![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 6 years ago
Closed 6 years ago
#2772 closed defect (fixed)
Crash in mark_plane_edge_cuts
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Volume Data | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Darwin-19.2.0-x86_64-i386-64bit
ChimeraX Version: 0.92 (2020-01-22)
Description
Last time you used ChimeraX it crashed.
I used the following command:
volume #4 region 167,0,0,135,290,299
Process: ChimeraX [6457]
Path: /Applications/ChimeraX_Daily.app/Contents/MacOS/ChimeraX
Identifier: edu.ucsf.cgl.ChimeraX
Version: 0.92.0 (0.92.0.0)
Code Type: X86-64 (Native)
Parent Process: ??? [1]
Responsible: ChimeraX [6457]
User ID: 501
Date/Time: 2020-01-24 16:46:36.523 +0100
OS Version: Mac OS X 10.15.2 (19C57)
Report Version: 12
Anonymous UUID: B59FBEBF-FE85-4028-A1BF-C2CE58F57606
Time Awake Since Boot: 170000 seconds
System Integrity Protection: enabled
Crashed Thread: 0 CrBrowserMain Dispatch queue: com.apple.main-thread
Exception Type: EXC_BAD_ACCESS (SIGSEGV)
Exception Codes: EXC_I386_GPFLT
Exception Note: EXC_CORPSE_NOTIFY
Thread 0 Crashed:: CrBrowserMain Dispatch queue: com.apple.main-thread
0 libsystem_kernel.dylib 0x00007fff671b57fa __pthread_kill + 10
1 libsystem_pthread.dylib 0x00007fff67272bc1 pthread_kill + 432
2 libsystem_c.dylib 0x00007fff670cc3a2 raise + 26
3 libsystem_platform.dylib 0x00007fff6726742d _sigtramp + 29
4 ??? 000000000000000000 0 + 0
5 _map.cpython-37m-darwin.so 0x0000000131fda40b Contour_Calculation::CSurface::mark_plane_edge_cuts(Contour_Calculation::Grid_Cell_List&, Contour_Calculation::Grid_Cell_List&, unsigned int) + 363
6 _map.cpython-37m-darwin.so 0x0000000131fd9d44 Contour_Calculation::CSurface::compute_surface() + 980
7 _map.cpython-37m-darwin.so 0x0000000131fd98d3 Contour_Calculation::CSurface::CSurface(float const*, unsigned int const*, long const*, float, bool, unsigned int) + 179
8 _map.cpython-37m-darwin.so 0x0000000131fc828f void contour_surface(Reference_Counted_Array::Array const&, float, bool, Contour_Calculation::Contour_Surface**) + 191
9 _map.cpython-37m-darwin.so 0x0000000131fc7300 surface_py + 496
10 org.python.python 0x000000010f0e0050 _PyMethodDef_RawFastCallKeywords + 624
11 org.python.python 0x000000010f0df3dc _PyCFunction_FastCallKeywords + 44
12 org.python.python 0x000000010f1a8fc9 call_function + 617
13 org.python.python 0x000000010f1a17a9 _PyEval_EvalFrameDefault + 5865
14 org.python.python 0x000000010f1a9c84 _PyEval_EvalCodeWithName + 2788
15 org.python.python 0x000000010f0df396 _PyFunction_FastCallKeywords + 230
16 org.python.python 0x000000010f1a9031 call_function + 721
17 org.python.python 0x000000010f1a1660 _PyEval_EvalFrameDefault + 5536
18 org.python.python 0x000000010f0df893 function_code_fastcall + 195
19 org.python.python 0x000000010f1a9031 call_function + 721
20 org.python.python 0x000000010f1a1660 _PyEval_EvalFrameDefault + 5536
21 org.python.python 0x000000010f0df893 function_code_fastcall + 195
22 org.python.python 0x000000010f1a9031 call_function + 721
23 org.python.python 0x000000010f1a1660 _PyEval_EvalFrameDefault + 5536
24 org.python.python 0x000000010f0df893 function_code_fastcall + 195
25 org.python.python 0x000000010f1a9031 call_function + 721
26 org.python.python 0x000000010f1a1660 _PyEval_EvalFrameDefault + 5536
27 org.python.python 0x000000010f1a9c84 _PyEval_EvalCodeWithName + 2788
28 org.python.python 0x000000010f0df396 _PyFunction_FastCallKeywords + 230
29 org.python.python 0x000000010f1a9031 call_function + 721
30 org.python.python 0x000000010f1a167a _PyEval_EvalFrameDefault + 5562
31 org.python.python 0x000000010f0df893 function_code_fastcall + 195
32 org.python.python 0x000000010f1a9031 call_function + 721
33 org.python.python 0x000000010f1a1660 _PyEval_EvalFrameDefault + 5536
34 org.python.python 0x000000010f0df893 function_code_fastcall + 195
35 org.python.python 0x000000010f1a9031 call_function + 721
36 org.python.python 0x000000010f1a1660 _PyEval_EvalFrameDefault + 5536
37 org.python.python 0x000000010f1a9c84 _PyEval_EvalCodeWithName + 2788
38 org.python.python 0x000000010f0df396 _PyFunction_FastCallKeywords + 230
39 org.python.python 0x000000010f1a9031 call_function + 721
40 org.python.python 0x000000010f1a1660 _PyEval_EvalFrameDefault + 5536
41 org.python.python 0x000000010f0df893 function_code_fastcall + 195
42 org.python.python 0x000000010f1a9031 call_function + 721
43 org.python.python 0x000000010f1a1660 _PyEval_EvalFrameDefault + 5536
44 org.python.python 0x000000010f0df893 function_code_fastcall + 195
45 org.python.python 0x000000010f1a9031 call_function + 721
46 org.python.python 0x000000010f1a1660 _PyEval_EvalFrameDefault + 5536
47 org.python.python 0x000000010f0df893 function_code_fastcall + 195
48 org.python.python 0x000000010f0e03b6 _PyObject_Call_Prepend + 150
49 org.python.python 0x000000010f0df4f8 PyObject_Call + 136
50 QtCore.so 0x0000000126ba2f17 PyQtSlot::call(_object*, _object*) const + 39
51 QtCore.so 0x0000000126ba2e26 PyQtSlot::invoke(void**, _object*, void*, bool) const + 374
52 QtCore.so 0x0000000126ba3925 PyQtSlotProxy::unislot(void**) + 85
53 QtCore.so 0x0000000126ba389a PyQtSlotProxy::qt_metacall(QMetaObject::Call, int, void**) + 58
54 QtCore 0x0000000124a835cd QMetaObject::activate(QObject*, int, int, void**) + 1773
55 QtCore 0x0000000124a8b682 QTimer::timerEvent(QTimerEvent*) + 98
56 QtCore.so 0x0000000126a99028 sipQTimer::timerEvent(QTimerEvent*) + 120
57 QtCore 0x0000000124a7bf46 QObject::event(QEvent*) + 102
58 QtCore.so 0x0000000126a98e9b sipQTimer::event(QEvent*) + 187
59 QtWidgets 0x0000000123d8876d QApplicationPrivate::notify_helper(QObject*, QEvent*) + 269
60 QtWidgets 0x0000000123d89b72 QApplication::notify(QObject*, QEvent*) + 594
61 QtWidgets.so 0x00000001239573ca sipQApplication::notify(QObject*, QEvent*) + 234
62 QtCore 0x0000000124a527c4 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 212
63 QtCore 0x0000000124aabdcf QTimerInfoList::activateTimers() + 991
64 libqcocoa.dylib 0x000000012e7cd4a2 0x12e799000 + 214178
65 com.apple.CoreFoundation 0x00007fff2fbacb21 __CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE0_PERFORM_FUNCTION__ + 17
66 com.apple.CoreFoundation 0x00007fff2fbacac0 __CFRunLoopDoSource0 + 103
67 com.apple.CoreFoundation 0x00007fff2fbac930 __CFRunLoopDoSources0 + 301
68 com.apple.CoreFoundation 0x00007fff2fbab740 __CFRunLoopRun + 1272
69 com.apple.CoreFoundation 0x00007fff2fbaabd3 CFRunLoopRunSpecific + 499
70 com.apple.HIToolbox 0x00007fff2e70165d RunCurrentEventLoopInMode + 292
71 com.apple.HIToolbox 0x00007fff2e70139d ReceiveNextEventCommon + 600
72 com.apple.HIToolbox 0x00007fff2e701127 _BlockUntilNextEventMatchingListInModeWithFilter + 64
73 com.apple.AppKit 0x00007fff2cd72eb4 _DPSNextEvent + 990
74 com.apple.AppKit 0x00007fff2cd71690 -[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 1352
75 com.apple.AppKit 0x00007fff2cd633ae -[NSApplication run] + 658
76 libqcocoa.dylib 0x000000012e7ce253 0x12e799000 + 217683
77 QtCore 0x0000000124a4dddf QEventLoop::exec(QFlags) + 431
78 QtCore 0x0000000124a52dd2 QCoreApplication::exec() + 130
79 QtWidgets.so 0x0000000123a467d2 meth_QApplication_exec_(_object*, _object*) + 82
80 org.python.python 0x000000010f0dfedb _PyMethodDef_RawFastCallKeywords + 251
81 org.python.python 0x000000010f0df3dc _PyCFunction_FastCallKeywords + 44
82 org.python.python 0x000000010f1a8fc9 call_function + 617
83 org.python.python 0x000000010f1a167a _PyEval_EvalFrameDefault + 5562
84 org.python.python 0x000000010f0df893 function_code_fastcall + 195
85 org.python.python 0x000000010f1a9031 call_function + 721
86 org.python.python 0x000000010f1a167a _PyEval_EvalFrameDefault + 5562
87 org.python.python 0x000000010f1a9c84 _PyEval_EvalCodeWithName + 2788
88 org.python.python 0x000000010f0df396 _PyFunction_FastCallKeywords + 230
89 org.python.python 0x000000010f1a9031 call_function + 721
90 org.python.python 0x000000010f1a170b _PyEval_EvalFrameDefault + 5707
91 org.python.python 0x000000010f1a9c84 _PyEval_EvalCodeWithName + 2788
92 org.python.python 0x000000010f1a0020 PyEval_EvalCode + 48
93 org.python.python 0x000000010f19d683 builtin_exec + 563
94 org.python.python 0x000000010f0e008e _PyMethodDef_RawFastCallKeywords + 686
95 org.python.python 0x000000010f0df3dc _PyCFunction_FastCallKeywords + 44
96 org.python.python 0x000000010f1a8fc9 call_function + 617
97 org.python.python 0x000000010f1a170b _PyEval_EvalFrameDefault + 5707
98 org.python.python 0x000000010f1a9c84 _PyEval_EvalCodeWithName + 2788
99 org.python.python 0x000000010f0df396 _PyFunction_FastCallKeywords + 230
100 org.python.python 0x000000010f1a9031 call_function + 721
101 org.python.python 0x000000010f1a170b _PyEval_EvalFrameDefault + 5707
102 org.python.python 0x000000010f1a9c84 _PyEval_EvalCodeWithName + 2788
103 org.python.python 0x000000010f0dee72 _PyFunction_FastCallDict + 450
104 org.python.python 0x000000010f1fe0e3 pymain_run_module + 147
105 org.python.python 0x000000010f1fd1a1 pymain_main + 5041
106 org.python.python 0x000000010f1fbde3 Py_Main + 51
107 edu.ucsf.cgl.ChimeraX 0x000000010f0b7dc8 main + 120
108 libdyld.dylib 0x00007fff6706e7fd start + 1
Thread 1:
0 libsystem_kernel.dylib 0x00007fff671b1ce6 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff67273185 _pthread_cond_wait + 701
2 libopenblasp-r0.3.7.dylib 0x00000001109c1c3b blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff67272e65 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6726e83b thread_start + 15
Thread 2:
0 libsystem_kernel.dylib 0x00007fff671b1ce6 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff67273185 _pthread_cond_wait + 701
2 libopenblasp-r0.3.7.dylib 0x00000001109c1c3b blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff67272e65 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6726e83b thread_start + 15
Thread 3:
0 libsystem_kernel.dylib 0x00007fff671b1ce6 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff67273185 _pthread_cond_wait + 701
2 libopenblasp-r0.3.7.dylib 0x00000001109c1c3b blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff67272e65 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6726e83b thread_start + 15
Thread 4:
0 libsystem_kernel.dylib 0x00007fff671b1ce6 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff67273185 _pthread_cond_wait + 701
2 libopenblasp-r0.3.7.dylib 0x00000001109c1c3b blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff67272e65 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6726e83b thread_start + 15
Thread 5:
0 libsystem_kernel.dylib 0x00007fff671b1ce6 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff67273185 _pthread_cond_wait + 701
2 libopenblasp-r0.3.7.dylib 0x00000001109c1c3b blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff67272e65 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6726e83b thread_start + 15
Thread 6:
0 libsystem_kernel.dylib 0x00007fff671b1ce6 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff67273185 _pthread_cond_wait + 701
2 libopenblasp-r0.3.7.dylib 0x00000001109c1c3b blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff67272e65 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6726e83b thread_start + 15
Thread 7:
0 libsystem_kernel.dylib 0x00007fff671b1ce6 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff67273185 _pthread_cond_wait + 701
2 libopenblasp-r0.3.7.dylib 0x00000001109c1c3b blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff67272e65 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff6726e83b thread_start + 15
Thread 8:
0 libsystem_pthread.dylib 0x00007fff6726e818 start_wqthread + 0
Thread 9:: com.apple.NSEventThread
0 libsystem_kernel.dylib 0x00007fff671af25a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff671af5d0 mach_msg + 60
2 com.apple.CoreFoundation 0x00007fff2fbacd0b __CFRunLoopServiceMachPort + 322
3 com.apple.CoreFoundation 0x00007fff2fbab8e7 __CFRunLoopRun + 1695
4 com.apple.CoreFoundation 0x00007fff2fbaabd3 CFRunLoopRunSpecific + 499
5 com.apple.AppKit 0x00007fff2cf15a72 _NSEventThread + 132
6 libsystem_pthread.dylib 0x00007fff67272e65 _pthread_start + 148
7 libsystem_pthread.dylib 0x00007fff6726e83b thread_start + 15
Thread 10:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff671af25a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff671af5d0 mach_msg + 60
2 QtWebEngineCore 0x000000012941b3ed 0x127270000 + 35304429
3 QtWebEngineCore 0x000000012941b2ef 0x127270000 + 35304175
4 QtWebEngineCore 0x00000001293cf11d 0x127270000 + 34992413
5 QtWebEngineCore 0x00000001293f8145 0x127270000 + 35160389
6 QtWebEngineCore 0x000000012944aa7c 0x127270000 + 35498620
7 QtWebEngineCore 0x000000012948a7c7 0x127270000 + 35760071
8 libsystem_pthread.dylib 0x00007fff67272e65 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff6726e83b thread_start + 15
Thread 11:: DnsConfigService
0 libsystem_kernel.dylib 0x00007fff671b3bce kevent + 10
1 QtWebEngineCore 0x00000001296dca59 0x127270000 + 38193753
2 QtWebEngineCore 0x00000001296d9d6d 0x127270000 + 38182253
3 QtWebEngineCore 0x0000000129490d8c 0x127270000 + 35786124
4 QtWebEngineCore 0x00000001293f8145 0x127270000 + 35160389
5 QtWebEngineCore 0x000000012944aa7c 0x127270000 + 35498620
6 QtWebEngineCore 0x000000012948a7c7 0x127270000 + 35760071
7 libsystem_pthread.dylib 0x00007fff67272e65 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff6726e83b thread_start + 15
Thread 12:: TaskSchedulerServiceThread
0 libsystem_kernel.dylib 0x00007fff671b3bce kevent + 10
1 QtWebEngineCore 0x00000001296dca59 0x127270000 + 38193753
2 QtWebEngineCore 0x00000001296d9d6d 0x127270000 + 38182253
3 QtWebEngineCore 0x0000000129490d74 0x127270000 + 35786100
4 QtWebEngineCore 0x00000001293f8145 0x127270000 + 35160389
5 QtWebEngineCore 0x0000000129439b34 0x127270000 + 35429172
6 QtWebEngineCore 0x000000012944aa7c 0x127270000 + 35498620
7 QtWebEngineCore 0x000000012948a7c7 0x127270000 + 35760071
8 libsystem_pthread.dylib 0x00007fff67272e65 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff6726e83b thread_start + 15
Thread 13:: TaskSchedulerForegroundWorker
0 libsystem_kernel.dylib 0x00007fff671af25a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff671af5d0 mach_msg + 60
2 QtWebEngineCore 0x000000012941b3ed 0x127270000 + 35304429
3 QtWebEngineCore 0x000000012941b4e1 0x127270000 + 35304673
4 QtWebEngineCore 0x0000000129432de8 0x127270000 + 35401192
5 QtWebEngineCore 0x000000012943371b 0x127270000 + 35403547
6 QtWebEngineCore 0x0000000129433384 0x127270000 + 35402628
7 QtWebEngineCore 0x000000012948a7c7 0x127270000 + 35760071
8 libsystem_pthread.dylib 0x00007fff67272e65 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff6726e83b thread_start + 15
Thread 14:: TaskSchedulerForegroundBlockingWorker
0 libsystem_kernel.dylib 0x00007fff671af25a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff671af5d0 mach_msg + 60
2 QtWebEngineCore 0x000000012941b3ed 0x127270000 + 35304429
3 QtWebEngineCore 0x000000012941b4e1 0x127270000 + 35304673
4 QtWebEngineCore 0x0000000129432de8 0x127270000 + 35401192
5 QtWebEngineCore 0x000000012943371b 0x127270000 + 35403547
6 QtWebEngineCore 0x0000000129433384 0x127270000 + 35402628
7 QtWebEngineCore 0x000000012948a7c7 0x127270000 + 35760071
8 libsystem_pthread.dylib 0x00007fff67272e65 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff6726e83b thread_start + 15
Thread 15:: TaskSchedulerForegroundBlockingWorker
0 libsystem_kernel.dylib 0x00007fff671af25a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff671af5d0 mach_msg + 60
2 QtWebEngineCore 0x000000012941b3ed 0x127270000 + 35304429
3 QtWebEngineCore 0x000000012941b4e1 0x127270000 + 35304673
4 QtWebEngineCore 0x0000000129432de8 0x127270000 + 35401192
5 QtWebEngineCore 0x000000012943371b 0x127270000 + 35403547
6 QtWebEngineCore 0x0000000129433384 0x127270000 + 35402628
7 QtWebEngineCore 0x000000012948a7c7 0x127270000 + 35760071
8 libsystem_pthread.dylib 0x00007fff67272e65 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff6726e83b thread_start + 15
Thread 16:: TaskSchedulerForegroundBlockingWorker
0 libsystem_kernel.dylib 0x00007fff671af25a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff671af5d0 mach_msg + 60
2 QtWebEngineCore 0x000000012941b3ed 0x127270000 + 35304429
3 QtWebEngineCore 0x000000012941b4e1 0x127270000 + 35304673
4 QtWebEngineCore 0x0000000129432de8 0x127270000 + 35401192
5 QtWebEngineCore 0x000000012943347f 0x127270000 + 35402879
6 QtWebEngineCore 0x0000000129433384 0x127270000 + 35402628
7 QtWebEngineCore 0x000000012948a7c7 0x127270000 + 35760071
8 libsystem_pthread.dylib 0x00007fff67272e65 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff6726e83b thread_start + 15
Thread 17:: TaskSchedulerBackgroundWorker
0 libsystem_kernel.dylib 0x00007fff671af25a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff671af5d0 mach_msg + 60
2 QtWebEngineCore 0x000000012941b3ed 0x127270000 + 35304429
3 QtWebEngineCore 0x000000012941b4e1 0x127270000 + 35304673
4 QtWebEngineCore 0x0000000129432de8 0x127270000 + 35401192
5 QtWebEngineCore 0x000000012943347f 0x127270000 + 35402879
6 QtWebEngineCore 0x00000001294332f4 0x127270000 + 35402484
7 QtWebEngineCore 0x000000012948a7c7 0x127270000 + 35760071
8 libsystem_pthread.dylib 0x00007fff67272e65 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff6726e83b thread_start + 15
Thread 18:: TaskSchedulerBackgroundBlockingWorker
0 libsystem_kernel.dylib 0x00007fff671af25a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff671af5d0 mach_msg + 60
2 QtWebEngineCore 0x000000012941b3ed 0x127270000 + 35304429
3 QtWebEngineCore 0x000000012941b4e1 0x127270000 + 35304673
4 QtWebEngineCore 0x0000000129432de8 0x127270000 + 35401192
5 QtWebEngineCore 0x000000012943347f 0x127270000 + 35402879
6 QtWebEngineCore 0x00000001294332f4 0x127270000 + 35402484
7 QtWebEngineCore 0x000000012948a7c7 0x127270000 + 35760071
8 libsystem_pthread.dylib 0x00007fff67272e65 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff6726e83b thread_start + 15
Thread 19:: Chrome_IOThread
0 libsystem_kernel.dylib 0x00007fff671b3bce kevent + 10
1 QtWebEngineCore 0x00000001296dca59 0x127270000 + 38193753
2 QtWebEngineCore 0x00000001296d9d6d 0x127270000 + 38182253
3 QtWebEngineCore 0x0000000129490d74 0x127270000 + 35786100
4 QtWebEngineCore 0x00000001293f8145 0x127270000 + 35160389
5 QtWebEngineCore 0x0000000128d5e5d4 0x127270000 + 28239316
6 QtWebEngineCore 0x000000012944aa7c 0x127270000 + 35498620
7 QtWebEngineCore 0x000000012948a7c7 0x127270000 + 35760071
8 libsystem_pthread.dylib 0x00007fff67272e65 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff6726e83b thread_start + 15
Thread 20:: TaskSchedulerSingleThreadSharedBackgroundBlocking0
0 libsystem_kernel.dylib 0x00007fff671af25a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff671af5d0 mach_msg + 60
2 QtWebEngineCore 0x000000012941b3ed 0x127270000 + 35304429
3 QtWebEngineCore 0x000000012941b2ef 0x127270000 + 35304175
4 QtWebEngineCore 0x0000000129432dda 0x127270000 + 35401178
5 QtWebEngineCore 0x000000012943347f 0x127270000 + 35402879
6 QtWebEngineCore 0x0000000129433324 0x127270000 + 35402532
7 QtWebEngineCore 0x000000012948a7c7 0x127270000 + 35760071
8 libsystem_pthread.dylib 0x00007fff67272e65 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff6726e83b thread_start + 15
Thread 21:: CompositorTileWorker1/73219
0 libsystem_kernel.dylib 0x00007fff671b1ce6 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff67273185 _pthread_cond_wait + 701
2 QtWebEngineCore 0x0000000129489058 0x127270000 + 35754072
3 QtWebEngineCore 0x000000012a411658 0x127270000 + 52041304
4 QtWebEngineCore 0x0000000129449754 0x127270000 + 35493716
5 QtWebEngineCore 0x000000012948a7c7 0x127270000 + 35760071
6 libsystem_pthread.dylib 0x00007fff67272e65 _pthread_start + 148
7 libsystem_pthread.dylib 0x00007fff6726e83b thread_start + 15
Thread 22:: AudioThread
0 libsystem_kernel.dylib 0x00007fff671af25a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff671af5d0 mach_msg + 60
2 QtWebEngineCore 0x000000012941b3ed 0x127270000 + 35304429
3 QtWebEngineCore 0x000000012941b2ef 0x127270000 + 35304175
4 QtWebEngineCore 0x00000001293cf11d 0x127270000 + 34992413
5 QtWebEngineCore 0x00000001293f8145 0x127270000 + 35160389
6 QtWebEngineCore 0x000000012944aa7c 0x127270000 + 35498620
7 QtWebEngineCore 0x000000012948a7c7 0x127270000 + 35760071
8 libsystem_pthread.dylib 0x00007fff67272e65 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff6726e83b thread_start + 15
Thread 23:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff671af25a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff671af5d0 mach_msg + 60
2 QtWebEngineCore 0x000000012941b3ed 0x127270000 + 35304429
3 QtWebEngineCore 0x000000012941b2ef 0x127270000 + 35304175
4 QtWebEngineCore 0x00000001293cf11d 0x127270000 + 34992413
5 QtWebEngineCore 0x00000001293f8145 0x127270000 + 35160389
6 QtWebEngineCore 0x000000012944aa7c 0x127270000 + 35498620
7 QtWebEngineCore 0x000000012948a7c7 0x127270000 + 35760071
8 libsystem_pthread.dylib 0x00007fff67272e65 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff6726e83b thread_start + 15
Thread 24:: Chrome_InProcGpuThread
0 libsystem_kernel.dylib 0x00007fff671af25a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff671af5d0 mach_msg + 60
2 QtWebEngineCore 0x000000012941b3ed 0x127270000 + 35304429
3 QtWebEngineCore 0x00000001293cf112 0x127270000 + 34992402
4 QtWebEngineCore 0x00000001293f8145 0x127270000 + 35160389
5 QtWebEngineCore 0x000000012944aa7c 0x127270000 + 35498620
6 QtWebEngineCore 0x000000012948a7c7 0x127270000 + 35760071
7 libsystem_pthread.dylib 0x00007fff67272e65 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff6726e83b thread_start + 15
Thread 25:: Chrome_ChildIOThread
0 libsystem_kernel.dylib 0x00007fff671b3bce kevent + 10
1 QtWebEngineCore 0x00000001296dca59 0x127270000 + 38193753
2 QtWebEngineCore 0x00000001296d9d6d 0x127270000 + 38182253
3 QtWebEngineCore 0x0000000129490d8c 0x127270000 + 35786124
4 QtWebEngineCore 0x00000001293f8145 0x127270000 + 35160389
5 QtWebEngineCore 0x000000012944aa7c 0x127270000 + 35498620
6 QtWebEngineCore 0x000000012948a7c7 0x127270000 + 35760071
7 libsystem_pthread.dylib 0x00007fff67272e65 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff6726e83b thread_start + 15
Thread 26:: TaskSchedulerSingleThreadForegroundBlocking1
0 libsystem_kernel.dylib 0x00007fff671af25a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff671af5d0 mach_msg + 60
2 QtWebEngineCore 0x000000012941b3ed 0x127270000 + 35304429
3 QtWebEngineCore 0x000000012941b2ef 0x127270000 + 35304175
4 QtWebEngineCore 0x0000000129432dda 0x127270000 + 35401178
5 QtWebEngineCore 0x000000012943371b 0x127270000 + 35403547
6 QtWebEngineCore 0x00000001294333e4 0x127270000 + 35402724
7 QtWebEngineCore 0x000000012948a7c7 0x127270000 + 35760071
8 libsystem_pthread.dylib 0x00007fff67272e65 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff6726e83b thread_start + 15
Thread 27:: QFileInfoGatherer
0 libsystem_kernel.dylib 0x00007fff671b1ce6 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff67273185 _pthread_cond_wait + 701
2 QtCore 0x0000000124893c9b 0x124869000 + 175259
3 QtCore 0x0000000124893bfc QWaitCondition::wait(QMutex*, QDeadlineTimer) + 108
4 QtWidgets 0x0000000123fb37a2 0x123d78000 + 2340770
5 QtCore 0x000000012488b4a3 0x124869000 + 140451
6 libsystem_pthread.dylib 0x00007fff67272e65 _pthread_start + 148
7 libsystem_pthread.dylib 0x00007fff6726e83b thread_start + 15
Thread 28:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff671af25a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff671af5d0 mach_msg + 60
2 QtWebEngineCore 0x000000012941b3ed 0x127270000 + 35304429
3 QtWebEngineCore 0x000000012941b2ef 0x127270000 + 35304175
4 QtWebEngineCore 0x00000001293cf11d 0x127270000 + 34992413
5 QtWebEngineCore 0x00000001293f8145 0x127270000 + 35160389
6 QtWebEngineCore 0x000000012944aa7c 0x127270000 + 35498620
7 QtWebEngineCore 0x000000012948a7c7 0x127270000 + 35760071
8 libsystem_pthread.dylib 0x00007fff67272e65 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff6726e83b thread_start + 15
Thread 29:
0 libsystem_pthread.dylib 0x00007fff6726e818 start_wqthread + 0
Thread 30:: TaskSchedulerForegroundWorker
0 libsystem_kernel.dylib 0x00007fff671af25a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff671af5d0 mach_msg + 60
2 QtWebEngineCore 0x000000012941b3ed 0x127270000 + 35304429
3 QtWebEngineCore 0x000000012941b4e1 0x127270000 + 35304673
4 QtWebEngineCore 0x0000000129432de8 0x127270000 + 35401192
5 QtWebEngineCore 0x000000012943347f 0x127270000 + 35402879
6 QtWebEngineCore 0x0000000129433384 0x127270000 + 35402628
7 QtWebEngineCore 0x000000012948a7c7 0x127270000 + 35760071
8 libsystem_pthread.dylib 0x00007fff67272e65 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff6726e83b thread_start + 15
Thread 31:
0 libsystem_pthread.dylib 0x00007fff6726e818 start_wqthread + 0
Thread 32:
0 libsystem_pthread.dylib 0x00007fff6726e818 start_wqthread + 0
Thread 0 crashed with X86 Thread State (64-bit):
rax: 0x0000000000000000 rbx: 0x000000010fdfcdc0 rcx: 0x00007fe190037a58 rdx: 0x0000000000000000
rdi: 0x0000000000000307 rsi: 0x000000000000000b rbp: 0x00007fe190037a80 rsp: 0x00007fe190037a58
r8: 0x00007fe190037f48 r9: 0x8e3695f38e2a97f7 r10: 0x000000010fdfcdc0 r11: 0x0000000000000246
r12: 0x0000000000000307 r13: 0x0000000000c49cbc r14: 0x000000000000000b r15: 0x0000000000000016
rip: 0x00007fff671b57fa rfl: 0x0000000000000246 cr2: 0x000000010f308124
Logical CPU: 0
Error Code: 0x02000148
Trap Number: 133
Binary Images:
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0x7fff67099000 - 0x7fff6709eff7 libmacho.dylib (949.0.1) /usr/lib/system/libmacho.dylib
0x7fff6709f000 - 0x7fff670a1ff7 libquarantine.dylib (110.40.3) /usr/lib/system/libquarantine.dylib
0x7fff670a2000 - 0x7fff670a3ff7 libremovefile.dylib (48) /usr/lib/system/libremovefile.dylib
0x7fff670a4000 - 0x7fff670bbfff libsystem_asl.dylib (377.60.2) /usr/lib/system/libsystem_asl.dylib
0x7fff670bc000 - 0x7fff670bcfff libsystem_blocks.dylib (74) /usr/lib/system/libsystem_blocks.dylib
0x7fff670bd000 - 0x7fff67144ff7 libsystem_c.dylib (1353.60.8) /usr/lib/system/libsystem_c.dylib
0x7fff67145000 - 0x7fff67148ffb libsystem_configuration.dylib (1061.40.2) /usr/lib/system/libsystem_configuration.dylib
0x7fff67149000 - 0x7fff6714cff7 libsystem_coreservices.dylib (114) /usr/lib/system/libsystem_coreservices.dylib
0x7fff6714d000 - 0x7fff67155fff libsystem_darwin.dylib (1353.60.8) /usr/lib/system/libsystem_darwin.dylib
0x7fff67156000 - 0x7fff6715dffb libsystem_dnssd.dylib (1096.60.2) /usr/lib/system/libsystem_dnssd.dylib
0x7fff6715e000 - 0x7fff6715fffb libsystem_featureflags.dylib (17) /usr/lib/system/libsystem_featureflags.dylib
0x7fff67160000 - 0x7fff671adfff libsystem_info.dylib (538) /usr/lib/system/libsystem_info.dylib
0x7fff671ae000 - 0x7fff671daff7 libsystem_kernel.dylib (6153.61.1) /usr/lib/system/libsystem_kernel.dylib
0x7fff671db000 - 0x7fff67222fcf libsystem_m.dylib (3178) /usr/lib/system/libsystem_m.dylib
0x7fff67223000 - 0x7fff6724afff libsystem_malloc.dylib (283.60.1) /usr/lib/system/libsystem_malloc.dylib
0x7fff6724b000 - 0x7fff67258ffb libsystem_networkextension.dylib (1095.60.2) /usr/lib/system/libsystem_networkextension.dylib
0x7fff67259000 - 0x7fff67262ff3 libsystem_notify.dylib (241) /usr/lib/system/libsystem_notify.dylib
0x7fff67263000 - 0x7fff6726cfef libsystem_platform.dylib (220) /usr/lib/system/libsystem_platform.dylib
0x7fff6726d000 - 0x7fff67277fff libsystem_pthread.dylib (416.60.2) /usr/lib/system/libsystem_pthread.dylib
0x7fff67278000 - 0x7fff6727cfff libsystem_sandbox.dylib (1217.61.1) /usr/lib/system/libsystem_sandbox.dylib
0x7fff6727d000 - 0x7fff6727ffff libsystem_secinit.dylib (62.60.1) /usr/lib/system/libsystem_secinit.dylib
0x7fff67280000 - 0x7fff67287ffb libsystem_symptoms.dylib (1238.60.1) /usr/lib/system/libsystem_symptoms.dylib
0x7fff67288000 - 0x7fff6729eff2 libsystem_trace.dylib (1147.60.3) /usr/lib/system/libsystem_trace.dylib
0x7fff672a0000 - 0x7fff672a5ffb libunwind.dylib (35.4) /usr/lib/system/libunwind.dylib
0x7fff672a6000 - 0x7fff672daffe libxpc.dylib (1738.61.1) /usr/lib/system/libxpc.dylib
External Modification Summary:
Calls made by other processes targeting this process:
task_for_pid: 2
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: 101722
thread_create: 0
thread_set_state: 0
VM Region Summary:
ReadOnly portion of Libraries: Total=893.4M resident=0K(0%) swapped_out_or_unallocated=893.4M(100%)
Writable regions: Total=4.8G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=4.8G(100%)
VIRTUAL REGION
REGION TYPE SIZE COUNT (non-coalesced)
=========== ======= =======
Accelerate framework 256K 2
Activity Tracing 256K 1
CG backing stores 57.1M 4
CG image 52K 3
CoreAnimation 64K 7
CoreGraphics 8K 1
CoreImage 24K 2
CoreUI image data 1600K 12
Foundation 4K 1
Kernel Alloc Once 8K 1
MALLOC 3.1G 129
MALLOC guard page 48K 10
MALLOC_MEDIUM (reserved) 800.0M 8 reserved VM address space (unallocated)
MALLOC_NANO (reserved) 384.0M 1 reserved VM address space (unallocated)
Memory Tag 242 12K 1
OpenGL GLSL 512K 6
PROTECTED_MEMORY 4K 1
STACK GUARD 128K 32
Stack 166.8M 33
Stack Guard 56.0M 1
VM_ALLOCATE 170.0M 380
VM_ALLOCATE (reserved) 160.0M 1 reserved VM address space (unallocated)
__DATA 64.7M 528
__DATA_CONST 128K 6
__FONT_DATA 4K 1
__GLSLBUILTINS 5176K 1
__LINKEDIT 372.9M 122
__OBJC_RO 32.0M 1
__OBJC_RW 1780K 2
__TEXT 520.5M 496
__UNICODE 564K 1
mapped file 83.0M 45
shared memory 652K 19
=========== ======= =======
TOTAL 5.9G 1859
TOTAL, minus reserved VM space 4.6G 1859
Log:
UCSF ChimeraX version: 0.92 (2020-01-22)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 ATI-3.4.19
OpenGL renderer: AMD Radeon Pro Vega 48 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Change History (2)
comment:1 by , 6 years ago
| Component: | Unassigned → Volume Data |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash in mark_plane_edge_cuts |
comment:2 by , 6 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
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Fixed.
I introduced a bug a few days ago in the volume contour surface calculation that caused this crash if the x-axis size of the data array is 0. Your command "volume #4 region 167,0,0,135,290,299" makes the x-axis size 0 since xmin = 167 and xmax = 135 (region option value is xmin,ymin,zmin,xmax,ymax,zmax).