![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
#3907 closed defect (nonchimerax)
Crash in graphics driver
| Reported by: | Eric Pettersen | Owned by: | Tom Goddard |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.15.7-x86_64-i386-64bit
ChimeraX Version: 1.2.dev202010262104 (2020-10-26 21:04:12 UTC)
Description
Last time you used ChimeraX it crashed.
Running the NIH3D script on a large structure (5y6p)
Process: ChimeraX [8276]
Path: /Users/USER/*/ChimeraX.app/Contents/MacOS/ChimeraX
Identifier: edu.ucsf.cgl.ChimeraX
Version: 1.2.0 (1.2.0.0)
Code Type: X86-64 (Native)
Parent Process: tcsh [642]
Responsible: Terminal [514]
User ID: 501
Date/Time: 2020-11-03 13:54:23.802 -0800
OS Version: Mac OS X 10.15.7 (19H2)
Report Version: 12
Anonymous UUID: 1001EC17-01AB-23EF-FBAF-2E1668FB0851
Time Awake Since Boot: 190000 seconds
System Integrity Protection: enabled
Crashed Thread: 0 CrBrowserMain Dispatch queue: com.apple.main-thread
Exception Type: EXC_BAD_INSTRUCTION (SIGILL)
Exception Codes: 0x0000000000000001, 0x0000000000000000
Exception Note: EXC_CORPSE_NOTIFY
Application Specific Information:
*** CFRetain() called with NULL ***
Thread 0 Crashed:: CrBrowserMain Dispatch queue: com.apple.main-thread
0 libsystem_kernel.dylib 0x00007fff699c433a __pthread_kill + 10
1 libsystem_pthread.dylib 0x00007fff69a80e60 pthread_kill + 430
2 libsystem_c.dylib 0x00007fff698db93e raise + 26
3 libsystem_platform.dylib 0x00007fff69a755fd _sigtramp + 29
4 ??? 000000000000000000 0 + 0
5 com.apple.driver.AppleIntelBDWGraphicsGLDriver 0x00007fff24a71eae IntelVertexArray::extractBuffers(GLDVertexArrayRec*, unsigned long long, unsigned long long) + 118
6 com.apple.driver.AppleIntelBDWGraphicsGLDriver 0x00007fff24a71e29 glrUpdateVertexArrayBuffers + 13
7 libGPUSupportMercury.dylib 0x00007fff50c4c9e0 gpusLoadCurrentVertexArray + 687
8 com.apple.driver.AppleIntelBDWGraphicsGLDriver 0x00007fff24a6483e updateDispatch + 1225
9 GLEngine 0x00007fff3a3d8506 gleDoSelectiveDispatchNoErrorCoreGL3 + 544
10 GLEngine 0x00007fff3a36b61f glValidateProgramARB_Exec + 350
11 _ctypes.cpython-38-darwin.so 0x0000000106611caf ffi_call_unix64 + 79
12 _ctypes.cpython-38-darwin.so 0x00000001066124fd ffi_call + 877
13 _ctypes.cpython-38-darwin.so 0x000000010660cdfc _ctypes_callproc + 844
14 _ctypes.cpython-38-darwin.so 0x0000000106606582 PyCFuncPtr_call + 1298
15 org.python.python 0x0000000100f4537b PyObject_Call + 171
16 org.python.python 0x0000000100f9d20e slot_tp_call + 222
17 org.python.python 0x0000000100f44ef6 _PyObject_MakeTpCall + 374
18 org.python.python 0x00000001010238c4 call_function + 660
19 org.python.python 0x0000000101020557 _PyEval_EvalFrameDefault + 26791
20 org.python.python 0x0000000100f45861 function_code_fastcall + 177
21 org.python.python 0x0000000101023792 call_function + 354
22 org.python.python 0x0000000101020533 _PyEval_EvalFrameDefault + 26755
23 org.python.python 0x0000000100f45861 function_code_fastcall + 177
24 org.python.python 0x0000000101023792 call_function + 354
25 org.python.python 0x0000000101020533 _PyEval_EvalFrameDefault + 26755
26 org.python.python 0x0000000100f45861 function_code_fastcall + 177
27 org.python.python 0x0000000101023792 call_function + 354
28 org.python.python 0x0000000101020533 _PyEval_EvalFrameDefault + 26755
29 org.python.python 0x0000000100f45861 function_code_fastcall + 177
30 org.python.python 0x0000000101023792 call_function + 354
31 org.python.python 0x0000000101020533 _PyEval_EvalFrameDefault + 26755
32 org.python.python 0x000000010102490e _PyEval_EvalCodeWithName + 3534
33 org.python.python 0x0000000100f459dd _PyFunction_Vectorcall + 253
34 org.python.python 0x0000000100f4823b method_vectorcall + 171
35 org.python.python 0x0000000101023792 call_function + 354
36 org.python.python 0x000000010102068e _PyEval_EvalFrameDefault + 27102
37 org.python.python 0x0000000100f45861 function_code_fastcall + 177
38 org.python.python 0x0000000101023792 call_function + 354
39 org.python.python 0x0000000101020533 _PyEval_EvalFrameDefault + 26755
40 org.python.python 0x0000000100f45861 function_code_fastcall + 177
41 org.python.python 0x0000000101023792 call_function + 354
42 org.python.python 0x0000000101020533 _PyEval_EvalFrameDefault + 26755
43 org.python.python 0x0000000100f45861 function_code_fastcall + 177
44 org.python.python 0x0000000101023792 call_function + 354
45 org.python.python 0x00000001010205f0 _PyEval_EvalFrameDefault + 26944
46 org.python.python 0x0000000100f45861 function_code_fastcall + 177
47 org.python.python 0x0000000101023792 call_function + 354
48 org.python.python 0x00000001010205f0 _PyEval_EvalFrameDefault + 26944
49 org.python.python 0x0000000100f45861 function_code_fastcall + 177
50 org.python.python 0x0000000101023792 call_function + 354
51 org.python.python 0x0000000101020533 _PyEval_EvalFrameDefault + 26755
52 org.python.python 0x000000010102490e _PyEval_EvalCodeWithName + 3534
53 org.python.python 0x0000000100f459dd _PyFunction_Vectorcall + 253
54 org.python.python 0x0000000100f4823b method_vectorcall + 171
55 org.python.python 0x0000000101023792 call_function + 354
56 org.python.python 0x000000010102068e _PyEval_EvalFrameDefault + 27102
57 org.python.python 0x0000000100f45861 function_code_fastcall + 177
58 org.python.python 0x0000000101023792 call_function + 354
59 org.python.python 0x0000000101020533 _PyEval_EvalFrameDefault + 26755
60 org.python.python 0x0000000100f45861 function_code_fastcall + 177
61 org.python.python 0x0000000101023792 call_function + 354
62 org.python.python 0x0000000101020533 _PyEval_EvalFrameDefault + 26755
63 org.python.python 0x000000010102490e _PyEval_EvalCodeWithName + 3534
64 org.python.python 0x0000000100f459dd _PyFunction_Vectorcall + 253
65 org.python.python 0x0000000100f45234 PyVectorcall_Call + 100
66 org.python.python 0x000000010102082f _PyEval_EvalFrameDefault + 27519
67 org.python.python 0x000000010102490e _PyEval_EvalCodeWithName + 3534
68 org.python.python 0x0000000100f459dd _PyFunction_Vectorcall + 253
69 org.python.python 0x0000000100f4823b method_vectorcall + 171
70 org.python.python 0x0000000101023792 call_function + 354
71 org.python.python 0x000000010102068e _PyEval_EvalFrameDefault + 27102
72 org.python.python 0x000000010102490e _PyEval_EvalCodeWithName + 3534
73 org.python.python 0x0000000100f459dd _PyFunction_Vectorcall + 253
74 org.python.python 0x0000000100f45234 PyVectorcall_Call + 100
75 org.python.python 0x000000010102082f _PyEval_EvalFrameDefault + 27519
76 org.python.python 0x000000010102490e _PyEval_EvalCodeWithName + 3534
77 org.python.python 0x0000000100f459dd _PyFunction_Vectorcall + 253
78 org.python.python 0x0000000100f4823b method_vectorcall + 171
79 org.python.python 0x0000000101023792 call_function + 354
80 org.python.python 0x000000010102068e _PyEval_EvalFrameDefault + 27102
81 org.python.python 0x000000010102490e _PyEval_EvalCodeWithName + 3534
82 org.python.python 0x0000000100f459dd _PyFunction_Vectorcall + 253
83 org.python.python 0x0000000101023792 call_function + 354
84 org.python.python 0x00000001010205f0 _PyEval_EvalFrameDefault + 26944
85 org.python.python 0x0000000100f45861 function_code_fastcall + 177
86 org.python.python 0x0000000101023792 call_function + 354
87 org.python.python 0x00000001010205f0 _PyEval_EvalFrameDefault + 26944
88 org.python.python 0x0000000100f45861 function_code_fastcall + 177
89 org.python.python 0x0000000101023792 call_function + 354
90 org.python.python 0x00000001010205f0 _PyEval_EvalFrameDefault + 26944
91 org.python.python 0x000000010102490e _PyEval_EvalCodeWithName + 3534
92 org.python.python 0x0000000101019c10 PyEval_EvalCode + 48
93 org.python.python 0x0000000101017040 builtin_exec + 592
94 org.python.python 0x0000000100f835a1 cfunction_vectorcall_FASTCALL + 177
95 org.python.python 0x0000000101023792 call_function + 354
96 org.python.python 0x00000001010205f0 _PyEval_EvalFrameDefault + 26944
97 org.python.python 0x000000010102490e _PyEval_EvalCodeWithName + 3534
98 org.python.python 0x0000000100f459dd _PyFunction_Vectorcall + 253
99 org.python.python 0x0000000101023792 call_function + 354
100 org.python.python 0x00000001010205f0 _PyEval_EvalFrameDefault + 26944
101 org.python.python 0x000000010102490e _PyEval_EvalCodeWithName + 3534
102 org.python.python 0x0000000100f459dd _PyFunction_Vectorcall + 253
103 org.python.python 0x0000000101023792 call_function + 354
104 org.python.python 0x000000010102068e _PyEval_EvalFrameDefault + 27102
105 org.python.python 0x000000010102490e _PyEval_EvalCodeWithName + 3534
106 org.python.python 0x0000000100f459dd _PyFunction_Vectorcall + 253
107 org.python.python 0x0000000100f45234 PyVectorcall_Call + 100
108 org.python.python 0x000000010102082f _PyEval_EvalFrameDefault + 27519
109 org.python.python 0x000000010102490e _PyEval_EvalCodeWithName + 3534
110 org.python.python 0x0000000100f459dd _PyFunction_Vectorcall + 253
111 org.python.python 0x0000000100f4823b method_vectorcall + 171
112 org.python.python 0x0000000101023792 call_function + 354
113 org.python.python 0x000000010102068e _PyEval_EvalFrameDefault + 27102
114 org.python.python 0x000000010102490e _PyEval_EvalCodeWithName + 3534
115 org.python.python 0x0000000100f459dd _PyFunction_Vectorcall + 253
116 org.python.python 0x0000000101023792 call_function + 354
117 org.python.python 0x00000001010205f0 _PyEval_EvalFrameDefault + 26944
118 org.python.python 0x000000010102490e _PyEval_EvalCodeWithName + 3534
119 org.python.python 0x0000000100f459dd _PyFunction_Vectorcall + 253
120 org.python.python 0x0000000101023792 call_function + 354
121 org.python.python 0x00000001010205f0 _PyEval_EvalFrameDefault + 26944
122 org.python.python 0x000000010102490e _PyEval_EvalCodeWithName + 3534
123 org.python.python 0x0000000101019c10 PyEval_EvalCode + 48
124 org.python.python 0x0000000101017040 builtin_exec + 592
125 org.python.python 0x0000000100f835a1 cfunction_vectorcall_FASTCALL + 177
126 org.python.python 0x0000000101023792 call_function + 354
127 org.python.python 0x00000001010205f0 _PyEval_EvalFrameDefault + 26944
128 org.python.python 0x000000010102490e _PyEval_EvalCodeWithName + 3534
129 org.python.python 0x0000000100f459dd _PyFunction_Vectorcall + 253
130 org.python.python 0x0000000101023792 call_function + 354
131 org.python.python 0x00000001010205f0 _PyEval_EvalFrameDefault + 26944
132 org.python.python 0x000000010102490e _PyEval_EvalCodeWithName + 3534
133 org.python.python 0x0000000100f459dd _PyFunction_Vectorcall + 253
134 org.python.python 0x0000000100f45234 PyVectorcall_Call + 100
135 org.python.python 0x0000000101089563 pymain_run_module + 179
136 org.python.python 0x0000000101088c58 Py_RunMain + 1416
137 org.python.python 0x0000000101089443 pymain_main + 403
138 org.python.python 0x000000010108929b Py_Main + 43
139 edu.ucsf.cgl.ChimeraX 0x0000000100f10d79 main + 121
140 libdyld.dylib 0x00007fff6987ccc9 start + 1
Thread 1:
0 libsystem_kernel.dylib 0x00007fff699c0882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff69a81425 _pthread_cond_wait + 698
2 libopenblas.0.dylib 0x000000010293a27b blas_thread_server + 507
3 libsystem_pthread.dylib 0x00007fff69a81109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff69a7cb8b thread_start + 15
Thread 2:
0 libsystem_kernel.dylib 0x00007fff699c0882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff69a81425 _pthread_cond_wait + 698
2 libopenblas.0.dylib 0x000000010293a27b blas_thread_server + 507
3 libsystem_pthread.dylib 0x00007fff69a81109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff69a7cb8b thread_start + 15
Thread 3:
0 libsystem_kernel.dylib 0x00007fff699c0882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff69a81425 _pthread_cond_wait + 698
2 libopenblas.0.dylib 0x000000010293a27b blas_thread_server + 507
3 libsystem_pthread.dylib 0x00007fff69a81109 _pthread_start + 148
4 libsystem_pthread.dylib 0x00007fff69a7cb8b thread_start + 15
Thread 4:: com.apple.NSEventThread
0 libsystem_kernel.dylib 0x00007fff699bddfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff699be170 mach_msg + 60
2 com.apple.CoreFoundation 0x00007fff2f7e2ef5 __CFRunLoopServiceMachPort + 247
3 com.apple.CoreFoundation 0x00007fff2f7e19c2 __CFRunLoopRun + 1319
4 com.apple.CoreFoundation 0x00007fff2f7e0e3e CFRunLoopRunSpecific + 462
5 com.apple.AppKit 0x00007fff2cbf4954 _NSEventThread + 132
6 libsystem_pthread.dylib 0x00007fff69a81109 _pthread_start + 148
7 libsystem_pthread.dylib 0x00007fff69a7cb8b thread_start + 15
Thread 5:: ThreadPoolServiceThread
0 libsystem_kernel.dylib 0x00007fff699c6b96 kevent64 + 10
1 QtWebEngineCore 0x000000011645c73a base::MessagePumpKqueue::DoInternalWork(base::MessagePump::Delegate::NextWorkInfo*) + 330
2 QtWebEngineCore 0x000000011645c597 base::MessagePumpKqueue::Run(base::MessagePump::Delegate*) + 167
3 QtWebEngineCore 0x00000001163e62af non-virtual thunk to base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 143
4 QtWebEngineCore 0x00000001163a9b6f base::RunLoop::Run() + 399
5 QtWebEngineCore 0x00000001163ef224 base::internal::ServiceThread::Run(base::RunLoop*) + 20
6 QtWebEngineCore 0x00000001164030dd base::Thread::ThreadMain() + 413
7 QtWebEngineCore 0x000000011644a4c7 base::(anonymous namespace)::ThreadFunc(void*) + 87
8 libsystem_pthread.dylib 0x00007fff69a81109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff69a7cb8b thread_start + 15
Thread 6:: ThreadPoolBackgroundWorker
0 libsystem_kernel.dylib 0x00007fff699bddfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff699be170 mach_msg + 60
2 QtWebEngineCore 0x0000000116451e65 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 405
3 QtWebEngineCore 0x00000001163fabe8 base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*) + 56
4 QtWebEngineCore 0x00000001163fb444 base::internal::WorkerThread::RunWorker() + 644
5 QtWebEngineCore 0x00000001163fb0b4 base::internal::WorkerThread::RunBackgroundPooledWorker() + 20
6 QtWebEngineCore 0x000000011644a4c7 base::(anonymous namespace)::ThreadFunc(void*) + 87
7 libsystem_pthread.dylib 0x00007fff69a81109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff69a7cb8b thread_start + 15
Thread 7:: Chrome_IOThread
0 libsystem_kernel.dylib 0x00007fff699c6b96 kevent64 + 10
1 QtWebEngineCore 0x000000011645c73a base::MessagePumpKqueue::DoInternalWork(base::MessagePump::Delegate::NextWorkInfo*) + 330
2 QtWebEngineCore 0x000000011645c597 base::MessagePumpKqueue::Run(base::MessagePump::Delegate*) + 167
3 QtWebEngineCore 0x00000001163e62af non-virtual thunk to base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 143
4 QtWebEngineCore 0x00000001163a9b6f base::RunLoop::Run() + 399
5 QtWebEngineCore 0x000000011a3573c4 content::BrowserProcessSubThread::IOThreadRun(base::RunLoop*) + 20
6 QtWebEngineCore 0x00000001164030dd base::Thread::ThreadMain() + 413
7 QtWebEngineCore 0x000000011644a4c7 base::(anonymous namespace)::ThreadFunc(void*) + 87
8 libsystem_pthread.dylib 0x00007fff69a81109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff69a7cb8b thread_start + 15
Thread 8:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff699bddfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff699be170 mach_msg + 60
2 QtWebEngineCore 0x0000000116451e65 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 405
3 QtWebEngineCore 0x0000000116451cbf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x000000011637fe4b base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171
5 QtWebEngineCore 0x00000001163e62af non-virtual thunk to base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 143
6 QtWebEngineCore 0x00000001163a9b6f base::RunLoop::Run() + 399
7 QtWebEngineCore 0x00000001164030dd base::Thread::ThreadMain() + 413
8 QtWebEngineCore 0x000000011644a4c7 base::(anonymous namespace)::ThreadFunc(void*) + 87
9 libsystem_pthread.dylib 0x00007fff69a81109 _pthread_start + 148
10 libsystem_pthread.dylib 0x00007fff69a7cb8b thread_start + 15
Thread 9:: CompositorTileWorker1
0 libsystem_kernel.dylib 0x00007fff699c0882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff69a81425 _pthread_cond_wait + 698
2 QtWebEngineCore 0x0000000116449555 base::ConditionVariable::Wait() + 53
3 QtWebEngineCore 0x000000011777ef38 non-virtual thunk to cc::SingleThreadTaskGraphRunner::Run() + 56
4 QtWebEngineCore 0x000000011644a4c7 base::(anonymous namespace)::ThreadFunc(void*) + 87
5 libsystem_pthread.dylib 0x00007fff69a81109 _pthread_start + 148
6 libsystem_pthread.dylib 0x00007fff69a7cb8b thread_start + 15
Thread 10:: Chrome_InProcGpuThread
0 libsystem_kernel.dylib 0x00007fff699bddfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff699be170 mach_msg + 60
2 QtWebEngineCore 0x0000000116451e65 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 405
3 QtWebEngineCore 0x0000000116451cbf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x000000011637fe4b base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171
5 QtWebEngineCore 0x00000001163e62af non-virtual thunk to base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 143
6 QtWebEngineCore 0x00000001163a9b6f base::RunLoop::Run() + 399
7 QtWebEngineCore 0x00000001164030dd base::Thread::ThreadMain() + 413
8 QtWebEngineCore 0x000000011644a4c7 base::(anonymous namespace)::ThreadFunc(void*) + 87
9 libsystem_pthread.dylib 0x00007fff69a81109 _pthread_start + 148
10 libsystem_pthread.dylib 0x00007fff69a7cb8b thread_start + 15
Thread 11:: Chrome_ChildIOThread
0 libsystem_kernel.dylib 0x00007fff699c6b96 kevent64 + 10
1 QtWebEngineCore 0x000000011645c73a base::MessagePumpKqueue::DoInternalWork(base::MessagePump::Delegate::NextWorkInfo*) + 330
2 QtWebEngineCore 0x000000011645c597 base::MessagePumpKqueue::Run(base::MessagePump::Delegate*) + 167
3 QtWebEngineCore 0x00000001163e62af non-virtual thunk to base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 143
4 QtWebEngineCore 0x00000001163a9b6f base::RunLoop::Run() + 399
5 QtWebEngineCore 0x00000001164030dd base::Thread::ThreadMain() + 413
6 QtWebEngineCore 0x000000011644a4c7 base::(anonymous namespace)::ThreadFunc(void*) + 87
7 libsystem_pthread.dylib 0x00007fff69a81109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff69a7cb8b thread_start + 15
Thread 12:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff699bddfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff699be170 mach_msg + 60
2 QtWebEngineCore 0x0000000116451e65 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 405
3 QtWebEngineCore 0x0000000116451cbf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x000000011637fe4b base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171
5 QtWebEngineCore 0x00000001163e62af non-virtual thunk to base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 143
6 QtWebEngineCore 0x00000001163a9b6f base::RunLoop::Run() + 399
7 QtWebEngineCore 0x00000001164030dd base::Thread::ThreadMain() + 413
8 QtWebEngineCore 0x000000011644a4c7 base::(anonymous namespace)::ThreadFunc(void*) + 87
9 libsystem_pthread.dylib 0x00007fff69a81109 _pthread_start + 148
10 libsystem_pthread.dylib 0x00007fff69a7cb8b thread_start + 15
Thread 13:: VizCompositorThread
0 libsystem_kernel.dylib 0x00007fff699bddfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff699be170 mach_msg + 60
2 QtWebEngineCore 0x0000000116451e65 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 405
3 QtWebEngineCore 0x0000000116451cbf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x000000011637fe4b base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171
5 QtWebEngineCore 0x00000001163e62af non-virtual thunk to base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 143
6 QtWebEngineCore 0x00000001163a9b6f base::RunLoop::Run() + 399
7 QtWebEngineCore 0x00000001164030dd base::Thread::ThreadMain() + 413
8 QtWebEngineCore 0x000000011644a4c7 base::(anonymous namespace)::ThreadFunc(void*) + 87
9 libsystem_pthread.dylib 0x00007fff69a81109 _pthread_start + 148
10 libsystem_pthread.dylib 0x00007fff69a7cb8b thread_start + 15
Thread 14:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff699bddfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff699be170 mach_msg + 60
2 QtWebEngineCore 0x0000000116451e65 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 405
3 QtWebEngineCore 0x0000000116451cbf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x000000011637fe4b base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171
5 QtWebEngineCore 0x00000001163e62af non-virtual thunk to base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 143
6 QtWebEngineCore 0x00000001163a9b6f base::RunLoop::Run() + 399
7 QtWebEngineCore 0x00000001164030dd base::Thread::ThreadMain() + 413
8 QtWebEngineCore 0x000000011644a4c7 base::(anonymous namespace)::ThreadFunc(void*) + 87
9 libsystem_pthread.dylib 0x00007fff69a81109 _pthread_start + 148
10 libsystem_pthread.dylib 0x00007fff69a7cb8b thread_start + 15
Thread 15:: ThreadPoolSingleThreadForegroundBlocking0
0 libsystem_kernel.dylib 0x00007fff699bddfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff699be170 mach_msg + 60
2 QtWebEngineCore 0x0000000116451e65 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 405
3 QtWebEngineCore 0x0000000116451cbf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x00000001163fabda base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*) + 42
5 QtWebEngineCore 0x00000001163fb444 base::internal::WorkerThread::RunWorker() + 644
6 QtWebEngineCore 0x00000001163fb1a4 base::internal::WorkerThread::RunDedicatedWorker() + 20
7 QtWebEngineCore 0x000000011644a4c7 base::(anonymous namespace)::ThreadFunc(void*) + 87
8 libsystem_pthread.dylib 0x00007fff69a81109 _pthread_start + 148
9 libsystem_pthread.dylib 0x00007fff69a7cb8b thread_start + 15
Thread 16:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fff699bddfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff699be170 mach_msg + 60
2 QtWebEngineCore 0x0000000116451e65 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 405
3 QtWebEngineCore 0x0000000116451cbf base::WaitableEvent::Wait() + 31
4 QtWebEngineCore 0x000000011637fe4b base::MessagePumpDefault::Run(base::MessagePump::Delegate*) + 171
5 QtWebEngineCore 0x00000001163e62af non-virtual thunk to base::sequence_manager::internal::ThreadControllerWithMessagePumpImpl::Run(bool, base::TimeDelta) + 143
6 QtWebEngineCore 0x00000001163a9b6f base::RunLoop::Run() + 399
7 QtWebEngineCore 0x00000001164030dd base::Thread::ThreadMain() + 413
8 QtWebEngineCore 0x000000011644a4c7 base::(anonymous namespace)::ThreadFunc(void*) + 87
9 libsystem_pthread.dylib 0x00007fff69a81109 _pthread_start + 148
10 libsystem_pthread.dylib 0x00007fff69a7cb8b thread_start + 15
Thread 17:: ThreadPoolForegroundWorker
0 libsystem_kernel.dylib 0x00007fff699bddfa mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff699be170 mach_msg + 60
2 QtWebEngineCore 0x0000000116451e65 base::WaitableEvent::TimedWait(base::TimeDelta const&) + 405
3 QtWebEngineCore 0x00000001163fabe8 base::internal::WorkerThread::Delegate::WaitForWork(base::WaitableEvent*) + 56
4 QtWebEngineCore 0x00000001163fb444 base::internal::WorkerThread::RunWorker() + 644
5 QtWebEngineCore 0x00000001163fb144 base::internal::WorkerThread::RunPooledWorker() + 20
6 QtWebEngineCore 0x000000011644a4c7 base::(anonymous namespace)::ThreadFunc(void*) + 87
7 libsystem_pthread.dylib 0x00007fff69a81109 _pthread_start + 148
8 libsystem_pthread.dylib 0x00007fff69a7cb8b thread_start + 15
Thread 18:
0 libsystem_pthread.dylib 0x00007fff69a7cb68 start_wqthread + 0
Thread 19:
0 libsystem_kernel.dylib 0x00007fff699c0882 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff69a81425 _pthread_cond_wait + 698
2 org.python.python 0x0000000101077a01 PyThread_acquire_lock_timed + 337
3 org.python.python 0x00000001010c46df acquire_timed + 111
4 org.python.python 0x00000001010c447c lock_PyThread_acquire_lock + 44
5 org.python.python 0x0000000100f4e6d4 method_vectorcall_VARARGS_KEYWORDS + 324
6 org.python.python 0x0000000101023792 call_function + 354
7 org.python.python 0x0000000101020533 _PyEval_EvalFrameDefault + 26755
8 org.python.python 0x000000010102490e _PyEval_EvalCodeWithName + 3534
9 org.python.python 0x0000000100f459dd _PyFunction_Vectorcall + 253
10 org.python.python 0x0000000101023792 call_function + 354
11 org.python.python 0x0000000101020533 _PyEval_EvalFrameDefault + 26755
12 org.python.python 0x000000010102490e _PyEval_EvalCodeWithName + 3534
13 org.python.python 0x0000000100f459dd _PyFunction_Vectorcall + 253
14 org.python.python 0x0000000101023792 call_function + 354
15 org.python.python 0x0000000101020533 _PyEval_EvalFrameDefault + 26755
16 org.python.python 0x0000000100f45861 function_code_fastcall + 177
17 org.python.python 0x0000000101023792 call_function + 354
18 org.python.python 0x0000000101020533 _PyEval_EvalFrameDefault + 26755
19 org.python.python 0x0000000100f45861 function_code_fastcall + 177
20 org.python.python 0x0000000101023792 call_function + 354
21 org.python.python 0x0000000101020533 _PyEval_EvalFrameDefault + 26755
22 org.python.python 0x0000000100f45861 function_code_fastcall + 177
23 org.python.python 0x0000000100f482d2 method_vectorcall + 322
24 org.python.python 0x0000000100f45234 PyVectorcall_Call + 100
25 org.python.python 0x00000001010c507a t_bootstrap + 74
26 org.python.python 0x0000000101077649 pythread_wrapper + 25
27 libsystem_pthread.dylib 0x00007fff69a81109 _pthread_start + 148
28 libsystem_pthread.dylib 0x00007fff69a7cb8b thread_start + 15
Thread 0 crashed with X86 Thread State (64-bit):
rax: 0x0000000000000000 rbx: 0x00000001080f7dc0 rcx: 0x00007fbb41f8da58 rdx: 0x0000000000000000
rdi: 0x0000000000000307 rsi: 0x0000000000000004 rbp: 0x00007fbb41f8da80 rsp: 0x00007fbb41f8da58
r8: 0x00007fbb41f8df48 r9: 0x5932d5e0006cac9f r10: 0x00000001080f7dc0 r11: 0x0000000000000246
r12: 0x0000000000000307 r13: 0xffffffffffffffff r14: 0x0000000000000004 r15: 0x0000000000000016
rip: 0x00007fff699c433a rfl: 0x0000000000000246 cr2: 0x000000010150db78
Logical CPU: 0
Error Code: 0x02000148
Trap Number: 133
Binary Images:
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0x7fff68c77000 - 0x7fff68c7affb libutil.dylib (57) /usr/lib/libutil.dylib
0x7fff68c7b000 - 0x7fff68c88ff7 libxar.1.dylib (425.2) /usr/lib/libxar.1.dylib
0x7fff68c8e000 - 0x7fff68d70fff libxml2.2.dylib (33.5) /usr/lib/libxml2.2.dylib
0x7fff68d74000 - 0x7fff68d9cfff libxslt.1.dylib (16.9) /usr/lib/libxslt.1.dylib
0x7fff68d9d000 - 0x7fff68dafff3 libz.1.dylib (76) /usr/lib/libz.1.dylib
0x7fff6965e000 - 0x7fff69663ff3 libcache.dylib (83) /usr/lib/system/libcache.dylib
0x7fff69664000 - 0x7fff6966ffff libcommonCrypto.dylib (60165.120.1) /usr/lib/system/libcommonCrypto.dylib
0x7fff69670000 - 0x7fff69677fff libcompiler_rt.dylib (101.2) /usr/lib/system/libcompiler_rt.dylib
0x7fff69678000 - 0x7fff69681ff7 libcopyfile.dylib (166.40.1) /usr/lib/system/libcopyfile.dylib
0x7fff69682000 - 0x7fff69714fdb libcorecrypto.dylib (866.140.1) /usr/lib/system/libcorecrypto.dylib
0x7fff69821000 - 0x7fff69861ff0 libdispatch.dylib (1173.100.2) /usr/lib/system/libdispatch.dylib
0x7fff69862000 - 0x7fff69898fff libdyld.dylib (750.6) /usr/lib/system/libdyld.dylib
0x7fff69899000 - 0x7fff69899ffb libkeymgr.dylib (30) /usr/lib/system/libkeymgr.dylib
0x7fff6989a000 - 0x7fff698a6ff3 libkxld.dylib (6153.141.2) /usr/lib/system/libkxld.dylib
0x7fff698a7000 - 0x7fff698a7ff7 liblaunch.dylib (1738.140.1) /usr/lib/system/liblaunch.dylib
0x7fff698a8000 - 0x7fff698adff7 libmacho.dylib (959.0.1) /usr/lib/system/libmacho.dylib
0x7fff698ae000 - 0x7fff698b0ff3 libquarantine.dylib (110.40.3) /usr/lib/system/libquarantine.dylib
0x7fff698b1000 - 0x7fff698b2ff7 libremovefile.dylib (48) /usr/lib/system/libremovefile.dylib
0x7fff698b3000 - 0x7fff698caff3 libsystem_asl.dylib (377.60.2) /usr/lib/system/libsystem_asl.dylib
0x7fff698cb000 - 0x7fff698cbff7 libsystem_blocks.dylib (74) /usr/lib/system/libsystem_blocks.dylib
0x7fff698cc000 - 0x7fff69953fff libsystem_c.dylib (1353.100.2) /usr/lib/system/libsystem_c.dylib
0x7fff69954000 - 0x7fff69957ffb libsystem_configuration.dylib (1061.141.1) /usr/lib/system/libsystem_configuration.dylib
0x7fff69958000 - 0x7fff6995bfff libsystem_coreservices.dylib (114) /usr/lib/system/libsystem_coreservices.dylib
0x7fff6995c000 - 0x7fff69964fff libsystem_darwin.dylib (1353.100.2) /usr/lib/system/libsystem_darwin.dylib
0x7fff69965000 - 0x7fff6996cfff libsystem_dnssd.dylib (1096.100.3) /usr/lib/system/libsystem_dnssd.dylib
0x7fff6996d000 - 0x7fff6996effb libsystem_featureflags.dylib (17) /usr/lib/system/libsystem_featureflags.dylib
0x7fff6996f000 - 0x7fff699bcff7 libsystem_info.dylib (538) /usr/lib/system/libsystem_info.dylib
0x7fff699bd000 - 0x7fff699e9ff7 libsystem_kernel.dylib (6153.141.2) /usr/lib/system/libsystem_kernel.dylib
0x7fff699ea000 - 0x7fff69a31fff libsystem_m.dylib (3178) /usr/lib/system/libsystem_m.dylib
0x7fff69a32000 - 0x7fff69a59fff libsystem_malloc.dylib (283.100.6) /usr/lib/system/libsystem_malloc.dylib
0x7fff69a5a000 - 0x7fff69a67ffb libsystem_networkextension.dylib (1095.140.2) /usr/lib/system/libsystem_networkextension.dylib
0x7fff69a68000 - 0x7fff69a71ff7 libsystem_notify.dylib (241.100.2) /usr/lib/system/libsystem_notify.dylib
0x7fff69a72000 - 0x7fff69a7afef libsystem_platform.dylib (220.100.1) /usr/lib/system/libsystem_platform.dylib
0x7fff69a7b000 - 0x7fff69a85fff libsystem_pthread.dylib (416.100.3) /usr/lib/system/libsystem_pthread.dylib
0x7fff69a86000 - 0x7fff69a8aff3 libsystem_sandbox.dylib (1217.141.2) /usr/lib/system/libsystem_sandbox.dylib
0x7fff69a8b000 - 0x7fff69a8dfff libsystem_secinit.dylib (62.100.2) /usr/lib/system/libsystem_secinit.dylib
0x7fff69a8e000 - 0x7fff69a95ffb libsystem_symptoms.dylib (1238.120.1) /usr/lib/system/libsystem_symptoms.dylib
0x7fff69a96000 - 0x7fff69aacff2 libsystem_trace.dylib (1147.120) /usr/lib/system/libsystem_trace.dylib
0x7fff69aae000 - 0x7fff69ab3ff7 libunwind.dylib (35.4) /usr/lib/system/libunwind.dylib
0x7fff69ab4000 - 0x7fff69ae9ffe libxpc.dylib (1738.140.1) /usr/lib/system/libxpc.dylib
External Modification Summary:
Calls made by other processes targeting this process:
task_for_pid: 80
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: 766415
thread_create: 0
thread_set_state: 0
VM Region Summary:
ReadOnly portion of Libraries: Total=989.5M resident=0K(0%) swapped_out_or_unallocated=989.5M(100%)
Writable regions: Total=12.7G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=12.7G(100%)
VIRTUAL REGION
REGION TYPE SIZE COUNT (non-coalesced)
=========== ======= =======
Accelerate framework 384K 3
Activity Tracing 256K 1
CG backing stores 336K 2
CG image 44K 6
CoreAnimation 80K 16
CoreGraphics 8K 1
CoreImage 8K 2
CoreUI image data 936K 14
Dispatch continuations 8192K 1
Foundation 4K 1
Kernel Alloc Once 8K 1
MALLOC 8.2G 1674
MALLOC guard page 32K 7
MALLOC_LARGE (reserved) 256K 1 reserved VM address space (unallocated)
Mach message 24K 3
OpenGL GLSL 256K 3
STACK GUARD 76K 19
Stack 130.6M 20
Stack Guard 56.0M 1
VM_ALLOCATE 4.4G 527
VM_ALLOCATE (reserved) 32.0M 1 reserved VM address space (unallocated)
__DATA 51.8M 540
__DATA_CONST 1260K 67
__FONT_DATA 4K 1
__GLSLBUILTINS 5176K 1
__LINKEDIT 474.3M 196
__OBJC_RO 32.3M 1
__OBJC_RW 1908K 2
__TEXT 515.6M 508
__UNICODE 564K 1
mapped file 396.9M 49
shared memory 656K 20
=========== ======= =======
TOTAL 14.2G 3690
TOTAL, minus reserved VM space 14.2G 3690
Log:
> runscript cx_unified.py --pdb 6e9d
> open pdbe_bio:6E9D autoStyle false
Summary of feedback from opening 6E9D fetched from pdbe_bio
---
warnings | Atom H is not in the residue template for GLY /A:226
Atom H is not in the residue template for GLY /AA:226
Atom H is not in the residue template for GLY /AB:226
Atom H is not in the residue template for GLY /B:226
Atom H is not in the residue template for GLY /BA:226
55 messages similar to the above omitted
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
note | Fetching compressed 6E9D bioassembly 1 from
https://www.ebi.ac.uk/pdbe/static/entry/download/6e9d-assembly-1.cif.gz
6E9D bioassembly 1 title:
Sub-2 Angstrom Ewald Curvature-Corrected Single-Particle Cryo-EM
Reconstruction of AAV-2 L336C [more info...]
Chain information for 6E9D bioassembly 1 #1
---
Chain | Description
A AA AB B BA BB C CA CB D DA DB E EA EB F FA FB G GA GB H HA HB I IA J JA K KA
L LA M MA N NA O OA P PA Q QA R RA S SA T TA U UA V VA W WA X XA Y YA Z ZA |
Capsid protein VP1
Opened 1 biological assemblies for 6E9D
> windowsize 512 512
> graphics bgColor white
> color name marine 0,50,100
Color 'marine' is opaque, 0% red, 50% green, and 100% blue
> color name forest 13.3,54.5,13.3
Color 'forest' is opaque, 13.3% red, 54.5% green, and 13.3% blue
> color name tangerine 95.3,51.8,0
Color 'tangerine' is opaque, 95.3% red, 51.8% green, and 0% blue
> color name grape 64.3,0,86.7
Color 'grape' is opaque, 64.3% red, 0% green, and 86.7% blue
> color name nih_blue 12.5,33.3,54.1
Color 'nih_blue' is opaque, 12.5% red, 33.3% green, and 54.1% blue
> color name jmol_carbon 56.5,56.5,56.5
Color 'jmol_carbon' is opaque, 56.5% red, 56.5% green, and 56.5% blue
> color name bond_purple 57.6,43.9,85.9
Color 'bond_purple' is opaque, 57.6% red, 43.9% green, and 85.9% blue
> color name struts_grey 48,48,48
Color 'struts_grey' is opaque, 48% red, 48% green, and 48% blue
> color name carbon_grey 22.2,22.2,22.2
Color 'carbon_grey' is opaque, 22.2% red, 22.2% green, and 22.2% blue
> delete solvent
> delete H
> delete ligand|ions
> select protein|nucleic-acid
245880 atoms, 253260 bonds, 30600 residues, 1 model selected
> select ~sel
Nothing selected
> delete sel
> ~select
Nothing selected
> ~nucleotides
> ~ribbon
> ~display
> surface #1 enclose #1 gridSpacing 2.5
> color nih_blue
> save 6E9D-surf.png width 512 height 512 supersample 3
> save 6E9D-surf.glb
> save 6E9D-surf.x3d
> color white
> color magenta
> color byattribute kd_hydrophobicity protein target rs palette
> 16,67,87:white:100,45,0 noValueColor magenta
30600 residues, 1 surfaces, atom kd_hydrophobicity range -4.5 to 4.5
> save 6E9D-surf-hydropathy.png width 512 height 512 supersample 3
> save 6E9D-surf-hydropathy.glb
> save 6E9D-surf-hydropathy.x3d
> rainbow chains @CA
Expected a keyword
UCSF ChimeraX version: 1.2.dev202010262104 (2020-10-26)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 INTEL-14.7.8
OpenGL renderer: Intel(R) Iris(TM) Pro Graphics 6200
OpenGL vendor: Intel Inc.Hardware:
Hardware Overview:
Model Name: iMac
Model Identifier: iMac16,2
Processor Name: Quad-Core Intel Core i5
Processor Speed: 2.8 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 4 MB
Memory: 16 GB
Boot ROM Version: 236.0.0.0.0
SMC Version (system): 2.32f21
Software:
System Software Overview:
System Version: macOS 10.15.7 (19H2)
Kernel Version: Darwin 19.6.0
Time since boot: 2 days 6:20
Graphics/Displays:
Intel Iris Pro Graphics 6200:
Chipset Model: Intel Iris Pro Graphics 6200
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x1622
Revision ID: 0x000a
Metal: Supported, feature set macOS GPUFamily1 v4
Displays:
iMac:
Display Type: LCD
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
Locale: ('en_US', 'UTF-8')
PyQt version: 5.15.1
Compiled Qt version: 5.15.1
Runtime Qt version: 5.15.1
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.0
Babel: 2.8.0
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.6.20
cftime: 1.2.1
chardet: 3.0.4
ChimeraX-AddH: 2.1.3
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.9.3
ChimeraX-AtomicLibrary: 1.1
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.2
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.0
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.1
ChimeraX-Clipper: 0.15.0
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-CommandLine: 1.1.3
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.2.dev202010262104
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.0.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-DataFormats: 1.0.1
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.0
ChimeraX-Hbonds: 2.1
ChimeraX-Help: 1.0
ChimeraX-HKCage: 1.0
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.1
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0
ChimeraX-ISOLDE: 1.0.2
ChimeraX-Label: 1.0
ChimeraX-ListInfo: 1.1
ChimeraX-Log: 1.1.1
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8
ChimeraX-Map: 1.0.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.0
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 1.1
ChimeraX-MDcrds: 2.1
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.0
ChimeraX-mmCIF: 2.2
ChimeraX-MMTF: 2.0
ChimeraX-Modeller: 1.0
ChimeraX-ModelPanel: 1.0
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.0
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0
ChimeraX-OpenCommand: 1.3.1
ChimeraX-PDB: 2.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.0.1
ChimeraX-Read-Pbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.2.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.2.1
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.0
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.0.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.2.2
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.0
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.0
ChimeraX-ToolshedUtils: 1.0
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.3.1
ChimeraX-uniprot: 2.0
ChimeraX-ViewDockX: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.3
comtypes: 1.1.7
cxservices: 1.0
cycler: 0.10.0
Cython: 0.29.21
decorator: 4.4.2
distlib: 0.3.1
docutils: 0.16
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 2.10.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.17
imagecodecs: 2020.5.30
imagecodecs-lite: 2020.1.31
imagesize: 1.2.0
ipykernel: 5.3.4
ipython: 7.18.1
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.7
jupyter-core: 4.6.3
kiwisolver: 1.2.0
line-profiler: 2.1.2
lxml: 4.5.2
MarkupSafe: 1.1.1
matplotlib: 3.3.2
msgpack: 1.0.0
netCDF4: 1.5.4
netifaces: 0.10.9
networkx: 2.5
numexpr: 2.7.1
numpy: 1.19.2
numpydoc: 1.1.0
openvr: 1.14.1501
packaging: 20.4
parso: 0.7.1
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 7.2.0
pip: 20.2.3
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.8
psutil: 5.7.2
ptyprocess: 0.6.0
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.7.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.15.1
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.1
python-dateutil: 2.8.1
pytz: 2020.1
pyzmq: 19.0.2
qtconsole: 4.7.7
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.5.2
setuptools: 50.3.0
sfftk-rw: 0.6.6.dev0
six: 1.15.0
snowballstemmer: 2.0.0
sortedcontainers: 2.2.2
Sphinx: 3.2.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 1.0.3
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.4
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2020.9.3
tinyarray: 1.2.3
tornado: 6.0.4
traitlets: 5.0.5
urllib3: 1.25.11
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.34.2
Change History (7)
comment:1 by , 5 years ago
| Component: | Unassigned → Graphics |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash in graphics driver |
comment:2 by , 5 years ago
| Resolution: | → nonchimerax |
|---|---|
| Status: | assigned → closed |
Says ChimeraX was using 14.2 Gbytes, a hefty amount.
* CFRetain() called with NULL *
suggests that perhaps a memory allocation failed and then the NULL pointer was passed to this CFRetain routine. As usual the crash is in Apple's graphics driver. I think when the graphics driver runs low on memory it is unstable. It's not supposed to crash -- there is an OpenGL GL_OUT_OF_MEMORY return value, but Apple's drivers seem to prefer to just crash. We have probably 50-100 such crashes reported. I don't have any thought on how to prevent these crashes. If an OpenGL call cannot allocate memory and crashes instead of returning GL_OUT_OF_MEMORY not much we can do. We have no way to predict how much memory is too much.
comment:3 by , 5 years ago
I am somewhat baffled why the logged commands are using so much memory. The only one that looks like it could use much memory is "surface #1 enclose #1 gridSpacing 2.5". The default grid spacing is 0.5 and I am surprised using 2.5 even works -- that really is going to mess with the rolling probe algorithm when you made the grid spacing as big as the probe diameter (1.4A radius). Making a solvent excluded surface on 5 million atoms is really asking for trouble. That is likely to use hundreds of millions of triangles, many Gbytes and be unusable when exported as glTF or other formats. Most generic applications that use 3D models really struggle with files over 100 Mbytes, and even if they can load them they are of little use for 3D printing, VR rendering, cell phone rendering, because it is too much detail. Probably a molmap lower resolution surface is the way to go for 5 million atoms.
comment:4 by , 5 years ago
For 3D printing a 100 Mbyte stl file used to take hours to compute tool paths for printing, very often ending in the software crashing, and the level of detail was way beyond what the printer could create (typically 1/100 inch resolution for a 2 inch model). And I think the printer software simply rejected files over 100 Mbytes. Just giving some ideas that limiting file size will be an important aim of the NIH 3D scripts.
comment:5 by , 5 years ago
Oops! Misread the log, structure has 500,000 atoms, not 5 million. I am surprise 500,000 uses so much memory. A full res SES surface (command: surf) causes ChimeraX only to use 2 Gbytes on my machine. Also surf enclose #1 takes only 1.5 Gbytes. I must be missing something he script is doing. Or maybe saving X3D or GLB takes lots of memory, could imagine that for X3D which is ascii and bloated.
comment:6 by , 5 years ago
This crash came from an old version of the script and I'm not 100% certain what surface command got issued. The current script issues "surf #1 enclose #1 res 8". That produces a 1.1GB(!) .x3d file. The original version of the script did some things to reduce scene complexity that the current script does not do, since the exact equivalents don't exist. Exactly what the targets are for scene complexity is one of the discussion topics for tomorrow's MSC meeting.
comment:7 by , 5 years ago
Saving X3D after "surface enclose #1" did take 15 Gbytes of memory and wrote a file 1.8 Gbytes in size. Saving GLB took about 1.5 Gbytes and wrote a file 0.95 Gbytes in size.
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Crashes very sporadic. Just ran the scripts with your latest updates and it didn't crash. You could tell by responsiveness that heavy memory pressure was being put on the machine.