![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 4 years ago
Closed 4 years ago
#5938 closed defect (nonchimerax)
Graphics driver crash, macOS 10.15.7, Intel Iris Graphics 6100
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | |
| Keywords: | Cc: | Eric Pettersen | |
| 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: 1.3 (2021-12-08 23:08:33 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted
Thread 0x000070000ce5e000 (most recent call first):
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 316 in wait
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 574 in wait
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 1284 in run
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Current thread 0x000000011da50dc0 (most recent call first):
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/opengl.py", line 235 in swap_buffers
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/opengl.py", line 496 in swap_buffers
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/view.py", line 179 in draw
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 73 in draw_new_frame
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 139 in _redraw_timer_callback
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 301 in event_loop
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 867 in init
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 1018 in
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main
Process: ChimeraX [63248]
Path: /Applications/ChimeraX-1.3.app/Contents/MacOS/ChimeraX
Identifier: ChimeraX
Version: 1.3.0 (1.3.0.0)
Code Type: X86-64 (Native)
Parent Process: ??? [1]
Responsible: ChimeraX [63248]
User ID: 501
Date/Time: 2022-01-17 15:45:36.149 -0500
OS Version: Mac OS X 10.15.7 (19H2)
Report Version: 12
Anonymous UUID: 7514A429-EA01-7F5A-AA39-25127A0E7BE5
Sleep/Wake UUID: A7410343-C0A2-4C81-889B-02241BD253F2
Time Awake Since Boot: 1300000 seconds
Time Since Wake: 1600 seconds
System Integrity Protection: enabled
Crashed Thread: 0 CrBrowserMain Dispatch queue: com.apple.main-thread
Exception Type: EXC_CRASH (SIGABRT)
Exception Codes: 0x0000000000000000, 0x0000000000000000
Exception Note: EXC_CORPSE_NOTIFY
Application Specific Information:
abort() called
Application Specific Signatures:
Graphics hardware encountered an error and was reset: 0x00000813
Thread 0 Crashed:: CrBrowserMain Dispatch queue: com.apple.main-thread
0 libsystem_kernel.dylib 0x00007fff67f6533a __pthread_kill + 10
1 libsystem_pthread.dylib 0x00007fff68021e60 pthread_kill + 430
2 libsystem_c.dylib 0x00007fff67e7c93e raise + 26
3 libsystem_platform.dylib 0x00007fff680165fd _sigtramp + 29
4 ??? 000000000000000000 0 + 0
5 libsystem_c.dylib 0x00007fff67eec808 abort + 120
6 libGPUSupportMercury.dylib 0x00007fff4f1eb0a5 gpusGenerateCrashLog.cold.1 + 95
7 libGPUSupportMercury.dylib 0x00007fff4f1e218f gpusGenerateCrashLog + 89
8 com.apple.driver.AppleIntelBDWGraphicsGLDriver 0x00007fff2342f650 gpusKillClientExt + 9
9 libGPUSupportMercury.dylib 0x00007fff4f1e36a1 gpusSubmitDataBuffers + 490
10 com.apple.driver.AppleIntelBDWGraphicsGLDriver 0x00007fff23007422 IntelCommandBuffer::getNew(GLDContextRec*) + 48
11 com.apple.driver.AppleIntelBDWGraphicsGLDriver 0x00007fff2300727c intelSubmitCommands + 171
12 com.apple.driver.AppleIntelBDWGraphicsGLDriver 0x00007fff2308ccfa gldPresentFramebufferData + 120
13 GLEngine 0x00007fff388ab8d1 glSwap_Exec + 97
14 com.apple.opengl 0x00007fff3888d473 CGLFlushDrawable + 59
15 com.apple.AppKit 0x00007fff2b39a75a -[NSOpenGLContext flushBuffer] + 20
16 libqcocoa.dylib 0x000000011c338f5d QCocoaGLContext::swapBuffers(QPlatformSurface*) + 541
17 QtGui 0x000000011a96c13c QOpenGLContext::swapBuffers(QSurface*) + 412
18 QtGui.abi3.so 0x000000011b06800f meth_QOpenGLContext_swapBuffers(_object*, _object*) + 95
19 org.python.python 0x000000010e57c06d cfunction_call + 125
20 org.python.python 0x000000010e53d17d _PyObject_MakeTpCall + 365
21 org.python.python 0x000000010e61561c call_function + 876
22 org.python.python 0x000000010e612ab3 _PyEval_EvalFrameDefault + 25219
23 org.python.python 0x000000010e616283 _PyEval_EvalCode + 2611
24 org.python.python 0x000000010e53d8d1 _PyFunction_Vectorcall + 289
25 org.python.python 0x000000010e61558c call_function + 732
26 org.python.python 0x000000010e612a92 _PyEval_EvalFrameDefault + 25186
27 org.python.python 0x000000010e53d948 function_code_fastcall + 104
28 org.python.python 0x000000010e61558c call_function + 732
29 org.python.python 0x000000010e612a92 _PyEval_EvalFrameDefault + 25186
30 org.python.python 0x000000010e616283 _PyEval_EvalCode + 2611
31 org.python.python 0x000000010e53d8d1 _PyFunction_Vectorcall + 289
32 org.python.python 0x000000010e53f98a method_vectorcall + 202
33 org.python.python 0x000000010e61558c call_function + 732
34 org.python.python 0x000000010e612be1 _PyEval_EvalFrameDefault + 25521
35 org.python.python 0x000000010e53d948 function_code_fastcall + 104
36 org.python.python 0x000000010e61558c call_function + 732
37 org.python.python 0x000000010e612a92 _PyEval_EvalFrameDefault + 25186
38 org.python.python 0x000000010e53d948 function_code_fastcall + 104
39 org.python.python 0x000000010e53f9d2 method_vectorcall + 274
40 QtCore.abi3.so 0x00000001178d8957 PyQtSlot::call(_object*, _object*) const + 39
41 QtCore.abi3.so 0x00000001178d8866 PyQtSlot::invoke(void**, _object*, void*, bool) const + 374
42 QtCore.abi3.so 0x00000001178d9455 PyQtSlotProxy::unislot(void**) + 85
43 QtCore.abi3.so 0x00000001178d93ca PyQtSlotProxy::qt_metacall(QMetaObject::Call, int, void**) + 58
44 QtCore 0x0000000117cbcf6e void doActivate(QObject*, int, void**) + 1118
45 QtCore 0x0000000117cc64c2 QTimer::timerEvent(QTimerEvent*) + 98
46 QtCore.abi3.so 0x00000001177c1bf9 sipQTimer::timerEvent(QTimerEvent*) + 121
47 QtCore 0x0000000117cb485f QObject::event(QEvent*) + 111
48 QtCore.abi3.so 0x00000001177c1a7a sipQTimer::event(QEvent*) + 186
49 QtWidgets 0x000000011a2b39ea QApplicationPrivate::notify_helper(QObject*, QEvent*) + 266
50 QtWidgets 0x000000011a2b4e11 QApplication::notify(QObject*, QEvent*) + 497
51 QtWidgets.abi3.so 0x0000000119e66db9 sipQApplication::notify(QObject*, QEvent*) + 233
52 QtCore 0x0000000117c89a34 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 212
53 QtCore 0x0000000117cef35f QTimerInfoList::activateTimers() + 991
54 libqcocoa.dylib 0x000000011c3178f2 QCocoaEventDispatcherPrivate::activateTimersSourceCallback(void*) + 18
55 com.apple.CoreFoundation 0x00007fff2dd7fd52 __CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE0_PERFORM_FUNCTION__ + 17
56 com.apple.CoreFoundation 0x00007fff2dd7fcf1 __CFRunLoopDoSource0 + 103
57 com.apple.CoreFoundation 0x00007fff2dd7fb0b __CFRunLoopDoSources0 + 209
58 com.apple.CoreFoundation 0x00007fff2dd7e83a __CFRunLoopRun + 927
59 com.apple.CoreFoundation 0x00007fff2dd7de3e CFRunLoopRunSpecific + 462
60 com.apple.HIToolbox 0x00007fff2c9aaabd RunCurrentEventLoopInMode + 292
61 com.apple.HIToolbox 0x00007fff2c9aa7d5 ReceiveNextEventCommon + 584
62 com.apple.HIToolbox 0x00007fff2c9aa579 _BlockUntilNextEventMatchingListInModeWithFilter + 64
63 com.apple.AppKit 0x00007fff2aff0039 _DPSNextEvent + 883
64 com.apple.AppKit 0x00007fff2afee880 -[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 1352
65 com.apple.AppKit 0x00007fff2afe058e -[NSApplication run] + 658
66 libqcocoa.dylib 0x000000011c31862f QCocoaEventDispatcher::processEvents(QFlags) + 2495
67 QtCore 0x0000000117c85acf QEventLoop::exec(QFlags) + 431
68 QtCore 0x0000000117c8a042 QCoreApplication::exec() + 130
69 QtWidgets.abi3.so 0x0000000119f58702 meth_QApplication_exec_(_object*, _object*) + 82
70 org.python.python 0x000000010e57c06d cfunction_call + 125
71 org.python.python 0x000000010e53d17d _PyObject_MakeTpCall + 365
72 org.python.python 0x000000010e61561c call_function + 876
73 org.python.python 0x000000010e612ab3 _PyEval_EvalFrameDefault + 25219
74 org.python.python 0x000000010e53d948 function_code_fastcall + 104
75 org.python.python 0x000000010e53f98a method_vectorcall + 202
76 org.python.python 0x000000010e61558c call_function + 732
77 org.python.python 0x000000010e612ab3 _PyEval_EvalFrameDefault + 25219
78 org.python.python 0x000000010e616283 _PyEval_EvalCode + 2611
79 org.python.python 0x000000010e53d8d1 _PyFunction_Vectorcall + 289
80 org.python.python 0x000000010e61558c call_function + 732
81 org.python.python 0x000000010e612b4b _PyEval_EvalFrameDefault + 25371
82 org.python.python 0x000000010e616283 _PyEval_EvalCode + 2611
83 org.python.python 0x000000010e60c70b PyEval_EvalCode + 139
84 org.python.python 0x000000010e609592 builtin_exec + 626
85 org.python.python 0x000000010e57b86a cfunction_vectorcall_FASTCALL + 218
86 org.python.python 0x000000010e61558c call_function + 732
87 org.python.python 0x000000010e612b4b _PyEval_EvalFrameDefault + 25371
88 org.python.python 0x000000010e616283 _PyEval_EvalCode + 2611
89 org.python.python 0x000000010e53d8d1 _PyFunction_Vectorcall + 289
90 org.python.python 0x000000010e61558c call_function + 732
91 org.python.python 0x000000010e612b4b _PyEval_EvalFrameDefault + 25371
92 org.python.python 0x000000010e616283 _PyEval_EvalCode + 2611
93 org.python.python 0x000000010e53d8d1 _PyFunction_Vectorcall + 289
94 org.python.python 0x000000010e67be20 pymain_run_module + 208
95 org.python.python 0x000000010e67b537 Py_RunMain + 1431
96 org.python.python 0x000000010e67bb3f pymain_main + 223
97 org.python.python 0x000000010e67ba4b Py_Main + 43
98 edu.ucsf.cgl.ChimeraX 0x000000010e4f4dc8 main + 120
99 libdyld.dylib 0x00007fff67e1dcc9 start + 1
Thread 1:
0 libsystem_kernel.dylib 0x00007fff67f61882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff68022425 _pthread_cond_wait + 698
2 libopenblas.0.dylib 0x000000010f1bda9f blas_thread_server + 207
3 libsystem_pthread.dylib 0x00007fff68022109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6801db8b thread_start + 15
Thread 2:: ThreadPoolServiceThread
0 libsystem_kernel.dylib 0x00007fff67f67b96 kevent64 + 10
1 QtWebEngineCore 0x00000001205b7e6a base::MessagePumpKqueue::DoInternalWork(base::MessagePump::Delegate::NextWorkInfo*) + 330
2 QtWebEngineCore 0x00000001205b7cc7 base::MessagePumpKqueue::Run(base::MessagePump::Delegate*) + 167
3 QtWebEngineCore 0x000000012054062b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
4 QtWebEngineCore 0x00000001205047cb base::RunLoop::Run() + 395
5 QtWebEngineCore 0x000000012054ba94 base::internal::ServiceThread::Run(base::RunLoop*) + 20
6 QtWebEngineCore 0x000000012055fa7d base::Thread::ThreadMain() + 413
7 QtWebEngineCore 0x00000001205a8e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
8 libsystem_pthread.dylib 0x00007fff68022109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff6801db8b thread_start + 15
Thread 3:: ThreadPoolBackgroundWorker
0 libsystem_kernel.dylib 0x00007fff67f5edfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff67f5f170 mach_msg + 60
2 QtWebEngineCore 0x00000001205ad492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x0000000120555778 base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*) + 56
4 QtWebEngineCore 0x0000000120556150 base::internal::WorkerThread::RunWorker() + 1024
5 QtWebEngineCore 0x0000000120555c44 base::internal::WorkerThread::RunBackgroundPooledWorker() + 20
6 QtWebEngineCore 0x00000001205a8e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
7 libsystem_pthread.dylib 0x00007fff68022109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff6801db8b thread_start + 15
Thread 4:: Chrome_IOThread
0 libsystem_kernel.dylib 0x00007fff67f67b96 kevent64 + 10
1 QtWebEngineCore 0x00000001205b7e6a base::MessagePumpKqueue::DoInternalWork(base::MessagePump::Delegate::NextWorkInfo*) + 330
2 QtWebEngineCore 0x00000001205b7cc7 base::MessagePumpKqueue::Run(base::MessagePump::Delegate*) + 167
3 QtWebEngineCore 0x000000012054062b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
4 QtWebEngineCore 0x00000001205047cb base::RunLoop::Run() + 395
5 QtWebEngineCore 0x0000000124484f06 content::BrowserProcessSubThread::IOThreadRun(base::RunLoop*) + 102
6 QtWebEngineCore 0x000000012055fa7d base::Thread::ThreadMain() + 413
7 QtWebEngineCore 0x00000001205a8e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
8 libsystem_pthread.dylib 0x00007fff68022109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff6801db8b thread_start + 15
Thread 5:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff67f5edfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff67f5f170 mach_msg + 60
2 QtWebEngineCore 0x00000001205ad492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x00000001205ad2cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x00000001204d51db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171
5 QtWebEngineCore 0x000000012054062b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
6 QtWebEngineCore 0x00000001205047cb base::RunLoop::Run() + 395
7 QtWebEngineCore 0x000000012055fa7d base::Thread::ThreadMain() + 413
8 QtWebEngineCore 0x00000001205a8e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
9 libsystem_pthread.dylib 0x00007fff68022109 _pthread_start + 148
10 libsystem_pthread.dylib 0x00007fff6801db8b thread_start + 15
Thread 6:: CompositorTileWorker1
0 libsystem_kernel.dylib 0x00007fff67f61882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff68022425 _pthread_cond_wait + 698
2 QtWebEngineCore 0x00000001205a4e18 base::ConditionVariable::Wait() + 104
3 QtWebEngineCore 0x000000012185c5f8 non-virtual thunk to cc::SingleThreadTaskGraphRunner::Run() + 56
4 QtWebEngineCore 0x00000001205a8e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
5 libsystem_pthread.dylib 0x00007fff68022109 _pthread_start + 148
6 libsystem_pthread.dylib 0x00007fff6801db8b thread_start + 15
Thread 7:: Chrome_InProcGpuThread
0 libsystem_kernel.dylib 0x00007fff67f5edfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff67f5f170 mach_msg + 60
2 QtWebEngineCore 0x00000001205ad492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x00000001204d520f base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 223
4 QtWebEngineCore 0x000000012054062b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
5 QtWebEngineCore 0x00000001205047cb base::RunLoop::Run() + 395
6 QtWebEngineCore 0x000000012055fa7d base::Thread::ThreadMain() + 413
7 QtWebEngineCore 0x00000001205a8e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
8 libsystem_pthread.dylib 0x00007fff68022109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff6801db8b thread_start + 15
Thread 8:: Chrome_ChildIOThread
0 libsystem_kernel.dylib 0x00007fff67f67b96 kevent64 + 10
1 QtWebEngineCore 0x00000001205b7e6a base::MessagePumpKqueue::DoInternalWork(base::MessagePump::Delegate::NextWorkInfo*) + 330
2 QtWebEngineCore 0x00000001205b7cc7 base::MessagePumpKqueue::Run(base::MessagePump::Delegate*) + 167
3 QtWebEngineCore 0x000000012054062b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
4 QtWebEngineCore 0x00000001205047cb base::RunLoop::Run() + 395
5 QtWebEngineCore 0x000000012055fa7d base::Thread::ThreadMain() + 413
6 QtWebEngineCore 0x00000001205a8e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
7 libsystem_pthread.dylib 0x00007fff68022109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff6801db8b thread_start + 15
Thread 9:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff67f5edfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff67f5f170 mach_msg + 60
2 QtWebEngineCore 0x00000001205ad492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x00000001205ad2cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x00000001204d51db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171
5 QtWebEngineCore 0x000000012054062b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
6 QtWebEngineCore 0x00000001205047cb base::RunLoop::Run() + 395
7 QtWebEngineCore 0x000000012055fa7d base::Thread::ThreadMain() + 413
8 QtWebEngineCore 0x00000001205a8e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
9 libsystem_pthread.dylib 0x00007fff68022109 _pthread_start + 148
10 libsystem_pthread.dylib 0x00007fff6801db8b thread_start + 15
Thread 10:: VizCompositorThread
0 libsystem_kernel.dylib 0x00007fff67f5edfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff67f5f170 mach_msg + 60
2 QtWebEngineCore 0x00000001205ad492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x00000001205ad2cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x00000001204d51db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171
5 QtWebEngineCore 0x000000012054062b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
6 QtWebEngineCore 0x00000001205047cb base::RunLoop::Run() + 395
7 QtWebEngineCore 0x000000012055fa7d base::Thread::ThreadMain() + 413
8 QtWebEngineCore 0x00000001205a8e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
9 libsystem_pthread.dylib 0x00007fff68022109 _pthread_start + 148
10 libsystem_pthread.dylib 0x00007fff6801db8b thread_start + 15
Thread 11:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff67f5edfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff67f5f170 mach_msg + 60
2 QtWebEngineCore 0x00000001205ad492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x00000001205ad2cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x00000001204d51db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171
5 QtWebEngineCore 0x000000012054062b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
6 QtWebEngineCore 0x00000001205047cb base::RunLoop::Run() + 395
7 QtWebEngineCore 0x000000012055fa7d base::Thread::ThreadMain() + 413
8 QtWebEngineCore 0x00000001205a8e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
9 libsystem_pthread.dylib 0x00007fff68022109 _pthread_start + 148
10 libsystem_pthread.dylib 0x00007fff6801db8b thread_start + 15
Thread 12:: ThreadPoolSingleThreadForegroundBlocking0
0 libsystem_kernel.dylib 0x00007fff67f5edfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff67f5f170 mach_msg + 60
2 QtWebEngineCore 0x00000001205ad492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x00000001205ad2cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x000000012055576a base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*) + 42
5 QtWebEngineCore 0x0000000120556150 base::internal::WorkerThread::RunWorker() + 1024
6 QtWebEngineCore 0x0000000120555d34 base::internal::WorkerThread::RunDedicatedWorker() + 20
7 QtWebEngineCore 0x00000001205a8e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
8 libsystem_pthread.dylib 0x00007fff68022109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff6801db8b thread_start + 15
Thread 13:: MemoryInfra
0 libsystem_kernel.dylib 0x00007fff67f5edfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff67f5f170 mach_msg + 60
2 QtWebEngineCore 0x00000001205ad492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x00000001205ad2cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x00000001204d51db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171
5 QtWebEngineCore 0x000000012054062b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
6 QtWebEngineCore 0x00000001205047cb base::RunLoop::Run() + 395
7 QtWebEngineCore 0x000000012055fa7d base::Thread::ThreadMain() + 413
8 QtWebEngineCore 0x00000001205a8e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
9 libsystem_pthread.dylib 0x00007fff68022109 _pthread_start + 148
10 libsystem_pthread.dylib 0x00007fff6801db8b thread_start + 15
Thread 14:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff67f5edfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff67f5f170 mach_msg + 60
2 QtWebEngineCore 0x00000001205ad492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x00000001205ad2cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x00000001204d51db base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171
5 QtWebEngineCore 0x000000012054062b base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 139
6 QtWebEngineCore 0x00000001205047cb base::RunLoop::Run() + 395
7 QtWebEngineCore 0x000000012055fa7d base::Thread::ThreadMain() + 413
8 QtWebEngineCore 0x00000001205a8e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
9 libsystem_pthread.dylib 0x00007fff68022109 _pthread_start + 148
10 libsystem_pthread.dylib 0x00007fff6801db8b thread_start + 15
Thread 15:: com.apple.NSEventThread
0 libsystem_kernel.dylib 0x00007fff67f5edfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff67f5f170 mach_msg + 60
2 com.apple.CoreFoundation 0x00007fff2dd7fef5 __CFRunLoopServiceMachPort + 247
3 com.apple.CoreFoundation 0x00007fff2dd7e9c2 __CFRunLoopRun + 1319
4 com.apple.CoreFoundation 0x00007fff2dd7de3e CFRunLoopRunSpecific + 462
5 com.apple.AppKit 0x00007fff2b191954 _NSEventThread + 132
6 libsystem_pthread.dylib 0x00007fff68022109 _pthread_start + 148
7 libsystem_pthread.dylib 0x00007fff6801db8b thread_start + 15
Thread 16:: ThreadPoolSingleThreadSharedBackgroundBlocking1
0 libsystem_kernel.dylib 0x00007fff67f5edfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff67f5f170 mach_msg + 60
2 QtWebEngineCore 0x00000001205ad492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x00000001205ad2cf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x000000012055576a base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*) + 42
5 QtWebEngineCore 0x0000000120555e3d base::internal::WorkerThread::RunWorker() + 237
6 QtWebEngineCore 0x0000000120555c74 base::internal::WorkerThread::RunBackgroundSharedWorker() + 20
7 QtWebEngineCore 0x00000001205a8e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
8 libsystem_pthread.dylib 0x00007fff68022109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff6801db8b thread_start + 15
Thread 17:
0 libsystem_kernel.dylib 0x00007fff67f61882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff68022425 _pthread_cond_wait + 698
2 libopenblas.0.dylib 0x000000015089e2eb blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff68022109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6801db8b thread_start + 15
Thread 18:: ThreadPoolForegroundWorker
0 libsystem_kernel.dylib 0x00007fff67f5edfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff67f5f170 mach_msg + 60
2 QtWebEngineCore 0x00000001205ad492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x0000000120555778 base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*) + 56
4 QtWebEngineCore 0x0000000120556150 base::internal::WorkerThread::RunWorker() + 1024
5 QtWebEngineCore 0x0000000120555cd4 base::internal::WorkerThread::RunPooledWorker() + 20
6 QtWebEngineCore 0x00000001205a8e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
7 libsystem_pthread.dylib 0x00007fff68022109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff6801db8b thread_start + 15
Thread 19:
0 libsystem_pthread.dylib 0x00007fff6801db68 start_wqthread + 0
Thread 20:: ThreadPoolForegroundWorker
0 libsystem_kernel.dylib 0x00007fff67f5edfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff67f5f170 mach_msg + 60
2 QtWebEngineCore 0x00000001205ad492 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 434
3 QtWebEngineCore 0x0000000120555778 base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*) + 56
4 QtWebEngineCore 0x0000000120556150 base::internal::WorkerThread::RunWorker() + 1024
5 QtWebEngineCore 0x0000000120555cd4 base::internal::WorkerThread::RunPooledWorker() + 20
6 QtWebEngineCore 0x00000001205a8e07 base::(anonymous namespace)::ThreadFunc(void*) + 87
7 libsystem_pthread.dylib 0x00007fff68022109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff6801db8b thread_start + 15
Thread 21:
0 libsystem_kernel.dylib 0x00007fff67f61882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff68022425 _pthread_cond_wait + 698
2 org.python.python 0x000000010e66bd6c PyThread_acquire_lock_timed + 700
3 org.python.python 0x000000010e6baa1f acquire_timed + 111
4 org.python.python 0x000000010e6bab30 lock_PyThread_acquire_lock + 48
5 org.python.python 0x000000010e545e54 method_vectorcall_VARARGS_KEYWORDS + 388
6 org.python.python 0x000000010e61558c call_function + 732
7 org.python.python 0x000000010e612a92 _PyEval_EvalFrameDefault + 25186
8 org.python.python 0x000000010e616283 _PyEval_EvalCode + 2611
9 org.python.python 0x000000010e53d8d1 _PyFunction_Vectorcall + 289
10 org.python.python 0x000000010e61558c call_function + 732
11 org.python.python 0x000000010e612a92 _PyEval_EvalFrameDefault + 25186
12 org.python.python 0x000000010e616283 _PyEval_EvalCode + 2611
13 org.python.python 0x000000010e53d8d1 _PyFunction_Vectorcall + 289
14 org.python.python 0x000000010e61558c call_function + 732
15 org.python.python 0x000000010e612a92 _PyEval_EvalFrameDefault + 25186
16 org.python.python 0x000000010e53d948 function_code_fastcall + 104
17 org.python.python 0x000000010e61558c call_function + 732
18 org.python.python 0x000000010e612a92 _PyEval_EvalFrameDefault + 25186
19 org.python.python 0x000000010e53d948 function_code_fastcall + 104
20 org.python.python 0x000000010e61558c call_function + 732
21 org.python.python 0x000000010e612a92 _PyEval_EvalFrameDefault + 25186
22 org.python.python 0x000000010e53d948 function_code_fastcall + 104
23 org.python.python 0x000000010e53f9d2 method_vectorcall + 274
24 org.python.python 0x000000010e6ba3c6 t_bootstrap + 70
25 org.python.python 0x000000010e66b8c9 pythread_wrapper + 25
26 libsystem_pthread.dylib 0x00007fff68022109 _pthread_start + 148
27 libsystem_pthread.dylib 0x00007fff6801db8b thread_start + 15
Thread 22:
0 libsystem_pthread.dylib 0x00007fff6801db68 start_wqthread + 0
Thread 23:
0 libsystem_pthread.dylib 0x00007fff6801db68 start_wqthread + 0
Thread 0 crashed with X86 Thread State (64-bit):
rax: 0x0000000000000000 rbx: 0x000000011da50dc0 rcx: 0x00007fa50f755a58 rdx: 0x0000000000000000
rdi: 0x0000000000000307 rsi: 0x0000000000000006 rbp: 0x00007fa50f755a80 rsp: 0x00007fa50f755a58
r8: 0x00007fa50f755f48 r9: 0x244b6f088a5aa7f5 r10: 0x000000011da50dc0 r11: 0x0000000000000246
r12: 0x0000000000000307 r13: 0x00007fa51233b3f8 r14: 0x0000000000000006 r15: 0x0000000000000016
rip: 0x00007fff67f6533a rfl: 0x0000000000000246 cr2: 0x00007fc98670a000
Logical CPU: 0
Error Code: 0x02000148
Trap Number: 133
Binary Images:
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0x7fff65bd1000 - 0x7fff65bdaff7 libheimdal-asn1.dylib (564.140.1) /usr/lib/libheimdal-asn1.dylib
0x7fff65bdb000 - 0x7fff65ccbfff libiconv.2.dylib (59) /usr/lib/libiconv.2.dylib
0x7fff65ccc000 - 0x7fff65f23fff libicucore.A.dylib (64260.0.1) /usr/lib/libicucore.A.dylib
0x7fff65f3d000 - 0x7fff65f3efff liblangid.dylib (133) /usr/lib/liblangid.dylib
0x7fff65f3f000 - 0x7fff65f57ff3 liblzma.5.dylib (16) /usr/lib/liblzma.5.dylib
0x7fff65f6f000 - 0x7fff66016ff7 libmecab.dylib (883.11) /usr/lib/libmecab.dylib
0x7fff66017000 - 0x7fff66279ff1 libmecabra.dylib (883.11) /usr/lib/libmecabra.dylib
0x7fff665e6000 - 0x7fff66615fff libncurses.5.4.dylib (57) /usr/lib/libncurses.5.4.dylib
0x7fff66745000 - 0x7fff66bc1ff5 libnetwork.dylib (1880.120.4) /usr/lib/libnetwork.dylib
0x7fff66bc2000 - 0x7fff66bd9fff libnetworkextension.dylib (1095.140.2) /usr/lib/libnetworkextension.dylib
0x7fff66c62000 - 0x7fff66c95fde libobjc.A.dylib (787.1) /usr/lib/libobjc.A.dylib
0x7fff66c96000 - 0x7fff66c97ff7 libodfde.dylib (26) /usr/lib/libodfde.dylib
0x7fff66ca8000 - 0x7fff66cacfff libpam.2.dylib (25.100.1) /usr/lib/libpam.2.dylib
0x7fff66caf000 - 0x7fff66ce5ff7 libpcap.A.dylib (89.120.1) /usr/lib/libpcap.A.dylib
0x7fff66d25000 - 0x7fff66d33ff9 libperfcheck.dylib (37.100.2) /usr/lib/libperfcheck.dylib
0x7fff66d34000 - 0x7fff66d37ff3 libpmenergy.dylib (214.120.1) /usr/lib/libpmenergy.dylib
0x7fff66d38000 - 0x7fff66d3afff libpmsample.dylib (214.120.1) /usr/lib/libpmsample.dylib
0x7fff66d69000 - 0x7fff66d81fff libresolv.9.dylib (67.40.1) /usr/lib/libresolv.9.dylib
0x7fff66d83000 - 0x7fff66dc7ff7 libsandbox.1.dylib (1217.141.2) /usr/lib/libsandbox.1.dylib
0x7fff66dc8000 - 0x7fff66ddaff7 libsasl2.2.dylib (213.120.1) /usr/lib/libsasl2.2.dylib
0x7fff66ddb000 - 0x7fff66ddcff7 libspindump.dylib (281.3) /usr/lib/libspindump.dylib
0x7fff66ddd000 - 0x7fff66fc7ff7 libsqlite3.dylib (308.5) /usr/lib/libsqlite3.dylib
0x7fff670bb000 - 0x7fff670e8ffb libssl.46.dylib (47.140.1) /usr/lib/libssl.46.dylib
0x7fff671bd000 - 0x7fff67217ff8 libusrtcp.dylib (1880.120.4) /usr/lib/libusrtcp.dylib
0x7fff67218000 - 0x7fff6721bffb libutil.dylib (57) /usr/lib/libutil.dylib
0x7fff6721c000 - 0x7fff67229ff7 libxar.1.dylib (425.2) /usr/lib/libxar.1.dylib
0x7fff6722f000 - 0x7fff67311fff libxml2.2.dylib (33.5) /usr/lib/libxml2.2.dylib
0x7fff67315000 - 0x7fff6733dfff libxslt.1.dylib (16.9) /usr/lib/libxslt.1.dylib
0x7fff6733e000 - 0x7fff67350ff3 libz.1.dylib (76) /usr/lib/libz.1.dylib
0x7fff67bff000 - 0x7fff67c04ff3 libcache.dylib (83) /usr/lib/system/libcache.dylib
0x7fff67c05000 - 0x7fff67c10fff libcommonCrypto.dylib (60165.120.1) /usr/lib/system/libcommonCrypto.dylib
0x7fff67c11000 - 0x7fff67c18fff libcompiler_rt.dylib (101.2) /usr/lib/system/libcompiler_rt.dylib
0x7fff67c19000 - 0x7fff67c22ff7 libcopyfile.dylib (166.40.1) /usr/lib/system/libcopyfile.dylib
0x7fff67c23000 - 0x7fff67cb5fdb libcorecrypto.dylib (866.140.1) /usr/lib/system/libcorecrypto.dylib
0x7fff67dc2000 - 0x7fff67e02ff0 libdispatch.dylib (1173.100.2) /usr/lib/system/libdispatch.dylib
0x7fff67e03000 - 0x7fff67e39fff libdyld.dylib (750.6) /usr/lib/system/libdyld.dylib
0x7fff67e3a000 - 0x7fff67e3affb libkeymgr.dylib (30) /usr/lib/system/libkeymgr.dylib
0x7fff67e3b000 - 0x7fff67e47ff3 libkxld.dylib (6153.141.2) /usr/lib/system/libkxld.dylib
0x7fff67e48000 - 0x7fff67e48ff7 liblaunch.dylib (1738.140.1) /usr/lib/system/liblaunch.dylib
0x7fff67e49000 - 0x7fff67e4eff7 libmacho.dylib (959.0.1) /usr/lib/system/libmacho.dylib
0x7fff67e4f000 - 0x7fff67e51ff3 libquarantine.dylib (110.40.3) /usr/lib/system/libquarantine.dylib
0x7fff67e52000 - 0x7fff67e53ff7 libremovefile.dylib (48) /usr/lib/system/libremovefile.dylib
0x7fff67e54000 - 0x7fff67e6bff3 libsystem_asl.dylib (377.60.2) /usr/lib/system/libsystem_asl.dylib
0x7fff67e6c000 - 0x7fff67e6cff7 libsystem_blocks.dylib (74) /usr/lib/system/libsystem_blocks.dylib
0x7fff67e6d000 - 0x7fff67ef4fff libsystem_c.dylib (1353.100.2) /usr/lib/system/libsystem_c.dylib
0x7fff67ef5000 - 0x7fff67ef8ffb libsystem_configuration.dylib (1061.141.1) /usr/lib/system/libsystem_configuration.dylib
0x7fff67ef9000 - 0x7fff67efcfff libsystem_coreservices.dylib (114) /usr/lib/system/libsystem_coreservices.dylib
0x7fff67efd000 - 0x7fff67f05fff libsystem_darwin.dylib (1353.100.2) /usr/lib/system/libsystem_darwin.dylib
0x7fff67f06000 - 0x7fff67f0dfff libsystem_dnssd.dylib (1096.100.3) /usr/lib/system/libsystem_dnssd.dylib
0x7fff67f0e000 - 0x7fff67f0fffb libsystem_featureflags.dylib (17) /usr/lib/system/libsystem_featureflags.dylib
0x7fff67f10000 - 0x7fff67f5dff7 libsystem_info.dylib (538) /usr/lib/system/libsystem_info.dylib
0x7fff67f5e000 - 0x7fff67f8aff7 libsystem_kernel.dylib (6153.141.2) /usr/lib/system/libsystem_kernel.dylib
0x7fff67f8b000 - 0x7fff67fd2fff libsystem_m.dylib (3178) /usr/lib/system/libsystem_m.dylib
0x7fff67fd3000 - 0x7fff67ffafff libsystem_malloc.dylib (283.100.6) /usr/lib/system/libsystem_malloc.dylib
0x7fff67ffb000 - 0x7fff68008ffb libsystem_networkextension.dylib (1095.140.2) /usr/lib/system/libsystem_networkextension.dylib
0x7fff68009000 - 0x7fff68012ff7 libsystem_notify.dylib (241.100.2) /usr/lib/system/libsystem_notify.dylib
0x7fff68013000 - 0x7fff6801bfef libsystem_platform.dylib (220.100.1) /usr/lib/system/libsystem_platform.dylib
0x7fff6801c000 - 0x7fff68026fff libsystem_pthread.dylib (416.100.3) /usr/lib/system/libsystem_pthread.dylib
0x7fff68027000 - 0x7fff6802bff3 libsystem_sandbox.dylib (1217.141.2) /usr/lib/system/libsystem_sandbox.dylib
0x7fff6802c000 - 0x7fff6802efff libsystem_secinit.dylib (62.100.2) /usr/lib/system/libsystem_secinit.dylib
0x7fff6802f000 - 0x7fff68036ffb libsystem_symptoms.dylib (1238.120.1) /usr/lib/system/libsystem_symptoms.dylib
0x7fff68037000 - 0x7fff6804dff2 libsystem_trace.dylib (1147.120) /usr/lib/system/libsystem_trace.dylib
0x7fff6804f000 - 0x7fff68054ff7 libunwind.dylib (35.4) /usr/lib/system/libunwind.dylib
0x7fff68055000 - 0x7fff6808affe libxpc.dylib (1738.140.1) /usr/lib/system/libxpc.dylib
External Modification Summary:
Calls made by other processes targeting this process:
task_for_pid: 13
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: 930041
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=1.0G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=1.0G(100%)
VIRTUAL REGION
REGION TYPE SIZE COUNT (non-coalesced)
=========== ======= =======
Accelerate framework 384K 3
Activity Tracing 256K 1
CG backing stores 880K 2
CG image 168K 14
CoreAnimation 220K 20
CoreGraphics 8K 1
CoreImage 28K 3
CoreUI image data 3088K 27
Foundation 28K 2
Kernel Alloc Once 8K 1
MALLOC 537.9M 1004
MALLOC guard page 32K 7
MALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated)
MALLOC_NANO (reserved) 256.0M 1 reserved VM address space (unallocated)
Mach message 24K 3
OpenGL GLSL 384K 5
STACK GUARD 92K 23
Stack 155.2M 24
Stack Guard 56.0M 1
VM_ALLOCATE 88.0M 173
VM_ALLOCATE (reserved) 32.0M 1 reserved VM address space (unallocated)
__DATA 55.1M 646
__DATA_CONST 40K 4
__FONT_DATA 4K 1
__GLSLBUILTINS 5176K 1
__LINKEDIT 498.1M 230
__OBJC_RO 32.3M 1
__OBJC_RW 1908K 2
__TEXT 654.8M 592
__UNICODE 564K 1
mapped file 392.7M 56
shared memory 2844K 25
=========== ======= =======
TOTAL 2.7G 2876
TOTAL, minus reserved VM space 2.4G 2876
===== Log before crash start =====
> lighting shadows false
> lighting depthCue false
> set bgColor alice blue
> ui mousemode right zoom
> windowsize 570 570
> camera ortho
> color name bluishwhite rgb(201, 218, 222)
Color 'bluishwhite' is opaque: rgb(78.8%, 85.5%, 87.1%) hex: #c9dade
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/charlesmidgett/OneDrive - Dartmouth College/2021 vibrio
> virulence regulator chapter/ToxT/Li 4mlo.cif"
Li 4mlo.cif title:
1.65A resolution structure of ToxT from Vibrio cholerae (P21 Form) [more
info...]
Chain information for Li 4mlo.cif #1
---
Chain | Description | UniProt
A | TCP pilus virulence regulatory protein | Q7BGC0_VIBCL
Non-standard residues in Li 4mlo.cif #1
---
CL — chloride ion
PAM — palmitoleic acid
> size stickRadius .3
Changed 2188 bond radii
> hide :HOH
> hide :12,269 target a
> hide :33 target a
> color cornflowerblue
> color byhetero
> color :304 violet
> color :304 purple
> color :304 byhetero
> color :1-300 darkorange
> color :1-300 byhetero
> dssp
> close
> open "/Users/charlesmidgett/OneDrive - Dartmouth College/2021 vibrio
> virulence regulator chapter/ToxT/Li 4mlo.cif" format mmcif
Li 4mlo.cif title:
1.65A resolution structure of ToxT from Vibrio cholerae (P21 Form) [more
info...]
Chain information for Li 4mlo.cif #1
---
Chain | Description | UniProt
A | TCP pilus virulence regulatory protein | Q7BGC0_VIBCL
Non-standard residues in Li 4mlo.cif #1
---
CL — chloride ion
PAM — palmitoleic acid
> hide :HOH
> hide :12,269,33 target a
> color 1-300 darkorange
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> color :1-300 darkorange
> color :PAM purple
> color byhetero
> open 3gbg
3gbg title:
Crystal Structure of ToxT from Vibrio Cholerae O395 [more info...]
Chain information for 3gbg #2
---
Chain | Description | UniProt
A | TCP pilus virulence regulatory protein | TCPN_VIBC3
Non-standard residues in 3gbg #2
---
PAM — palmitoleic acid
> ui tool show Matchmaker
> matchmaker #!2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Li 4mlo.cif, chain A (#1) with 3gbg, chain A (#2), sequence
alignment score = 1346.2
RMSD between 248 pruned atom pairs is 0.568 angstroms; (across all 257 pairs:
0.992)
> color #2 1-300 cornflowerblue
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> color #2:1-300 cornflowerblue
> hide :12,269 target a
> color #2:PAM hotpink
> color byhetero
> pwd
Current working directory is: /Users/charlesmidgett/Desktop
> cd "/Users/charlesmidgett/OneDrive - Dartmouth College/2021 vibrio virulence
> regulator chapter/ToxT"
Current working directory is: /Users/charlesmidgett/OneDrive - Dartmouth
College/2021 vibrio virulence regulator chapter/ToxT
> save lowden_Li_toxt_comp.cxs
> hide :HOH
> save lowden_Li_toxt_comp.cxs
> size stickRadius .3
Changed 4369 bond radii
> graphics silhouettes true
> save lowden_Li_toxt_comp.cxs
> save "ToxT pics/ToxT_overallview1.png" width 2400 transparentBackground true
> supersample 9
> roll y 180 1
> save "ToxT pics/ToxT_overallview2.png" width 2400 transparentBackground true
> supersample 9
> close
> open "/Users/charlesmidgett/OneDrive - Dartmouth College/2021 vibrio
> virulence regulator chapter/ToxT/ToxT overlay.cxs"
opened ChimeraX session
> color #7:1-300 darkorange
> color #6:1-300 cornflowerblue
> show #7 target r
> show #7:PAM target a
> hide #1 models
> show #1 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> show #2
> show #2 target r
> hide #2 target a
> save "ToxT overlay.cxs"
> hide #1,3,4,5,6
> hide #1,3,4,5,6 target ar
> color #7:PAM purple
> color byhetero
> show #7:30,231 target a
> ~show #7:30,231 target a
> show #7:31,230 target a
> show #2:32,231 target a
> size stickRadius .3
Changed 15821 bond radii
> windowsize 570 500
> windowsize 500 570
===== Log before crash end =====
Log:
> lighting shadows false
> lighting depthCue false
> set bgColor alice blue
> ui mousemode right zoom
> windowsize 570 570
> camera ortho
> color name bluishwhite rgb(201, 218, 222)
Color 'bluishwhite' is opaque: rgb(78.8%, 85.5%, 87.1%) hex: #c9dade
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 INTEL-14.7.8
OpenGL renderer: Intel(R) Iris(TM) Graphics 6100
OpenGL vendor: Intel Inc.Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro12,1
Processor Name: Dual-Core Intel Core i5
Processor Speed: 2.7 GHz
Number of Processors: 1
Total Number of Cores: 2
L2 Cache (per Core): 256 KB
L3 Cache: 3 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
Boot ROM Version: 192.0.0.0.0
SMC Version (system): 2.28f7
Software:
System Software Overview:
System Version: macOS 10.15.7 (19H2)
Kernel Version: Darwin 19.6.0
Time since boot: 48 days 5:06
Graphics/Displays:
Intel Iris Graphics 6100:
Chipset Model: Intel Iris Graphics 6100
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x162b
Revision ID: 0x0009
Metal: Supported, feature set macOS GPUFamily1 v4
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
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: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2021.5.30
cftime: 1.5.1.1
charset-normalizer: 2.0.9
ChimeraX-AddCharge: 1.2.2
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.31
ChimeraX-AtomicLibrary: 4.2
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.6.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.2
ChimeraX-Clipper: 0.17.0
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5
ChimeraX-CommandLine: 1.1.5
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.3
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-Cytoscape: 0.1
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.5
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: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.3
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.4
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.4
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.4
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.2.6
ChimeraX-ModelPanel: 1.2.1
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: 2.0.2
ChimeraX-OpenCommand: 1.7
ChimeraX-PDB: 2.6.5
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
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
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.4.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.6.1
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: 1.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.13.7
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0.1
ChimeraX-VIPERdb: 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: 0.4.4
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.24
decorator: 5.1.0
docutils: 0.17.1
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 3.6.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.21
imagecodecs: 2021.4.28
imagesize: 1.3.0
ipykernel: 5.5.5
ipython: 7.23.1
ipython-genutils: 0.2.0
jedi: 0.18.0
Jinja2: 3.0.1
jupyter-client: 6.1.12
jupyter-core: 4.9.1
kiwisolver: 1.3.2
lxml: 4.6.3
lz4: 3.1.3
MarkupSafe: 2.0.1
matplotlib: 3.4.3
matplotlib-inline: 0.1.3
msgpack: 1.0.2
netCDF4: 1.5.7
networkx: 2.6.3
numexpr: 2.8.0
numpy: 1.21.2
openvr: 1.16.801
packaging: 21.0
ParmEd: 3.2.0
parso: 0.8.3
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 8.3.2
pip: 21.2.4
pkginfo: 1.7.1
prompt-toolkit: 3.0.23
psutil: 5.8.0
ptyprocess: 0.7.0
pycollada: 0.7.1
pydicom: 2.1.2
Pygments: 2.10.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.6
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.2
pytz: 2021.3
pyzmq: 22.3.0
qtconsole: 5.1.1
QtPy: 1.11.3
RandomWords: 0.3.0
requests: 2.26.0
scipy: 1.7.1
setuptools: 57.5.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.2.0
sphinx-autodoc-typehints: 1.12.0
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
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
suds-jurko: 0.6
tifffile: 2021.4.8
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.7
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.0
wheel-filename: 1.3.0
Change History (4)
comment:1 by , 4 years ago
| Component: | Unassigned → Graphics |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Graphics hardware encountered an error and was reset |
comment:2 by , 4 years ago
| Cc: | added |
|---|
comment:4 by , 4 years ago
| Resolution: | → nonchimerax |
|---|---|
| Status: | assigned → closed |
| Summary: | Graphics hardware encountered an error and was reset → Graphics driver crash, macOS 10.15.7, Intel Iris Graphics 6100 |
Apple graphics driver crash. Graphics window had just been resized.
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Didn't get mail when I modified this ticket initially, so modifying again to see if I get any.