![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 6 years ago
Closed 6 years ago
#2594 closed defect (duplicate)
Crash opening model
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Input/Output | 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-18.7.0-x86_64-i386-64bit
ChimeraX Version: 0.91 (2019-09-21)
Description
Tried to use the command line to open a model file.
Process: ChimeraX [86388]
Path: /Applications/ChimeraX.app/Contents/MacOS/ChimeraX
Identifier: edu.ucsf.cgl.ChimeraX
Version: 0.91.0 (0.91.0.0)
Code Type: X86-64 (Native)
Parent Process: ??? [1]
Responsible: ChimeraX [86388]
User ID: 501
Date/Time: 2019-11-20 16:46:15.808 -0800
OS Version: Mac OS X 10.14.6 (18G87)
Report Version: 12
Bridge OS Version: 3.6 (16P6568)
Anonymous UUID: 19B202EA-2AEA-B7E4-0983-A274FDA27900
Sleep/Wake UUID: 30825749-8C50-4C25-A351-69E345DBD920
Time Awake Since Boot: 56000 seconds
Time Since Wake: 1200 seconds
System Integrity Protection: enabled
Crashed Thread: 0 CrBrowserMain Dispatch queue: com.apple.main-thread
Exception Type: EXC_BAD_ACCESS (SIGSEGV)
Exception Codes: KERN_INVALID_ADDRESS at 0x0000000000000000
Exception Note: EXC_CORPSE_NOTIFY
VM Regions Near 0:
-->
__TEXT 0000000106fcf000-0000000106fd0000 [ 4K] r-x/rwx SM=COW /Applications/ChimeraX.app/Contents/MacOS/ChimeraX
Thread 0 Crashed:: CrBrowserMain Dispatch queue: com.apple.main-thread
0 libsystem_kernel.dylib 0x00007fff584852c6 __pthread_kill + 10
1 libsystem_pthread.dylib 0x00007fff58540bf1 pthread_kill + 284
2 libsystem_c.dylib 0x00007fff583a2d8a raise + 26
3 libsystem_platform.dylib 0x00007fff58535b5d _sigtramp + 29
4 ??? 000000000000000000 0 + 0
5 GLEngine 0x00007fff3611adf7 glDrawArrays_ACC_Exec + 713
6 QtGui 0x0000000114a3d3cb 0x1146e4000 + 3511243
7 QtGui 0x00000001149cffa5 0x1146e4000 + 3063717
8 QtGui 0x00000001149cf17a QPlatformBackingStore::composeAndFlush(QWindow*, QRegion const&, QPoint const&, QPlatformTextureList*, bool) + 2314
9 QtWidgets 0x000000011415b8a3 0x114143000 + 100515
10 QtWidgets 0x000000011415bc1e 0x114143000 + 101406
11 QtWidgets 0x00000001141611f7 0x114143000 + 123383
12 QtWidgets 0x000000011418fabd QWidget::event(QEvent*) + 1645
13 QtWidgets 0x00000001142a0bf5 QMainWindow::event(QEvent*) + 277
14 QtWidgets.so 0x0000000111b28e70 sipQMainWindow::event(QEvent*) + 192
15 QtWidgets 0x000000011415376d QApplicationPrivate::notify_helper(QObject*, QEvent*) + 269
16 QtWidgets 0x0000000114154b72 QApplication::notify(QObject*, QEvent*) + 594
17 QtWidgets.so 0x0000000111bd43ca sipQApplication::notify(QObject*, QEvent*) + 234
18 QtCore 0x0000000114e1d7c4 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 212
19 QtCore 0x0000000114e1e9fe QCoreApplicationPrivate::sendPostedEvents(QObject*, int, QThreadData*) + 878
20 libqcocoa.dylib 0x000000011e94bd69 0x11e916000 + 220521
21 libqcocoa.dylib 0x000000011e94c4d8 0x11e916000 + 222424
22 com.apple.CoreFoundation 0x00007fff2c411683 __CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE0_PERFORM_FUNCTION__ + 17
23 com.apple.CoreFoundation 0x00007fff2c411629 __CFRunLoopDoSource0 + 108
24 com.apple.CoreFoundation 0x00007fff2c3f5043 __CFRunLoopDoSources0 + 283
25 com.apple.CoreFoundation 0x00007fff2c3f45b5 __CFRunLoopRun + 1189
26 com.apple.CoreFoundation 0x00007fff2c3f3ebe CFRunLoopRunSpecific + 455
27 com.apple.HIToolbox 0x00007fff2b6531ab RunCurrentEventLoopInMode + 292
28 com.apple.HIToolbox 0x00007fff2b652ee5 ReceiveNextEventCommon + 603
29 com.apple.HIToolbox 0x00007fff2b652c76 _BlockUntilNextEventMatchingListInModeWithFilter + 64
30 com.apple.AppKit 0x00007fff299eb79d _DPSNextEvent + 1135
31 com.apple.AppKit 0x00007fff299ea48b -[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 1361
32 com.apple.AppKit 0x00007fff299e45a8 -[NSApplication run] + 699
33 libqcocoa.dylib 0x000000011e94b253 0x11e916000 + 217683
34 QtCore 0x0000000114e18ddf QEventLoop::exec(QFlags) + 431
35 QtCore 0x0000000114e1ddd2 QCoreApplication::exec() + 130
36 QtWidgets.so 0x0000000111cc37d2 meth_QApplication_exec_(_object*, _object*) + 82
37 org.python.python 0x0000000106ff4edb _PyMethodDef_RawFastCallKeywords + 251
38 org.python.python 0x0000000106ff43dc _PyCFunction_FastCallKeywords + 44
39 org.python.python 0x00000001070bdfc9 call_function + 617
40 org.python.python 0x00000001070b667a _PyEval_EvalFrameDefault + 5562
41 org.python.python 0x0000000106ff4893 function_code_fastcall + 195
42 org.python.python 0x00000001070be031 call_function + 721
43 org.python.python 0x00000001070b667a _PyEval_EvalFrameDefault + 5562
44 org.python.python 0x00000001070bec84 _PyEval_EvalCodeWithName + 2788
45 org.python.python 0x0000000106ff4396 _PyFunction_FastCallKeywords + 230
46 org.python.python 0x00000001070be031 call_function + 721
47 org.python.python 0x00000001070b670b _PyEval_EvalFrameDefault + 5707
48 org.python.python 0x00000001070bec84 _PyEval_EvalCodeWithName + 2788
49 org.python.python 0x00000001070b5020 PyEval_EvalCode + 48
50 org.python.python 0x00000001070b2683 builtin_exec + 563
51 org.python.python 0x0000000106ff508e _PyMethodDef_RawFastCallKeywords + 686
52 org.python.python 0x0000000106ff43dc _PyCFunction_FastCallKeywords + 44
53 org.python.python 0x00000001070bdfc9 call_function + 617
54 org.python.python 0x00000001070b670b _PyEval_EvalFrameDefault + 5707
55 org.python.python 0x00000001070bec84 _PyEval_EvalCodeWithName + 2788
56 org.python.python 0x0000000106ff4396 _PyFunction_FastCallKeywords + 230
57 org.python.python 0x00000001070be031 call_function + 721
58 org.python.python 0x00000001070b670b _PyEval_EvalFrameDefault + 5707
59 org.python.python 0x00000001070bec84 _PyEval_EvalCodeWithName + 2788
60 org.python.python 0x0000000106ff3e72 _PyFunction_FastCallDict + 450
61 org.python.python 0x00000001071130e3 pymain_run_module + 147
62 org.python.python 0x00000001071121a1 pymain_main + 5041
63 org.python.python 0x0000000107110de3 Py_Main + 51
64 edu.ucsf.cgl.ChimeraX 0x0000000106fcfe01 main + 593
65 libdyld.dylib 0x00007fff5834a3d5 start + 1
Thread 1:
0 libsystem_kernel.dylib 0x00007fff5848286a __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff5854156e _pthread_cond_wait + 722
2 libopenblasp-r0.3.7.dev.dylib 0x00000001088ccc0b blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff5853e2eb _pthread_body + 126
4 libsystem_pthread.dylib 0x00007fff58541249 _pthread_start + 66
5 libsystem_pthread.dylib 0x00007fff5853d40d thread_start + 13
Thread 2:
0 libsystem_kernel.dylib 0x00007fff5848286a __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff5854156e _pthread_cond_wait + 722
2 libopenblasp-r0.3.7.dev.dylib 0x00000001088ccc0b blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff5853e2eb _pthread_body + 126
4 libsystem_pthread.dylib 0x00007fff58541249 _pthread_start + 66
5 libsystem_pthread.dylib 0x00007fff5853d40d thread_start + 13
Thread 3:
0 libsystem_kernel.dylib 0x00007fff5848286a __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff5854156e _pthread_cond_wait + 722
2 libopenblasp-r0.3.7.dev.dylib 0x00000001088ccc0b blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff5853e2eb _pthread_body + 126
4 libsystem_pthread.dylib 0x00007fff58541249 _pthread_start + 66
5 libsystem_pthread.dylib 0x00007fff5853d40d thread_start + 13
Thread 4:: com.apple.NSEventThread
0 libsystem_kernel.dylib 0x00007fff5847f22a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff5847f76c mach_msg + 60
2 com.apple.CoreFoundation 0x00007fff2c3f51ee __CFRunLoopServiceMachPort + 328
3 com.apple.CoreFoundation 0x00007fff2c3f475c __CFRunLoopRun + 1612
4 com.apple.CoreFoundation 0x00007fff2c3f3ebe CFRunLoopRunSpecific + 455
5 com.apple.AppKit 0x00007fff299f34c2 _NSEventThread + 175
6 libsystem_pthread.dylib 0x00007fff5853e2eb _pthread_body + 126
7 libsystem_pthread.dylib 0x00007fff58541249 _pthread_start + 66
8 libsystem_pthread.dylib 0x00007fff5853d40d thread_start + 13
Thread 5:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff5847f22a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff5847f76c mach_msg + 60
2 QtWebEngineCore 0x0000000117bc13ed 0x115a16000 + 35304429
3 QtWebEngineCore 0x0000000117bc12ef 0x115a16000 + 35304175
4 QtWebEngineCore 0x0000000117b7511d 0x115a16000 + 34992413
5 QtWebEngineCore 0x0000000117b9e145 0x115a16000 + 35160389
6 QtWebEngineCore 0x0000000117bf0a7c 0x115a16000 + 35498620
7 QtWebEngineCore 0x0000000117c307c7 0x115a16000 + 35760071
8 libsystem_pthread.dylib 0x00007fff5853e2eb _pthread_body + 126
9 libsystem_pthread.dylib 0x00007fff58541249 _pthread_start + 66
10 libsystem_pthread.dylib 0x00007fff5853d40d thread_start + 13
Thread 6:: DnsConfigService
0 libsystem_kernel.dylib 0x00007fff5848578e kevent + 10
1 QtWebEngineCore 0x0000000117e82a59 0x115a16000 + 38193753
2 QtWebEngineCore 0x0000000117e7fd6d 0x115a16000 + 38182253
3 QtWebEngineCore 0x0000000117c36d8c 0x115a16000 + 35786124
4 QtWebEngineCore 0x0000000117b9e145 0x115a16000 + 35160389
5 QtWebEngineCore 0x0000000117bf0a7c 0x115a16000 + 35498620
6 QtWebEngineCore 0x0000000117c307c7 0x115a16000 + 35760071
7 libsystem_pthread.dylib 0x00007fff5853e2eb _pthread_body + 126
8 libsystem_pthread.dylib 0x00007fff58541249 _pthread_start + 66
9 libsystem_pthread.dylib 0x00007fff5853d40d thread_start + 13
Thread 7:: TaskSchedulerServiceThread
0 libsystem_kernel.dylib 0x00007fff5848578e kevent + 10
1 QtWebEngineCore 0x0000000117e82a59 0x115a16000 + 38193753
2 QtWebEngineCore 0x0000000117e7fd6d 0x115a16000 + 38182253
3 QtWebEngineCore 0x0000000117c36d74 0x115a16000 + 35786100
4 QtWebEngineCore 0x0000000117b9e145 0x115a16000 + 35160389
5 QtWebEngineCore 0x0000000117bdfb34 0x115a16000 + 35429172
6 QtWebEngineCore 0x0000000117bf0a7c 0x115a16000 + 35498620
7 QtWebEngineCore 0x0000000117c307c7 0x115a16000 + 35760071
8 libsystem_pthread.dylib 0x00007fff5853e2eb _pthread_body + 126
9 libsystem_pthread.dylib 0x00007fff58541249 _pthread_start + 66
10 libsystem_pthread.dylib 0x00007fff5853d40d thread_start + 13
Thread 8:: TaskSchedulerForegroundWorker
0 libsystem_kernel.dylib 0x00007fff5847f22a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff5847f76c mach_msg + 60
2 QtWebEngineCore 0x0000000117bc13ed 0x115a16000 + 35304429
3 QtWebEngineCore 0x0000000117bc14e1 0x115a16000 + 35304673
4 QtWebEngineCore 0x0000000117bd8de8 0x115a16000 + 35401192
5 QtWebEngineCore 0x0000000117bd971b 0x115a16000 + 35403547
6 QtWebEngineCore 0x0000000117bd9384 0x115a16000 + 35402628
7 QtWebEngineCore 0x0000000117c307c7 0x115a16000 + 35760071
8 libsystem_pthread.dylib 0x00007fff5853e2eb _pthread_body + 126
9 libsystem_pthread.dylib 0x00007fff58541249 _pthread_start + 66
10 libsystem_pthread.dylib 0x00007fff5853d40d thread_start + 13
Thread 9:: TaskSchedulerForegroundBlockingWorker
0 libsystem_kernel.dylib 0x00007fff5847f22a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff5847f76c mach_msg + 60
2 QtWebEngineCore 0x0000000117bc13ed 0x115a16000 + 35304429
3 QtWebEngineCore 0x0000000117bc14e1 0x115a16000 + 35304673
4 QtWebEngineCore 0x0000000117bd8de8 0x115a16000 + 35401192
5 QtWebEngineCore 0x0000000117bd971b 0x115a16000 + 35403547
6 QtWebEngineCore 0x0000000117bd9384 0x115a16000 + 35402628
7 QtWebEngineCore 0x0000000117c307c7 0x115a16000 + 35760071
8 libsystem_pthread.dylib 0x00007fff5853e2eb _pthread_body + 126
9 libsystem_pthread.dylib 0x00007fff58541249 _pthread_start + 66
10 libsystem_pthread.dylib 0x00007fff5853d40d thread_start + 13
Thread 10:: TaskSchedulerBackgroundWorker
0 libsystem_kernel.dylib 0x00007fff5847f22a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff5847f76c mach_msg + 60
2 QtWebEngineCore 0x0000000117bc13ed 0x115a16000 + 35304429
3 QtWebEngineCore 0x0000000117bc14e1 0x115a16000 + 35304673
4 QtWebEngineCore 0x0000000117bd8de8 0x115a16000 + 35401192
5 QtWebEngineCore 0x0000000117bd971b 0x115a16000 + 35403547
6 QtWebEngineCore 0x0000000117bd92f4 0x115a16000 + 35402484
7 QtWebEngineCore 0x0000000117c307c7 0x115a16000 + 35760071
8 libsystem_pthread.dylib 0x00007fff5853e2eb _pthread_body + 126
9 libsystem_pthread.dylib 0x00007fff58541249 _pthread_start + 66
10 libsystem_pthread.dylib 0x00007fff5853d40d thread_start + 13
Thread 11:: TaskSchedulerBackgroundBlockingWorker
0 libsystem_kernel.dylib 0x00007fff5847f22a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff5847f76c mach_msg + 60
2 QtWebEngineCore 0x0000000117bc13ed 0x115a16000 + 35304429
3 QtWebEngineCore 0x0000000117bc14e1 0x115a16000 + 35304673
4 QtWebEngineCore 0x0000000117bd8de8 0x115a16000 + 35401192
5 QtWebEngineCore 0x0000000117bd971b 0x115a16000 + 35403547
6 QtWebEngineCore 0x0000000117bd92f4 0x115a16000 + 35402484
7 QtWebEngineCore 0x0000000117c307c7 0x115a16000 + 35760071
8 libsystem_pthread.dylib 0x00007fff5853e2eb _pthread_body + 126
9 libsystem_pthread.dylib 0x00007fff58541249 _pthread_start + 66
10 libsystem_pthread.dylib 0x00007fff5853d40d thread_start + 13
Thread 12:: Chrome_IOThread
0 libsystem_kernel.dylib 0x00007fff5848578e kevent + 10
1 QtWebEngineCore 0x0000000117e82a59 0x115a16000 + 38193753
2 QtWebEngineCore 0x0000000117e7fd6d 0x115a16000 + 38182253
3 QtWebEngineCore 0x0000000117c36d74 0x115a16000 + 35786100
4 QtWebEngineCore 0x0000000117b9e145 0x115a16000 + 35160389
5 QtWebEngineCore 0x00000001175045d4 0x115a16000 + 28239316
6 QtWebEngineCore 0x0000000117bf0a7c 0x115a16000 + 35498620
7 QtWebEngineCore 0x0000000117c307c7 0x115a16000 + 35760071
8 libsystem_pthread.dylib 0x00007fff5853e2eb _pthread_body + 126
9 libsystem_pthread.dylib 0x00007fff58541249 _pthread_start + 66
10 libsystem_pthread.dylib 0x00007fff5853d40d thread_start + 13
Thread 13:: TaskSchedulerSingleThreadSharedBackgroundBlocking0
0 libsystem_kernel.dylib 0x00007fff5847f22a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff5847f76c mach_msg + 60
2 QtWebEngineCore 0x0000000117bc13ed 0x115a16000 + 35304429
3 QtWebEngineCore 0x0000000117bc12ef 0x115a16000 + 35304175
4 QtWebEngineCore 0x0000000117bd8dda 0x115a16000 + 35401178
5 QtWebEngineCore 0x0000000117bd947f 0x115a16000 + 35402879
6 QtWebEngineCore 0x0000000117bd9324 0x115a16000 + 35402532
7 QtWebEngineCore 0x0000000117c307c7 0x115a16000 + 35760071
8 libsystem_pthread.dylib 0x00007fff5853e2eb _pthread_body + 126
9 libsystem_pthread.dylib 0x00007fff58541249 _pthread_start + 66
10 libsystem_pthread.dylib 0x00007fff5853d40d thread_start + 13
Thread 14:: CompositorTileWorker1/72451
0 libsystem_kernel.dylib 0x00007fff5848286a __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff5854156e _pthread_cond_wait + 722
2 QtWebEngineCore 0x0000000117c2f058 0x115a16000 + 35754072
3 QtWebEngineCore 0x0000000118bb7658 0x115a16000 + 52041304
4 QtWebEngineCore 0x0000000117bef754 0x115a16000 + 35493716
5 QtWebEngineCore 0x0000000117c307c7 0x115a16000 + 35760071
6 libsystem_pthread.dylib 0x00007fff5853e2eb _pthread_body + 126
7 libsystem_pthread.dylib 0x00007fff58541249 _pthread_start + 66
8 libsystem_pthread.dylib 0x00007fff5853d40d thread_start + 13
Thread 15:: AudioThread
0 libsystem_kernel.dylib 0x00007fff5847f22a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff5847f76c mach_msg + 60
2 QtWebEngineCore 0x0000000117bc13ed 0x115a16000 + 35304429
3 QtWebEngineCore 0x0000000117bc12ef 0x115a16000 + 35304175
4 QtWebEngineCore 0x0000000117b7511d 0x115a16000 + 34992413
5 QtWebEngineCore 0x0000000117b9e145 0x115a16000 + 35160389
6 QtWebEngineCore 0x0000000117bf0a7c 0x115a16000 + 35498620
7 QtWebEngineCore 0x0000000117c307c7 0x115a16000 + 35760071
8 libsystem_pthread.dylib 0x00007fff5853e2eb _pthread_body + 126
9 libsystem_pthread.dylib 0x00007fff58541249 _pthread_start + 66
10 libsystem_pthread.dylib 0x00007fff5853d40d thread_start + 13
Thread 16:: Chrome_InProcGpuThread
0 libsystem_kernel.dylib 0x00007fff5847f22a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff5847f76c mach_msg + 60
2 QtWebEngineCore 0x0000000117bc13ed 0x115a16000 + 35304429
3 QtWebEngineCore 0x0000000117b75112 0x115a16000 + 34992402
4 QtWebEngineCore 0x0000000117b9e145 0x115a16000 + 35160389
5 QtWebEngineCore 0x0000000117bf0a7c 0x115a16000 + 35498620
6 QtWebEngineCore 0x0000000117c307c7 0x115a16000 + 35760071
7 libsystem_pthread.dylib 0x00007fff5853e2eb _pthread_body + 126
8 libsystem_pthread.dylib 0x00007fff58541249 _pthread_start + 66
9 libsystem_pthread.dylib 0x00007fff5853d40d thread_start + 13
Thread 17:: Chrome_ChildIOThread
0 libsystem_kernel.dylib 0x00007fff5848578e kevent + 10
1 QtWebEngineCore 0x0000000117e82a59 0x115a16000 + 38193753
2 QtWebEngineCore 0x0000000117e7fd6d 0x115a16000 + 38182253
3 QtWebEngineCore 0x0000000117c36d8c 0x115a16000 + 35786124
4 QtWebEngineCore 0x0000000117b9e145 0x115a16000 + 35160389
5 QtWebEngineCore 0x0000000117bf0a7c 0x115a16000 + 35498620
6 QtWebEngineCore 0x0000000117c307c7 0x115a16000 + 35760071
7 libsystem_pthread.dylib 0x00007fff5853e2eb _pthread_body + 126
8 libsystem_pthread.dylib 0x00007fff58541249 _pthread_start + 66
9 libsystem_pthread.dylib 0x00007fff5853d40d thread_start + 13
Thread 18:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff5847f22a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff5847f76c mach_msg + 60
2 QtWebEngineCore 0x0000000117bc13ed 0x115a16000 + 35304429
3 QtWebEngineCore 0x0000000117bc12ef 0x115a16000 + 35304175
4 QtWebEngineCore 0x0000000117b7511d 0x115a16000 + 34992413
5 QtWebEngineCore 0x0000000117b9e145 0x115a16000 + 35160389
6 QtWebEngineCore 0x0000000117bf0a7c 0x115a16000 + 35498620
7 QtWebEngineCore 0x0000000117c307c7 0x115a16000 + 35760071
8 libsystem_pthread.dylib 0x00007fff5853e2eb _pthread_body + 126
9 libsystem_pthread.dylib 0x00007fff58541249 _pthread_start + 66
10 libsystem_pthread.dylib 0x00007fff5853d40d thread_start + 13
Thread 19:: TaskSchedulerSingleThreadForegroundBlocking1
0 libsystem_kernel.dylib 0x00007fff5847f22a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff5847f76c mach_msg + 60
2 QtWebEngineCore 0x0000000117bc13ed 0x115a16000 + 35304429
3 QtWebEngineCore 0x0000000117bc12ef 0x115a16000 + 35304175
4 QtWebEngineCore 0x0000000117bd8dda 0x115a16000 + 35401178
5 QtWebEngineCore 0x0000000117bd971b 0x115a16000 + 35403547
6 QtWebEngineCore 0x0000000117bd93e4 0x115a16000 + 35402724
7 QtWebEngineCore 0x0000000117c307c7 0x115a16000 + 35760071
8 libsystem_pthread.dylib 0x00007fff5853e2eb _pthread_body + 126
9 libsystem_pthread.dylib 0x00007fff58541249 _pthread_start + 66
10 libsystem_pthread.dylib 0x00007fff5853d40d thread_start + 13
Thread 20:: QFileInfoGatherer
0 libsystem_kernel.dylib 0x00007fff5848286a __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff5854156e _pthread_cond_wait + 722
2 QtCore 0x0000000114c5ec9b 0x114c34000 + 175259
3 QtCore 0x0000000114c5ebfc QWaitCondition::wait(QMutex*, QDeadlineTimer) + 108
4 QtWidgets 0x000000011437e7a2 0x114143000 + 2340770
5 QtCore 0x0000000114c564a3 0x114c34000 + 140451
6 libsystem_pthread.dylib 0x00007fff5853e2eb _pthread_body + 126
7 libsystem_pthread.dylib 0x00007fff58541249 _pthread_start + 66
8 libsystem_pthread.dylib 0x00007fff5853d40d thread_start + 13
Thread 21:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff5847f22a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff5847f76c mach_msg + 60
2 QtWebEngineCore 0x0000000117bc13ed 0x115a16000 + 35304429
3 QtWebEngineCore 0x0000000117bc12ef 0x115a16000 + 35304175
4 QtWebEngineCore 0x0000000117b7511d 0x115a16000 + 34992413
5 QtWebEngineCore 0x0000000117b9e145 0x115a16000 + 35160389
6 QtWebEngineCore 0x0000000117bf0a7c 0x115a16000 + 35498620
7 QtWebEngineCore 0x0000000117c307c7 0x115a16000 + 35760071
8 libsystem_pthread.dylib 0x00007fff5853e2eb _pthread_body + 126
9 libsystem_pthread.dylib 0x00007fff58541249 _pthread_start + 66
10 libsystem_pthread.dylib 0x00007fff5853d40d thread_start + 13
Thread 22:: QFileInfoGatherer
0 libsystem_kernel.dylib 0x00007fff5848286a __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff5854156e _pthread_cond_wait + 722
2 QtCore 0x0000000114c5ec9b 0x114c34000 + 175259
3 QtCore 0x0000000114c5ebfc QWaitCondition::wait(QMutex*, QDeadlineTimer) + 108
4 QtWidgets 0x000000011437e7a2 0x114143000 + 2340770
5 QtCore 0x0000000114c564a3 0x114c34000 + 140451
6 libsystem_pthread.dylib 0x00007fff5853e2eb _pthread_body + 126
7 libsystem_pthread.dylib 0x00007fff58541249 _pthread_start + 66
8 libsystem_pthread.dylib 0x00007fff5853d40d thread_start + 13
Thread 23:: Dispatch queue: com.apple.opengl.cvmDoWork
0 libsystem_kernel.dylib 0x00007fff5847f22a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff5847f76c mach_msg + 60
2 libdispatch.dylib 0x00007fff583113e7 _dispatch_mach_send_and_wait_for_reply + 609
3 libdispatch.dylib 0x00007fff58311882 dispatch_mach_send_with_result_and_wait_for_reply + 50
4 libxpc.dylib 0x00007fff5857c647 xpc_connection_send_message_with_reply_sync + 178
5 libCoreVMClient.dylib 0x00007fff354a8541 cvms_element_build_and_get_internal + 229
6 libCoreVMClient.dylib 0x00007fff354a844d cvms_element_build_from_source + 185
7 libCVMSPluginSupport.dylib 0x00007fff354a0033 cvm_deferred_build_modular(void*) + 509
8 libdispatch.dylib 0x00007fff582fd63d _dispatch_client_callout + 8
9 libdispatch.dylib 0x00007fff583038e0 _dispatch_lane_serial_drain + 602
10 libdispatch.dylib 0x00007fff58304396 _dispatch_lane_invoke + 385
11 libdispatch.dylib 0x00007fff5830c6ed _dispatch_workloop_worker_thread + 598
12 libsystem_pthread.dylib 0x00007fff5853d611 _pthread_wqthread + 421
13 libsystem_pthread.dylib 0x00007fff5853d3fd start_wqthread + 13
Thread 24:: TaskSchedulerForegroundWorker
0 libsystem_kernel.dylib 0x00007fff5847f22a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff5847f76c mach_msg + 60
2 QtWebEngineCore 0x0000000117bc13ed 0x115a16000 + 35304429
3 QtWebEngineCore 0x0000000117bc14e1 0x115a16000 + 35304673
4 QtWebEngineCore 0x0000000117bd8de8 0x115a16000 + 35401192
5 QtWebEngineCore 0x0000000117bd947f 0x115a16000 + 35402879
6 QtWebEngineCore 0x0000000117bd9384 0x115a16000 + 35402628
7 QtWebEngineCore 0x0000000117c307c7 0x115a16000 + 35760071
8 libsystem_pthread.dylib 0x00007fff5853e2eb _pthread_body + 126
9 libsystem_pthread.dylib 0x00007fff58541249 _pthread_start + 66
10 libsystem_pthread.dylib 0x00007fff5853d40d thread_start + 13
Thread 25:
0 libsystem_pthread.dylib 0x00007fff5853d3f0 start_wqthread + 0
Thread 26:: TaskSchedulerForegroundBlockingWorker
0 libsystem_kernel.dylib 0x00007fff5847f22a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff5847f76c mach_msg + 60
2 QtWebEngineCore 0x0000000117bc13ed 0x115a16000 + 35304429
3 QtWebEngineCore 0x0000000117bc14e1 0x115a16000 + 35304673
4 QtWebEngineCore 0x0000000117bd8de8 0x115a16000 + 35401192
5 QtWebEngineCore 0x0000000117bd947f 0x115a16000 + 35402879
6 QtWebEngineCore 0x0000000117bd9384 0x115a16000 + 35402628
7 QtWebEngineCore 0x0000000117c307c7 0x115a16000 + 35760071
8 libsystem_pthread.dylib 0x00007fff5853e2eb _pthread_body + 126
9 libsystem_pthread.dylib 0x00007fff58541249 _pthread_start + 66
10 libsystem_pthread.dylib 0x00007fff5853d40d thread_start + 13
Thread 0 crashed with X86 Thread State (64-bit):
rax: 0x0000000000000000 rbx: 0x000000011211a5c0 rcx: 0x0000000107445a48 rdx: 0x0000000000000000
rdi: 0x0000000000000307 rsi: 0x000000000000000b rbp: 0x0000000107445a80 rsp: 0x0000000107445a48
r8: 0x0000000107445f48 r9: 0x508d5edb7415b792 r10: 0x000000011211a66c r11: 0x0000000000000287
r12: 0x0000000000000307 r13: 0x000000010640108b r14: 0x000000000000000b r15: 0x000000000000002d
rip: 0x00007fff584852c6 rfl: 0x0000000000000286 cr2: 0x000000010721d124
Logical CPU: 0
Error Code: 0x02000148
Trap Number: 133
Binary Images:
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0x107e4e000 - 0x107e4fff3 +_queue.cpython-37m-darwin.so (0) /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_queue.cpython-37m-darwin.so
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0x111851000 - 0x111910fff +libarrays.dylib (0) /Applications/ChimeraX.app/Contents/lib/libarrays.dylib
0x111a91000 - 0x111d16ffb +QtWidgets.so (0) /Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/PyQt5/QtWidgets.so
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0x112078000 - 0x1120e26ef dyld (655.1.1) /usr/lib/dyld
0x114143000 - 0x114581ff7 +QtWidgets (0) /Applications/ChimeraX.app/Contents/lib/python3.7/site-packages/PyQt5/Qt/lib/QtWidgets.framework/Versions/5/QtWidgets
0x1146e4000 - 0x114b30fe7 +QtGui (0) /Applications/ChimeraX.app/Contents/lib/python3.7/site-packages/PyQt5/Qt/lib/QtGui.framework/Versions/5/QtGui
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0x7fff5837b000 - 0x7fff58392ff3 libsystem_asl.dylib (356.200.4) /usr/lib/system/libsystem_asl.dylib
0x7fff58393000 - 0x7fff58393ff7 libsystem_blocks.dylib (73) /usr/lib/system/libsystem_blocks.dylib
0x7fff58394000 - 0x7fff5841bfff libsystem_c.dylib (1272.250.1) /usr/lib/system/libsystem_c.dylib
0x7fff5841c000 - 0x7fff5841fffb libsystem_configuration.dylib (963.270.3) /usr/lib/system/libsystem_configuration.dylib
0x7fff58420000 - 0x7fff58423ff7 libsystem_coreservices.dylib (66) /usr/lib/system/libsystem_coreservices.dylib
0x7fff58424000 - 0x7fff5842afff libsystem_darwin.dylib (1272.250.1) /usr/lib/system/libsystem_darwin.dylib
0x7fff5842b000 - 0x7fff58431ff7 libsystem_dnssd.dylib (878.270.2) /usr/lib/system/libsystem_dnssd.dylib
0x7fff58432000 - 0x7fff5847dffb libsystem_info.dylib (517.200.9) /usr/lib/system/libsystem_info.dylib
0x7fff5847e000 - 0x7fff584a6ff7 libsystem_kernel.dylib (4903.270.47) /usr/lib/system/libsystem_kernel.dylib
0x7fff584a7000 - 0x7fff584f2ff7 libsystem_m.dylib (3158.200.7) /usr/lib/system/libsystem_m.dylib
0x7fff584f3000 - 0x7fff5851dfff libsystem_malloc.dylib (166.270.1) /usr/lib/system/libsystem_malloc.dylib
0x7fff5851e000 - 0x7fff58528ff7 libsystem_networkextension.dylib (767.250.2) /usr/lib/system/libsystem_networkextension.dylib
0x7fff58529000 - 0x7fff58530fff libsystem_notify.dylib (172.200.21) /usr/lib/system/libsystem_notify.dylib
0x7fff58531000 - 0x7fff5853afef libsystem_platform.dylib (177.270.1) /usr/lib/system/libsystem_platform.dylib
0x7fff5853b000 - 0x7fff58545ff7 libsystem_pthread.dylib (330.250.2) /usr/lib/system/libsystem_pthread.dylib
0x7fff58546000 - 0x7fff58549ff7 libsystem_sandbox.dylib (851.270.1) /usr/lib/system/libsystem_sandbox.dylib
0x7fff5854a000 - 0x7fff5854cff3 libsystem_secinit.dylib (30.260.2) /usr/lib/system/libsystem_secinit.dylib
0x7fff5854d000 - 0x7fff58554ff3 libsystem_symptoms.dylib (820.267.1) /usr/lib/system/libsystem_symptoms.dylib
0x7fff58555000 - 0x7fff5856afff libsystem_trace.dylib (906.260.1) /usr/lib/system/libsystem_trace.dylib
0x7fff5856c000 - 0x7fff58571ffb libunwind.dylib (35.4) /usr/lib/system/libunwind.dylib
0x7fff58572000 - 0x7fff585a1fff libxpc.dylib (1336.261.2) /usr/lib/system/libxpc.dylib
External Modification Summary:
Calls made by other processes targeting this process:
task_for_pid: 7
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: 41564
thread_create: 0
thread_set_state: 0
VM Region Summary:
ReadOnly portion of Libraries: Total=733.8M resident=0K(0%) swapped_out_or_unallocated=733.8M(100%)
Writable regions: Total=1.2G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=1.2G(100%)
VIRTUAL REGION
REGION TYPE SIZE COUNT (non-coalesced)
=========== ======= =======
Accelerate framework 384K 2
Activity Tracing 256K 1
CG backing stores 9532K 9
CG image 304K 34
CoreAnimation 512K 65
CoreGraphics 8K 1
CoreImage 132K 29
CoreUI image data 1652K 36
CoreUI image file 372K 7
Foundation 20K 2
Kernel Alloc Once 8K 1
MALLOC 563.7M 249
MALLOC guard page 32K 8
MALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated)
MALLOC_NANO (reserved) 256.0M 1 reserved VM address space (unallocated)
Memory Tag 242 12K 1
OpenGL GLSL 512K 6
PROTECTED_MEMORY 4K 1
STACK GUARD 104K 26
Stack 156.2M 27
Stack Guard 56.0M 1
VM_ALLOCATE 234.5M 210
VM_ALLOCATE (reserved) 32.0M 1 reserved VM address space (unallocated)
__DATA 51.6M 512
__FONT_DATA 4K 1
__GLSLBUILTINS 5176K 1
__LINKEDIT 241.4M 135
__TEXT 492.3M 488
__UNICODE 564K 1
mapped file 81.9M 72
shared memory 696K 19
=========== ======= =======
TOTAL 2.1G 1948
TOTAL, minus reserved VM space 1.9G 1948
Log:
Startup Messages
---
warnings | 'clip' is a prefix of an existing command 'clipper'
'rota' is a prefix of an existing command 'rotamers'
UCSF ChimeraX version: 0.91 (2019-09-21)
© 2016-2019 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/lynnettj/Documents/Grad
School/Research/CryoEM/Modeling/plus3_displaced/Displaced_Global.mrc"
Opened Displaced_Global.mrc, grid size 256,256,256, pixel 1.06, shown at level
0.0116, step 1, values float32
OpenGL version: 4.1 INTEL-12.10.12
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655
OpenGL vendor: Intel Inc.
Change History (4)
comment:1 by , 6 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Input/Output |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash opening model |
comment:2 by , 6 years ago
| Status: | accepted → feedback |
|---|
Hi Lynette,
Thanks for reporting this. Can you tell me what kind of model it was you were opening (MRC, PDB, etc.)? Was this in the middle of a long session or just right at the beginning? Does that file crash ChimeraX reliably or was it just that one time?
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
follow-up: 3 comment:3 by , 6 years ago
Hi Eric,
I was trying to open a PDB file in the middle of a session I had been using for a while. This was the first time this crash happened to me in general and with this specific model. Let me know if you need any more information.
Best,
Lynnette
_________________________
Lynnette N. Jackson
Ph.D. Student, Puglisi Lab
Structural Biology Department
On Nov 21, 2019, at 10:21 AM, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu<mailto:ChimeraX-bugs-admin@cgl.ucsf.edu>> wrote:
#2594: Crash opening model
-----------------------------------+----------------------------
Reporter: lynnettj@… | Owner: Eric Pettersen
Type: defect | Status: feedback
Priority: normal | Milestone:
Component: Input/Output | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
-----------------------------------+----------------------------
Changes (by Eric Pettersen):
* status: accepted => feedback
Comment:
Hi Lynette,
Thanks for reporting this. Can you tell me what kind of model it
was you were opening (MRC, PDB, etc.)? Was this in the middle of a long
session or just right at the beginning? Does that file crash ChimeraX
reliably or was it just that one time?
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/2594#comment:2>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
comment:4 by , 6 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | feedback → closed |
Hi Lynette,
Thanks for the info. From the behavior you describe and the information in the bug report, this looks to be a bug in the window toolkit we're using (Qt) or in the Apple graphics driver for your graphics card, and not in ChimeraX code per se. So, there's little we can do about it except wait for updates to Qt or for Apple to issues updates for your driver. So here's hoping the problem doesn't bite you too often until one of those things happens...
--Eric
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Reported by Lynette Jackson.