![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 5 years ago
Closed 3 years ago
#3768 closed defect (can't reproduce)
OpenMM/OpenCL crash
| 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-17.7.0-x86_64-i386-64bit
ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Process: ChimeraX [85830]
Path: /Applications/ChimeraX-1.0.app/Contents/MacOS/ChimeraX
Identifier: edu.ucsf.cgl.ChimeraX
Version: 1.0.0 (1.0.0.0)
Code Type: X86-64 (Native)
Parent Process: ??? [1]
Responsible: ChimeraX [85830]
User ID: 501
Date/Time: 2020-09-25 11:28:37.335 +0100
OS Version: Mac OS X 10.13.6 (17G14019)
Report Version: 12
Anonymous UUID: B3AE2F25-6339-0527-9417-9B4CA56EE2FE
Sleep/Wake UUID: 54F40691-178C-45F8-B0DE-48547CA3E3ED
Time Awake Since Boot: 3100000 seconds
Time Since Wake: 12000 seconds
System Integrity Protection: enabled
Crashed Thread: 0 CrBrowserMain Dispatch queue: opencl_runtime
Exception Type: EXC_CRASH (SIGABRT)
Exception Codes: 0x0000000000000000, 0x0000000000000000
Exception Note: EXC_CORPSE_NOTIFY
Application Specific Information:
abort() called
Application Specific Signatures:
Graphics kernel error: 0xfffffffe
Thread 0 Crashed:: CrBrowserMain Dispatch queue: opencl_runtime
0 libsystem_kernel.dylib 0x00007fff575c3b66 __pthread_kill + 10
1 libsystem_pthread.dylib 0x00007fff5778e080 pthread_kill + 333
2 libsystem_c.dylib 0x00007fff574d16fe raise + 26
3 libsystem_platform.dylib 0x00007fff57781f5a _sigtramp + 26
4 ??? 000000000000000000 0 + 0
5 libsystem_c.dylib 0x00007fff5751f1ae abort + 127
6 libGPUSupportMercury.dylib 0x00007fff47ffc0f1 gpusGenerateCrashLog + 168
7 com.apple.driver.AppleIntelHD5000GraphicsGLDriver 0x000000011d15fc5d gpusKillClientExt + 9
8 libGPUSupportMercury.dylib 0x00007fff47ffcab0 gpusQueueSubmitDataBuffers + 171
9 com.apple.driver.AppleIntelHD5000GraphicsGLDriver 0x000000011cde9b4b IntelCLCommandBuffer::getNew(GLDQueueRec*) + 31
10 com.apple.driver.AppleIntelHD5000GraphicsGLDriver 0x000000011cde9a33 intelSubmitCLCommands(GLDQueueRec*, unsigned int) + 69
11 com.apple.driver.AppleIntelHD5000GraphicsGLDriver 0x000000011cde997e CHAL_INTEL::ChalContext::ChalFlush() + 82
12 com.apple.driver.AppleIntelHD5000GraphicsGLDriver 0x000000011cde98e9 gldFinishQueue + 43
13 com.apple.opencl 0x00007fff37cb70c1 0x7fff37ca9000 + 57537
14 com.apple.opencl 0x00007fff37cb7d8a 0x7fff37ca9000 + 60810
15 com.apple.opencl 0x00007fff37cd47bd 0x7fff37ca9000 + 178109
16 com.apple.opencl 0x00007fff37cd7a90 0x7fff37ca9000 + 191120
17 libdispatch.dylib 0x00007fff57439db8 _dispatch_client_callout + 8
18 libdispatch.dylib 0x00007fff5744d1e1 _dispatch_queue_barrier_sync_invoke_and_complete + 60
19 com.apple.opencl 0x00007fff37cd790a 0x7fff37ca9000 + 190730
20 com.apple.opencl 0x00007fff37cd3a49 0x7fff37ca9000 + 174665
21 com.apple.opencl 0x00007fff37cc9a97 clEnqueueWriteBuffer + 777
22 libOpenMMOpenCL.dylib 0x0000000141845d78 OpenMM::OpenCLArray::upload(void const*, bool) + 104
23 libOpenMMOpenCL.dylib 0x000000014191ef82 OpenMM::OpenCLCalcCustomCompoundBondForceKernel::initialize(OpenMM::System const&, OpenMM::CustomCompoundBondForce const&) + 2146
24 libOpenMM.dylib 0x00000001414eb089 OpenMM::CustomCompoundBondForceImpl::initialize(OpenMM::ContextImpl&) + 489
25 libOpenMM.dylib 0x00000001414d7228 OpenMM::ContextImpl::initialize() + 1160
26 libOpenMM.dylib 0x00000001414d35b3 OpenMM::Context::Context(OpenMM::System const&, OpenMM::Integrator&, OpenMM::Platform&, std::__1::map, std::__1::allocator >, std::__1::basic_string, std::__1::allocator >, std::__1::less, std::__1::allocator > >, std::__1::allocator, std::__1::allocator > const, std::__1::basic_string, std::__1::allocator > > > > const&) + 227
27 _openmm.cpython-37m-darwin.so 0x00000001411c171b _wrap_new_Context(_object*, _object*) + 1275
28 org.python.python 0x000000010342ac23 PyCFunction_Call + 387
29 org.python.python 0x00000001034fcaca _PyEval_EvalFrameDefault + 27370
30 org.python.python 0x00000001035009bc _PyEval_EvalCodeWithName + 3276
31 org.python.python 0x000000010342a377 _PyFunction_FastCallDict + 455
32 org.python.python 0x000000010342b883 _PyObject_Call_Prepend + 131
33 org.python.python 0x000000010347ee3f slot_tp_init + 175
34 org.python.python 0x000000010347a534 type_call + 292
35 org.python.python 0x000000010342a6df _PyObject_FastCallKeywords + 575
36 org.python.python 0x00000001034ffb5d call_function + 765
37 org.python.python 0x00000001034fc7a7 _PyEval_EvalFrameDefault + 26567
38 org.python.python 0x00000001035009bc _PyEval_EvalCodeWithName + 3276
39 org.python.python 0x000000010342a377 _PyFunction_FastCallDict + 455
40 org.python.python 0x000000010342b883 _PyObject_Call_Prepend + 131
41 org.python.python 0x000000010347ee3f slot_tp_init + 175
42 org.python.python 0x000000010347a534 type_call + 292
43 org.python.python 0x000000010342a6df _PyObject_FastCallKeywords + 575
44 org.python.python 0x00000001034ffb5d call_function + 765
45 org.python.python 0x00000001034fc7a7 _PyEval_EvalFrameDefault + 26567
46 org.python.python 0x000000010342ad61 function_code_fastcall + 177
47 org.python.python 0x00000001034ffb64 call_function + 772
48 org.python.python 0x00000001034fc78a _PyEval_EvalFrameDefault + 26538
49 org.python.python 0x000000010342ad61 function_code_fastcall + 177
50 org.python.python 0x00000001034ffb64 call_function + 772
51 org.python.python 0x00000001034fc78a _PyEval_EvalFrameDefault + 26538
52 org.python.python 0x000000010342ad61 function_code_fastcall + 177
53 org.python.python 0x00000001034ffb64 call_function + 772
54 org.python.python 0x00000001034fc78a _PyEval_EvalFrameDefault + 26538
55 org.python.python 0x000000010342ad61 function_code_fastcall + 177
56 org.python.python 0x00000001034ffb64 call_function + 772
57 org.python.python 0x00000001034fc78a _PyEval_EvalFrameDefault + 26538
58 org.python.python 0x00000001035009bc _PyEval_EvalCodeWithName + 3276
59 org.python.python 0x000000010342a377 _PyFunction_FastCallDict + 455
60 org.python.python 0x00000001034fc9ca _PyEval_EvalFrameDefault + 27114
61 org.python.python 0x00000001035009bc _PyEval_EvalCodeWithName + 3276
62 org.python.python 0x000000010342a879 _PyFunction_FastCallKeywords + 217
63 org.python.python 0x00000001034ffb64 call_function + 772
64 org.python.python 0x00000001034fc78a _PyEval_EvalFrameDefault + 26538
65 org.python.python 0x00000001035009bc _PyEval_EvalCodeWithName + 3276
66 org.python.python 0x000000010342a377 _PyFunction_FastCallDict + 455
67 org.python.python 0x000000010342b883 _PyObject_Call_Prepend + 131
68 org.python.python 0x000000010342a9d8 PyObject_Call + 136
69 QtCore.so 0x000000011195ff17 PyQtSlot::call(_object*, _object*) const + 39
70 QtCore.so 0x000000011195fe26 PyQtSlot::invoke(void**, _object*, void*, bool) const + 374
71 QtCore.so 0x0000000111960925 PyQtSlotProxy::unislot(void**) + 85
72 QtCore.so 0x000000011196089a PyQtSlotProxy::qt_metacall(QMetaObject::Call, int, void**) + 58
73 QtCore 0x00000001114322dd QMetaObject::activate(QObject*, int, int, void**) + 1773
74 QtCore 0x000000011143282c QMetaObject::activate(QObject*, int, int, void**) + 3132
75 QtWidgets 0x000000011085fa67 QWidgetLineControl::processKeyEvent(QKeyEvent*) + 551
76 QtWidgets 0x0000000110856722 QLineEdit::keyPressEvent(QKeyEvent*) + 34
77 QtWidgets 0x000000011075149f QWidget::event(QEvent*) + 527
78 QtWidgets 0x0000000110855a87 QLineEdit::event(QEvent*) + 727
79 QtWidgets 0x000000011081a540 QComboBox::keyPressEvent(QKeyEvent*) + 784
80 QtWidgets.so 0x00000001103b723b meth_QComboBox_keyPressEvent(_object*, _object*) + 139
81 org.python.python 0x000000010342b392 _PyMethodDef_RawFastCallKeywords + 226
82 org.python.python 0x000000010342a8b9 _PyCFunction_FastCallKeywords + 41
83 org.python.python 0x00000001034ffaf0 call_function + 656
84 org.python.python 0x00000001034fc7a7 _PyEval_EvalFrameDefault + 26567
85 org.python.python 0x00000001035009bc _PyEval_EvalCodeWithName + 3276
86 org.python.python 0x000000010342a377 _PyFunction_FastCallDict + 455
87 org.python.python 0x000000010342b883 _PyObject_Call_Prepend + 131
88 org.python.python 0x000000010342a9d8 PyObject_Call + 136
89 sip.so 0x0000000111820f7a call_method + 76
90 sip.so 0x000000011181cd07 sip_api_call_procedure_method + 152
91 QtWidgets.so 0x00000001102ba9a7 sipQComboBox::keyPressEvent(QKeyEvent*) + 103
92 QtWidgets 0x000000011075149f QWidget::event(QEvent*) + 527
93 QtWidgets 0x0000000110819ea4 QComboBox::event(QEvent*) + 372
94 QtWidgets.so 0x00000001102b9eb0 sipQComboBox::event(QEvent*) + 192
95 QtWidgets 0x000000011071570d QApplicationPrivate::notify_helper(QObject*, QEvent*) + 269
96 QtWidgets 0x0000000110716c5c QApplication::notify(QObject*, QEvent*) + 924
97 QtWidgets.so 0x00000001102d53ca sipQApplication::notify(QObject*, QEvent*) + 234
98 QtCore 0x00000001114014c4 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 212
99 QtWidgets 0x00000001107702a1 0x110705000 + 438945
100 QtWidgets 0x000000011076f691 0x110705000 + 435857
101 QtWidgets 0x000000011071570d QApplicationPrivate::notify_helper(QObject*, QEvent*) + 269
102 QtWidgets 0x0000000110716b12 QApplication::notify(QObject*, QEvent*) + 594
103 QtWidgets.so 0x00000001102d53ca sipQApplication::notify(QObject*, QEvent*) + 234
104 QtCore 0x00000001114014c4 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 212
105 QtGui 0x0000000110ceb41f QGuiApplicationPrivate::processKeyEvent(QWindowSystemInterfacePrivate::KeyEvent*) + 191
106 QtGui 0x0000000110cd16db QWindowSystemInterface::sendWindowSystemEvents(QFlags) + 219
107 QtGui 0x0000000110ccc615 QWindowSystemInterface::flushWindowSystemEvents(QFlags) + 581
108 libqcocoa.dylib 0x000000011b0910d8 0x11b062000 + 192728
109 libqcocoa.dylib 0x000000011b0912a8 0x11b062000 + 193192
110 com.apple.AppKit 0x00007fff2d3e143d -[NSWindow(NSEventRouting) _reallySendEvent:isDelayedEvent:] + 5040
111 com.apple.AppKit 0x00007fff2d3dfc70 -[NSWindow(NSEventRouting) sendEvent:] + 497
112 libqcocoa.dylib 0x000000011b0946b5 0x11b062000 + 206517
113 com.apple.AppKit 0x00007fff2d241236 -[NSApplication(NSEvent) sendEvent:] + 2462
114 libqcocoa.dylib 0x000000011b09b70a 0x11b062000 + 235274
115 com.apple.AppKit 0x00007fff2caa187d -[NSApplication run] + 812
116 libqcocoa.dylib 0x000000011b097de3 0x11b062000 + 220643
117 QtCore 0x00000001113fcadf QEventLoop::exec(QFlags) + 431
118 QtCore 0x0000000111401ad2 QCoreApplication::exec() + 130
119 QtWidgets.so 0x00000001103c47d2 meth_QApplication_exec_(_object*, _object*) + 82
120 org.python.python 0x000000010342b392 _PyMethodDef_RawFastCallKeywords + 226
121 org.python.python 0x000000010342a8b9 _PyCFunction_FastCallKeywords + 41
122 org.python.python 0x00000001034ffaf0 call_function + 656
123 org.python.python 0x00000001034fc7a7 _PyEval_EvalFrameDefault + 26567
124 org.python.python 0x000000010342ad61 function_code_fastcall + 177
125 org.python.python 0x00000001034ffb64 call_function + 772
126 org.python.python 0x00000001034fc7a7 _PyEval_EvalFrameDefault + 26567
127 org.python.python 0x00000001035009bc _PyEval_EvalCodeWithName + 3276
128 org.python.python 0x000000010342a879 _PyFunction_FastCallKeywords + 217
129 org.python.python 0x00000001034ffb64 call_function + 772
130 org.python.python 0x00000001034fc83e _PyEval_EvalFrameDefault + 26718
131 org.python.python 0x00000001035009bc _PyEval_EvalCodeWithName + 3276
132 org.python.python 0x00000001034f5f40 PyEval_EvalCode + 48
133 org.python.python 0x00000001034f34d7 builtin_exec + 583
134 org.python.python 0x000000010342b545 _PyMethodDef_RawFastCallKeywords + 661
135 org.python.python 0x000000010342a8b9 _PyCFunction_FastCallKeywords + 41
136 org.python.python 0x00000001034ffaf0 call_function + 656
137 org.python.python 0x00000001034fc83e _PyEval_EvalFrameDefault + 26718
138 org.python.python 0x00000001035009bc _PyEval_EvalCodeWithName + 3276
139 org.python.python 0x000000010342a879 _PyFunction_FastCallKeywords + 217
140 org.python.python 0x00000001034ffb64 call_function + 772
141 org.python.python 0x00000001034fc83e _PyEval_EvalFrameDefault + 26718
142 org.python.python 0x00000001035009bc _PyEval_EvalCodeWithName + 3276
143 org.python.python 0x000000010342a377 _PyFunction_FastCallDict + 455
144 org.python.python 0x000000010355aa83 pymain_run_module + 147
145 org.python.python 0x0000000103559b6c pymain_main + 5900
146 org.python.python 0x0000000103558453 Py_Main + 51
147 edu.ucsf.cgl.ChimeraX 0x00000001033f9dc8 main + 120
148 libdyld.dylib 0x00007fff57473015 start + 1
Thread 1:
0 libsystem_kernel.dylib 0x00007fff575c3a16 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff5778c589 _pthread_cond_wait + 732
2 libopenblasp-r0.3.7.dylib 0x0000000104f8ac3b blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff5778b661 _pthread_body + 340
4 libsystem_pthread.dylib 0x00007fff5778b50d _pthread_start + 377
5 libsystem_pthread.dylib 0x00007fff5778abf9 thread_start + 13
Thread 2:
0 libsystem_kernel.dylib 0x00007fff575c3a16 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff5778c589 _pthread_cond_wait + 732
2 libopenblasp-r0.3.7.dylib 0x0000000104f8ac3b blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff5778b661 _pthread_body + 340
4 libsystem_pthread.dylib 0x00007fff5778b50d _pthread_start + 377
5 libsystem_pthread.dylib 0x00007fff5778abf9 thread_start + 13
Thread 3:
0 libsystem_kernel.dylib 0x00007fff575c3a16 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff5778c589 _pthread_cond_wait + 732
2 libopenblasp-r0.3.7.dylib 0x0000000104f8ac3b blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff5778b661 _pthread_body + 340
4 libsystem_pthread.dylib 0x00007fff5778b50d _pthread_start + 377
5 libsystem_pthread.dylib 0x00007fff5778abf9 thread_start + 13
Thread 4:: com.apple.NSEventThread
0 libsystem_kernel.dylib 0x00007fff575ba1fa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff575b9714 mach_msg + 60
2 com.apple.CoreFoundation 0x00007fff2f516405 __CFRunLoopServiceMachPort + 341
3 com.apple.CoreFoundation 0x00007fff2f515757 __CFRunLoopRun + 1783
4 com.apple.CoreFoundation 0x00007fff2f514dd3 CFRunLoopRunSpecific + 483
5 com.apple.AppKit 0x00007fff2cbe9fc4 _NSEventThread + 184
6 libsystem_pthread.dylib 0x00007fff5778b661 _pthread_body + 340
7 libsystem_pthread.dylib 0x00007fff5778b50d _pthread_start + 377
8 libsystem_pthread.dylib 0x00007fff5778abf9 thread_start + 13
Thread 5:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff575ba1fa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff575b9714 mach_msg + 60
2 QtWebEngineCore 0x00000001141f62ad 0x11204b000 + 35304109
3 QtWebEngineCore 0x00000001141f61af 0x11204b000 + 35303855
4 QtWebEngineCore 0x00000001141a9fdd 0x11204b000 + 34992093
5 QtWebEngineCore 0x00000001141d3005 0x11204b000 + 35160069
6 QtWebEngineCore 0x000000011422593c 0x11204b000 + 35498300
7 QtWebEngineCore 0x0000000114265697 0x11204b000 + 35759767
8 libsystem_pthread.dylib 0x00007fff5778b661 _pthread_body + 340
9 libsystem_pthread.dylib 0x00007fff5778b50d _pthread_start + 377
10 libsystem_pthread.dylib 0x00007fff5778abf9 thread_start + 13
Thread 6:: DnsConfigService
0 libsystem_kernel.dylib 0x00007fff575c4bea kevent + 10
1 QtWebEngineCore 0x00000001144b7929 0x11204b000 + 38193449
2 QtWebEngineCore 0x00000001144b4c3d 0x11204b000 + 38181949
3 QtWebEngineCore 0x000000011426bc5c 0x11204b000 + 35785820
4 QtWebEngineCore 0x00000001141d3005 0x11204b000 + 35160069
5 QtWebEngineCore 0x000000011422593c 0x11204b000 + 35498300
6 QtWebEngineCore 0x0000000114265697 0x11204b000 + 35759767
7 libsystem_pthread.dylib 0x00007fff5778b661 _pthread_body + 340
8 libsystem_pthread.dylib 0x00007fff5778b50d _pthread_start + 377
9 libsystem_pthread.dylib 0x00007fff5778abf9 thread_start + 13
Thread 7:: TaskSchedulerServiceThread
0 libsystem_kernel.dylib 0x00007fff575c4bea kevent + 10
1 QtWebEngineCore 0x00000001144b7929 0x11204b000 + 38193449
2 QtWebEngineCore 0x00000001144b4c3d 0x11204b000 + 38181949
3 QtWebEngineCore 0x000000011426bc44 0x11204b000 + 35785796
4 QtWebEngineCore 0x00000001141d3005 0x11204b000 + 35160069
5 QtWebEngineCore 0x00000001142149f4 0x11204b000 + 35428852
6 QtWebEngineCore 0x000000011422593c 0x11204b000 + 35498300
7 QtWebEngineCore 0x0000000114265697 0x11204b000 + 35759767
8 libsystem_pthread.dylib 0x00007fff5778b661 _pthread_body + 340
9 libsystem_pthread.dylib 0x00007fff5778b50d _pthread_start + 377
10 libsystem_pthread.dylib 0x00007fff5778abf9 thread_start + 13
Thread 8:: TaskSchedulerForegroundWorker
0 libsystem_kernel.dylib 0x00007fff575ba1fa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff575b9714 mach_msg + 60
2 QtWebEngineCore 0x00000001141f62ad 0x11204b000 + 35304109
3 QtWebEngineCore 0x00000001141f63a1 0x11204b000 + 35304353
4 QtWebEngineCore 0x000000011420dca8 0x11204b000 + 35400872
5 QtWebEngineCore 0x000000011420e5db 0x11204b000 + 35403227
6 QtWebEngineCore 0x000000011420e244 0x11204b000 + 35402308
7 QtWebEngineCore 0x0000000114265697 0x11204b000 + 35759767
8 libsystem_pthread.dylib 0x00007fff5778b661 _pthread_body + 340
9 libsystem_pthread.dylib 0x00007fff5778b50d _pthread_start + 377
10 libsystem_pthread.dylib 0x00007fff5778abf9 thread_start + 13
Thread 9:: TaskSchedulerForegroundBlockingWorker
0 libsystem_kernel.dylib 0x00007fff575ba1fa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff575b9714 mach_msg + 60
2 QtWebEngineCore 0x00000001141f62ad 0x11204b000 + 35304109
3 QtWebEngineCore 0x00000001141f63a1 0x11204b000 + 35304353
4 QtWebEngineCore 0x000000011420dca8 0x11204b000 + 35400872
5 QtWebEngineCore 0x000000011420e5db 0x11204b000 + 35403227
6 QtWebEngineCore 0x000000011420e244 0x11204b000 + 35402308
7 QtWebEngineCore 0x0000000114265697 0x11204b000 + 35759767
8 libsystem_pthread.dylib 0x00007fff5778b661 _pthread_body + 340
9 libsystem_pthread.dylib 0x00007fff5778b50d _pthread_start + 377
10 libsystem_pthread.dylib 0x00007fff5778abf9 thread_start + 13
Thread 10:: TaskSchedulerBackgroundWorker
0 libsystem_kernel.dylib 0x00007fff575ba1fa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff575b9714 mach_msg + 60
2 QtWebEngineCore 0x00000001141f62ad 0x11204b000 + 35304109
3 QtWebEngineCore 0x00000001141f63a1 0x11204b000 + 35304353
4 QtWebEngineCore 0x000000011420dca8 0x11204b000 + 35400872
5 QtWebEngineCore 0x000000011420e5db 0x11204b000 + 35403227
6 QtWebEngineCore 0x000000011420e1b4 0x11204b000 + 35402164
7 QtWebEngineCore 0x0000000114265697 0x11204b000 + 35759767
8 libsystem_pthread.dylib 0x00007fff5778b661 _pthread_body + 340
9 libsystem_pthread.dylib 0x00007fff5778b50d _pthread_start + 377
10 libsystem_pthread.dylib 0x00007fff5778abf9 thread_start + 13
Thread 11:: TaskSchedulerBackgroundBlockingWorker
0 libsystem_kernel.dylib 0x00007fff575ba1fa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff575b9714 mach_msg + 60
2 QtWebEngineCore 0x00000001141f62ad 0x11204b000 + 35304109
3 QtWebEngineCore 0x00000001141f63a1 0x11204b000 + 35304353
4 QtWebEngineCore 0x000000011420dca8 0x11204b000 + 35400872
5 QtWebEngineCore 0x000000011420e5db 0x11204b000 + 35403227
6 QtWebEngineCore 0x000000011420e1b4 0x11204b000 + 35402164
7 QtWebEngineCore 0x0000000114265697 0x11204b000 + 35759767
8 libsystem_pthread.dylib 0x00007fff5778b661 _pthread_body + 340
9 libsystem_pthread.dylib 0x00007fff5778b50d _pthread_start + 377
10 libsystem_pthread.dylib 0x00007fff5778abf9 thread_start + 13
Thread 12:: Chrome_IOThread
0 libsystem_kernel.dylib 0x00007fff575c4bea kevent + 10
1 QtWebEngineCore 0x00000001144b7929 0x11204b000 + 38193449
2 QtWebEngineCore 0x00000001144b4c3d 0x11204b000 + 38181949
3 QtWebEngineCore 0x000000011426bc44 0x11204b000 + 35785796
4 QtWebEngineCore 0x00000001141d3005 0x11204b000 + 35160069
5 QtWebEngineCore 0x0000000113b38fa4 0x11204b000 + 28237732
6 QtWebEngineCore 0x000000011422593c 0x11204b000 + 35498300
7 QtWebEngineCore 0x0000000114265697 0x11204b000 + 35759767
8 libsystem_pthread.dylib 0x00007fff5778b661 _pthread_body + 340
9 libsystem_pthread.dylib 0x00007fff5778b50d _pthread_start + 377
10 libsystem_pthread.dylib 0x00007fff5778abf9 thread_start + 13
Thread 13:: TaskSchedulerSingleThreadSharedBackgroundBlocking0
0 libsystem_kernel.dylib 0x00007fff575ba1fa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff575b9714 mach_msg + 60
2 QtWebEngineCore 0x00000001141f62ad 0x11204b000 + 35304109
3 QtWebEngineCore 0x00000001141f61af 0x11204b000 + 35303855
4 QtWebEngineCore 0x000000011420dc9a 0x11204b000 + 35400858
5 QtWebEngineCore 0x000000011420e33f 0x11204b000 + 35402559
6 QtWebEngineCore 0x000000011420e1e4 0x11204b000 + 35402212
7 QtWebEngineCore 0x0000000114265697 0x11204b000 + 35759767
8 libsystem_pthread.dylib 0x00007fff5778b661 _pthread_body + 340
9 libsystem_pthread.dylib 0x00007fff5778b50d _pthread_start + 377
10 libsystem_pthread.dylib 0x00007fff5778abf9 thread_start + 13
Thread 14:: CompositorTileWorker1/73731
0 libsystem_kernel.dylib 0x00007fff575c3a16 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff5778c589 _pthread_cond_wait + 732
2 QtWebEngineCore 0x0000000114263f28 0x11204b000 + 35753768
3 QtWebEngineCore 0x00000001151ec628 0x11204b000 + 52041256
4 QtWebEngineCore 0x0000000114224614 0x11204b000 + 35493396
5 QtWebEngineCore 0x0000000114265697 0x11204b000 + 35759767
6 libsystem_pthread.dylib 0x00007fff5778b661 _pthread_body + 340
7 libsystem_pthread.dylib 0x00007fff5778b50d _pthread_start + 377
8 libsystem_pthread.dylib 0x00007fff5778abf9 thread_start + 13
Thread 15:: AudioThread
0 libsystem_kernel.dylib 0x00007fff575ba1fa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff575b9714 mach_msg + 60
2 QtWebEngineCore 0x00000001141f62ad 0x11204b000 + 35304109
3 QtWebEngineCore 0x00000001141f61af 0x11204b000 + 35303855
4 QtWebEngineCore 0x00000001141a9fdd 0x11204b000 + 34992093
5 QtWebEngineCore 0x00000001141d3005 0x11204b000 + 35160069
6 QtWebEngineCore 0x000000011422593c 0x11204b000 + 35498300
7 QtWebEngineCore 0x0000000114265697 0x11204b000 + 35759767
8 libsystem_pthread.dylib 0x00007fff5778b661 _pthread_body + 340
9 libsystem_pthread.dylib 0x00007fff5778b50d _pthread_start + 377
10 libsystem_pthread.dylib 0x00007fff5778abf9 thread_start + 13
Thread 16:: Chrome_InProcGpuThread
0 libsystem_kernel.dylib 0x00007fff575ba1fa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff575b9714 mach_msg + 60
2 QtWebEngineCore 0x00000001141f62ad 0x11204b000 + 35304109
3 QtWebEngineCore 0x00000001141a9fd2 0x11204b000 + 34992082
4 QtWebEngineCore 0x00000001141d3005 0x11204b000 + 35160069
5 QtWebEngineCore 0x000000011422593c 0x11204b000 + 35498300
6 QtWebEngineCore 0x0000000114265697 0x11204b000 + 35759767
7 libsystem_pthread.dylib 0x00007fff5778b661 _pthread_body + 340
8 libsystem_pthread.dylib 0x00007fff5778b50d _pthread_start + 377
9 libsystem_pthread.dylib 0x00007fff5778abf9 thread_start + 13
Thread 17:: Chrome_ChildIOThread
0 libsystem_kernel.dylib 0x00007fff575c4bea kevent + 10
1 QtWebEngineCore 0x00000001144b7929 0x11204b000 + 38193449
2 QtWebEngineCore 0x00000001144b4c3d 0x11204b000 + 38181949
3 QtWebEngineCore 0x000000011426bc5c 0x11204b000 + 35785820
4 QtWebEngineCore 0x00000001141d3005 0x11204b000 + 35160069
5 QtWebEngineCore 0x000000011422593c 0x11204b000 + 35498300
6 QtWebEngineCore 0x0000000114265697 0x11204b000 + 35759767
7 libsystem_pthread.dylib 0x00007fff5778b661 _pthread_body + 340
8 libsystem_pthread.dylib 0x00007fff5778b50d _pthread_start + 377
9 libsystem_pthread.dylib 0x00007fff5778abf9 thread_start + 13
Thread 18:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff575ba1fa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff575b9714 mach_msg + 60
2 QtWebEngineCore 0x00000001141f62ad 0x11204b000 + 35304109
3 QtWebEngineCore 0x00000001141f61af 0x11204b000 + 35303855
4 QtWebEngineCore 0x00000001141a9fdd 0x11204b000 + 34992093
5 QtWebEngineCore 0x00000001141d3005 0x11204b000 + 35160069
6 QtWebEngineCore 0x000000011422593c 0x11204b000 + 35498300
7 QtWebEngineCore 0x0000000114265697 0x11204b000 + 35759767
8 libsystem_pthread.dylib 0x00007fff5778b661 _pthread_body + 340
9 libsystem_pthread.dylib 0x00007fff5778b50d _pthread_start + 377
10 libsystem_pthread.dylib 0x00007fff5778abf9 thread_start + 13
Thread 19:: TaskSchedulerSingleThreadForegroundBlocking1
0 libsystem_kernel.dylib 0x00007fff575ba1fa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff575b9714 mach_msg + 60
2 QtWebEngineCore 0x00000001141f62ad 0x11204b000 + 35304109
3 QtWebEngineCore 0x00000001141f61af 0x11204b000 + 35303855
4 QtWebEngineCore 0x000000011420dc9a 0x11204b000 + 35400858
5 QtWebEngineCore 0x000000011420e5db 0x11204b000 + 35403227
6 QtWebEngineCore 0x000000011420e2a4 0x11204b000 + 35402404
7 QtWebEngineCore 0x0000000114265697 0x11204b000 + 35759767
8 libsystem_pthread.dylib 0x00007fff5778b661 _pthread_body + 340
9 libsystem_pthread.dylib 0x00007fff5778b50d _pthread_start + 377
10 libsystem_pthread.dylib 0x00007fff5778abf9 thread_start + 13
Thread 20:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff575ba1fa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff575b9714 mach_msg + 60
2 QtWebEngineCore 0x00000001141f62ad 0x11204b000 + 35304109
3 QtWebEngineCore 0x00000001141f61af 0x11204b000 + 35303855
4 QtWebEngineCore 0x00000001141a9fdd 0x11204b000 + 34992093
5 QtWebEngineCore 0x00000001141d3005 0x11204b000 + 35160069
6 QtWebEngineCore 0x000000011422593c 0x11204b000 + 35498300
7 QtWebEngineCore 0x0000000114265697 0x11204b000 + 35759767
8 libsystem_pthread.dylib 0x00007fff5778b661 _pthread_body + 340
9 libsystem_pthread.dylib 0x00007fff5778b50d _pthread_start + 377
10 libsystem_pthread.dylib 0x00007fff5778abf9 thread_start + 13
Thread 21:: TaskSchedulerForegroundWorker
0 libsystem_kernel.dylib 0x00007fff575ba1fa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff575b9714 mach_msg + 60
2 QtWebEngineCore 0x00000001141f62ad 0x11204b000 + 35304109
3 QtWebEngineCore 0x00000001141f63a1 0x11204b000 + 35304353
4 QtWebEngineCore 0x000000011420dca8 0x11204b000 + 35400872
5 QtWebEngineCore 0x000000011420e5db 0x11204b000 + 35403227
6 QtWebEngineCore 0x000000011420e244 0x11204b000 + 35402308
7 QtWebEngineCore 0x0000000114265697 0x11204b000 + 35759767
8 libsystem_pthread.dylib 0x00007fff5778b661 _pthread_body + 340
9 libsystem_pthread.dylib 0x00007fff5778b50d _pthread_start + 377
10 libsystem_pthread.dylib 0x00007fff5778abf9 thread_start + 13
Thread 22:
0 libsystem_kernel.dylib 0x00007fff575c3a16 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff5778c589 _pthread_cond_wait + 732
2 libopenblasp-r0.3.7.dylib 0x0000000142335c3b blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff5778b661 _pthread_body + 340
4 libsystem_pthread.dylib 0x00007fff5778b50d _pthread_start + 377
5 libsystem_pthread.dylib 0x00007fff5778abf9 thread_start + 13
Thread 23:
0 libsystem_kernel.dylib 0x00007fff575c3a16 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff5778c589 _pthread_cond_wait + 732
2 libopenblasp-r0.3.7.dylib 0x0000000142335c3b blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff5778b661 _pthread_body + 340
4 libsystem_pthread.dylib 0x00007fff5778b50d _pthread_start + 377
5 libsystem_pthread.dylib 0x00007fff5778abf9 thread_start + 13
Thread 24:
0 libsystem_kernel.dylib 0x00007fff575c3a16 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff5778c589 _pthread_cond_wait + 732
2 libopenblasp-r0.3.7.dylib 0x0000000142335c3b blas_thread_server + 619
3 libsystem_pthread.dylib 0x00007fff5778b661 _pthread_body + 340
4 libsystem_pthread.dylib 0x00007fff5778b50d _pthread_start + 377
5 libsystem_pthread.dylib 0x00007fff5778abf9 thread_start + 13
Thread 25:
0 libsystem_kernel.dylib 0x00007fff575c428a __workq_kernreturn + 10
1 libsystem_pthread.dylib 0x00007fff5778b20e _pthread_wqthread + 1552
2 libsystem_pthread.dylib 0x00007fff5778abe9 start_wqthread + 13
Thread 26:
0 libsystem_kernel.dylib 0x00007fff575c3a16 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff5778c589 _pthread_cond_wait + 732
2 org.python.python 0x00000001034f5610 take_gil + 240
3 org.python.python 0x00000001034f5b6f PyEval_RestoreThread + 31
4 org.python.python 0x000000010358f969 acquire_timed + 121
5 org.python.python 0x000000010358f6dc lock_PyThread_acquire_lock + 44
6 org.python.python 0x000000010342b582 _PyMethodDef_RawFastCallKeywords + 722
7 org.python.python 0x0000000103431581 _PyMethodDescr_FastCallKeywords + 81
8 org.python.python 0x00000001034ffb8e call_function + 814
9 org.python.python 0x00000001034fc78a _PyEval_EvalFrameDefault + 26538
10 org.python.python 0x00000001035009bc _PyEval_EvalCodeWithName + 3276
11 org.python.python 0x000000010342a879 _PyFunction_FastCallKeywords + 217
12 org.python.python 0x00000001034ffb64 call_function + 772
13 org.python.python 0x00000001034fc78a _PyEval_EvalFrameDefault + 26538
14 org.python.python 0x00000001035009bc _PyEval_EvalCodeWithName + 3276
15 org.python.python 0x000000010342a879 _PyFunction_FastCallKeywords + 217
16 org.python.python 0x00000001034ffb64 call_function + 772
17 org.python.python 0x00000001034fc78a _PyEval_EvalFrameDefault + 26538
18 org.python.python 0x000000010342ad61 function_code_fastcall + 177
19 org.python.python 0x00000001034ffb64 call_function + 772
20 org.python.python 0x00000001034fc78a _PyEval_EvalFrameDefault + 26538
21 org.python.python 0x000000010342ad61 function_code_fastcall + 177
22 org.python.python 0x00000001034ffb64 call_function + 772
23 org.python.python 0x00000001034fc78a _PyEval_EvalFrameDefault + 26538
24 org.python.python 0x000000010342ad61 function_code_fastcall + 177
25 org.python.python 0x000000010342b883 _PyObject_Call_Prepend + 131
26 org.python.python 0x000000010342a9d8 PyObject_Call + 136
27 org.python.python 0x0000000103590207 t_bootstrap + 71
28 org.python.python 0x0000000103543cb9 pythread_wrapper + 25
29 libsystem_pthread.dylib 0x00007fff5778b661 _pthread_body + 340
30 libsystem_pthread.dylib 0x00007fff5778b50d _pthread_start + 377
31 libsystem_pthread.dylib 0x00007fff5778abf9 thread_start + 13
Thread 27:
0 libsystem_kernel.dylib 0x00007fff575c3a16 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff5778c589 _pthread_cond_wait + 732
2 libOpenMM.dylib 0x0000000141537d21 OpenMM::threadBody(void*) + 65
3 libsystem_pthread.dylib 0x00007fff5778b661 _pthread_body + 340
4 libsystem_pthread.dylib 0x00007fff5778b50d _pthread_start + 377
5 libsystem_pthread.dylib 0x00007fff5778abf9 thread_start + 13
Thread 28:
0 libsystem_kernel.dylib 0x00007fff575c3a16 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff5778c589 _pthread_cond_wait + 732
2 libOpenMM.dylib 0x0000000141537d21 OpenMM::threadBody(void*) + 65
3 libsystem_pthread.dylib 0x00007fff5778b661 _pthread_body + 340
4 libsystem_pthread.dylib 0x00007fff5778b50d _pthread_start + 377
5 libsystem_pthread.dylib 0x00007fff5778abf9 thread_start + 13
Thread 29:
0 libsystem_kernel.dylib 0x00007fff575c3a16 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff5778c589 _pthread_cond_wait + 732
2 libOpenMM.dylib 0x0000000141537d21 OpenMM::threadBody(void*) + 65
3 libsystem_pthread.dylib 0x00007fff5778b661 _pthread_body + 340
4 libsystem_pthread.dylib 0x00007fff5778b50d _pthread_start + 377
5 libsystem_pthread.dylib 0x00007fff5778abf9 thread_start + 13
Thread 30:
0 libsystem_kernel.dylib 0x00007fff575c3a16 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff5778c589 _pthread_cond_wait + 732
2 libOpenMM.dylib 0x0000000141537d21 OpenMM::threadBody(void*) + 65
3 libsystem_pthread.dylib 0x00007fff5778b661 _pthread_body + 340
4 libsystem_pthread.dylib 0x00007fff5778b50d _pthread_start + 377
5 libsystem_pthread.dylib 0x00007fff5778abf9 thread_start + 13
Thread 31:
0 libsystem_kernel.dylib 0x00007fff575c3a16 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff5778c589 _pthread_cond_wait + 732
2 libOpenMM.dylib 0x0000000141537d21 OpenMM::threadBody(void*) + 65
3 libsystem_pthread.dylib 0x00007fff5778b661 _pthread_body + 340
4 libsystem_pthread.dylib 0x00007fff5778b50d _pthread_start + 377
5 libsystem_pthread.dylib 0x00007fff5778abf9 thread_start + 13
Thread 32:
0 libsystem_kernel.dylib 0x00007fff575c3a16 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff5778c589 _pthread_cond_wait + 732
2 libOpenMM.dylib 0x0000000141537d21 OpenMM::threadBody(void*) + 65
3 libsystem_pthread.dylib 0x00007fff5778b661 _pthread_body + 340
4 libsystem_pthread.dylib 0x00007fff5778b50d _pthread_start + 377
5 libsystem_pthread.dylib 0x00007fff5778abf9 thread_start + 13
Thread 33:
0 libsystem_kernel.dylib 0x00007fff575c3a16 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff5778c589 _pthread_cond_wait + 732
2 libOpenMM.dylib 0x0000000141537d21 OpenMM::threadBody(void*) + 65
3 libsystem_pthread.dylib 0x00007fff5778b661 _pthread_body + 340
4 libsystem_pthread.dylib 0x00007fff5778b50d _pthread_start + 377
5 libsystem_pthread.dylib 0x00007fff5778abf9 thread_start + 13
Thread 34:
0 libsystem_kernel.dylib 0x00007fff575c3a16 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff5778c589 _pthread_cond_wait + 732
2 libOpenMM.dylib 0x0000000141537d21 OpenMM::threadBody(void*) + 65
3 libsystem_pthread.dylib 0x00007fff5778b661 _pthread_body + 340
4 libsystem_pthread.dylib 0x00007fff5778b50d _pthread_start + 377
5 libsystem_pthread.dylib 0x00007fff5778abf9 thread_start + 13
Thread 35:
0 libsystem_kernel.dylib 0x00007fff575c3a16 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff5778c589 _pthread_cond_wait + 732
2 libOpenMMOpenCL.dylib 0x00000001418653cd threadBody(void*) + 109
3 libsystem_pthread.dylib 0x00007fff5778b661 _pthread_body + 340
4 libsystem_pthread.dylib 0x00007fff5778b50d _pthread_start + 377
5 libsystem_pthread.dylib 0x00007fff5778abf9 thread_start + 13
Thread 0 crashed with X86 Thread State (64-bit):
rax: 0x0000000000000000 rbx: 0x00007fff8fea6380 rcx: 0x0000000103895a48 rdx: 0x0000000000000000
rdi: 0x0000000000000307 rsi: 0x0000000000000006 rbp: 0x0000000103895a80 rsp: 0x0000000103895a48
r8: 0x0000000103895f48 r9: 0x0000000000000010 r10: 0x00007fff8fea63c8 r11: 0x0000000000000206
r12: 0x0000000000000307 r13: 0x00007ffeec800fa0 r14: 0x0000000000000006 r15: 0x000000000000002d
rip: 0x00007fff575c3b66 rfl: 0x0000000000000206 cr2: 0x00000001036037c8
Logical CPU: 0
Error Code: 0x02000148
Trap Number: 133
Binary Images:
0x1033f9000 - 0x1033f9ff3 +edu.ucsf.cgl.ChimeraX (1.0.0 - 1.0.0.0) /Applications/ChimeraX-1.0.app/Contents/MacOS/ChimeraX
0x103407000 - 0x103602fff +org.python.python (3.7.7, [c] 2001-2019 Python Software Foundation. - 3.7.7) /Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/Python
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0x103b8f000 - 0x103b90ff7 +_bz2.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_bz2.cpython-37m-darwin.so
0x103b99000 - 0x103b9cfff +_lzma.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_lzma.cpython-37m-darwin.so
0x103ba7000 - 0x103ba7ffb +grp.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/grp.cpython-37m-darwin.so
0x103bef000 - 0x103bf4ffb +math.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/math.cpython-37m-darwin.so
0x103c00000 - 0x103c02ff3 +_hashlib.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_hashlib.cpython-37m-darwin.so
0x103c0b000 - 0x103c68ff7 +libssl.1.1.dylib (0) /Applications/ChimeraX-1.0.app/Contents/lib/libssl.1.1.dylib
0x103c97000 - 0x103e5eaf3 +libcrypto.1.1.dylib (0) /Applications/ChimeraX-1.0.app/Contents/lib/libcrypto.1.1.dylib
0x103ef7000 - 0x103efcff3 +_blake2.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_blake2.cpython-37m-darwin.so
0x103f06000 - 0x103f16ff3 +_sha3.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_sha3.cpython-37m-darwin.so
0x103f21000 - 0x103f21ffb +_bisect.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_bisect.cpython-37m-darwin.so
0x103f29000 - 0x103f2affb +_random.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_random.cpython-37m-darwin.so
0x103f33000 - 0x103f39ff3 +libqgif.dylib (0) /Applications/ChimeraX-1.0.app/Contents/lib/python3.7/site-packages/PyQt5/Qt/plugins/imageformats/libqgif.dylib
0x103f42000 - 0x103f49ffb +libqicns.dylib (0) /Applications/ChimeraX-1.0.app/Contents/lib/python3.7/site-packages/PyQt5/Qt/plugins/imageformats/libqicns.dylib
0x103f53000 - 0x103f58ff3 +libqico.dylib (0) /Applications/ChimeraX-1.0.app/Contents/lib/python3.7/site-packages/PyQt5/Qt/plugins/imageformats/libqico.dylib
0x103f61000 - 0x103f66ff7 +libqmacheif.dylib (0) /Applications/ChimeraX-1.0.app/Contents/lib/python3.7/site-packages/PyQt5/Qt/plugins/imageformats/libqmacheif.dylib
0x103f6f000 - 0x103f72ff3 +libqwbmp.dylib (0) /Applications/ChimeraX-1.0.app/Contents/lib/python3.7/site-packages/PyQt5/Qt/plugins/imageformats/libqwbmp.dylib
0x10403b000 - 0x104041ffb +_json.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_json.cpython-37m-darwin.so
0x10408a000 - 0x104097ff3 +_ssl.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_ssl.cpython-37m-darwin.so
0x1040ad000 - 0x1040b6ffb +_socket.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_socket.cpython-37m-darwin.so
0x104108000 - 0x10410bfff +select.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/select.cpython-37m-darwin.so
0x104115000 - 0x104119ff3 +_struct.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_struct.cpython-37m-darwin.so
0x104127000 - 0x10412bff7 +binascii.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/binascii.cpython-37m-darwin.so
0x104234000 - 0x104242ff3 +_datetime.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_datetime.cpython-37m-darwin.so
0x104292000 - 0x104292ff3 +_scproxy.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_scproxy.cpython-37m-darwin.so
0x1042ec000 - 0x1042edff3 +_queue.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_queue.cpython-37m-darwin.so
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0x7fff558c1000 - 0x7fff55a52fff libcrypto.35.dylib (22.50.3) /usr/lib/libcrypto.35.dylib
0x7fff55bed000 - 0x7fff55bf8ff7 libcsfde.dylib (546.50.1) /usr/lib/libcsfde.dylib
0x7fff55bf9000 - 0x7fff55c4eff3 libcups.2.dylib (462.2.10) /usr/lib/libcups.2.dylib
0x7fff55c79000 - 0x7fff55ccdfff libcurl.4.dylib (105.40.2) /usr/lib/libcurl.4.dylib
0x7fff55d8e000 - 0x7fff55d8efff libenergytrace.dylib (16) /usr/lib/libenergytrace.dylib
0x7fff55d8f000 - 0x7fff55da8ff3 libexpat.1.dylib (16.1.1.1) /usr/lib/libexpat.1.dylib
0x7fff55dc0000 - 0x7fff55dc4ff7 libgermantok.dylib (17) /usr/lib/libgermantok.dylib
0x7fff55dc5000 - 0x7fff55dcaff3 libheimdal-asn1.dylib (520.50.9) /usr/lib/libheimdal-asn1.dylib
0x7fff55df6000 - 0x7fff55ee7ff7 libiconv.2.dylib (51.50.1) /usr/lib/libiconv.2.dylib
0x7fff55ee8000 - 0x7fff5610fffb libicucore.A.dylib (59181.0.1) /usr/lib/libicucore.A.dylib
0x7fff5615c000 - 0x7fff5615dfff liblangid.dylib (128) /usr/lib/liblangid.dylib
0x7fff5615e000 - 0x7fff56177ffb liblzma.5.dylib (10) /usr/lib/liblzma.5.dylib
0x7fff56178000 - 0x7fff5618eff7 libmarisa.dylib (9) /usr/lib/libmarisa.dylib
0x7fff5618f000 - 0x7fff5623efff libmecab.1.0.0.dylib (779.7.6) /usr/lib/libmecab.1.0.0.dylib
0x7fff5623f000 - 0x7fff56467ff7 libmecabra.dylib (779.7.6) /usr/lib/libmecabra.dylib
0x7fff5663f000 - 0x7fff567bafff libnetwork.dylib (1229.70.2) /usr/lib/libnetwork.dylib
0x7fff56841000 - 0x7fff56c2f7e7 libobjc.A.dylib (723) /usr/lib/libobjc.A.dylib
0x7fff56c30000 - 0x7fff56c31fff libodfde.dylib (24.50.1) /usr/lib/libodfde.dylib
0x7fff56c42000 - 0x7fff56c46fff libpam.2.dylib (22) /usr/lib/libpam.2.dylib
0x7fff56c49000 - 0x7fff56c81ff7 libpcap.A.dylib (79.20.3) /usr/lib/libpcap.A.dylib
0x7fff56d00000 - 0x7fff56d1cffb libresolv.9.dylib (65.1) /usr/lib/libresolv.9.dylib
0x7fff56d1e000 - 0x7fff56d57ff3 libsandbox.1.dylib (765.70.1) /usr/lib/libsandbox.1.dylib
0x7fff56d58000 - 0x7fff56d6afff libsasl2.2.dylib (211.0.2) /usr/lib/libsasl2.2.dylib
0x7fff56d6b000 - 0x7fff56d6cff3 libspindump.dylib (252) /usr/lib/libspindump.dylib
0x7fff56d6d000 - 0x7fff56f00ff7 libsqlite3.dylib (274.8.1) /usr/lib/libsqlite3.dylib
0x7fff56f5c000 - 0x7fff56fafffb libssl.35.dylib (22.50.3) /usr/lib/libssl.35.dylib
0x7fff570d4000 - 0x7fff57134ff3 libusrtcp.dylib (1229.70.2) /usr/lib/libusrtcp.dylib
0x7fff57135000 - 0x7fff57138ffb libutil.dylib (51.20.1) /usr/lib/libutil.dylib
0x7fff57139000 - 0x7fff57146ff3 libxar.1.dylib (417.1) /usr/lib/libxar.1.dylib
0x7fff5714a000 - 0x7fff57231fff libxml2.2.dylib (31.19) /usr/lib/libxml2.2.dylib
0x7fff57232000 - 0x7fff5725afff libxslt.1.dylib (15.16) /usr/lib/libxslt.1.dylib
0x7fff5725b000 - 0x7fff5726dffb libz.1.dylib (70) /usr/lib/libz.1.dylib
0x7fff57309000 - 0x7fff5730dff7 libcache.dylib (80) /usr/lib/system/libcache.dylib
0x7fff5730e000 - 0x7fff57318ff3 libcommonCrypto.dylib (60118.50.1) /usr/lib/system/libcommonCrypto.dylib
0x7fff57319000 - 0x7fff57320fff libcompiler_rt.dylib (62) /usr/lib/system/libcompiler_rt.dylib
0x7fff57321000 - 0x7fff5732affb libcopyfile.dylib (146.50.5) /usr/lib/system/libcopyfile.dylib
0x7fff5732b000 - 0x7fff573b0ffb libcorecrypto.dylib (562.70.3) /usr/lib/system/libcorecrypto.dylib
0x7fff57438000 - 0x7fff57471ff7 libdispatch.dylib (913.60.3) /usr/lib/system/libdispatch.dylib
0x7fff57472000 - 0x7fff5748fff7 libdyld.dylib (551.5) /usr/lib/system/libdyld.dylib
0x7fff57490000 - 0x7fff57490ffb libkeymgr.dylib (28) /usr/lib/system/libkeymgr.dylib
0x7fff57491000 - 0x7fff5749dff3 libkxld.dylib (4570.71.82.5) /usr/lib/system/libkxld.dylib
0x7fff5749e000 - 0x7fff5749eff7 liblaunch.dylib (1205.70.16) /usr/lib/system/liblaunch.dylib
0x7fff5749f000 - 0x7fff574a3ffb libmacho.dylib (906) /usr/lib/system/libmacho.dylib
0x7fff574a4000 - 0x7fff574a6fff libquarantine.dylib (86.70.1) /usr/lib/system/libquarantine.dylib
0x7fff574a7000 - 0x7fff574a8ff3 libremovefile.dylib (45) /usr/lib/system/libremovefile.dylib
0x7fff574a9000 - 0x7fff574c0fff libsystem_asl.dylib (356.70.1) /usr/lib/system/libsystem_asl.dylib
0x7fff574c1000 - 0x7fff574c1fff libsystem_blocks.dylib (67) /usr/lib/system/libsystem_blocks.dylib
0x7fff574c2000 - 0x7fff5754bff7 libsystem_c.dylib (1244.50.9) /usr/lib/system/libsystem_c.dylib
0x7fff5754c000 - 0x7fff5754fffb libsystem_configuration.dylib (963.50.9) /usr/lib/system/libsystem_configuration.dylib
0x7fff57550000 - 0x7fff57553ffb libsystem_coreservices.dylib (51) /usr/lib/system/libsystem_coreservices.dylib
0x7fff57554000 - 0x7fff57555fff libsystem_darwin.dylib (1244.50.9) /usr/lib/system/libsystem_darwin.dylib
0x7fff57556000 - 0x7fff5755cffb libsystem_dnssd.dylib (878.70.4) /usr/lib/system/libsystem_dnssd.dylib
0x7fff5755d000 - 0x7fff575a6ff7 libsystem_info.dylib (517.30.1) /usr/lib/system/libsystem_info.dylib
0x7fff575a7000 - 0x7fff575cdff7 libsystem_kernel.dylib (4570.71.82.5) /usr/lib/system/libsystem_kernel.dylib
0x7fff575ce000 - 0x7fff57619fcb libsystem_m.dylib (3147.50.1) /usr/lib/system/libsystem_m.dylib
0x7fff5761a000 - 0x7fff57639ff7 libsystem_malloc.dylib (140.50.7) /usr/lib/system/libsystem_malloc.dylib
0x7fff5763a000 - 0x7fff5776aff7 libsystem_network.dylib (1229.70.2) /usr/lib/system/libsystem_network.dylib
0x7fff5776b000 - 0x7fff57775ffb libsystem_networkextension.dylib (767.70.2) /usr/lib/system/libsystem_networkextension.dylib
0x7fff57776000 - 0x7fff5777fff3 libsystem_notify.dylib (172) /usr/lib/system/libsystem_notify.dylib
0x7fff57780000 - 0x7fff57787ff7 libsystem_platform.dylib (161.50.1) /usr/lib/system/libsystem_platform.dylib
0x7fff57788000 - 0x7fff57793fff libsystem_pthread.dylib (301.50.1) /usr/lib/system/libsystem_pthread.dylib
0x7fff57794000 - 0x7fff57797fff libsystem_sandbox.dylib (765.70.1) /usr/lib/system/libsystem_sandbox.dylib
0x7fff57798000 - 0x7fff57799ff3 libsystem_secinit.dylib (30) /usr/lib/system/libsystem_secinit.dylib
0x7fff5779a000 - 0x7fff577a1ff7 libsystem_symptoms.dylib (820.60.3) /usr/lib/system/libsystem_symptoms.dylib
0x7fff577a2000 - 0x7fff577b6ff7 libsystem_trace.dylib (829.70.2) /usr/lib/system/libsystem_trace.dylib
0x7fff577b8000 - 0x7fff577bdff7 libunwind.dylib (35.3) /usr/lib/system/libunwind.dylib
0x7fff577be000 - 0x7fff577ebfff libxpc.dylib (1205.70.16) /usr/lib/system/libxpc.dylib
External Modification Summary:
Calls made by other processes targeting this process:
task_for_pid: 3
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: 2265676
thread_create: 0
thread_set_state: 0
VM Region Summary:
ReadOnly portion of Libraries: Total=797.9M resident=0K(0%) swapped_out_or_unallocated=797.9M(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 384K 3
Activity Tracing 256K 2
CG backing stores 12.7M 9
CG image 148K 19
CoreAnimation 172K 37
CoreGraphics 8K 2
CoreImage 140K 34
CoreUI image data 3124K 38
CoreUI image file 216K 6
Foundation 4K 2
Image IO 16K 2
Kernel Alloc Once 8K 2
MALLOC 3.0G 227
MALLOC guard page 48K 11
MALLOC_LARGE (reserved) 420K 3 reserved VM address space (unallocated)
Memory Tag 242 12K 2
Memory Tag 251 12K 2
OpenCL 1.1G 24
OpenCL (reserved) 4504K 18 reserved VM address space (unallocated)
OpenGL GLSL 512K 7
PROTECTED_MEMORY 4K 2
STACK GUARD 140K 36
Stack 157.8M 37
Stack Guard 56.0M 2
VM_ALLOCATE 369.0M 269
VM_ALLOCATE (reserved) 128.0M 3 reserved VM address space (unallocated)
__DATA 49.1M 598
__FONT_DATA 4K 2
__GLSLBUILTINS 2588K 2
__LINKEDIT 233.8M 219
__TEXT 564.0M 551
__UNICODE 560K 2
mapped file 83.1M 79
shared memory 1200K 20
=========== ======= =======
TOTAL 5.7G 2238
TOTAL, minus reserved VM space 5.6G 2238
System Profile:
Network Service: Thunderbolt Ethernet, Ethernet, en4
Network Service: Wi-Fi, AirPort, en0
Thunderbolt Bus: MacBook Pro, Apple Inc., 27.1
Boot Volume File System Type: apfs
Memory Module: BANK 0/DIMM0, 8 GB, DDR3, 1600 MHz, 0x80AD, 0x484D54343147533642465238412D50422020
Memory Module: BANK 1/DIMM0, 8 GB, DDR3, 1600 MHz, 0x80AD, 0x484D54343147533642465238412D50422020
USB Device: USB 3.0 Bus
USB Device: Apple Internal Keyboard / Trackpad
USB Device: Bluetooth USB Host Controller
USB Device: USB Receiver
Serial ATA Device: APPLE SSD SM1024G, 1 TB
Model: MacBookPro11,4, BootROM 199.0.0.0.0, 4 processors, Intel Core i7, 2.8 GHz, 16 GB, SMC 2.29f24
Graphics: Intel Iris Pro, Intel Iris Pro, Built-In
AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x152), Broadcom BCM43xx 1.0 (7.77.37.33.1a1)
Bluetooth: Version 6.0.7f22, 3 services, 27 devices, 1 incoming serial ports
Log:
UCSF ChimeraX version: 1.0 (2020-06-04)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/misupov/work/biomex/yarden_em/manuscript/revision/maps/maps and
> coordinates for review 26_8_2020/6ZZ7_NAD_supp.pdb"
6ZZ7_NAD_supp.pdb title:
\--- [more info...]
Chain information for 6ZZ7_NAD_supp.pdb #1
---
Chain | Description
A B C D E F G H | No description available
Non-standard residues in 6ZZ7_NAD_supp.pdb #1
---
NAD — (NAD)
OpenGL version: 4.1 INTEL-10.36.32
OpenGL renderer: Intel Iris Pro OpenGL Engine
OpenGL vendor: Intel Inc.Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro11,4
Processor Name: Intel Core i7
Processor Speed: 2.8 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 6 MB
Memory: 16 GB
Boot ROM Version: 199.0.0.0.0
SMC Version (system): 2.29f24
Software:
System Software Overview:
System Version: macOS 10.13.6 (17G14019)
Kernel Version: Darwin 17.7.0
Time since boot: 62 days 7:43
Graphics/Displays:
Intel Iris Pro:
Chipset Model: Intel Iris Pro
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x0d26
Revision ID: 0x0008
Metal: Supported, feature set macOS GPUFamily1 v3
Displays:
PLX2783H:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60 Hz
Framebuffer Depth: 24-Bit Color (ARGB8888)
Display Serial Number: 1128161001888
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: No
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8
Change History (6)
comment:1 by , 5 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Third Party |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → OpenMM/OpenCL crash |
comment:2 by , 5 years ago
Not sure, but my best guess here is that the GPU ran out of memory - although (while slow) the Intel GPUs on MacBooks are usually pretty good at handling large systems. Were you attempting to start a simulation covering all of a large model and map when this happened?
follow-up: 3 comment:3 by , 5 years ago
This was a relatively large model 8x400 residues
in X-ray map at 3.2 (really 3.8) A. Previous refinement of the whole
model went well, but not this one after addition of some poorly visible helices.
The refinement of full model in a different project (an EM model 8 X 600 residues
at 2.7 A) also went well.
It may be that starting geometry was not very good.
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 29 September 2020 16:43
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; misupov@ex.ac.uk <misupov@ex.ac.uk>; tic20@cam.ac.uk <tic20@cam.ac.uk>
Subject: Re: [ChimeraX] #3768: OpenMM/OpenCL crash
CAUTION: This email originated from outside of the organisation. Do not click links or open attachments unless you recognise the sender and know the content is safe.
#3768: OpenMM/OpenCL crash
----------------------------------+---------------------------
Reporter: misupov@… | Owner: Tristan Croll
Type: defect | Status: assigned
Priority: normal | Milestone:
Component: Third Party | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
----------------------------------+---------------------------
Comment (by Tristan Croll):
Not sure, but my best guess here is that the GPU ran out of memory -
although (while slow) the Intel GPUs on MacBooks are usually pretty good
at handling large systems. Were you attempting to start a simulation
covering all of a large model and map when this happened?
--
Ticket URL: <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fplato.cgl.ucsf.edu%2Ftrac%2FChimeraX%2Fticket%2F3768%23comment%3A2&data=02%7C01%7CM.Isupov%40exeter.ac.uk%7C2b786844d5fe4995fb3308d8648e97a2%7C912a5d77fb984eeeaf321334d8f04a53%7C0%7C0%7C637369910898629112&sdata=eEhcLrIDr0vAq%2FZsuWdb1k3b9tDO6Jfe3Fvlt2y9E38%3D&reserved=0>
ChimeraX <https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimerax%2F&data=02%7C01%7CM.Isupov%40exeter.ac.uk%7C2b786844d5fe4995fb3308d8648e97a2%7C912a5d77fb984eeeaf321334d8f04a53%7C0%7C0%7C637369910898639105&sdata=8P%2BSFMOdY9ux5yccV%2BBv9SGZ7qTaFOo%2BoP2bTmVnN00%3D&reserved=0>
ChimeraX Issue Tracker
follow-up: 4 comment:4 by , 5 years ago
Hmm... that doesn't sound like it would be big enough to cause memory problems. If the geometry was bad it's possible the system exploded (although I haven't seen that happen in a long time) - but that usually doesn't lead to a hard crash like this (typically you'll get a Python error with "Particle coordinate is NaN"). Mysterious. If possible, would you mind sharing the model with me (directly at tic20@cam.ac.uk) for debugging purposes? In the meantime, you could try carefully untangling the clashing regions - the "isolde ignore {sel}" command is useful for this. Where you have a severe clash, select one of the offending regions and do "isolde ignore sel" to exclude it from simulations, then select the other part and start a simulation to pull it free (pinning it out of the way if you have to). Then stop the simulation, do "isolde ~ignore" to reinstate all residues for simulations, and continue on.
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 29 September 2020 16:54
To: misupov@ex.ac.uk <misupov@ex.ac.uk>; Tristan Croll <tic20@cam.ac.uk>
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #3768: OpenMM/OpenCL crash
#3768: OpenMM/OpenCL crash
----------------------------------+---------------------------
Reporter: misupov@… | Owner: Tristan Croll
Type: defect | Status: assigned
Priority: normal | Milestone:
Component: Third Party | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
----------------------------------+---------------------------
Comment (by M.Isupov@…):
{{{
This was a relatively large model 8x400 residues
in X-ray map at 3.2 (really 3.8) A. Previous refinement of the whole
model went well, but not this one after addition of some poorly visible
helices.
The refinement of full model in a different project (an EM model 8 X 600
residues
at 2.7 A) also went well.
It may be that starting geometry was not very good.
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 29 September 2020 16:43
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; misupov@ex.ac.uk
<misupov@ex.ac.uk>; tic20@cam.ac.uk <tic20@cam.ac.uk>
Subject: Re: [ChimeraX] #3768: OpenMM/OpenCL crash
CAUTION: This email originated from outside of the organisation. Do not
click links or open attachments unless you recognise the sender and know
the content is safe.
#3768: OpenMM/OpenCL crash
----------------------------------+---------------------------
Reporter: misupov@… | Owner: Tristan Croll
Type: defect | Status: assigned
Priority: normal | Milestone:
Component: Third Party | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
----------------------------------+---------------------------
Comment (by Tristan Croll):
Not sure, but my best guess here is that the GPU ran out of memory -
although (while slow) the Intel GPUs on MacBooks are usually pretty good
at handling large systems. Were you attempting to start a simulation
covering all of a large model and map when this happened?
--
Ticket URL:
<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fplato.cgl.ucsf.edu%2Ftrac%2FChimeraX%2Fticket%2F3768%23comment%3A2&data=02%7C01%7CM.Isupov%40exeter.ac.uk%7C2b786844d5fe4995fb3308d8648e97a2%7C912a5d77fb984eeeaf321334d8f04a53%7C0%7C0%7C637369910898629112&sdata=eEhcLrIDr0vAq%2FZsuWdb1k3b9tDO6Jfe3Fvlt2y9E38%3D&reserved=0>
ChimeraX
<https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimerax%2F&data=02%7C01%7CM.Isupov%40exeter.ac.uk%7C2b786844d5fe4995fb3308d8648e97a2%7C912a5d77fb984eeeaf321334d8f04a53%7C0%7C0%7C637369910898639105&sdata=8P%2BSFMOdY9ux5yccV%2BBv9SGZ7qTaFOo%2BoP2bTmVnN00%3D&reserved=0>
ChimeraX Issue Tracker
}}}
--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/3768#comment:3>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
follow-up: 5 comment:5 by , 5 years ago
Thank you for the advice.
The model is not mine, I cannot share it
until publilcation, sorry.
However I can run it then and it the program still crashes
provide it.
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 29 September 2020 17:04
To: misupov@ex.ac.uk <misupov@ex.ac.uk>; tic20@cam.ac.uk <tic20@cam.ac.uk>
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #3768: OpenMM/OpenCL crash
CAUTION: This email originated from outside of the organisation. Do not click links or open attachments unless you recognise the sender and know the content is safe.
#3768: OpenMM/OpenCL crash
----------------------------------+---------------------------
Reporter: misupov@… | Owner: Tristan Croll
Type: defect | Status: assigned
Priority: normal | Milestone:
Component: Third Party | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
----------------------------------+---------------------------
Comment (by Tristan Croll):
{{{
Hmm... that doesn't sound like it would be big enough to cause memory
problems. If the geometry was bad it's possible the system exploded
(although I haven't seen that happen in a long time) - but that usually
doesn't lead to a hard crash like this (typically you'll get a Python
error with "Particle coordinate is NaN"). Mysterious. If possible, would
you mind sharing the model with me (directly at tic20@cam.ac.uk) for
debugging purposes? In the meantime, you could try carefully untangling
the clashing regions - the "isolde ignore {sel}" command is useful for
this. Where you have a severe clash, select one of the offending regions
and do "isolde ignore sel" to exclude it from simulations, then select the
other part and start a simulation to pull it free (pinning it out of the
way if you have to). Then stop the simulation, do "isolde ~ignore" to
reinstate all residues for simulations, and continue on.
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 29 September 2020 16:54
To: misupov@ex.ac.uk <misupov@ex.ac.uk>; Tristan Croll <tic20@cam.ac.uk>
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #3768: OpenMM/OpenCL crash
#3768: OpenMM/OpenCL crash
----------------------------------+---------------------------
Reporter: misupov@… | Owner: Tristan Croll
Type: defect | Status: assigned
Priority: normal | Milestone:
Component: Third Party | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
----------------------------------+---------------------------
Comment (by M.Isupov@…):
{{{
This was a relatively large model 8x400 residues
in X-ray map at 3.2 (really 3.8) A. Previous refinement of the whole
model went well, but not this one after addition of some poorly visible
helices.
The refinement of full model in a different project (an EM model 8 X 600
residues
at 2.7 A) also went well.
It may be that starting geometry was not very good.
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 29 September 2020 16:43
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; misupov@ex.ac.uk
<misupov@ex.ac.uk>; tic20@cam.ac.uk <tic20@cam.ac.uk>
Subject: Re: [ChimeraX] #3768: OpenMM/OpenCL crash
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#3768: OpenMM/OpenCL crash
----------------------------------+---------------------------
Reporter: misupov@… | Owner: Tristan Croll
Type: defect | Status: assigned
Priority: normal | Milestone:
Component: Third Party | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
----------------------------------+---------------------------
Comment (by Tristan Croll):
Not sure, but my best guess here is that the GPU ran out of memory -
although (while slow) the Intel GPUs on MacBooks are usually pretty good
at handling large systems. Were you attempting to start a simulation
covering all of a large model and map when this happened?
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comment:6 by , 3 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
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Reported by Mikhail Isupov