![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 5 years ago
Closed 4 years ago
#3520 closed defect (fixed)
Some kind of graphics crash running ISOLDE
| Reported by: | Owned by: | Tristan Croll | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Third Party | Version: | 0.93 |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Darwin-19.5.0-x86_64-i386-64bit
ChimeraX Version: 0.93 (2020-04-03)
Description
I was running ISOLDE with a small molecule bound protein structure on a MacBook Pro.
Process: ChimeraX [90814]
Path: /private/var/folders/*/ChimeraX-0.93.app/Contents/MacOS/ChimeraX
Identifier: ChimeraX
Version: ???
Code Type: X86-64 (Native)
Parent Process: ??? [1]
Responsible: ChimeraX [90814]
User ID: 1979659624
Date/Time: 2020-07-15 22:09:29.303 +0300
OS Version: Mac OS X 10.15.5 (19F101)
Report Version: 12
Bridge OS Version: 4.5 (17P5300)
Anonymous UUID: EDA71157-7254-FBD7-9940-05741977D717
Sleep/Wake UUID: A28DD2FB-8F9B-4EFE-ADD3-5DA1D8DE71E7
Time Awake Since Boot: 1100000 seconds
Time Since Wake: 4400 seconds
System Integrity Protection: enabled
Notes: Translocated Process
Crashed Thread: 45 Dispatch queue: opencl_runtime
Exception Type: EXC_CRASH (SIGABRT)
Exception Codes: 0x0000000000000000, 0x0000000000000000
Exception Note: EXC_CORPSE_NOTIFY
Application Specific Information:
abort() called
Application Specific Signatures:
Graphics kernel error: 0xfffffffa
Thread 0:: CrBrowserMain Dispatch queue: com.apple.main-thread
0 org.python.python 0x0000000103610ab8 listiter_next + 40
1 org.python.python 0x00000001035dfb10 PyIter_Next + 16
2 org.python.python 0x0000000103622d2f dict_merge + 415
3 org.python.python 0x00000001036518b6 merge_class_dict + 54
4 org.python.python 0x0000000103650f02 type___dir__ + 34
5 org.python.python 0x00000001035f5a5f _PyMethodDef_RawFastCallDict + 655
6 org.python.python 0x00000001035f4a8e _PyObject_FastCallDict + 270
7 org.python.python 0x0000000103633051 PyObject_Dir + 49
8 org.python.python 0x00000001036bd7d9 builtin_dir + 57
9 org.python.python 0x00000001035f5d62 _PyMethodDef_RawFastCallKeywords + 226
10 org.python.python 0x00000001035f5289 _PyCFunction_FastCallKeywords + 41
11 org.python.python 0x00000001036ca300 call_function + 656
12 org.python.python 0x00000001036c704e _PyEval_EvalFrameDefault + 26718
13 org.python.python 0x00000001035f5731 function_code_fastcall + 177
14 org.python.python 0x00000001036ca374 call_function + 772
15 org.python.python 0x00000001036c6f9a _PyEval_EvalFrameDefault + 26538
16 org.python.python 0x00000001036cb1cc _PyEval_EvalCodeWithName + 3276
17 org.python.python 0x00000001035f4d47 _PyFunction_FastCallDict + 455
18 org.python.python 0x00000001035f6253 _PyObject_Call_Prepend + 131
19 org.python.python 0x00000001035f4ae2 _PyObject_FastCallDict + 354
20 org.python.python 0x00000001035f70cb object_vacall + 619
21 org.python.python 0x00000001035f72d0 PyObject_CallFunctionObjArgs + 144
22 org.python.python 0x0000000103648547 slot_tp_getattr_hook + 711
23 org.python.python 0x00000001036325c3 _PyObject_LookupAttr + 115
24 org.python.python 0x00000001036bdeb5 builtin_hasattr + 117
25 org.python.python 0x00000001035f5f15 _PyMethodDef_RawFastCallKeywords + 661
26 org.python.python 0x00000001035f5289 _PyCFunction_FastCallKeywords + 41
27 org.python.python 0x00000001036ca300 call_function + 656
28 org.python.python 0x00000001036c704e _PyEval_EvalFrameDefault + 26718
29 org.python.python 0x00000001036cb1cc _PyEval_EvalCodeWithName + 3276
30 org.python.python 0x00000001035f5249 _PyFunction_FastCallKeywords + 217
31 org.python.python 0x00000001036ca374 call_function + 772
32 org.python.python 0x00000001036c0d64 _PyEval_EvalFrameDefault + 1396
33 org.python.python 0x00000001035f5731 function_code_fastcall + 177
34 org.python.python 0x00000001036ca374 call_function + 772
35 org.python.python 0x00000001036c6fb7 _PyEval_EvalFrameDefault + 26567
36 org.python.python 0x00000001035f5731 function_code_fastcall + 177
37 org.python.python 0x00000001036ca374 call_function + 772
38 org.python.python 0x00000001036c6f9a _PyEval_EvalFrameDefault + 26538
39 org.python.python 0x00000001035f5731 function_code_fastcall + 177
40 org.python.python 0x00000001035f6253 _PyObject_Call_Prepend + 131
41 org.python.python 0x00000001035f53a8 PyObject_Call + 136
42 QtCore.so 0x000000011b43ff17 PyQtSlot::call(_object*, _object*) const + 39
43 QtCore.so 0x000000011b43fe26 PyQtSlot::invoke(void**, _object*, void*, bool) const + 374
44 QtCore.so 0x000000011b440925 PyQtSlotProxy::unislot(void**) + 85
45 QtCore.so 0x000000011b44089a PyQtSlotProxy::qt_metacall(QMetaObject::Call, int, void**) + 58
46 QtCore 0x000000011938f37d QMetaObject::activate(QObject*, int, int, void**) + 1773
47 QtCore 0x0000000119397432 QTimer::timerEvent(QTimerEvent*) + 98
48 QtCore.so 0x000000011b336028 sipQTimer::timerEvent(QTimerEvent*) + 120
49 QtCore 0x0000000119387cf6 QObject::event(QEvent*) + 102
50 QtCore.so 0x000000011b335e9b sipQTimer::event(QEvent*) + 187
51 QtWidgets 0x000000011867470d QApplicationPrivate::notify_helper(QObject*, QEvent*) + 269
52 QtWidgets 0x0000000118675b12 QApplication::notify(QObject*, QEvent*) + 594
53 QtWidgets.so 0x00000001182343ca sipQApplication::notify(QObject*, QEvent*) + 234
54 QtCore 0x000000011935e564 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 212
55 QtCore 0x00000001193b7b7f QTimerInfoList::activateTimers() + 991
56 libqcocoa.dylib 0x00000001231e8472 0x1231b4000 + 214130
57 com.apple.CoreFoundation 0x00007fff390afde2 __CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE0_PERFORM_FUNCTION__ + 17
58 com.apple.CoreFoundation 0x00007fff390afd81 __CFRunLoopDoSource0 + 103
59 com.apple.CoreFoundation 0x00007fff390afb9b __CFRunLoopDoSources0 + 209
60 com.apple.CoreFoundation 0x00007fff390ae8ca __CFRunLoopRun + 927
61 com.apple.CoreFoundation 0x00007fff390adece CFRunLoopRunSpecific + 462
62 com.apple.HIToolbox 0x00007fff37cdcabd RunCurrentEventLoopInMode + 292
63 com.apple.HIToolbox 0x00007fff37cdc7d5 ReceiveNextEventCommon + 584
64 com.apple.HIToolbox 0x00007fff37cdc579 _BlockUntilNextEventMatchingListInModeWithFilter + 64
65 com.apple.AppKit 0x00007fff36324829 _DPSNextEvent + 883
66 com.apple.AppKit 0x00007fff36323070 -[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 1352
67 com.apple.AppKit 0x00007fff36314d7e -[NSApplication run] + 658
68 libqcocoa.dylib 0x00000001231e9223 0x1231b4000 + 217635
69 QtCore 0x0000000119359b7f QEventLoop::exec(QFlags) + 431
70 QtCore 0x000000011935eb72 QCoreApplication::exec() + 130
71 QtWidgets.so 0x00000001183237d2 meth_QApplication_exec_(_object*, _object*) + 82
72 org.python.python 0x00000001035f5d62 _PyMethodDef_RawFastCallKeywords + 226
73 org.python.python 0x00000001035f5289 _PyCFunction_FastCallKeywords + 41
74 org.python.python 0x00000001036ca300 call_function + 656
75 org.python.python 0x00000001036c6fb7 _PyEval_EvalFrameDefault + 26567
76 org.python.python 0x00000001035f5731 function_code_fastcall + 177
77 org.python.python 0x00000001036ca374 call_function + 772
78 org.python.python 0x00000001036c6fb7 _PyEval_EvalFrameDefault + 26567
79 org.python.python 0x00000001036cb1cc _PyEval_EvalCodeWithName + 3276
80 org.python.python 0x00000001035f5249 _PyFunction_FastCallKeywords + 217
81 org.python.python 0x00000001036ca374 call_function + 772
82 org.python.python 0x00000001036c704e _PyEval_EvalFrameDefault + 26718
83 org.python.python 0x00000001036cb1cc _PyEval_EvalCodeWithName + 3276
84 org.python.python 0x00000001036c0750 PyEval_EvalCode + 48
85 org.python.python 0x00000001036bdce7 builtin_exec + 583
86 org.python.python 0x00000001035f5f15 _PyMethodDef_RawFastCallKeywords + 661
87 org.python.python 0x00000001035f5289 _PyCFunction_FastCallKeywords + 41
88 org.python.python 0x00000001036ca300 call_function + 656
89 org.python.python 0x00000001036c704e _PyEval_EvalFrameDefault + 26718
90 org.python.python 0x00000001036cb1cc _PyEval_EvalCodeWithName + 3276
91 org.python.python 0x00000001035f5249 _PyFunction_FastCallKeywords + 217
92 org.python.python 0x00000001036ca374 call_function + 772
93 org.python.python 0x00000001036c704e _PyEval_EvalFrameDefault + 26718
94 org.python.python 0x00000001036cb1cc _PyEval_EvalCodeWithName + 3276
95 org.python.python 0x00000001035f4d47 _PyFunction_FastCallDict + 455
96 org.python.python 0x0000000103725293 pymain_run_module + 147
97 org.python.python 0x000000010372437c pymain_main + 5900
98 org.python.python 0x0000000103722c63 Py_Main + 51
99 edu.ucsf.cgl.ChimeraX 0x00000001035c7dc8 main + 120
100 libdyld.dylib 0x00007fff72f11cc9 start + 1
Thread 1:: com.apple.NSEventThread
0 libsystem_kernel.dylib 0x00007fff73052dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff73053170 mach_msg + 60
2 com.apple.CoreFoundation 0x00007fff390aff85 __CFRunLoopServiceMachPort + 247
3 com.apple.CoreFoundation 0x00007fff390aea52 __CFRunLoopRun + 1319
4 com.apple.CoreFoundation 0x00007fff390adece CFRunLoopRunSpecific + 462
5 com.apple.AppKit 0x00007fff364c6144 _NSEventThread + 132
6 libsystem_pthread.dylib 0x00007fff73116109 _pthread_start + 148
7 libsystem_pthread.dylib 0x00007fff73111b8b thread_start + 15
Thread 2:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff73052dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff73053170 mach_msg + 60
2 QtWebEngineCore 0x000000011dd16d7d 0x11bb6b000 + 35306877
3 QtWebEngineCore 0x000000011dd16c7f 0x11bb6b000 + 35306623
4 QtWebEngineCore 0x000000011dccaaad 0x11bb6b000 + 34994861
5 QtWebEngineCore 0x000000011dcf3ad5 0x11bb6b000 + 35162837
6 QtWebEngineCore 0x000000011dd4640c 0x11bb6b000 + 35501068
7 QtWebEngineCore 0x000000011dd86167 0x11bb6b000 + 35762535
8 libsystem_pthread.dylib 0x00007fff73116109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff73111b8b thread_start + 15
Thread 3:: DnsConfigService
0 libsystem_kernel.dylib 0x00007fff73057766 kevent + 10
1 QtWebEngineCore 0x000000011dfd83f9 0x11bb6b000 + 38196217
2 QtWebEngineCore 0x000000011dfd570d 0x11bb6b000 + 38184717
3 QtWebEngineCore 0x000000011dd8c72c 0x11bb6b000 + 35788588
4 QtWebEngineCore 0x000000011dcf3ad5 0x11bb6b000 + 35162837
5 QtWebEngineCore 0x000000011dd4640c 0x11bb6b000 + 35501068
6 QtWebEngineCore 0x000000011dd86167 0x11bb6b000 + 35762535
7 libsystem_pthread.dylib 0x00007fff73116109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff73111b8b thread_start + 15
Thread 4:: TaskSchedulerServiceThread
0 libsystem_kernel.dylib 0x00007fff73057766 kevent + 10
1 QtWebEngineCore 0x000000011dfd83f9 0x11bb6b000 + 38196217
2 QtWebEngineCore 0x000000011dfd570d 0x11bb6b000 + 38184717
3 QtWebEngineCore 0x000000011dd8c714 0x11bb6b000 + 35788564
4 QtWebEngineCore 0x000000011dcf3ad5 0x11bb6b000 + 35162837
5 QtWebEngineCore 0x000000011dd354c4 0x11bb6b000 + 35431620
6 QtWebEngineCore 0x000000011dd4640c 0x11bb6b000 + 35501068
7 QtWebEngineCore 0x000000011dd86167 0x11bb6b000 + 35762535
8 libsystem_pthread.dylib 0x00007fff73116109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff73111b8b thread_start + 15
Thread 5:: TaskSchedulerForegroundWorker
0 libsystem_kernel.dylib 0x00007fff73052dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff73053170 mach_msg + 60
2 QtWebEngineCore 0x000000011dd16d7d 0x11bb6b000 + 35306877
3 QtWebEngineCore 0x000000011dd16e71 0x11bb6b000 + 35307121
4 QtWebEngineCore 0x000000011dd2e778 0x11bb6b000 + 35403640
5 QtWebEngineCore 0x000000011dd2f0ab 0x11bb6b000 + 35405995
6 QtWebEngineCore 0x000000011dd2ed14 0x11bb6b000 + 35405076
7 QtWebEngineCore 0x000000011dd86167 0x11bb6b000 + 35762535
8 libsystem_pthread.dylib 0x00007fff73116109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff73111b8b thread_start + 15
Thread 6:: TaskSchedulerBackgroundWorker
0 libsystem_kernel.dylib 0x00007fff73052dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff73053170 mach_msg + 60
2 QtWebEngineCore 0x000000011dd16d7d 0x11bb6b000 + 35306877
3 QtWebEngineCore 0x000000011dd16e71 0x11bb6b000 + 35307121
4 QtWebEngineCore 0x000000011dd2e778 0x11bb6b000 + 35403640
5 QtWebEngineCore 0x000000011dd2f0ab 0x11bb6b000 + 35405995
6 QtWebEngineCore 0x000000011dd2ec84 0x11bb6b000 + 35404932
7 QtWebEngineCore 0x000000011dd86167 0x11bb6b000 + 35762535
8 libsystem_pthread.dylib 0x00007fff73116109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff73111b8b thread_start + 15
Thread 7:: TaskSchedulerBackgroundBlockingWorker
0 libsystem_kernel.dylib 0x00007fff73052dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff73053170 mach_msg + 60
2 QtWebEngineCore 0x000000011dd16d7d 0x11bb6b000 + 35306877
3 QtWebEngineCore 0x000000011dd16e71 0x11bb6b000 + 35307121
4 QtWebEngineCore 0x000000011dd2e778 0x11bb6b000 + 35403640
5 QtWebEngineCore 0x000000011dd2f0ab 0x11bb6b000 + 35405995
6 QtWebEngineCore 0x000000011dd2ec84 0x11bb6b000 + 35404932
7 QtWebEngineCore 0x000000011dd86167 0x11bb6b000 + 35762535
8 libsystem_pthread.dylib 0x00007fff73116109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff73111b8b thread_start + 15
Thread 8:: Chrome_IOThread
0 libsystem_kernel.dylib 0x00007fff73057766 kevent + 10
1 QtWebEngineCore 0x000000011dfd83f9 0x11bb6b000 + 38196217
2 QtWebEngineCore 0x000000011dfd570d 0x11bb6b000 + 38184717
3 QtWebEngineCore 0x000000011dd8c714 0x11bb6b000 + 35788564
4 QtWebEngineCore 0x000000011dcf3ad5 0x11bb6b000 + 35162837
5 QtWebEngineCore 0x000000011d659a74 0x11bb6b000 + 28240500
6 QtWebEngineCore 0x000000011dd4640c 0x11bb6b000 + 35501068
7 QtWebEngineCore 0x000000011dd86167 0x11bb6b000 + 35762535
8 libsystem_pthread.dylib 0x00007fff73116109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff73111b8b thread_start + 15
Thread 9:: TaskSchedulerSingleThreadSharedBackgroundBlocking0
0 libsystem_kernel.dylib 0x00007fff73052dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff73053170 mach_msg + 60
2 QtWebEngineCore 0x000000011dd16d7d 0x11bb6b000 + 35306877
3 QtWebEngineCore 0x000000011dd16c7f 0x11bb6b000 + 35306623
4 QtWebEngineCore 0x000000011dd2e76a 0x11bb6b000 + 35403626
5 QtWebEngineCore 0x000000011dd2ee0f 0x11bb6b000 + 35405327
6 QtWebEngineCore 0x000000011dd2ecb4 0x11bb6b000 + 35404980
7 QtWebEngineCore 0x000000011dd86167 0x11bb6b000 + 35762535
8 libsystem_pthread.dylib 0x00007fff73116109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff73111b8b thread_start + 15
Thread 10:: CompositorTileWorker1/68611
0 libsystem_kernel.dylib 0x00007fff73055882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff73116425 _pthread_cond_wait + 698
2 QtWebEngineCore 0x000000011dd849f8 0x11bb6b000 + 35756536
3 QtWebEngineCore 0x000000011ed0cfe8 0x11bb6b000 + 52043752
4 QtWebEngineCore 0x000000011dd450e4 0x11bb6b000 + 35496164
5 QtWebEngineCore 0x000000011dd86167 0x11bb6b000 + 35762535
6 libsystem_pthread.dylib 0x00007fff73116109 _pthread_start + 148
7 libsystem_pthread.dylib 0x00007fff73111b8b thread_start + 15
Thread 11:: AudioThread
0 libsystem_kernel.dylib 0x00007fff73052dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff73053170 mach_msg + 60
2 QtWebEngineCore 0x000000011dd16d7d 0x11bb6b000 + 35306877
3 QtWebEngineCore 0x000000011dd16c7f 0x11bb6b000 + 35306623
4 QtWebEngineCore 0x000000011dccaaad 0x11bb6b000 + 34994861
5 QtWebEngineCore 0x000000011dcf3ad5 0x11bb6b000 + 35162837
6 QtWebEngineCore 0x000000011dd4640c 0x11bb6b000 + 35501068
7 QtWebEngineCore 0x000000011dd86167 0x11bb6b000 + 35762535
8 libsystem_pthread.dylib 0x00007fff73116109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff73111b8b thread_start + 15
Thread 12:: Chrome_InProcGpuThread
0 libsystem_kernel.dylib 0x00007fff73052dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff73053170 mach_msg + 60
2 QtWebEngineCore 0x000000011dd16d7d 0x11bb6b000 + 35306877
3 QtWebEngineCore 0x000000011dccaaa2 0x11bb6b000 + 34994850
4 QtWebEngineCore 0x000000011dcf3ad5 0x11bb6b000 + 35162837
5 QtWebEngineCore 0x000000011dd4640c 0x11bb6b000 + 35501068
6 QtWebEngineCore 0x000000011dd86167 0x11bb6b000 + 35762535
7 libsystem_pthread.dylib 0x00007fff73116109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff73111b8b thread_start + 15
Thread 13:: Chrome_ChildIOThread
0 libsystem_kernel.dylib 0x00007fff73057766 kevent + 10
1 QtWebEngineCore 0x000000011dfd83f9 0x11bb6b000 + 38196217
2 QtWebEngineCore 0x000000011dfd570d 0x11bb6b000 + 38184717
3 QtWebEngineCore 0x000000011dd8c72c 0x11bb6b000 + 35788588
4 QtWebEngineCore 0x000000011dcf3ad5 0x11bb6b000 + 35162837
5 QtWebEngineCore 0x000000011dd4640c 0x11bb6b000 + 35501068
6 QtWebEngineCore 0x000000011dd86167 0x11bb6b000 + 35762535
7 libsystem_pthread.dylib 0x00007fff73116109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff73111b8b thread_start + 15
Thread 14:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff73052dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff73053170 mach_msg + 60
2 QtWebEngineCore 0x000000011dd16d7d 0x11bb6b000 + 35306877
3 QtWebEngineCore 0x000000011dd16c7f 0x11bb6b000 + 35306623
4 QtWebEngineCore 0x000000011dccaaad 0x11bb6b000 + 34994861
5 QtWebEngineCore 0x000000011dcf3ad5 0x11bb6b000 + 35162837
6 QtWebEngineCore 0x000000011dd4640c 0x11bb6b000 + 35501068
7 QtWebEngineCore 0x000000011dd86167 0x11bb6b000 + 35762535
8 libsystem_pthread.dylib 0x00007fff73116109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff73111b8b thread_start + 15
Thread 15:: TaskSchedulerSingleThreadForegroundBlocking1
0 libsystem_kernel.dylib 0x00007fff73052dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff73053170 mach_msg + 60
2 QtWebEngineCore 0x000000011dd16d7d 0x11bb6b000 + 35306877
3 QtWebEngineCore 0x000000011dd16c7f 0x11bb6b000 + 35306623
4 QtWebEngineCore 0x000000011dd2e76a 0x11bb6b000 + 35403626
5 QtWebEngineCore 0x000000011dd2f0ab 0x11bb6b000 + 35405995
6 QtWebEngineCore 0x000000011dd2ed74 0x11bb6b000 + 35405172
7 QtWebEngineCore 0x000000011dd86167 0x11bb6b000 + 35762535
8 libsystem_pthread.dylib 0x00007fff73116109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff73111b8b thread_start + 15
Thread 16:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff73052dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff73053170 mach_msg + 60
2 QtWebEngineCore 0x000000011dd16d7d 0x11bb6b000 + 35306877
3 QtWebEngineCore 0x000000011dd16c7f 0x11bb6b000 + 35306623
4 QtWebEngineCore 0x000000011dccaaad 0x11bb6b000 + 34994861
5 QtWebEngineCore 0x000000011dcf3ad5 0x11bb6b000 + 35162837
6 QtWebEngineCore 0x000000011dd4640c 0x11bb6b000 + 35501068
7 QtWebEngineCore 0x000000011dd86167 0x11bb6b000 + 35762535
8 libsystem_pthread.dylib 0x00007fff73116109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff73111b8b thread_start + 15
Thread 17:: PowerSaveBlocker
0 libsystem_kernel.dylib 0x00007fff73052dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff73053170 mach_msg + 60
2 QtWebEngineCore 0x000000011dd16d7d 0x11bb6b000 + 35306877
3 QtWebEngineCore 0x000000011dd16c7f 0x11bb6b000 + 35306623
4 QtWebEngineCore 0x000000011dccaaad 0x11bb6b000 + 34994861
5 QtWebEngineCore 0x000000011dcf3ad5 0x11bb6b000 + 35162837
6 QtWebEngineCore 0x000000011dd4640c 0x11bb6b000 + 35501068
7 QtWebEngineCore 0x000000011dd86167 0x11bb6b000 + 35762535
8 libsystem_pthread.dylib 0x00007fff73116109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff73111b8b thread_start + 15
Thread 18:: TaskSchedulerForegroundBlockingWorker
0 libsystem_kernel.dylib 0x00007fff73052dfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff73053170 mach_msg + 60
2 QtWebEngineCore 0x000000011dd16d7d 0x11bb6b000 + 35306877
3 QtWebEngineCore 0x000000011dd16e71 0x11bb6b000 + 35307121
4 QtWebEngineCore 0x000000011dd2e778 0x11bb6b000 + 35403640
5 QtWebEngineCore 0x000000011dd2f0ab 0x11bb6b000 + 35405995
6 QtWebEngineCore 0x000000011dd2ed14 0x11bb6b000 + 35405076
7 QtWebEngineCore 0x000000011dd86167 0x11bb6b000 + 35762535
8 libsystem_pthread.dylib 0x00007fff73116109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff73111b8b thread_start + 15
Thread 19:
0 libsystem_kernel.dylib 0x00007fff73055882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff73116425 _pthread_cond_wait + 698
2 libOpenMM.dylib 0x000000013b441b3f OpenMM::threadBody(void*) + 207
3 libsystem_pthread.dylib 0x00007fff73116109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff73111b8b thread_start + 15
Thread 20:
0 libsystem_kernel.dylib 0x00007fff73055882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff73116425 _pthread_cond_wait + 698
2 libOpenMM.dylib 0x000000013b441b3f OpenMM::threadBody(void*) + 207
3 libsystem_pthread.dylib 0x00007fff73116109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff73111b8b thread_start + 15
Thread 21:
0 libsystem_kernel.dylib 0x00007fff73055882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff73116425 _pthread_cond_wait + 698
2 libOpenMM.dylib 0x000000013b441b3f OpenMM::threadBody(void*) + 207
3 libsystem_pthread.dylib 0x00007fff73116109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff73111b8b thread_start + 15
Thread 22:
0 libsystem_kernel.dylib 0x00007fff73055882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff73116425 _pthread_cond_wait + 698
2 libOpenMM.dylib 0x000000013b441b3f OpenMM::threadBody(void*) + 207
3 libsystem_pthread.dylib 0x00007fff73116109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff73111b8b thread_start + 15
Thread 23:
0 libsystem_kernel.dylib 0x00007fff73055882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff73116425 _pthread_cond_wait + 698
2 libOpenMM.dylib 0x000000013b441b3f OpenMM::threadBody(void*) + 207
3 libsystem_pthread.dylib 0x00007fff73116109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff73111b8b thread_start + 15
Thread 24:
0 libsystem_kernel.dylib 0x00007fff73055882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff73116425 _pthread_cond_wait + 698
2 libOpenMM.dylib 0x000000013b441b3f OpenMM::threadBody(void*) + 207
3 libsystem_pthread.dylib 0x00007fff73116109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff73111b8b thread_start + 15
Thread 25:
0 libsystem_kernel.dylib 0x00007fff73055882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff73116425 _pthread_cond_wait + 698
2 libOpenMM.dylib 0x000000013b441b3f OpenMM::threadBody(void*) + 207
3 libsystem_pthread.dylib 0x00007fff73116109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff73111b8b thread_start + 15
Thread 26:
0 libsystem_kernel.dylib 0x00007fff73055882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff73116425 _pthread_cond_wait + 698
2 libOpenMM.dylib 0x000000013b441b3f OpenMM::threadBody(void*) + 207
3 libsystem_pthread.dylib 0x00007fff73116109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff73111b8b thread_start + 15
Thread 27:
0 libsystem_kernel.dylib 0x00007fff73055882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff73116425 _pthread_cond_wait + 698
2 libOpenMM.dylib 0x000000013b441b3f OpenMM::threadBody(void*) + 207
3 libsystem_pthread.dylib 0x00007fff73116109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff73111b8b thread_start + 15
Thread 28:
0 libsystem_kernel.dylib 0x00007fff73055882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff73116425 _pthread_cond_wait + 698
2 libOpenMM.dylib 0x000000013b441b3f OpenMM::threadBody(void*) + 207
3 libsystem_pthread.dylib 0x00007fff73116109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff73111b8b thread_start + 15
Thread 29:
0 libsystem_kernel.dylib 0x00007fff73055882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff73116425 _pthread_cond_wait + 698
2 libOpenMM.dylib 0x000000013b441b3f OpenMM::threadBody(void*) + 207
3 libsystem_pthread.dylib 0x00007fff73116109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff73111b8b thread_start + 15
Thread 30:
0 libsystem_kernel.dylib 0x00007fff73055882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff73116425 _pthread_cond_wait + 698
2 libOpenMM.dylib 0x000000013b441b3f OpenMM::threadBody(void*) + 207
3 libsystem_pthread.dylib 0x00007fff73116109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff73111b8b thread_start + 15
Thread 31:
0 libsystem_kernel.dylib 0x00007fff73055882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff73116425 _pthread_cond_wait + 698
2 libOpenMM.dylib 0x000000013b441b3f OpenMM::threadBody(void*) + 207
3 libsystem_pthread.dylib 0x00007fff73116109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff73111b8b thread_start + 15
Thread 32:
0 libsystem_kernel.dylib 0x00007fff73055882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff73116425 _pthread_cond_wait + 698
2 libOpenMM.dylib 0x000000013b441b3f OpenMM::threadBody(void*) + 207
3 libsystem_pthread.dylib 0x00007fff73116109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff73111b8b thread_start + 15
Thread 33:
0 libsystem_kernel.dylib 0x00007fff73055882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff73116425 _pthread_cond_wait + 698
2 libOpenMM.dylib 0x000000013b441b3f OpenMM::threadBody(void*) + 207
3 libsystem_pthread.dylib 0x00007fff73116109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff73111b8b thread_start + 15
Thread 34:
0 libsystem_kernel.dylib 0x00007fff73055882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff73116425 _pthread_cond_wait + 698
2 libOpenMM.dylib 0x000000013b441b3f OpenMM::threadBody(void*) + 207
3 libsystem_pthread.dylib 0x00007fff73116109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff73111b8b thread_start + 15
Thread 35:
0 libsystem_kernel.dylib 0x00007fff73055882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff73116425 _pthread_cond_wait + 698
2 libOpenMMOpenCL.dylib 0x000000013b6ea41d threadBody(void*) + 109
3 libsystem_pthread.dylib 0x00007fff73116109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff73111b8b thread_start + 15
Thread 36:
0 libsystem_kernel.dylib 0x00007fff73052f02 swtch_pri + 10
1 libsystem_pthread.dylib 0x00007fff73113698 sched_yield + 11
2 libopenblasp-r0.3.7.dylib 0x0000000107f7bc05 blas_thread_server + 565
3 libsystem_pthread.dylib 0x00007fff73116109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff73111b8b thread_start + 15
Thread 37:
0 libsystem_kernel.dylib 0x00007fff73052f02 swtch_pri + 10
1 libsystem_pthread.dylib 0x00007fff73113698 sched_yield + 11
2 libopenblasp-r0.3.7.dylib 0x0000000107f7bc05 blas_thread_server + 565
3 libsystem_pthread.dylib 0x00007fff73116109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff73111b8b thread_start + 15
Thread 38:
0 libsystem_kernel.dylib 0x00007fff73055882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff73116425 _pthread_cond_wait + 698
2 libopenblasp-r0.3.7.dylib 0x0000000107f7bc3b blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff73116109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff73111b8b thread_start + 15
Thread 39:
0 libsystem_kernel.dylib 0x00007fff73055882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff73116425 _pthread_cond_wait + 698
2 libopenblasp-r0.3.7.dylib 0x0000000107f7bc3b blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff73116109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff73111b8b thread_start + 15
Thread 40:
0 libsystem_kernel.dylib 0x00007fff73055882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff73116425 _pthread_cond_wait + 698
2 libopenblasp-r0.3.7.dylib 0x0000000107f7bc3b blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff73116109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff73111b8b thread_start + 15
Thread 41:
0 libsystem_kernel.dylib 0x00007fff73055882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff73116425 _pthread_cond_wait + 698
2 libopenblasp-r0.3.7.dylib 0x0000000107f7bc3b blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff73116109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff73111b8b thread_start + 15
Thread 42:
0 libsystem_kernel.dylib 0x00007fff73055882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff73116425 _pthread_cond_wait + 698
2 libopenblasp-r0.3.7.dylib 0x0000000107f7bc3b blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff73116109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff73111b8b thread_start + 15
Thread 43:
0 libsystem_pthread.dylib 0x00007fff73111b68 start_wqthread + 0
Thread 44:
0 libsystem_pthread.dylib 0x00007fff73111b68 start_wqthread + 0
Thread 45 Crashed:: Dispatch queue: opencl_runtime
0 libsystem_kernel.dylib 0x00007fff7305933a __pthread_kill + 10
1 libsystem_pthread.dylib 0x00007fff73115e60 pthread_kill + 430
2 libsystem_c.dylib 0x00007fff72f7093e raise + 26
3 libsystem_platform.dylib 0x00007fff7310a5fd _sigtramp + 29
4 ??? 0x0000000000000001 0 + 1
5 libsystem_c.dylib 0x00007fff72fe0808 abort + 120
6 libGPUSupportMercury.dylib 0x00007fff5a3310a5 gpusGenerateCrashLog.cold.1 + 95
7 libGPUSupportMercury.dylib 0x00007fff5a32818f gpusGenerateCrashLog + 89
8 com.apple.AMDRadeonX6000GLDriver 0x00000001252aad5d gpusKillClientExt + 9
9 libGPUSupportMercury.dylib 0x00007fff5a328b38 gpusQueueSubmitDataBuffers + 159
10 com.apple.AMDRadeonX6000GLDriver 0x000000012527b5b2 glrAMDCompSubmitPackets + 228
11 com.apple.AMDRadeonX6000GLDriver 0x000000012527b49a glrAMDFlush + 30
12 com.apple.AMDRadeonX6000GLDriver 0x000000012527b840 gldFlushQueue + 37
13 com.apple.AMDRadeonX6000GLDriver 0x000000012527b85f gldFinishQueue + 19
14 com.apple.opencl 0x00007fff4256aacd 0x7fff42559000 + 72397
15 com.apple.opencl 0x00007fff4256af0c 0x7fff42559000 + 73484
16 com.apple.opencl 0x00007fff425843ff 0x7fff42559000 + 177151
17 com.apple.opencl 0x00007fff4258605d 0x7fff42559000 + 184413
18 libdispatch.dylib 0x00007fff72eb8658 _dispatch_client_callout + 8
19 libdispatch.dylib 0x00007fff72ec46ec _dispatch_lane_barrier_sync_invoke_and_complete + 60
20 com.apple.opencl 0x00007fff42585ee9 0x7fff42559000 + 184041
21 com.apple.opencl 0x00007fff42583531 0x7fff42559000 + 173361
22 com.apple.opencl 0x00007fff4257abd6 clEnqueueReadBuffer + 751
23 libOpenMMOpenCL.dylib 0x000000013b6cb2d8 OpenMM::OpenCLArray::download(void*, bool) const + 104
24 libOpenMMOpenCL.dylib 0x000000013b713304 OpenMM::OpenCLIntegrationUtilities::getLastStepSize() + 84
25 libOpenMMOpenCL.dylib 0x000000013b7cc273 OpenMM::OpenCLIntegrateVariableLangevinStepKernel::execute(OpenMM::ContextImpl&, OpenMM::VariableLangevinIntegrator const&, double) + 2035
26 libOpenMM.dylib 0x000000013b442b30 OpenMM::VariableLangevinIntegrator::step(int) + 144
27 libopenmm.dylib 0x000000012e649c19 isolde::OpenMM_Thread_Handler::_step_threaded(unsigned long, bool) + 345
28 libopenmm.dylib 0x000000012e64dfbd void* std::__1::__thread_proxy >, void (isolde::OpenMM_Thread_Handler::*)(unsigned long, bool), isolde::OpenMM_Thread_Handler*, unsigned long, bool> >(void*) + 77
29 libsystem_pthread.dylib 0x00007fff73116109 _pthread_start + 148
30 libsystem_pthread.dylib 0x00007fff73111b8b thread_start + 15
Thread 45 crashed with X86 Thread State (64-bit):
rax: 0x0000000000000000 rbx: 0x000070000e286000 rcx: 0x000070000e284f48 rdx: 0x0000000000000000
rdi: 0x000000000001a9ab rsi: 0x0000000000000006 rbp: 0x000070000e284f70 rsp: 0x000070000e284f48
r8: 0x000070000e285430 r9: 0x0a897b68e7e1dc03 r10: 0x000070000e286000 r11: 0x0000000000000246
r12: 0x000000000001a9ab r13: 0x00007fa1ca6041b0 r14: 0x0000000000000006 r15: 0x0000000000000016
rip: 0x00007fff7305933a rfl: 0x0000000000000246 cr2: 0x00007f97872fc09b
Logical CPU: 0
Error Code: 0x02000148
Trap Number: 133
Binary Images:
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0x7fff73107000 - 0x7fff7310ffef libsystem_platform.dylib (220.100.1) /usr/lib/system/libsystem_platform.dylib
0x7fff73110000 - 0x7fff7311afff libsystem_pthread.dylib (416.100.3) /usr/lib/system/libsystem_pthread.dylib
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0x7fff73149000 - 0x7fff7317effe libxpc.dylib (1738.120.8) /usr/lib/system/libxpc.dylib
External Modification Summary:
Calls made by other processes targeting this process:
task_for_pid: 17
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: 1765139
thread_create: 0
thread_set_state: 0
VM Region Summary:
ReadOnly portion of Libraries: Total=1.0G resident=0K(0%) swapped_out_or_unallocated=1.0G(100%)
Writable regions: Total=4.0G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=4.0G(100%)
VIRTUAL REGION
REGION TYPE SIZE COUNT (non-coalesced)
=========== ======= =======
Accelerate framework 384K 3
Activity Tracing 256K 1
CG backing stores 1232K 2
CG image 548K 33
CoreAnimation 4160K 72
CoreGraphics 8K 1
CoreImage 28K 3
CoreUI image data 3836K 34
Foundation 24K 2
Kernel Alloc Once 8K 1
MALLOC 2.5G 1512
MALLOC guard page 32K 6
MALLOC_LARGE (reserved) 640K 1 reserved VM address space (unallocated)
MALLOC_NANO (reserved) 384.0M 1 reserved VM address space (unallocated)
Memory Tag 242 12K 1
Memory Tag 251 12K 1
OpenCL 122.5M 67
OpenCL (reserved) 24K 4 reserved VM address space (unallocated)
OpenGL GLSL 512K 6
PROTECTED_MEMORY 4K 1
STACK GUARD 56.2M 46
Stack 158.4M 46
VM_ALLOCATE 703.7M 856
VM_ALLOCATE (reserved) 160.0M 2 reserved VM address space (unallocated)
__DATA 67.1M 640
__DATA_CONST 132K 6
__FONT_DATA 4K 1
__GLSLBUILTINS 5176K 1
__LINKEDIT 425.9M 218
__OBJC_RO 32.2M 1
__OBJC_RW 1888K 1
__TEXT 606.3M 593
__UNICODE 564K 1
mapped file 118.9M 54
shared memory 668K 21
=========== ======= =======
TOTAL 5.3G 4239
TOTAL, minus reserved VM space 4.8G 4239
Log:
UCSF ChimeraX version: 0.93 (2020-04-03)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 ATI-3.9.15
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Change History (6)
comment:1 by , 5 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Third Party |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Some kind of graphics crash running ISOLDE |
| Version: | → 0.93 |
comment:2 by , 5 years ago
follow-up: 3 comment:3 by , 5 years ago
There are two other bug reports #3505 and #3521 this week where OpenGL reported "out of memory" at ChimeraX startup. These make no sense. Possibly a window size of -1 or erroneous huge value was passed to an OpenGL buffer allocating routine. But it is strange to get two reports of that in one week on Windows and Linux with different older ChimeraX versions. It looks like the errors don't report the OpenGL call that actually caused the error. Doesn't seem these errors are related to your OpenCL error but who knows.
follow-up: 4 comment:4 by , 5 years ago
Current ChimeraX 1.0 uses OpenMM 7.4.1 which has a fix to the runaway OpenMM memory use during large forces added by Peter Eastman. ChimeraX 0.93 has OpenMM 7.4.0 that does not have the fix. Looks like ISOLDE is not available yet for ChimeraX 1.0.
follow-up: 5 comment:5 by , 5 years ago
Working on it... progress is slower than I'd like. On 2020-07-16 19:36, ChimeraX wrote:
comment:6 by , 4 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
Sorry for the necropost - just cleaning up some ancient history (this has been fixed for ages now).
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Took a little digging, but 0xfffffffa works out to -6, corresponding to CL_OUT_OF_HOST_MEMORY (thrown while OpenMM was performing a simulation step). Note, that's *host* (i.e. system) memory - out of *device* memory would be -5. I've only ever seen a report of this error twice (the other happened on a Linux machine while starting a simulation, and only caused a Python traceback rather than a complete crash). It seems rather surprising on the face of it... is this an especially large model? Did you have a lot of other stuff open? Honestly not entirely sure what to do about it, to be frank.
... actually, one thing does come to mind. There's a bug in the version of OpenMM we're currently using (fixed in their newer versions, which we can't yet update to due to Linux compiler incompatibility) that causes the memory usage to explode if the simulation "explodes" - that is, you do something that creates an enormous force causing everything to fly apart. Rather hard to do these days (I've put quite a bit of effort into catching excessive velocities and triggering an automatic energy minimisation to reel things back in, but it *is* possible, particularly if you're aggressively tugging on atoms very close to other atoms that are fixed in space. Could this have been what happened here?