![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 7 years ago
Closed 7 years ago
#1444 closed defect (can't reproduce)
Crash running OpenMM simulation
| Reported by: | Owned by: | Tristan Croll | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Third Party | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Darwin-18.0.0-x86_64-i386-64bit
ChimeraX Version: 0.8 (2018-11-11)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Process: ChimeraX [21034]
Path: /Volumes/VOLUME/*/ChimeraX.app/Contents/MacOS/ChimeraX
Identifier: ChimeraX
Version: ???
Code Type: X86-64 (Native)
Parent Process: ??? [1]
Responsible: ChimeraX [21034]
User ID: 312535630
Date/Time: 2018-11-13 14:51:37.693 +0100
OS Version: Mac OS X 10.14 (18A391)
Report Version: 12
Bridge OS Version: 3.0 (14Y667)
Anonymous UUID: C55BD4FD-5235-FB12-5562-74AC346B79EF
Sleep/Wake UUID: 08D5BE86-6381-48BC-9503-9D6623E034B2
Time Awake Since Boot: 110000 seconds
Time Since Wake: 8100 seconds
System Integrity Protection: enabled
Notes: Translocated Process
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:
terminating
abort() called
Thread 0 Crashed:: CrBrowserMain Dispatch queue: com.apple.main-thread
0 libsystem_kernel.dylib 0x00007fff63656b86 __pthread_kill + 10
1 libsystem_pthread.dylib 0x00007fff6370cc50 pthread_kill + 285
2 libsystem_c.dylib 0x00007fff63573096 raise + 26
3 libsystem_platform.dylib 0x00007fff63701b3d _sigtramp + 29
4 ??? 000000000000000000 0 + 0
5 libsystem_c.dylib 0x00007fff635c01c9 abort + 127
6 libc++abi.dylib 0x00007fff60c43231 abort_message + 231
7 libc++abi.dylib 0x00007fff60c432f4 default_terminate_handler() + 48
8 libc++abi.dylib 0x00007fff60c4edfe std::__terminate(void (*)()) + 8
9 libc++abi.dylib 0x00007fff60c4ee85 std::terminate() + 69
10 libopenmm.dylib 0x000000011c550004 openmm_thread_handler_step + 20
11 _ctypes.cpython-36m-darwin.so 0x000000010ed24f5f ffi_call_unix64 + 79
12 _ctypes.cpython-36m-darwin.so 0x000000010ed257ba ffi_call + 858
13 _ctypes.cpython-36m-darwin.so 0x000000010ed20943 _ctypes_callproc + 787
14 _ctypes.cpython-36m-darwin.so 0x000000010ed1a739 PyCFuncPtr_call + 1049
15 org.python.python 0x000000010790a2a4 _PyObject_FastCallDict + 292
16 org.python.python 0x00000001079dc30b call_function + 427
17 org.python.python 0x00000001079d525c _PyEval_EvalFrameDefault + 4988
18 org.python.python 0x00000001079dd91d _PyFunction_FastCallDict + 813
19 org.python.python 0x000000010790a2da _PyObject_FastCallDict + 346
20 org.python.python 0x000000010790a40c _PyObject_Call_Prepend + 156
21 org.python.python 0x000000010790a035 PyObject_Call + 101
22 org.python.python 0x00000001079d54e3 _PyEval_EvalFrameDefault + 5635
23 org.python.python 0x00000001079dd52f fast_function + 511
24 org.python.python 0x00000001079dc312 call_function + 434
25 org.python.python 0x00000001079d525c _PyEval_EvalFrameDefault + 4988
26 org.python.python 0x00000001079dd52f fast_function + 511
27 org.python.python 0x00000001079dc312 call_function + 434
28 org.python.python 0x00000001079d525c _PyEval_EvalFrameDefault + 4988
29 org.python.python 0x00000001079dce20 _PyEval_EvalCodeWithName + 2592
30 org.python.python 0x00000001079dd835 _PyFunction_FastCallDict + 581
31 org.python.python 0x000000010790a2da _PyObject_FastCallDict + 346
32 org.python.python 0x000000010790a40c _PyObject_Call_Prepend + 156
33 org.python.python 0x000000010790a035 PyObject_Call + 101
34 org.python.python 0x00000001079d54e3 _PyEval_EvalFrameDefault + 5635
35 org.python.python 0x00000001079dce20 _PyEval_EvalCodeWithName + 2592
36 org.python.python 0x00000001079dd4b2 fast_function + 386
37 org.python.python 0x00000001079dc312 call_function + 434
38 org.python.python 0x00000001079d525c _PyEval_EvalFrameDefault + 4988
39 org.python.python 0x00000001079dd52f fast_function + 511
40 org.python.python 0x00000001079dc312 call_function + 434
41 org.python.python 0x00000001079d525c _PyEval_EvalFrameDefault + 4988
42 org.python.python 0x00000001079dd52f fast_function + 511
43 org.python.python 0x00000001079dc312 call_function + 434
44 org.python.python 0x00000001079d525c _PyEval_EvalFrameDefault + 4988
45 org.python.python 0x00000001079dce20 _PyEval_EvalCodeWithName + 2592
46 org.python.python 0x00000001079dd4b2 fast_function + 386
47 org.python.python 0x00000001079dc312 call_function + 434
48 org.python.python 0x00000001079d525c _PyEval_EvalFrameDefault + 4988
49 org.python.python 0x00000001079dd52f fast_function + 511
50 org.python.python 0x00000001079dc312 call_function + 434
51 org.python.python 0x00000001079d525c _PyEval_EvalFrameDefault + 4988
52 org.python.python 0x00000001079dd91d _PyFunction_FastCallDict + 813
53 org.python.python 0x000000010790a2da _PyObject_FastCallDict + 346
54 org.python.python 0x000000010790a40c _PyObject_Call_Prepend + 156
55 org.python.python 0x000000010790a035 PyObject_Call + 101
56 QtCore.so 0x0000000111982828 PyQtSlot::call(_object*, _object*) const + 40
57 QtCore.so 0x0000000111982727 PyQtSlot::invoke(void**, _object*, void*, bool) const + 391
58 QtCore.so 0x0000000111983268 PyQtSlotProxy::unislot(void**) + 88
59 QtCore.so 0x00000001119831da PyQtSlotProxy::qt_metacall(QMetaObject::Call, int, void**) + 58
60 QtCore 0x00000001114ea3d6 QMetaObject::activate(QObject*, int, int, void**) + 2230
61 QtCore 0x00000001114f2042 QTimer::timerEvent(QTimerEvent*) + 98
62 QtCore.so 0x0000000111882a68 sipQTimer::timerEvent(QTimerEvent*) + 120
63 QtCore 0x00000001114e2696 QObject::event(QEvent*) + 102
64 QtCore.so 0x00000001118828db sipQTimer::event(QEvent*) + 187
65 QtWidgets 0x0000000110836b82 QApplicationPrivate::notify_helper(QObject*, QEvent*) + 306
66 QtWidgets 0x0000000110837e9f QApplication::notify(QObject*, QEvent*) + 383
67 QtWidgets.so 0x0000000110408f8a sipQApplication::notify(QObject*, QEvent*) + 234
68 QtCore 0x00000001114b9a7f QCoreApplication::notifyInternal2(QObject*, QEvent*) + 159
69 QtCore 0x000000011150fb1a QTimerInfoList::activateTimers() + 890
70 libqcocoa.dylib 0x0000000119ba1862 0x119b7b000 + 157794
71 com.apple.CoreFoundation 0x00007fff364a0405 __CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE0_PERFORM_FUNCTION__ + 17
72 com.apple.CoreFoundation 0x00007fff364a03ab __CFRunLoopDoSource0 + 108
73 com.apple.CoreFoundation 0x00007fff36483e51 __CFRunLoopDoSources0 + 195
74 com.apple.CoreFoundation 0x00007fff364833fa __CFRunLoopRun + 1219
75 com.apple.CoreFoundation 0x00007fff36482ce4 CFRunLoopRunSpecific + 463
76 com.apple.HIToolbox 0x00007fff3571c895 RunCurrentEventLoopInMode + 293
77 com.apple.HIToolbox 0x00007fff3571c5cb ReceiveNextEventCommon + 618
78 com.apple.HIToolbox 0x00007fff3571c348 _BlockUntilNextEventMatchingListInModeWithFilter + 64
79 com.apple.AppKit 0x00007fff339d995b _DPSNextEvent + 997
80 com.apple.AppKit 0x00007fff339d86fa -[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 1362
81 com.apple.AppKit 0x00007fff339d275d -[NSApplication run] + 699
82 libqcocoa.dylib 0x0000000119ba253d 0x119b7b000 + 161085
83 QtCore 0x00000001114b5742 QEventLoop::exec(QFlags) + 418
84 QtCore 0x00000001114ba172 QCoreApplication::exec() + 402
85 QtWidgets.so 0x00000001104f6dc2 meth_QApplication_exec_(_object*, _object*) + 82
86 org.python.python 0x0000000107952b06 _PyCFunction_FastCallDict + 166
87 org.python.python 0x00000001079dc337 call_function + 471
88 org.python.python 0x00000001079d525c _PyEval_EvalFrameDefault + 4988
89 org.python.python 0x00000001079dd52f fast_function + 511
90 org.python.python 0x00000001079dc312 call_function + 434
91 org.python.python 0x00000001079d525c _PyEval_EvalFrameDefault + 4988
92 org.python.python 0x00000001079dce20 _PyEval_EvalCodeWithName + 2592
93 org.python.python 0x00000001079dd4b2 fast_function + 386
94 org.python.python 0x00000001079dc312 call_function + 434
95 org.python.python 0x00000001079d525c _PyEval_EvalFrameDefault + 4988
96 org.python.python 0x00000001079dce20 _PyEval_EvalCodeWithName + 2592
97 org.python.python 0x00000001079d3e50 PyEval_EvalCode + 48
98 org.python.python 0x00000001079d163b builtin_exec + 555
99 org.python.python 0x0000000107952b06 _PyCFunction_FastCallDict + 166
100 org.python.python 0x00000001079dc337 call_function + 471
101 org.python.python 0x00000001079d525c _PyEval_EvalFrameDefault + 4988
102 org.python.python 0x00000001079dce20 _PyEval_EvalCodeWithName + 2592
103 org.python.python 0x00000001079dd4b2 fast_function + 386
104 org.python.python 0x00000001079dc312 call_function + 434
105 org.python.python 0x00000001079d525c _PyEval_EvalFrameDefault + 4988
106 org.python.python 0x00000001079dce20 _PyEval_EvalCodeWithName + 2592
107 org.python.python 0x00000001079d3e97 PyEval_EvalCodeEx + 55
108 org.python.python 0x000000010793227e function_call + 350
109 org.python.python 0x000000010790a035 PyObject_Call + 101
110 org.python.python 0x0000000107a22b53 RunModule + 147
111 org.python.python 0x0000000107a223ec Py_Main + 2588
112 edu.ucsf.cgl.ChimeraX 0x00000001078f5e16 main + 278
113 libdyld.dylib 0x00007fff63518085 start + 1
Thread 1:: com.apple.NSEventThread
0 libsystem_kernel.dylib 0x00007fff63650c2a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff63651174 mach_msg + 60
2 com.apple.CoreFoundation 0x00007fff3648405e __CFRunLoopServiceMachPort + 337
3 com.apple.CoreFoundation 0x00007fff364835ad __CFRunLoopRun + 1654
4 com.apple.CoreFoundation 0x00007fff36482ce4 CFRunLoopRunSpecific + 463
5 com.apple.AppKit 0x00007fff339e2581 _NSEventThread + 160
6 libsystem_pthread.dylib 0x00007fff6370a33d _pthread_body + 126
7 libsystem_pthread.dylib 0x00007fff6370d2a7 _pthread_start + 70
8 libsystem_pthread.dylib 0x00007fff63709425 thread_start + 13
Thread 2:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff63658b8e poll + 10
1 QtCore 0x000000011150cb40 qt_safe_poll(pollfd*, unsigned int, timespec const*) + 544
2 QtCore 0x000000011150e1b9 QEventDispatcherUNIX::processEvents(QFlags) + 857
3 QtCore 0x00000001114b5742 QEventLoop::exec(QFlags) + 418
4 QtWebEngineCore 0x0000000112338c4a 0x112317000 + 138314
5 QtWebEngineCore 0x0000000112f3410e 0x112317000 + 12701966
6 QtWebEngineCore 0x0000000112f58531 0x112317000 + 12850481
7 QtWebEngineCore 0x0000000112f8c36b 0x112317000 + 13063019
8 QtWebEngineCore 0x0000000112f85667 0x112317000 + 13035111
9 libsystem_pthread.dylib 0x00007fff6370a33d _pthread_body + 126
10 libsystem_pthread.dylib 0x00007fff6370d2a7 _pthread_start + 70
11 libsystem_pthread.dylib 0x00007fff63709425 thread_start + 13
Thread 3:: DnsConfigService
0 libsystem_kernel.dylib 0x00007fff63657052 kevent + 10
1 QtWebEngineCore 0x0000000113445469 0x112317000 + 18015337
2 QtWebEngineCore 0x000000011344275d 0x112317000 + 18003805
3 QtWebEngineCore 0x0000000112f3699f 0x112317000 + 12712351
4 QtWebEngineCore 0x0000000112f3410e 0x112317000 + 12701966
5 QtWebEngineCore 0x0000000112f58531 0x112317000 + 12850481
6 QtWebEngineCore 0x0000000112f8c36b 0x112317000 + 13063019
7 QtWebEngineCore 0x0000000112f85667 0x112317000 + 13035111
8 libsystem_pthread.dylib 0x00007fff6370a33d _pthread_body + 126
9 libsystem_pthread.dylib 0x00007fff6370d2a7 _pthread_start + 70
10 libsystem_pthread.dylib 0x00007fff63709425 thread_start + 13
Thread 4:: Chrome_DBThread
0 libsystem_kernel.dylib 0x00007fff63650c2a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff63651174 mach_msg + 60
2 com.apple.CoreFoundation 0x00007fff3648405e __CFRunLoopServiceMachPort + 337
3 com.apple.CoreFoundation 0x00007fff364835ad __CFRunLoopRun + 1654
4 com.apple.CoreFoundation 0x00007fff36482ce4 CFRunLoopRunSpecific + 463
5 QtWebEngineCore 0x0000000112f3790f 0x112317000 + 12716303
6 QtWebEngineCore 0x0000000112f372a4 0x112317000 + 12714660
7 QtWebEngineCore 0x0000000112f3410e 0x112317000 + 12701966
8 QtWebEngineCore 0x0000000112f58531 0x112317000 + 12850481
9 QtWebEngineCore 0x0000000112604958 0x112317000 + 3070296
10 QtWebEngineCore 0x0000000112604d1f 0x112317000 + 3071263
11 QtWebEngineCore 0x0000000112f8c36b 0x112317000 + 13063019
12 QtWebEngineCore 0x0000000112f85667 0x112317000 + 13035111
13 libsystem_pthread.dylib 0x00007fff6370a33d _pthread_body + 126
14 libsystem_pthread.dylib 0x00007fff6370d2a7 _pthread_start + 70
15 libsystem_pthread.dylib 0x00007fff63709425 thread_start + 13
Thread 5:: Chrome_FileThread
0 libsystem_kernel.dylib 0x00007fff63657052 kevent + 10
1 QtWebEngineCore 0x0000000113445469 0x112317000 + 18015337
2 QtWebEngineCore 0x000000011344275d 0x112317000 + 18003805
3 QtWebEngineCore 0x0000000112f3699f 0x112317000 + 12712351
4 QtWebEngineCore 0x0000000112f3410e 0x112317000 + 12701966
5 QtWebEngineCore 0x0000000112f58531 0x112317000 + 12850481
6 QtWebEngineCore 0x00000001126049d8 0x112317000 + 3070424
7 QtWebEngineCore 0x0000000112604d2f 0x112317000 + 3071279
8 QtWebEngineCore 0x0000000112f8c36b 0x112317000 + 13063019
9 QtWebEngineCore 0x0000000112f85667 0x112317000 + 13035111
10 libsystem_pthread.dylib 0x00007fff6370a33d _pthread_body + 126
11 libsystem_pthread.dylib 0x00007fff6370d2a7 _pthread_start + 70
12 libsystem_pthread.dylib 0x00007fff63709425 thread_start + 13
Thread 6:: Chrome_FileUserBlockingThread
0 libsystem_kernel.dylib 0x00007fff63650c2a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff63651174 mach_msg + 60
2 com.apple.CoreFoundation 0x00007fff3648405e __CFRunLoopServiceMachPort + 337
3 com.apple.CoreFoundation 0x00007fff364835ad __CFRunLoopRun + 1654
4 com.apple.CoreFoundation 0x00007fff36482ce4 CFRunLoopRunSpecific + 463
5 QtWebEngineCore 0x0000000112f3790f 0x112317000 + 12716303
6 QtWebEngineCore 0x0000000112f372a4 0x112317000 + 12714660
7 QtWebEngineCore 0x0000000112f3410e 0x112317000 + 12701966
8 QtWebEngineCore 0x0000000112f58531 0x112317000 + 12850481
9 QtWebEngineCore 0x0000000112604a58 0x112317000 + 3070552
10 QtWebEngineCore 0x0000000112604d3f 0x112317000 + 3071295
11 QtWebEngineCore 0x0000000112f8c36b 0x112317000 + 13063019
12 QtWebEngineCore 0x0000000112f85667 0x112317000 + 13035111
13 libsystem_pthread.dylib 0x00007fff6370a33d _pthread_body + 126
14 libsystem_pthread.dylib 0x00007fff6370d2a7 _pthread_start + 70
15 libsystem_pthread.dylib 0x00007fff63709425 thread_start + 13
Thread 7:: Chrome_ProcessLauncherThread
0 libsystem_kernel.dylib 0x00007fff63650c2a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff63651174 mach_msg + 60
2 com.apple.CoreFoundation 0x00007fff3648405e __CFRunLoopServiceMachPort + 337
3 com.apple.CoreFoundation 0x00007fff364835ad __CFRunLoopRun + 1654
4 com.apple.CoreFoundation 0x00007fff36482ce4 CFRunLoopRunSpecific + 463
5 QtWebEngineCore 0x0000000112f3790f 0x112317000 + 12716303
6 QtWebEngineCore 0x0000000112f372a4 0x112317000 + 12714660
7 QtWebEngineCore 0x0000000112f3410e 0x112317000 + 12701966
8 QtWebEngineCore 0x0000000112f58531 0x112317000 + 12850481
9 QtWebEngineCore 0x0000000112604ad8 0x112317000 + 3070680
10 QtWebEngineCore 0x0000000112604d4c 0x112317000 + 3071308
11 QtWebEngineCore 0x0000000112f8c36b 0x112317000 + 13063019
12 QtWebEngineCore 0x0000000112f85667 0x112317000 + 13035111
13 libsystem_pthread.dylib 0x00007fff6370a33d _pthread_body + 126
14 libsystem_pthread.dylib 0x00007fff6370d2a7 _pthread_start + 70
15 libsystem_pthread.dylib 0x00007fff63709425 thread_start + 13
Thread 8:: Chrome_CacheThread
0 libsystem_kernel.dylib 0x00007fff63650c2a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff63651174 mach_msg + 60
2 com.apple.CoreFoundation 0x00007fff3648405e __CFRunLoopServiceMachPort + 337
3 com.apple.CoreFoundation 0x00007fff364835ad __CFRunLoopRun + 1654
4 com.apple.CoreFoundation 0x00007fff36482ce4 CFRunLoopRunSpecific + 463
5 QtWebEngineCore 0x0000000112f3790f 0x112317000 + 12716303
6 QtWebEngineCore 0x0000000112f372a4 0x112317000 + 12714660
7 QtWebEngineCore 0x0000000112f3410e 0x112317000 + 12701966
8 QtWebEngineCore 0x0000000112f58531 0x112317000 + 12850481
9 QtWebEngineCore 0x0000000112604b58 0x112317000 + 3070808
10 QtWebEngineCore 0x0000000112604d59 0x112317000 + 3071321
11 QtWebEngineCore 0x0000000112f8c36b 0x112317000 + 13063019
12 QtWebEngineCore 0x0000000112f85667 0x112317000 + 13035111
13 libsystem_pthread.dylib 0x00007fff6370a33d _pthread_body + 126
14 libsystem_pthread.dylib 0x00007fff6370d2a7 _pthread_start + 70
15 libsystem_pthread.dylib 0x00007fff63709425 thread_start + 13
Thread 9:: Chrome_IOThread
0 libsystem_kernel.dylib 0x00007fff63657052 kevent + 10
1 QtWebEngineCore 0x0000000113445469 0x112317000 + 18015337
2 QtWebEngineCore 0x000000011344275d 0x112317000 + 18003805
3 QtWebEngineCore 0x0000000112f3699f 0x112317000 + 12712351
4 QtWebEngineCore 0x0000000112f3410e 0x112317000 + 12701966
5 QtWebEngineCore 0x0000000112f58531 0x112317000 + 12850481
6 QtWebEngineCore 0x0000000112604bd8 0x112317000 + 3070936
7 QtWebEngineCore 0x0000000112604d66 0x112317000 + 3071334
8 QtWebEngineCore 0x0000000112f8c36b 0x112317000 + 13063019
9 QtWebEngineCore 0x0000000112f85667 0x112317000 + 13035111
10 libsystem_pthread.dylib 0x00007fff6370a33d _pthread_body + 126
11 libsystem_pthread.dylib 0x00007fff6370d2a7 _pthread_start + 70
12 libsystem_pthread.dylib 0x00007fff63709425 thread_start + 13
Thread 10:: IndexedDB
0 libsystem_kernel.dylib 0x00007fff63650c2a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff63651174 mach_msg + 60
2 com.apple.CoreFoundation 0x00007fff3648405e __CFRunLoopServiceMachPort + 337
3 com.apple.CoreFoundation 0x00007fff364835ad __CFRunLoopRun + 1654
4 com.apple.CoreFoundation 0x00007fff36482ce4 CFRunLoopRunSpecific + 463
5 QtWebEngineCore 0x0000000112f3790f 0x112317000 + 12716303
6 QtWebEngineCore 0x0000000112f372a4 0x112317000 + 12714660
7 QtWebEngineCore 0x0000000112f3410e 0x112317000 + 12701966
8 QtWebEngineCore 0x0000000112f58531 0x112317000 + 12850481
9 QtWebEngineCore 0x0000000112f8c36b 0x112317000 + 13063019
10 QtWebEngineCore 0x0000000112f85667 0x112317000 + 13035111
11 libsystem_pthread.dylib 0x00007fff6370a33d _pthread_body + 126
12 libsystem_pthread.dylib 0x00007fff6370d2a7 _pthread_start + 70
13 libsystem_pthread.dylib 0x00007fff63709425 thread_start + 13
Thread 11:: BrowserBlockingWorker1/70915
0 libsystem_kernel.dylib 0x00007fff636541b2 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6370d5cb _pthread_cond_wait + 724
2 QtWebEngineCore 0x0000000112f86c1f 0x112317000 + 13040671
3 QtWebEngineCore 0x0000000112f862e6 0x112317000 + 13038310
4 QtWebEngineCore 0x0000000112f8a18d 0x112317000 + 13054349
5 QtWebEngineCore 0x0000000112f85667 0x112317000 + 13035111
6 libsystem_pthread.dylib 0x00007fff6370a33d _pthread_body + 126
7 libsystem_pthread.dylib 0x00007fff6370d2a7 _pthread_start + 70
8 libsystem_pthread.dylib 0x00007fff63709425 thread_start + 13
Thread 12:: CompositorTileWorker1/70147
0 libsystem_kernel.dylib 0x00007fff636541b2 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6370d5cb _pthread_cond_wait + 724
2 QtWebEngineCore 0x0000000113b25cf8 0x112317000 + 25226488
3 QtWebEngineCore 0x0000000112f8a18d 0x112317000 + 13054349
4 QtWebEngineCore 0x0000000112f85667 0x112317000 + 13035111
5 libsystem_pthread.dylib 0x00007fff6370a33d _pthread_body + 126
6 libsystem_pthread.dylib 0x00007fff6370d2a7 _pthread_start + 70
7 libsystem_pthread.dylib 0x00007fff63709425 thread_start + 13
Thread 13:: AudioThread
0 libsystem_kernel.dylib 0x00007fff63650c2a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff63651174 mach_msg + 60
2 com.apple.CoreFoundation 0x00007fff3648405e __CFRunLoopServiceMachPort + 337
3 com.apple.CoreFoundation 0x00007fff364835ad __CFRunLoopRun + 1654
4 com.apple.CoreFoundation 0x00007fff36482ce4 CFRunLoopRunSpecific + 463
5 QtWebEngineCore 0x0000000112f3790f 0x112317000 + 12716303
6 QtWebEngineCore 0x0000000112f372a4 0x112317000 + 12714660
7 QtWebEngineCore 0x0000000112f3410e 0x112317000 + 12701966
8 QtWebEngineCore 0x0000000112f58531 0x112317000 + 12850481
9 QtWebEngineCore 0x0000000112f8c36b 0x112317000 + 13063019
10 QtWebEngineCore 0x0000000112f85667 0x112317000 + 13035111
11 libsystem_pthread.dylib 0x00007fff6370a33d _pthread_body + 126
12 libsystem_pthread.dylib 0x00007fff6370d2a7 _pthread_start + 70
13 libsystem_pthread.dylib 0x00007fff63709425 thread_start + 13
Thread 14:: Chrome_InProcGpuThread
0 libsystem_kernel.dylib 0x00007fff63650c2a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff63651174 mach_msg + 60
2 com.apple.CoreFoundation 0x00007fff3648405e __CFRunLoopServiceMachPort + 337
3 com.apple.CoreFoundation 0x00007fff364835ad __CFRunLoopRun + 1654
4 com.apple.CoreFoundation 0x00007fff36482ce4 CFRunLoopRunSpecific + 463
5 QtWebEngineCore 0x0000000112f3790f 0x112317000 + 12716303
6 QtWebEngineCore 0x0000000112f372a4 0x112317000 + 12714660
7 QtWebEngineCore 0x0000000112f3410e 0x112317000 + 12701966
8 QtWebEngineCore 0x0000000112f58531 0x112317000 + 12850481
9 QtWebEngineCore 0x0000000112f8c36b 0x112317000 + 13063019
10 QtWebEngineCore 0x0000000112f85667 0x112317000 + 13035111
11 libsystem_pthread.dylib 0x00007fff6370a33d _pthread_body + 126
12 libsystem_pthread.dylib 0x00007fff6370d2a7 _pthread_start + 70
13 libsystem_pthread.dylib 0x00007fff63709425 thread_start + 13
Thread 15:: Chrome_ChildIOThread
0 libsystem_kernel.dylib 0x00007fff63657052 kevent + 10
1 QtWebEngineCore 0x0000000113445469 0x112317000 + 18015337
2 QtWebEngineCore 0x000000011344275d 0x112317000 + 18003805
3 QtWebEngineCore 0x0000000112f3699f 0x112317000 + 12712351
4 QtWebEngineCore 0x0000000112f3410e 0x112317000 + 12701966
5 QtWebEngineCore 0x0000000112f58531 0x112317000 + 12850481
6 QtWebEngineCore 0x0000000112f8c36b 0x112317000 + 13063019
7 QtWebEngineCore 0x0000000112f85667 0x112317000 + 13035111
8 libsystem_pthread.dylib 0x00007fff6370a33d _pthread_body + 126
9 libsystem_pthread.dylib 0x00007fff6370d2a7 _pthread_start + 70
10 libsystem_pthread.dylib 0x00007fff63709425 thread_start + 13
Thread 16:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff63658b8e poll + 10
1 QtCore 0x000000011150cb40 qt_safe_poll(pollfd*, unsigned int, timespec const*) + 544
2 QtCore 0x000000011150e1b9 QEventDispatcherUNIX::processEvents(QFlags) + 857
3 QtCore 0x00000001114b5742 QEventLoop::exec(QFlags) + 418
4 QtWebEngineCore 0x0000000112338c4a 0x112317000 + 138314
5 QtWebEngineCore 0x0000000112f3410e 0x112317000 + 12701966
6 QtWebEngineCore 0x0000000112f58531 0x112317000 + 12850481
7 QtWebEngineCore 0x0000000112f8c36b 0x112317000 + 13063019
8 QtWebEngineCore 0x0000000112f85667 0x112317000 + 13035111
9 libsystem_pthread.dylib 0x00007fff6370a33d _pthread_body + 126
10 libsystem_pthread.dylib 0x00007fff6370d2a7 _pthread_start + 70
11 libsystem_pthread.dylib 0x00007fff63709425 thread_start + 13
Thread 17:: BrowserBlockingWorker2/66747
0 libsystem_kernel.dylib 0x00007fff636541b2 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6370d5cb _pthread_cond_wait + 724
2 QtWebEngineCore 0x0000000112f86c1f 0x112317000 + 13040671
3 QtWebEngineCore 0x0000000112f862e6 0x112317000 + 13038310
4 QtWebEngineCore 0x0000000112f8a18d 0x112317000 + 13054349
5 QtWebEngineCore 0x0000000112f85667 0x112317000 + 13035111
6 libsystem_pthread.dylib 0x00007fff6370a33d _pthread_body + 126
7 libsystem_pthread.dylib 0x00007fff6370d2a7 _pthread_start + 70
8 libsystem_pthread.dylib 0x00007fff63709425 thread_start + 13
Thread 18:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff63658b8e poll + 10
1 QtCore 0x000000011150cb40 qt_safe_poll(pollfd*, unsigned int, timespec const*) + 544
2 QtCore 0x000000011150e1b9 QEventDispatcherUNIX::processEvents(QFlags) + 857
3 QtCore 0x00000001114b5742 QEventLoop::exec(QFlags) + 418
4 QtWebEngineCore 0x0000000112338c4a 0x112317000 + 138314
5 QtWebEngineCore 0x0000000112f3410e 0x112317000 + 12701966
6 QtWebEngineCore 0x0000000112f58531 0x112317000 + 12850481
7 QtWebEngineCore 0x0000000112f8c36b 0x112317000 + 13063019
8 QtWebEngineCore 0x0000000112f85667 0x112317000 + 13035111
9 libsystem_pthread.dylib 0x00007fff6370a33d _pthread_body + 126
10 libsystem_pthread.dylib 0x00007fff6370d2a7 _pthread_start + 70
11 libsystem_pthread.dylib 0x00007fff63709425 thread_start + 13
Thread 19:: PowerSaveBlocker
0 libsystem_kernel.dylib 0x00007fff63650c2a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff63651174 mach_msg + 60
2 com.apple.CoreFoundation 0x00007fff3648405e __CFRunLoopServiceMachPort + 337
3 com.apple.CoreFoundation 0x00007fff364835ad __CFRunLoopRun + 1654
4 com.apple.CoreFoundation 0x00007fff36482ce4 CFRunLoopRunSpecific + 463
5 QtWebEngineCore 0x0000000112f3790f 0x112317000 + 12716303
6 QtWebEngineCore 0x0000000112f372a4 0x112317000 + 12714660
7 QtWebEngineCore 0x0000000112f3410e 0x112317000 + 12701966
8 QtWebEngineCore 0x0000000112f58531 0x112317000 + 12850481
9 QtWebEngineCore 0x0000000112f8c36b 0x112317000 + 13063019
10 QtWebEngineCore 0x0000000112f85667 0x112317000 + 13035111
11 libsystem_pthread.dylib 0x00007fff6370a33d _pthread_body + 126
12 libsystem_pthread.dylib 0x00007fff6370d2a7 _pthread_start + 70
13 libsystem_pthread.dylib 0x00007fff63709425 thread_start + 13
Thread 20:
0 libsystem_kernel.dylib 0x00007fff63650d32 swtch_pri + 10
1 libsystem_pthread.dylib 0x00007fff6370cef3 sched_yield + 11
2 libopenblasp-r0.3.0.dev.dylib 0x00000001087696f5 blas_thread_server + 133
3 libsystem_pthread.dylib 0x00007fff6370a33d _pthread_body + 126
4 libsystem_pthread.dylib 0x00007fff6370d2a7 _pthread_start + 70
5 libsystem_pthread.dylib 0x00007fff63709425 thread_start + 13
Thread 21:
0 libsystem_kernel.dylib 0x00007fff636541b2 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6370d5cb _pthread_cond_wait + 724
2 libOpenMM.dylib 0x000000012d8f369f OpenMM::threadBody(void*) + 207
3 libsystem_pthread.dylib 0x00007fff6370a33d _pthread_body + 126
4 libsystem_pthread.dylib 0x00007fff6370d2a7 _pthread_start + 70
5 libsystem_pthread.dylib 0x00007fff63709425 thread_start + 13
Thread 22:
0 libsystem_kernel.dylib 0x00007fff636541b2 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6370d5cb _pthread_cond_wait + 724
2 libOpenMM.dylib 0x000000012d8f369f OpenMM::threadBody(void*) + 207
3 libsystem_pthread.dylib 0x00007fff6370a33d _pthread_body + 126
4 libsystem_pthread.dylib 0x00007fff6370d2a7 _pthread_start + 70
5 libsystem_pthread.dylib 0x00007fff63709425 thread_start + 13
Thread 23:
0 libsystem_kernel.dylib 0x00007fff636541b2 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6370d5cb _pthread_cond_wait + 724
2 libOpenMM.dylib 0x000000012d8f369f OpenMM::threadBody(void*) + 207
3 libsystem_pthread.dylib 0x00007fff6370a33d _pthread_body + 126
4 libsystem_pthread.dylib 0x00007fff6370d2a7 _pthread_start + 70
5 libsystem_pthread.dylib 0x00007fff63709425 thread_start + 13
Thread 24:
0 libsystem_kernel.dylib 0x00007fff636541b2 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6370d5cb _pthread_cond_wait + 724
2 libOpenMM.dylib 0x000000012d8f369f OpenMM::threadBody(void*) + 207
3 libsystem_pthread.dylib 0x00007fff6370a33d _pthread_body + 126
4 libsystem_pthread.dylib 0x00007fff6370d2a7 _pthread_start + 70
5 libsystem_pthread.dylib 0x00007fff63709425 thread_start + 13
Thread 25:
0 libsystem_kernel.dylib 0x00007fff636541b2 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6370d5cb _pthread_cond_wait + 724
2 libOpenMMOpenCL.dylib 0x000000012dd25b9d threadBody(void*) + 109
3 libsystem_pthread.dylib 0x00007fff6370a33d _pthread_body + 126
4 libsystem_pthread.dylib 0x00007fff6370d2a7 _pthread_start + 70
5 libsystem_pthread.dylib 0x00007fff63709425 thread_start + 13
Thread 26:
0 libsystem_kernel.dylib 0x00007fff636541b2 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6370d5cb _pthread_cond_wait + 724
2 libOpenMM.dylib 0x000000012d8f369f OpenMM::threadBody(void*) + 207
3 libsystem_pthread.dylib 0x00007fff6370a33d _pthread_body + 126
4 libsystem_pthread.dylib 0x00007fff6370d2a7 _pthread_start + 70
5 libsystem_pthread.dylib 0x00007fff63709425 thread_start + 13
Thread 27:
0 libsystem_kernel.dylib 0x00007fff636541b2 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6370d5cb _pthread_cond_wait + 724
2 libOpenMM.dylib 0x000000012d8f369f OpenMM::threadBody(void*) + 207
3 libsystem_pthread.dylib 0x00007fff6370a33d _pthread_body + 126
4 libsystem_pthread.dylib 0x00007fff6370d2a7 _pthread_start + 70
5 libsystem_pthread.dylib 0x00007fff63709425 thread_start + 13
Thread 28:
0 libsystem_kernel.dylib 0x00007fff636541b2 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6370d5cb _pthread_cond_wait + 724
2 libOpenMM.dylib 0x000000012d8f369f OpenMM::threadBody(void*) + 207
3 libsystem_pthread.dylib 0x00007fff6370a33d _pthread_body + 126
4 libsystem_pthread.dylib 0x00007fff6370d2a7 _pthread_start + 70
5 libsystem_pthread.dylib 0x00007fff63709425 thread_start + 13
Thread 29:
0 libsystem_kernel.dylib 0x00007fff636541b2 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6370d5cb _pthread_cond_wait + 724
2 libOpenMM.dylib 0x000000012d8f369f OpenMM::threadBody(void*) + 207
3 libsystem_pthread.dylib 0x00007fff6370a33d _pthread_body + 126
4 libsystem_pthread.dylib 0x00007fff6370d2a7 _pthread_start + 70
5 libsystem_pthread.dylib 0x00007fff63709425 thread_start + 13
Thread 30:
0 libsystem_kernel.dylib 0x00007fff636541b2 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6370d5cb _pthread_cond_wait + 724
2 libOpenMMOpenCL.dylib 0x000000012dd25b9d threadBody(void*) + 109
3 libsystem_pthread.dylib 0x00007fff6370a33d _pthread_body + 126
4 libsystem_pthread.dylib 0x00007fff6370d2a7 _pthread_start + 70
5 libsystem_pthread.dylib 0x00007fff63709425 thread_start + 13
Thread 31:
0 libsystem_pthread.dylib 0x00007fff63709408 start_wqthread + 0
1 ??? 0x0000000054485244 0 + 1414025796
Thread 32:
0 libsystem_pthread.dylib 0x00007fff63709408 start_wqthread + 0
1 ??? 0x0000000054485244 0 + 1414025796
Thread 33:
0 libsystem_pthread.dylib 0x00007fff63709408 start_wqthread + 0
1 ??? 0x0000000054485244 0 + 1414025796
Thread 34:
0 libsystem_pthread.dylib 0x00007fff63709408 start_wqthread + 0
1 ??? 0x0000600000d823a0 0 + 105553130431392
Thread 35:
0 libsystem_pthread.dylib 0x00007fff63709408 start_wqthread + 0
Thread 36:
0 libsystem_kernel.dylib 0x00007fff636541b2 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff6370d5cb _pthread_cond_wait + 724
2 org.python.python 0x0000000107a1eca6 PyThread_acquire_lock_timed + 390
3 org.python.python 0x0000000107a256e6 acquire_timed + 134
4 org.python.python 0x0000000107a2546c lock_PyThread_acquire_lock + 44
5 org.python.python 0x0000000107952c2f _PyCFunction_FastCallDict + 463
6 org.python.python 0x00000001079dc337 call_function + 471
7 org.python.python 0x00000001079d525c _PyEval_EvalFrameDefault + 4988
8 org.python.python 0x00000001079dce20 _PyEval_EvalCodeWithName + 2592
9 org.python.python 0x00000001079dd4b2 fast_function + 386
10 org.python.python 0x00000001079dc312 call_function + 434
11 org.python.python 0x00000001079d525c _PyEval_EvalFrameDefault + 4988
12 org.python.python 0x00000001079dce20 _PyEval_EvalCodeWithName + 2592
13 org.python.python 0x00000001079dd4b2 fast_function + 386
14 org.python.python 0x00000001079dc312 call_function + 434
15 org.python.python 0x00000001079d525c _PyEval_EvalFrameDefault + 4988
16 org.python.python 0x00000001079dd52f fast_function + 511
17 org.python.python 0x00000001079dc312 call_function + 434
18 org.python.python 0x00000001079d525c _PyEval_EvalFrameDefault + 4988
19 org.python.python 0x00000001079dd52f fast_function + 511
20 org.python.python 0x00000001079dc312 call_function + 434
21 org.python.python 0x00000001079d525c _PyEval_EvalFrameDefault + 4988
22 org.python.python 0x00000001079dd91d _PyFunction_FastCallDict + 813
23 org.python.python 0x000000010790a2da _PyObject_FastCallDict + 346
24 org.python.python 0x000000010790a40c _PyObject_Call_Prepend + 156
25 org.python.python 0x000000010790a035 PyObject_Call + 101
26 org.python.python 0x0000000107a25fc6 t_bootstrap + 70
27 libsystem_pthread.dylib 0x00007fff6370a33d _pthread_body + 126
28 libsystem_pthread.dylib 0x00007fff6370d2a7 _pthread_start + 70
29 libsystem_pthread.dylib 0x00007fff63709425 thread_start + 13
Thread 37:
0 libclipper.dylib 0x000000012c32ca40 clipper::AtomShapeFn::rho(clipper::Coord_orth const&) const + 320
1 libclipper.dylib 0x000000012c3bfc59 clipper::EDcalc_aniso::operator()(clipper::Xmap&, clipper::Atom_list const&) const + 793
2 libclipper_cx.dylib 0x000000011c49fd87 clipper_cx::SFcalc_obs_bulk_vdw::operator()(clipper::HKL_data >&, clipper::HKL_data > const&, clipper::Atom_list const&) + 599
3 libclipper_cx.dylib 0x000000011c48fd74 clipper_cx::Xtal_thread_mgr::recalculate_all_(clipper::Atom_list const&) + 68
4 libclipper_cx.dylib 0x000000011c499378 0x11c488000 + 70520
5 libclipper_cx.dylib 0x000000011c49960e void* std::__1::__thread_proxy >, void (std::__1::__async_assoc_state >::*)(), std::__1::__async_assoc_state >*> >(void*) + 62
6 libsystem_pthread.dylib 0x00007fff6370a33d _pthread_body + 126
7 libsystem_pthread.dylib 0x00007fff6370d2a7 _pthread_start + 70
8 libsystem_pthread.dylib 0x00007fff63709425 thread_start + 13
Thread 38:
0 contour_thread.cpython-36m-darwin.so 0x000000012a1730b2 0x12a15b000 + 98482
1 contour_thread.cpython-36m-darwin.so 0x000000012a15ca04 0x12a15b000 + 6660
2 contour_thread.cpython-36m-darwin.so 0x000000012a171d0b 0x12a15b000 + 93451
3 contour_thread.cpython-36m-darwin.so 0x000000012a171f9e 0x12a15b000 + 94110
4 libsystem_pthread.dylib 0x00007fff6370a33d _pthread_body + 126
5 libsystem_pthread.dylib 0x00007fff6370d2a7 _pthread_start + 70
6 libsystem_pthread.dylib 0x00007fff63709425 thread_start + 13
Thread 39:
0 libsystem_kernel.dylib 0x00007fff63650c2a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff63651174 mach_msg + 60
2 com.apple.framework.IOKit 0x00007fff38ec1edb io_connect_method + 374
3 com.apple.framework.IOKit 0x00007fff38ec283b IOConnectCallScalarMethod + 76
4 com.apple.IOAccelerator 0x00007fff542aa2fa IOAccelContextFinishFenceEvent + 41
5 libGPUSupportMercury.dylib 0x00007fff51ef507a gldFinishFenceOnQueue + 127
6 com.apple.opencl 0x00007fff3f006ec4 0x7fff3eff3000 + 81604
7 com.apple.opencl 0x00007fff3f01d244 0x7fff3eff3000 + 172612
8 com.apple.opencl 0x00007fff3f01d0e8 clWaitForEvents + 185
9 libOpenMMOpenCL.dylib 0x000000012de221c8 OpenMM::OpenCLNonbondedUtilities::computeInteractions(int, bool, bool) + 568
10 libOpenMMOpenCL.dylib 0x000000012dd608da OpenMM::OpenCLCalcForcesAndEnergyKernel::finishComputation(OpenMM::ContextImpl&, bool, bool, int, bool&) + 90
11 libOpenMM.dylib 0x000000012d88fbea OpenMM::ContextImpl::calcForcesAndEnergy(bool, bool, int) + 234
12 libOpenMM.dylib 0x000000012d8f45de OpenMM::VariableLangevinIntegrator::step(int) + 94
13 libopenmm.dylib 0x000000011c54df08 isolde::OpenMM_Thread_Handler::_step_threaded(unsigned long, bool) + 408
14 libopenmm.dylib 0x000000011c551e77 void* std::__1::__thread_proxy >, void (isolde::OpenMM_Thread_Handler::*)(unsigned long, bool), isolde::OpenMM_Thread_Handler*, unsigned long, bool> >(void*) + 71
15 libsystem_pthread.dylib 0x00007fff6370a33d _pthread_body + 126
16 libsystem_pthread.dylib 0x00007fff6370d2a7 _pthread_start + 70
17 libsystem_pthread.dylib 0x00007fff63709425 thread_start + 13
Thread 40:: Dispatch queue: opencl_runtime
0 libsystem_kernel.dylib 0x00007fff63650c2a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff63651174 mach_msg + 60
2 com.apple.framework.IOKit 0x00007fff38ec1edb io_connect_method + 374
3 com.apple.framework.IOKit 0x00007fff38ec1d03 IOConnectCallMethod + 186
4 com.apple.IOAccelerator 0x00007fff542aa136 IOAccelContextFinish + 73
5 com.apple.driver.AppleIntelKBLGraphicsGLDriver 0x00007fff2ddfec9e gldFinishQueue + 72
6 com.apple.opencl 0x00007fff3f005543 0x7fff3eff3000 + 75075
7 com.apple.opencl 0x00007fff3f00598d 0x7fff3eff3000 + 76173
8 com.apple.opencl 0x00007fff3f01f060 0x7fff3eff3000 + 180320
9 com.apple.opencl 0x00007fff3f020d52 0x7fff3eff3000 + 187730
10 libdispatch.dylib 0x00007fff634c9dcb _dispatch_client_callout + 8
11 libdispatch.dylib 0x00007fff634d5d7d _dispatch_sync_invoke_and_complete_recurse + 65
12 libdispatch.dylib 0x00007fff634d58e3 _dispatch_sync_f_slow + 195
13 com.apple.opencl 0x00007fff3f020bd6 0x7fff3eff3000 + 187350
14 com.apple.opencl 0x00007fff3f01e19a 0x7fff3eff3000 + 176538
15 com.apple.opencl 0x00007fff3f015523 clEnqueueReadBuffer + 820
16 libOpenMMOpenCL.dylib 0x000000012dd0c700 OpenMM::OpenCLArray::download(void*, bool) const + 96
17 libOpenMMOpenCL.dylib 0x000000012dd53004 OpenMM::OpenCLIntegrationUtilities::getLastStepSize() + 84
18 libOpenMMOpenCL.dylib 0x000000012ddf7c56 OpenMM::OpenCLIntegrateVariableLangevinStepKernel::execute(OpenMM::ContextImpl&, OpenMM::VariableLangevinIntegrator const&, double) + 2086
19 libOpenMM.dylib 0x000000012d8f4618 OpenMM::VariableLangevinIntegrator::step(int) + 152
20 libopenmm.dylib 0x000000011c54df08 isolde::OpenMM_Thread_Handler::_step_threaded(unsigned long, bool) + 408
21 libopenmm.dylib 0x000000011c551e77 void* std::__1::__thread_proxy >, void (isolde::OpenMM_Thread_Handler::*)(unsigned long, bool), isolde::OpenMM_Thread_Handler*, unsigned long, bool> >(void*) + 71
22 libsystem_pthread.dylib 0x00007fff6370a33d _pthread_body + 126
23 libsystem_pthread.dylib 0x00007fff6370d2a7 _pthread_start + 70
24 libsystem_pthread.dylib 0x00007fff63709425 thread_start + 13
Thread 0 crashed with X86 Thread State (64-bit):
rax: 0x0000000000000000 rbx: 0x00000001122ec5c0 rcx: 0x0000000107cfca48 rdx: 0x0000000000000000
rdi: 0x0000000000000307 rsi: 0x0000000000000006 rbp: 0x0000000107cfca80 rsp: 0x0000000107cfca48
r8: 0x0000000107cfcf48 r9: 0xf746dcbff4a7b7bb r10: 0x00000001122ec66c r11: 0x0000000000000206
r12: 0x0000000000000307 r13: 0x0000003000000008 r14: 0x0000000000000006 r15: 0x000000000000002d
rip: 0x00007fff63656b86 rfl: 0x0000000000000206 cr2: 0x000000011beced80
Logical CPU: 0
Error Code: 0x0100001f
Trap Number: 133
Binary Images:
0x1078f5000 - 0x1078f5ff3 +edu.ucsf.cgl.ChimeraX (0.8.0 - 0.8.0.0) /var/folders/*/ChimeraX.app/Contents/MacOS/ChimeraX
0x1078fb000 - 0x107abfff7 +org.python.python (3.6.4, [c] 2001-2017 Python Software Foundation. - 3.6.4) /var/folders/*/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/Python
0x107ec3000 - 0x107ec4ff7 +_heapq.cpython-36m-darwin.so (0) /var/folders/*/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/lib-dynload/_heapq.cpython-36m-darwin.so
0x107fc8000 - 0x107feefff +_pdbio.cpython-36m-darwin.so (0) /var/folders/*/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/atomic/pdb/_pdbio.cpython-36m-darwin.so
0x108008000 - 0x10800cff3 +libqmacjp2.dylib (0) /var/folders/*/ChimeraX.app/Contents/lib/python3.6/site-packages/PyQt5/Qt/plugins/imageformats/libqmacjp2.dylib
0x108111000 - 0x108111fff +_bisect.cpython-36m-darwin.so (0) /var/folders/*/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/lib-dynload/_bisect.cpython-36m-darwin.so
0x108114000 - 0x108118fff +math.cpython-36m-darwin.so (0) /var/folders/*/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/lib-dynload/math.cpython-36m-darwin.so
0x10811f000 - 0x108125ff7 +libpdbconnect.dylib (0) /var/folders/*/ChimeraX.app/Contents/lib/python3.6/site-packages/chimerax/atomic/pdb/lib/libpdbconnect.dylib
0x108170000 - 0x108176fff +libqgif.dylib (0) /var/folders/*/ChimeraX.app/Contents/lib/python3.6/site-packages/PyQt5/Qt/plugins/imageformats/libqgif.dylib
0x10817a000 - 0x108181ffb +libqicns.dylib (0) /var/folders/*/ChimeraX.app/Contents/lib/python3.6/site-packages/PyQt5/Qt/plugins/imageformats/libqicns.dylib
0x1081c9000 - 0x108364ff7 +multiarray.cpython-36m-darwin.so (???) /var/folders/*/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/numpy/core/multiarray.cpython-36m-darwin.so
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0x7fff5f510000 - 0x7fff5f5f9fff com.apple.ViewBridge (400.1 - 400.1) /System/Library/PrivateFrameworks/ViewBridge.framework/Versions/A/ViewBridge
0x7fff5fe14000 - 0x7fff5fe17fff com.apple.dt.XCTTargetBootstrap (1.0 - 1) /System/Library/PrivateFrameworks/XCTTargetBootstrap.framework/Versions/A/XCTTargetBootstrap
0x7fff60248000 - 0x7fff6024aff3 com.apple.loginsupport (1.0 - 1) /System/Library/PrivateFrameworks/login.framework/Versions/A/Frameworks/loginsupport.framework/Versions/A/loginsupport
0x7fff6024b000 - 0x7fff60260fff com.apple.login (3.0 - 3.0) /System/Library/PrivateFrameworks/login.framework/Versions/A/login
0x7fff60504000 - 0x7fff6053cfff libCRFSuite.dylib (41.15.4) /usr/lib/libCRFSuite.dylib
0x7fff6053f000 - 0x7fff6054aff7 libChineseTokenizer.dylib (28.15.3) /usr/lib/libChineseTokenizer.dylib
0x7fff6054b000 - 0x7fff605d7ff7 libCoreStorage.dylib (546.50.1) /usr/lib/libCoreStorage.dylib
0x7fff605db000 - 0x7fff605dcff7 libDiagnosticMessagesClient.dylib (107) /usr/lib/libDiagnosticMessagesClient.dylib
0x7fff60613000 - 0x7fff607d6ff7 libFosl_dynamic.dylib (18.3.2) /usr/lib/libFosl_dynamic.dylib
0x7fff607f7000 - 0x7fff607fefff libMatch.1.dylib (31.200.1) /usr/lib/libMatch.1.dylib
0x7fff6082c000 - 0x7fff6084bffb libMobileGestalt.dylib (645.200.76) /usr/lib/libMobileGestalt.dylib
0x7fff6084c000 - 0x7fff6084cfff libOpenScriptingUtil.dylib (178) /usr/lib/libOpenScriptingUtil.dylib
0x7fff6098d000 - 0x7fff6098effb libSystem.B.dylib (1252.200.5) /usr/lib/libSystem.B.dylib
0x7fff60a18000 - 0x7fff60a19fff libThaiTokenizer.dylib (2.15.1) /usr/lib/libThaiTokenizer.dylib
0x7fff60a2c000 - 0x7fff60a42ffb libapple_nghttp2.dylib (1.24.1) /usr/lib/libapple_nghttp2.dylib
0x7fff60a43000 - 0x7fff60a6cffb libarchive.2.dylib (54.200.3) /usr/lib/libarchive.2.dylib
0x7fff60a6d000 - 0x7fff60aecfef libate.dylib (1.13.8) /usr/lib/libate.dylib
0x7fff60af0000 - 0x7fff60af0ff3 libauto.dylib (187) /usr/lib/libauto.dylib
0x7fff60bc8000 - 0x7fff60bd8ff3 libbsm.0.dylib (39.200.18) /usr/lib/libbsm.0.dylib
0x7fff60bd9000 - 0x7fff60be7fff libbz2.1.0.dylib (38.200.3) /usr/lib/libbz2.1.0.dylib
0x7fff60be8000 - 0x7fff60c3fff7 libc++.1.dylib (400.9.4) /usr/lib/libc++.1.dylib
0x7fff60c40000 - 0x7fff60c55fff libc++abi.dylib (400.17) /usr/lib/libc++abi.dylib
0x7fff60c56000 - 0x7fff60c56ff3 libcharset.1.dylib (51.200.6) /usr/lib/libcharset.1.dylib
0x7fff60c57000 - 0x7fff60c67ffb libcmph.dylib (6.15.1) /usr/lib/libcmph.dylib
0x7fff60c68000 - 0x7fff60c80ffb libcompression.dylib (52.200.13) /usr/lib/libcompression.dylib
0x7fff60f2b000 - 0x7fff60f41fff libcoretls.dylib (155.200.6) /usr/lib/libcoretls.dylib
0x7fff60f42000 - 0x7fff60f43ff3 libcoretls_cfhelpers.dylib (155.200.6) /usr/lib/libcoretls_cfhelpers.dylib
0x7fff610e2000 - 0x7fff61272ff3 libcrypto.35.dylib (22.200.4) /usr/lib/libcrypto.35.dylib
0x7fff615a6000 - 0x7fff615b1ff7 libcsfde.dylib (546.50.1) /usr/lib/libcsfde.dylib
0x7fff615ba000 - 0x7fff61610ffb libcups.2.dylib (462.9) /usr/lib/libcups.2.dylib
0x7fff61748000 - 0x7fff61748fff libenergytrace.dylib (17.200.1) /usr/lib/libenergytrace.dylib
0x7fff61749000 - 0x7fff61762ffb libexpat.1.dylib (16.1.1) /usr/lib/libexpat.1.dylib
0x7fff6177a000 - 0x7fff6177fff7 libgermantok.dylib (17.15.2) /usr/lib/libgermantok.dylib
0x7fff61780000 - 0x7fff61785ff7 libheimdal-asn1.dylib (520.200.17) /usr/lib/libheimdal-asn1.dylib
0x7fff617b1000 - 0x7fff618a2ff7 libiconv.2.dylib (51.200.6) /usr/lib/libiconv.2.dylib
0x7fff618a3000 - 0x7fff61b06ffb libicucore.A.dylib (62107.0.1) /usr/lib/libicucore.A.dylib
0x7fff61b53000 - 0x7fff61b54fff liblangid.dylib (128.15.1) /usr/lib/liblangid.dylib
0x7fff61b55000 - 0x7fff61b6dfff liblzma.5.dylib (10.200.3) /usr/lib/liblzma.5.dylib
0x7fff61b85000 - 0x7fff61c35fff libmecab.1.0.0.dylib (779.15.23) /usr/lib/libmecab.1.0.0.dylib
0x7fff61c36000 - 0x7fff61e73fff libmecabra.dylib (779.15.23) /usr/lib/libmecabra.dylib
0x7fff6204b000 - 0x7fff623a3fff libnetwork.dylib (1229.200.109) /usr/lib/libnetwork.dylib
0x7fff62434000 - 0x7fff62bbafe7 libobjc.A.dylib (750) /usr/lib/libobjc.A.dylib
0x7fff62bcd000 - 0x7fff62bd1ffb libpam.2.dylib (22.200.1) /usr/lib/libpam.2.dylib
0x7fff62bd4000 - 0x7fff62c0aff7 libpcap.A.dylib (79.200.4) /usr/lib/libpcap.A.dylib
0x7fff62d24000 - 0x7fff62d3cffb libresolv.9.dylib (65.200.2) /usr/lib/libresolv.9.dylib
0x7fff62d3e000 - 0x7fff62d7aff7 libsandbox.1.dylib (851.201.1) /usr/lib/libsandbox.1.dylib
0x7fff62d8e000 - 0x7fff62d8fffb libspindump.dylib (266) /usr/lib/libspindump.dylib
0x7fff62d90000 - 0x7fff62f67fe7 libsqlite3.dylib (274.20) /usr/lib/libsqlite3.dylib
0x7fff631f4000 - 0x7fff631f7ffb libutil.dylib (51.200.4) /usr/lib/libutil.dylib
0x7fff631f8000 - 0x7fff63205fff libxar.1.dylib (404) /usr/lib/libxar.1.dylib
0x7fff6320a000 - 0x7fff632edfff libxml2.2.dylib (32.6) /usr/lib/libxml2.2.dylib
0x7fff632ee000 - 0x7fff63316ff3 libxslt.1.dylib (16.1) /usr/lib/libxslt.1.dylib
0x7fff63317000 - 0x7fff63329ffb libz.1.dylib (70.200.4) /usr/lib/libz.1.dylib
0x7fff6339a000 - 0x7fff6339eff3 libcache.dylib (81) /usr/lib/system/libcache.dylib
0x7fff6339f000 - 0x7fff633a9ff3 libcommonCrypto.dylib (60118.200.6) /usr/lib/system/libcommonCrypto.dylib
0x7fff633aa000 - 0x7fff633b1fff libcompiler_rt.dylib (63.4) /usr/lib/system/libcompiler_rt.dylib
0x7fff633b2000 - 0x7fff633bbff3 libcopyfile.dylib (146.200.3) /usr/lib/system/libcopyfile.dylib
0x7fff633bc000 - 0x7fff63440fff libcorecrypto.dylib (602.200.50) /usr/lib/system/libcorecrypto.dylib
0x7fff634c6000 - 0x7fff63500ff7 libdispatch.dylib (1008.200.78) /usr/lib/system/libdispatch.dylib
0x7fff63501000 - 0x7fff63530fff libdyld.dylib (625.13) /usr/lib/system/libdyld.dylib
0x7fff63531000 - 0x7fff63531ffb libkeymgr.dylib (30) /usr/lib/system/libkeymgr.dylib
0x7fff63532000 - 0x7fff6353eff7 libkxld.dylib (4903.201.2) /usr/lib/system/libkxld.dylib
0x7fff6353f000 - 0x7fff6353fff7 liblaunch.dylib (1336.201.2) /usr/lib/system/liblaunch.dylib
0x7fff63540000 - 0x7fff63545fff libmacho.dylib (917) /usr/lib/system/libmacho.dylib
0x7fff63546000 - 0x7fff63548ff3 libquarantine.dylib (86.200.11) /usr/lib/system/libquarantine.dylib
0x7fff63549000 - 0x7fff6354aff3 libremovefile.dylib (45.200.2) /usr/lib/system/libremovefile.dylib
0x7fff6354b000 - 0x7fff63562ff3 libsystem_asl.dylib (356.200.4) /usr/lib/system/libsystem_asl.dylib
0x7fff63563000 - 0x7fff63563fff libsystem_blocks.dylib (73) /usr/lib/system/libsystem_blocks.dylib
0x7fff63564000 - 0x7fff635ecfff libsystem_c.dylib (1272.200.26) /usr/lib/system/libsystem_c.dylib
0x7fff635ed000 - 0x7fff635f0ff7 libsystem_configuration.dylib (963.200.27) /usr/lib/system/libsystem_configuration.dylib
0x7fff635f1000 - 0x7fff635f4ff7 libsystem_coreservices.dylib (66) /usr/lib/system/libsystem_coreservices.dylib
0x7fff635f5000 - 0x7fff635fbffb libsystem_darwin.dylib (1272.200.26) /usr/lib/system/libsystem_darwin.dylib
0x7fff635fc000 - 0x7fff63602ff7 libsystem_dnssd.dylib (878.200.35) /usr/lib/system/libsystem_dnssd.dylib
0x7fff63603000 - 0x7fff6364fff3 libsystem_info.dylib (517.200.9) /usr/lib/system/libsystem_info.dylib
0x7fff63650000 - 0x7fff63677ff7 libsystem_kernel.dylib (4903.201.2) /usr/lib/system/libsystem_kernel.dylib
0x7fff63678000 - 0x7fff636c3ff7 libsystem_m.dylib (3158.200.7) /usr/lib/system/libsystem_m.dylib
0x7fff636c4000 - 0x7fff636e8ff7 libsystem_malloc.dylib (166.200.60) /usr/lib/system/libsystem_malloc.dylib
0x7fff636e9000 - 0x7fff636f4ffb libsystem_networkextension.dylib (767.200.40) /usr/lib/system/libsystem_networkextension.dylib
0x7fff636f5000 - 0x7fff636fcfff libsystem_notify.dylib (172.200.21) /usr/lib/system/libsystem_notify.dylib
0x7fff636fd000 - 0x7fff63706fef libsystem_platform.dylib (177.200.16) /usr/lib/system/libsystem_platform.dylib
0x7fff63707000 - 0x7fff63711fff libsystem_pthread.dylib (330.201.1) /usr/lib/system/libsystem_pthread.dylib
0x7fff63712000 - 0x7fff63715ff7 libsystem_sandbox.dylib (851.201.1) /usr/lib/system/libsystem_sandbox.dylib
0x7fff63716000 - 0x7fff63718ff7 libsystem_secinit.dylib (30.200.13) /usr/lib/system/libsystem_secinit.dylib
0x7fff63719000 - 0x7fff63720ff7 libsystem_symptoms.dylib (820.207.88) /usr/lib/system/libsystem_symptoms.dylib
0x7fff63721000 - 0x7fff63736ff7 libsystem_trace.dylib (906.200.86) /usr/lib/system/libsystem_trace.dylib
0x7fff63738000 - 0x7fff6373dffb libunwind.dylib (35.4) /usr/lib/system/libunwind.dylib
0x7fff6373e000 - 0x7fff6376efff libxpc.dylib (1336.201.2) /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: 131285
thread_create: 0
thread_set_state: 0
VM Region Summary:
ReadOnly portion of Libraries: Total=739.4M resident=0K(0%) swapped_out_or_unallocated=739.4M(100%)
Writable regions: Total=2.0G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=2.0G(100%)
VIRTUAL REGION
REGION TYPE SIZE COUNT (non-coalesced)
=========== ======= =======
Accelerate framework 256K 3
Activity Tracing 256K 2
CG backing stores 34.1M 12
CG image 200K 24
CoreAnimation 164K 17
CoreGraphics 8K 2
CoreImage 52K 8
CoreUI image data 3564K 37
CoreUI image file 416K 6
Foundation 24K 3
Kernel Alloc Once 8K 2
MALLOC 924.5M 574
MALLOC guard page 32K 9
MALLOC_LARGE (reserved) 384K 3 reserved VM address space (unallocated)
MALLOC_NANO (reserved) 384.0M 2 reserved VM address space (unallocated)
Memory Tag 242 12K 2
OpenCL 361.5M 105
OpenCL (reserved) 60K 13 reserved VM address space (unallocated)
OpenGL GLSL 512K 7
STACK GUARD 160K 41
Stack 167.8M 42
Stack Guard 56.0M 2
VM_ALLOCATE 166.7M 283
__DATA 45.1M 475
__FONT_DATA 4K 2
__GLSLBUILTINS 5176K 2
__LINKEDIT 239.4M 145
__TEXT 499.9M 450
__UNICODE 560K 2
mapped file 83.1M 47
shared memory 776K 19
=========== ======= =======
TOTAL 2.9G 2310
TOTAL, minus reserved VM space 2.5G 2310
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 0.8 (2018-11-11)
How to cite UCSF ChimeraX
OpenGL version: 4.1 INTEL-12.0.34
OpenGL renderer: Intel(R) Iris(TM) Graphics 650
OpenGL vendor: Intel Inc.
Change History (5)
comment:1 by , 7 years ago
| Platform: | → all |
|---|---|
| Project: | → ChimeraX |
comment:2 by , 7 years ago
| Cc: | added |
|---|
comment:3 by , 7 years ago
| Component: | Unassigned → Third Party |
|---|---|
| Owner: | set to |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash running OpenMM simulation |
comment:4 by , 7 years ago
| Cc: | added; removed |
|---|---|
| Owner: | changed from to |
Tristan, the reporter of this bug did not provide email. So all you have to go on is this bug report. It is probably not enough to conclude anything. It crashed in openmm_thread_handler_step(). There were some other calculations going on in threads 37 - 40 that you might look at in the crash report to see if the could have interfered with the data used by the crashed thread. If you don't see anything just close the ticket.
comment:5 by , 7 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
Hard to say what's going on here. I've tried out a few likely scenarios on my Mac:
- starting a simulation on a sub-selection of an un-minimized structure (causing the coordinates to run out of control - the fact that this is still possible is something I need to fix. My code catches such situations reliably in Linux, but there must be some subtle difference in OpenCL implementation on the Mac...);
- closing ChimeraX while a simulation is running (everything closes perfectly gracefully)
- deleting the model while a simulation is running (ugly Python traceback, but no crash)
It's possible that it's not directly related to OpenMM at all. Thread 14 crashed at the same time:
Thread 14:: Chrome_InProcGpuThread 0 libsystem_kernel.dylib 0x00007fff63650c2a mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff63651174 mach_msg + 60
... which looks to be part of Qt's Chromium browser. It looks quite similar to an old (but apparently fixed) Qt bug described at https://github.com/spyder-ide/spyder/issues/3880. Can't reproduce it either, though - I've tried sleeping/resuming a few times over, with both the browser and a simulation running, on battery or on mains power. No crashes. In any case, it's telling that two GPU threads (14 and 40) crashed at the same time...
Might also be specific to the graphics card - the machine that crashed uses the Intel Iris 650, mine uses Intel HD Graphics 6000. I suspect this might have come from the person who happened to be sitting beside me at the workshop - he had a MacBook Pro with the Iris 650, and everything in ChimeraX was running slow (on full lighting with 2BBV from the quickstart guide, he was getting maybe 10-15 fps rotating the model).
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Looks like this crashed while running an ISOLDE simulation. Is there anything you can tell me about what you were doing immediately preceding the crash?