (10.15 - 227) /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/Ink.framework/Versions/A/Ink
0x1a3d47000 - 0x1a3d4afff com.apple.CommonPanels (1.2.6 - 101) /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/CommonPanels.framework/Versions/A/CommonPanels
0x1a3d4b000 - 0x1a3d52fff com.apple.ImageCapture (1711.5.2 - 1711.5.2) /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/ImageCapture.framework/Versions/A/ImageCapture
0x1a3d53000 - 0x1a4e27fff com.apple.JavaScriptCore (16611 - 16611.3.10.1.3) /System/Library/Frameworks/JavaScriptCore.framework/Versions/A/JavaScriptCore
0x1a4e95000 - 0x1a4fa9fff com.apple.AVFCapture (1.0 - 82.6) /System/Library/PrivateFrameworks/AVFCapture.framework/Versions/A/AVFCapture
0x1a4faa000 - 0x1a503bfff com.apple.Quagga (47 - 47) /System/Library/PrivateFrameworks/Quagga.framework/Versions/A/Quagga
0x1a503c000 - 0x1a5273fff com.apple.CMCapture (1.0 - 82.6) /System/Library/PrivateFrameworks/CMCapture.framework/Versions/A/CMCapture
0x1a5604000 - 0x1a56affff com.apple.accounts.AccountsDaemon (113 - 113) /System/Library/PrivateFrameworks/AccountsDaemon.framework/Versions/A/AccountsDaemon
0x1a56b0000 - 0x1a56b2fff com.apple.OAuth (25 - 25) /System/Library/PrivateFrameworks/OAuth.framework/Versions/A/OAuth
0x1a5c8d000 - 0x1a5c99fff com.apple.HID (1.0 - 1) /System/Library/PrivateFrameworks/HID.framework/Versions/A/HID
0x1a5c9a000 - 0x1a5d99fff com.apple.QuickLookUIFramework (5.0 - 928.4) /System/Library/Frameworks/Quartz.framework/Versions/A/Frameworks/QuickLookUI.framework/Versions/A/QuickLookUI
0x1a5d9a000 - 0x1a5db8fff com.apple.IOGPU (21.11 - 21.11) /System/Library/PrivateFrameworks/IOGPU.framework/Versions/A/IOGPU
0x1a616a000 - 0x1a61e9fff com.apple.coredav (1.0.1 - 889) /System/Library/PrivateFrameworks/CoreDAV.framework/Versions/A/CoreDAV
0x1a61ea000 - 0x1a6241fff com.apple.ExchangeWebServices (8.0 - 814.100.1) /System/Library/PrivateFrameworks/ExchangeWebServices.framework/Versions/A/ExchangeWebServices
0x1a6242000 - 0x1a6284fff com.apple.MediaServices (1.0 - 1) /System/Library/PrivateFrameworks/MediaServices.framework/Versions/A/MediaServices
0x1a6392000 - 0x1a6392fff com.apple.marco (10.0 - 1000) /System/Library/PrivateFrameworks/Marco.framework/Versions/A/Marco
0x1a6584000 - 0x1a65c1fff com.apple.contacts.ContactsAutocomplete (1.0 - 1152.4) /System/Library/PrivateFrameworks/ContactsAutocomplete.framework/Versions/A/ContactsAutocomplete
0x1a65c2000 - 0x1a65cefff com.apple.KerberosHelper (4.0 - 1.0) /System/Library/PrivateFrameworks/KerberosHelper.framework/Versions/A/KerberosHelper
0x1a65cf000 - 0x1a6612fff com.apple.ResponseKit (1.0 - 165.2) /System/Library/PrivateFrameworks/ResponseKit.framework/Versions/A/ResponseKit
0x1a6613000 - 0x1a6634fff com.apple.proactive.support.ProactiveEventTracker (1.0 - 294.7) /System/Library/PrivateFrameworks/ProactiveEventTracker.framework/Versions/A/ProactiveEventTracker
0x1a6a58000 - 0x1a6a5cfff com.apple.PhoneNumbers (1.0 - 1) /System/Library/PrivateFrameworks/PhoneNumbers.framework/Versions/A/PhoneNumbers
0x1a6a5d000 - 0x1a6a64fff com.apple.URLFormatting (146 - 146.22) /System/Library/PrivateFrameworks/URLFormatting.framework/Versions/A/URLFormatting
0x1a6a65000 - 0x1a6a76fff com.apple.accessibility.AXCoreUtilities (1.0 - 1) /System/Library/PrivateFrameworks/AXCoreUtilities.framework/Versions/A/AXCoreUtilities
0x1a6a77000 - 0x1a6a91fff libAccessibility.dylib (2885.49) /usr/lib/libAccessibility.dylib
0x1a932b000 - 0x1a934bfff com.apple.quicklook.QuickLookSupport (1.0 - 135.5) /System/Library/PrivateFrameworks/QuickLookSupport.framework/Versions/A/QuickLookSupport
0x1a934c000 - 0x1a93dffff com.apple.AirPlaySync (1.0 - 2780.10) /System/Library/PrivateFrameworks/AirPlaySync.framework/Versions/A/AirPlaySync
0x1a9f9b000 - 0x1aa01afff com.apple.CorePDF (4.0 - 529) /System/Library/PrivateFrameworks/CorePDF.framework/Versions/A/CorePDF
0x1aa01b000 - 0x1aa01efff com.apple.print.framework.Print (15 - 271) /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/Print.framework/Versions/A/Print
0x1aa01f000 - 0x1aa022fff com.apple.Carbon (160 - 164) /System/Library/Frameworks/Carbon.framework/Versions/A/Carbon
0x1aa123000 - 0x1aa123fff com.apple.avfoundation (2.0 - 2020.10) /System/Library/Frameworks/AVFoundation.framework/Versions/A/AVFoundation
0x1aa2e9000 - 0x1aa305fff com.apple.private.SystemPolicy (1.0 - 1) /System/Library/PrivateFrameworks/SystemPolicy.framework/Versions/A/SystemPolicy
0x1aa44c000 - 0x1aa4a4fff com.apple.AccessibilitySharedSupport (1.0 - 1) /System/Library/PrivateFrameworks/AccessibilitySharedSupport.framework/Versions/A/AccessibilitySharedSupport
0x1aa4a5000 - 0x1aa4c4fff com.apple.sidecar-core (1.0 - 231) /System/Library/PrivateFrameworks/SidecarCore.framework/Versions/A/SidecarCore
0x1aa4c5000 - 0x1aa4ccfff com.apple.QuickLookNonBaseSystem (1.0 - 1) /System/Library/PrivateFrameworks/QuickLookNonBaseSystem.framework/Versions/A/QuickLookNonBaseSystem
0x1aa903000 - 0x1aa908fff com.apple.FeatureFlagsSupport (1.0 - 28.60.1) /System/Library/PrivateFrameworks/FeatureFlagsSupport.framework/Versions/A/FeatureFlagsSupport
0x1aaa7c000 - 0x1aaa97fff com.apple.SafariServices.framework (16611 - 16611.3.10.1.3) /System/Library/Frameworks/SafariServices.framework/Versions/A/SafariServices
0x1aac56000 - 0x1aac61fff com.apple.MallocStackLogging (1.0 - 1) /System/Library/PrivateFrameworks/MallocStackLogging.framework/Versions/A/MallocStackLogging
0x1aac76000 - 0x1aac88fff libmis.dylib (274.140.2) /usr/lib/libmis.dylib
0x1aaca6000 - 0x1aaddafff com.apple.CoreHandwriting (161 - 1.2) /System/Library/PrivateFrameworks/CoreHandwriting.framework/Versions/A/CoreHandwriting
0x1aaddb000 - 0x1aafe1fff com.apple.imageKit (3.0 - 1100) /System/Library/Frameworks/Quartz.framework/Versions/A/Frameworks/ImageKit.framework/Versions/A/ImageKit
0x1aafe2000 - 0x1ab0ecfff com.apple.PencilKit (1.0 - 1) /System/Library/Frameworks/PencilKit.framework/Versions/A/PencilKit
0x1ab0ed000 - 0x1ab0fefff com.apple.sidecar-ui (1.0 - 231) /System/Library/PrivateFrameworks/SidecarUI.framework/Versions/A/SidecarUI
0x1ab752000 - 0x1ab7abfff com.apple.ImageCaptureCore (1711.5.2 - 1711.5.2) /System/Library/Frameworks/ImageCaptureCore.framework/Versions/A/ImageCaptureCore
0x1ab7ac000 - 0x1ab7d1fff com.apple.quartzfilters (1.10.0 - 98) /System/Library/Frameworks/Quartz.framework/Versions/A/Frameworks/QuartzFilters.framework/Versions/A/QuartzFilters
0x1aba1f000 - 0x1abb91fff com.apple.MediaPlayer (1.0 - 1.0) /System/Library/Frameworks/MediaPlayer.framework/Versions/A/MediaPlayer
0x1abb92000 - 0x1abe56fff com.apple.iTunesCloud (1.0 - 1) /System/Library/PrivateFrameworks/iTunesCloud.framework/Versions/A/iTunesCloud
0x1abeaa000 - 0x1abfc6fff com.apple.AnnotationKit (1.0 - 383.6) /System/Library/PrivateFrameworks/AnnotationKit.framework/Versions/A/AnnotationKit
0x1abfc7000 - 0x1ac47ffff com.apple.QuartzComposer (5.1 - 383) /System/Library/Frameworks/Quartz.framework/Versions/A/Frameworks/QuartzComposer.framework/Versions/A/QuartzComposer
0x1ac480000 - 0x1ac560fff com.apple.PDFKit (1.0 - 950.40.3) /System/Library/Frameworks/PDFKit.framework/Versions/A/PDFKit
0x1ad2bd000 - 0x1ad33ffff com.apple.TextInput (1.0 - 1.0) /System/Library/PrivateFrameworks/TextInput.framework/Versions/A/TextInput
0x1ae36a000 - 0x1ae36dfff com.apple.quartzframework (1.5 - 25) /System/Library/Frameworks/Quartz.framework/Versions/A/Quartz
0x1ae669000 - 0x1ae682fff libCGInterfaces.dylib (544.4) /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vImage.framework/Versions/A/Libraries/libCGInterfaces.dylib
0x1afd3b000 - 0x1b0926fff libfaceCore.dylib (4.3.1) /System/Library/Frameworks/Vision.framework/libfaceCore.dylib
0x1b0927000 - 0x1b0a22fff com.apple.TextRecognition (1.0 - 157) /System/Library/PrivateFrameworks/TextRecognition.framework/Versions/A/TextRecognition
0x1b0a23000 - 0x1b0a3afff com.apple.Futhark (1.0 - 1) /System/Library/PrivateFrameworks/Futhark.framework/Versions/A/Futhark
0x1b0abf000 - 0x1b0cdefff com.apple.RawCamera.bundle (9.10.0 - 1450.3) /System/Library/CoreServices/RawCamera.bundle/Contents/MacOS/RawCamera
0x1b1587000 - 0x1b158bfff com.apple.DAAPKit (1.0 - 1) /System/Library/PrivateFrameworks/DAAPKit.framework/Versions/A/DAAPKit
0x1b2eab000 - 0x1b2eaefff libpmenergy.dylib (227.140.1) /usr/lib/libpmenergy.dylib
0x1b4b3b000 - 0x1b4b76fff com.apple.osanalytics.OSAnalytics (1.0 - 1) /System/Library/PrivateFrameworks/OSAnalytics.framework/Versions/A/OSAnalytics
0x1b53c0000 - 0x1b53dbfff com.apple.network.statistics.framework (1.2 - 1) /System/Library/PrivateFrameworks/NetworkStatistics.framework/Versions/A/NetworkStatistics
0x1be406000 - 0x1be433fff com.apple.HelpData (2.3 - 201) /System/Library/PrivateFrameworks/HelpData.framework/Versions/A/HelpData
0x1be434000 - 0x1be44efff com.apple.shortcut (2.16 - 118) /System/Library/PrivateFrameworks/Shortcut.framework/Versions/A/Shortcut
0x1be44f000 - 0x1be4edfff com.apple.Symbolication (12.5 - 64544.70.1) /System/Library/PrivateFrameworks/Symbolication.framework/Versions/A/Symbolication
0x1be6eb000 - 0x1be6eefff libpmsample.dylib (227.140.1) /usr/lib/libpmsample.dylib
0x1c0c10000 - 0x1c0c4afff com.apple.ReplayKit (1.0 - 1) /System/Library/Frameworks/ReplayKit.framework/Versions/A/ReplayKit
0x1c2290000 - 0x1c2293fff com.apple.ForceFeedback (1.0.6 - 1.0.6) /System/Library/Frameworks/ForceFeedback.framework/Versions/A/ForceFeedback
0x1c4dbf000 - 0x1c4ddafff libJapaneseConverter.dylib (90) /System/Library/CoreServices/Encodings/libJapaneseConverter.dylib
0x1ca235000 - 0x1ca247fff libTraditionalChineseConverter.dylib (90) /System/Library/CoreServices/Encodings/libTraditionalChineseConverter.dylib
0x1ca248000 - 0x1ca26dfff libKoreanConverter.dylib (90) /System/Library/CoreServices/Encodings/libKoreanConverter.dylib
0x1ca270000 - 0x1ca27ffff libSimplifiedChineseConverter.dylib (90) /System/Library/CoreServices/Encodings/libSimplifiedChineseConverter.dylib
0x1ce6a4000 - 0x1ce6a8fff libmetal_timestamp.dylib (31001.192.1) /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/31001/Libraries/libmetal_timestamp.dylib
0x1d08f6000 - 0x1d08fcfff libCoreFSCache.dylib (200.10) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCoreFSCache.dylib
0x1d08fd000 - 0x1d0902fff libCoreVMClient.dylib (200.10) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCoreVMClient.dylib
0x1d0903000 - 0x1d0912fff com.apple.opengl (18.5.9 - 18.5.9) /System/Library/Frameworks/OpenGL.framework/Versions/A/OpenGL
0x1d0913000 - 0x1d0915fff libCVMSPluginSupport.dylib (18.5.9) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCVMSPluginSupport.dylib
0x1d0916000 - 0x1d091efff libGFXShared.dylib (18.5.9) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGFXShared.dylib
0x1d091f000 - 0x1d0957fff libGLImage.dylib (18.5.9) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLImage.dylib
0x1d0958000 - 0x1d0990fff libGLU.dylib (18.5.9) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLU.dylib
0x1d0991000 - 0x1d0afdfff libGLProgrammability.dylib (18.5.9) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLProgrammability.dylib
0x1d0afe000 - 0x1d0b08fff libGL.dylib (18.5.9) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib
0x1d0b09000 - 0x1d0c73fff GLEngine (18.5.9) /System/Library/Frameworks/OpenGL.framework/Versions/A/Resources/GLEngine.bundle/GLEngine
0x1d0c74000 - 0x1d0c98fff GLRendererFloat (18.5.9) /System/Library/Frameworks/OpenGL.framework/Versions/A/Resources/GLRendererFloat.bundle/GLRendererFloat
0x1d0c99000 - 0x1d0cf8fff com.apple.opencl (4.6 - 4.6) /System/Library/Frameworks/OpenCL.framework/Versions/A/OpenCL
0x1d1777000 - 0x1d177efff com.apple.agl (3.3.4 - AGL-3.3.3) /System/Library/Frameworks/AGL.framework/Versions/A/AGL
0x1d177f000 - 0x1d1865fff com.apple.audio.AVFAudio (1.0 - 477.88) /System/Library/Frameworks/AVFAudio.framework/Versions/A/AVFAudio
0x1d3d43000 - 0x1d3d4efff com.apple.CMImaging (1.0 - 82.6) /System/Library/PrivateFrameworks/CMImaging.framework/Versions/A/CMImaging
0x1d9f4e000 - 0x1d9f59fff com.apple.SymptomAnalytics (1.0 - 1431.140.1) /System/Library/PrivateFrameworks/Symptoms.framework/Frameworks/SymptomAnalytics.framework/Versions/A/SymptomAnalytics
0x1da173000 - 0x1da18cfff com.apple.SymptomPresentationFeed (1.0 - 1431.140.1) /System/Library/PrivateFrameworks/Symptoms.framework/Frameworks/SymptomPresentationFeed.framework/Versions/A/SymptomPresentationFeed
0x1e1d68000 - 0x1e1d6ffff libRosetta.dylib (203.58) /usr/lib/libRosetta.dylib
0x28b624000 - 0x28b627fff +lib_util.dylib (0) /Users/USER/Library/Application Support/ChimeraX/*/lib_util.dylib
0x28e6fc000 - 0x28e717fff com.apple.security.csparser (3.0 - 59754.140.13) /System/Library/Frameworks/Security.framework/PlugIns/csparser.bundle/Contents/MacOS/csparser
0x290404000 - 0x290413fff +numpy_formathandler.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/OpenGL_accelerate/numpy_formathandler.cpython-39-darwin.so
0x2906b8000 - 0x2906bffff +nones_formathandler.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/OpenGL_accelerate/nones_formathandler.cpython-39-darwin.so
0x29b948000 - 0x29b973fff +libccp4.dylib (0) /Users/USER/Library/Application Support/ChimeraX/*/libccp4.dylib
0x29cf7c000 - 0x29cfb7fff +libclipper_cx.dylib (0) /Users/USER/Library/Application Support/ChimeraX/*/libclipper_cx.dylib
0x29d0c4000 - 0x29d0c7fff +_c_internal_utils.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/matplotlib/_c_internal_utils.cpython-39-darwin.so
0x29d734000 - 0x29d7d3fff +libmmdb2.dylib (0) /Users/USER/Library/Application Support/ChimeraX/*/libmmdb2.dylib
0x29db00000 - 0x29db2bfff +mcsplit.cpython-39-darwin.so (0) /Users/USER/Library/Application Support/ChimeraX/*/mcsplit.cpython-39-darwin.so
0x29dcd8000 - 0x29dce7fff +_ribbons.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/atomic/_ribbons.cpython-39-darwin.so
0x29dd28000 - 0x29de7ffff +libclipper.dylib (0) /Users/USER/Library/Application Support/ChimeraX/*/libclipper.dylib
0x29e0f0000 - 0x29e10bfff +_path.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/matplotlib/_path.cpython-39-darwin.so
0x2a2300000 - 0x2a270ffff +clipper_python.cpython-39-darwin.so (0) /Users/USER/Library/Application Support/ChimeraX/*/clipper_python.cpython-39-darwin.so
0x2a2a00000 - 0x2a2a87fff +ft2font.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/matplotlib/ft2font.cpython-39-darwin.so
0x2a2ac0000 - 0x2a2ad7fff +_cext.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/kiwisolver/_cext.cpython-39-darwin.so
0x2a2f40000 - 0x2a2f5bfff +_image.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/matplotlib/_image.cpython-39-darwin.so
0x2a3130000 - 0x2a3157fff +_backend_agg.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/matplotlib/backends/_backend_agg.cpython-39-darwin.so
0x2a3608000 - 0x2a366bfff +mmcif.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/mmcif/mmcif.cpython-39-darwin.so
0x2a369c000 - 0x2a36bffff +_pdbio.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/pdb/_pdbio.cpython-39-darwin.so
0x2a7dc8000 - 0x2a7e1bfff +_mmcif.cpython-39-darwin.so (0) /Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/mmcif/_mmcif.cpython-39-darwin.so
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: 0
thread_create: 0
thread_set_state: 0
VM Region Summary:
ReadOnly portion of Libraries: Total=1.1G resident=0K(0%) swapped_out_or_unallocated=1.1G(100%)
Writable regions: Total=2.3G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=2.3G(100%)
VIRTUAL REGION
REGION TYPE SIZE COUNT (non-coalesced)
=========== ======= =======
Accelerate framework 256K 2
Activity Tracing 256K 1
CG backing stores 3264K 6
CG image 480K 22
CoreAnimation 208K 13
CoreGraphics 32K 2
CoreUI image data 3744K 28
Foundation 16K 1
Kernel Alloc Once 32K 1
MALLOC 620.4M 90
MALLOC guard page 192K 10
MALLOC_MEDIUM (reserved) 872.0M 8 reserved VM address space (unallocated)
MALLOC_NANO (reserved) 256.0M 1 reserved VM address space (unallocated)
Mach message 64K 4
OpenGL GLSL 384K 4
STACK GUARD 688K 43
Stack 188.0M 44
Stack Guard 56.0M 1
VM_ALLOCATE 279.5M 588
VM_ALLOCATE (reserved) 128.0M 2 reserved VM address space (unallocated)
__AUTH 1031K 266
__AUTH_CONST 15.2M 461
__DATA 19.4M 625
__DATA_CONST 25.7M 623
__DATA_DIRTY 1813K 213
__FONT_DATA 4K 1
__GLSLBUILTINS 5176K 1
__LINKEDIT 525.2M 173
__OBJC_CONST 3311K 257
__OBJC_RO 75.1M 1
__OBJC_RW 2576K 1
__TEXT 581.0M 646
__UNICODE 588K 1
mapped file 1.7G 257
shared memory 3248K 25
=========== ======= =======
TOTAL 5.2G 4422
TOTAL, minus reserved VM space 4.0G 4422
===== Log before crash start =====
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> ui tool show ISOLDE
> set selectionWidth 4
Populating font family aliases took 604 ms. Replace uses of missing font
family "Carlito" with one that exists to avoid this cost.
> open
> /Users/seiyahirai/Desktop/Research/Kimura_T/E97K/modeling/Large/E97K_job112_postprocess_masked.mrc
Opened E97K_job112_postprocess_masked.mrc as #1, grid size 256,256,256, pixel
1.06, shown at level 0.00434, step 1, values float32
> open
> /Users/seiyahirai/Desktop/Research/Kimura_T/E97K/modeling/Large/E97Km7_ISOLDE_A93-99.pdb
Chain information for E97Km7_ISOLDE_A93-99.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 71.7.1
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro17,1
Chip: Apple M1
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 6723.140.2
OS Loader Version: 6723.140.2
Software:
System Software Overview:
System Version: macOS 11.5.1 (20G80)
Kernel Version: Darwin 20.6.0
Time since boot: 9 days 22:46
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Family: Supported, Metal GPUFamily Apple 7
Displays:
Color LCD:
Resolution: 2880 x 1800
UI Looks like: 1440 x 900 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.1.0
Babel: 2.11.0
backcall: 0.2.0
blockdiag: 3.0.0
build: 0.8.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 2.1.1
ChimeraX-AddCharge: 1.4
ChimeraX-AddH: 2.2.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.6
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.41.5
ChimeraX-AtomicLibrary: 8.0.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.7.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.1
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.19.0
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.2
ChimeraX-CommandLine: 1.2.4
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.5
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.3
ChimeraX-DockPrep: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.5
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.1
ChimeraX-MatchMaker: 2.0.9
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.8
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.6
ChimeraX-ModelPanel: 1.3.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.1
ChimeraX-MouseModes: 1.1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.9.1
ChimeraX-PDB: 2.6.8
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.7.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.1.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.24.3
ChimeraX-uniprot: 2.2.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.1.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.1
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0.1
colorama: 0.4.5
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.32
debugpy: 1.6.4
decorator: 5.1.1
docutils: 0.19
entrypoints: 0.4
executing: 1.2.0
filelock: 3.7.1
fonttools: 4.38.0
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.33
imagecodecs: 2022.7.31
imagesize: 1.4.1
importlib-metadata: 5.1.0
ipykernel: 6.15.3
ipython: 8.4.0
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.1.2
jupyter-client: 7.3.4
jupyter-core: 5.1.0
kiwisolver: 1.4.4
line-profiler: 3.5.1
lxml: 4.9.1
lz4: 4.0.2
MarkupSafe: 2.1.1
matplotlib: 3.5.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.0
networkx: 2.8.5
numexpr: 2.8.4
numpy: 1.23.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.2.0
pip: 22.2.2
pkginfo: 1.8.3
platformdirs: 2.5.4
prompt-toolkit: 3.0.33
psutil: 5.9.1
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.12.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2022.6
pyzmq: 24.0.1
qtconsole: 5.3.1
QtPy: 2.3.0
RandomWords: 0.4.0
requests: 2.28.1
scipy: 1.9.0
setuptools: 65.1.1
setuptools-scm: 7.0.5
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 5.1.1
sphinx-autodoc-typehints: 1.19.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tifffile: 2022.7.31
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
typing-extensions: 4.4.0
urllib3: 1.26.13
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
zipp: 3.11.0
Change History (11)
comment:1 by , 3 years ago
| Platform: | → all |
|---|---|
| Project: | → ChimeraX |
comment:2 by , 3 years ago
comment:3 by , 3 years ago
Did exactly the same scenario as #8345 - ran ChimeraX 1.5 straight from the .dmg, same series of commands. Repeated 3 times, no problem. Honestly, I don't know where to go with this one.
For what it's worth, my system details are below. Slightly newer model, more up to date OS... is it possible this is caused by some system bug that's been patched?
OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,1
Chip: Apple M1 Pro
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 32 GB
System Firmware Version: 7459.141.1
OS Loader Version: 7459.141.1
Software:
System Software Overview:
System Version: macOS 12.5.1 (21G83)
Kernel Version: Darwin 21.6.0
Time since boot: 9 minutes
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Family: Supported, Metal GPUFamily Apple 7
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.1.0
Babel: 2.11.0
backcall: 0.2.0
blockdiag: 3.0.0
build: 0.8.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 2.1.1
ChimeraX-AddCharge: 1.4
ChimeraX-AddH: 2.2.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.6
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.41.5
ChimeraX-AtomicLibrary: 8.0.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.7.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.1
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.19.0
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.2
ChimeraX-CommandLine: 1.2.4
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.5
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.3
ChimeraX-DockPrep: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.5
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.1
ChimeraX-MatchMaker: 2.0.9
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.8
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.6
ChimeraX-ModelPanel: 1.3.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.1
ChimeraX-MouseModes: 1.1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.9.1
ChimeraX-PDB: 2.6.8
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.7.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.1.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.24.3
ChimeraX-uniprot: 2.2.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.1.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.1
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0.1
colorama: 0.4.5
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.32
debugpy: 1.6.4
decorator: 5.1.1
docutils: 0.19
entrypoints: 0.4
executing: 1.2.0
filelock: 3.7.1
fonttools: 4.38.0
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.33
imagecodecs: 2022.7.31
imagesize: 1.4.1
importlib-metadata: 5.1.0
ipykernel: 6.15.3
ipython: 8.4.0
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.1.2
jupyter-client: 7.3.4
jupyter-core: 5.1.0
kiwisolver: 1.4.4
line-profiler: 3.5.1
lxml: 4.9.1
lz4: 4.0.2
MarkupSafe: 2.1.1
matplotlib: 3.5.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.0
networkx: 2.8.5
numexpr: 2.8.4
numpy: 1.23.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.2.0
pip: 22.2.2
pkginfo: 1.8.3
platformdirs: 2.5.4
prompt-toolkit: 3.0.33
psutil: 5.9.1
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.12.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2022.6
pyzmq: 24.0.1
qtconsole: 5.3.1
QtPy: 2.3.0
RandomWords: 0.4.0
requests: 2.28.1
scipy: 1.9.0
setuptools: 65.1.1
setuptools-scm: 7.0.5
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 5.1.1
sphinx-autodoc-typehints: 1.19.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tifffile: 2022.7.31
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
typing-extensions: 4.4.0
urllib3: 1.26.13
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
zipp: 3.11.0
comment:4 by , 3 years ago
I think probably the biggest hint is coming from #8345/#8347 - these are using ISOLDE's built-in cryo-EM demo model 6out. That doesn't have any anisou atoms to start with, so Atoms._set_aniso_u6() should be getting called on a zero-length Atoms array and returning immediately. But instead it's crashing, which suggests to me that either some of the atoms are getting trashed, or there's some more obscure library linking issue happening. The aniso_u sanity check happens *before* the model is temporarily removed from the session to be placed back under the Clipper SymmetryManager, which means that at this point Clipper really hasn't done anything to it at all. So it's just running remove_invalid_anisou(session, model.atoms) from https://github.com/tristanic/chimerax-clipper/blob/master/src/sanity_check.py (and failing at line 12). Makes no sense.
comment:5 by , 3 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Structure Editing |
| Owner: | set to |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash clearing aniso_u6 |
comment:6 by , 3 years ago
I constructed empty Atoms collections and set their aniso_u6 to None, and that worked fine on my Mac at home, but it's Intel.
follow-up: 8 comment:8 by , 3 years ago
I also tested setting aniso_u6=None on an empty Atoms array (many times over) on my ARM Mac. No crashes. On Wed, 8 Feb 2023 at 17:28, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote:
comment:9 by , 3 years ago
One other thing that all the reported clashes seem to have in common (except for one where the log wasn't written so I couldn't tell): the model was opened from a PDB file, not mmCIF. I currently have a loop running opening a new model (fetched by ID from the wwPDB) at each graphics update and running the "clipper spot" command on it. Keeping them all open to really stress-test it... up to 320 open models with no sign of trouble.
follow-up: 10 comment:10 by , 3 years ago
Once again I am officially stumped. I’ve tried opening and processing a few hundred random models in a loop - no problem. I’ve tried the “isolde demo cryo_em_intro” command a few dozen times (both manually and as a perframe command) - no problem. I’ve tried filling the aniso_u6 fields for a really big PDB model with numpy.random.rand() junk - no problem. I’ve tried every random PDB file I happened to have lying around on my machine - no problem. I’m thinking this has to be some obscure model, firmware or OS version-specific bug. On Thu, 2 Mar 2023 at 19:15, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote:
comment:11 by , 3 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
The ctypes call of clear_atom_aniso_u6 wasn't specifying the type of the second argument: https://github.com/RBVI/ChimeraX/commit/eaa5c4b59144fa9d6d856ef368bdc1d189784a24
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Well, that's interesting. Same bug, but this time ChimeraX appears to be installed and running from the right place. Will try again to reproduce it, but it's definitely a weird one - the Clipper code leading up to the failure hasn't been changed in years, and doesn't do anything unusual (no atom additions or deletions - just filtering all atoms on
has_aniso_u, then on the value of the aniso_u determinant, and clearing theaniso_u6for any atoms where the determinant is <1e-6.One thing I notice is that (unless I've missed something) all the reports of this bug have been on Apple Silicon CPUs... but I have no idea why. Will run some trials on my MacBook to see if I can figure out what triggers it.