Atom deleted during atoms.radii lookup

[Tom Goddard]

Loading exosome.ihm (attached) loads several mmCIF files and generates a numpy deprecation warning in the Structure code.

VisibleDeprecationWarning: boolean index did not match indexed array along dimension 0;
dimension is 26829 but corresponding boolean dimension is 26828
r[dm == Atom.BALL_STYLE] *= self.ball_scale

This happens because atoms.radii has a different length than atoms.draw_modes (computed on two consecutive lines). Debugging print statements reveal that before the r = atoms.radii line len(atoms) = 26829, but after that line len(atoms) = 26828, one less. Putting an abort in molc.cpp filter_array() reveals that the atom seems be deleted when in ~Ring(). Somehow a ring deletion in computing atom radii mistakenly causes an atom pointer to be removed from the atoms array when really the code was trying to remove a Ring * from any numpy arrays.

Seems like something might be amiss in the C++ code that removes deleted pointers from numpy arrays.

Here is the Python and C++ traceback when abort() called.

$ cx
cx
GVA info: Successfully connected to the Intel plugin, offline Gen7
removed 19366 numpy array elements
removed 19366 numpy array elements
removed 1 numpy array elements
Fatal Python error: Aborted

Thread 0x0000700009553000 (most recent call first):

File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/threading.py", line 299 in wait
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/threading.py", line 551 in wait
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/threading.py", line 1180 in run
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/threading.py", line 916 in _bootstrap_inner
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/threading.py", line 884 in _bootstrap

Current thread 0x00007fffaef3d3c0 (most recent call first):

File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/atomic/molc.py", line 126 in get_prop
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/atomic/structure.py", line 377 in _atom_display_radii
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/atomic/structure.py", line 344 in _update_atom_graphics
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/atomic/structure.py", line 275 in _make_drawing
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/atomic/structure.py", line 68 in init
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/atomic/structure.py", line 1842 in init
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/atomic/mmcif.py", line 50 in <listcomp>
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/atomic/mmcif.py", line 50 in open_mmcif
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/io.py", line 330 in open_data
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/atomic/mmcif.py", line 102 in fetch_mmcif
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/ihm/ihm.py", line 854 in models
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/ihm/ihm.py", line 205 in read_experimental_models
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/ihm/ihm.py", line 151 in read_starting_models
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/ihm/ihm.py", line 61 in init
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/ihm/ihm.py", line 36 in read_ihm
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/ihm/init.py", line 24 in open_file
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/toolshed/info.py", line 259 in open_shim
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/toolshed/info.py", line 262 in open_cb
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/io.py", line 330 in open_data
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/io.py", line 370 in open_multiple_data
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/models.py", line 345 in open
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/commands/open.py", line 111 in open
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/commands/cli.py", line 2354 in run
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/cmd_line/tool.py", line 161 in execute
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/cmd_line/tool.py", line 64 in keyPressEvent
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/ui/gui.py", line 167 in event_loop
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/ChimeraX_main.py", line 552 in init
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/ChimeraX_main.py", line 643 in <module>
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/runpy.py", line 85 in _run_code
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/runpy.py", line 193 in _run_module_as_main

Abort trap: 6

C++ traceback:

Process: ChimeraX [61406]
Path: /Users/USER/*/ChimeraX.app/Contents/MacOS/ChimeraX
Identifier: edu.ucsf.cgl.ChimeraX
Version: 0.1.0 (0.1.0.0)
Code Type: X86-64 (Native)
Parent Process: bash [18251]
Responsible: ChimeraX [61406]
User ID: 501

Date/Time: 2017-04-07 14:06:04.007 -0700
OS Version: Mac OS X 10.12.2 (16C67)
Report Version: 12
Anonymous UUID: ADCA02F2-9A59-6574-CF8F-380125498A20

Sleep/Wake UUID: 9E378455-13E3-4623-9871-61574B08CF5B

Time Awake Since Boot: 5000000 seconds

System Integrity Protection: enabled

Crashed Thread: 0 CrBrowserMain Dispatch queue: com.apple.main-thread

Exception Type: EXC_CRASH (SIGABRT)
Exception Codes: 0x0000000000000000, 0x0000000000000000
Exception Note: EXC_CORPSE_NOTIFY

Application Specific Information:
abort() called

Thread 0 Crashed:: CrBrowserMain Dispatch queue: com.apple.main-thread
0 libsystem_kernel.dylib 0x00007fffa6223dd6 pthread_kill + 10
1 libsystem_pthread.dylib 0x00007fffa630f787 pthread_kill + 90
2 libsystem_c.dylib 0x00007fffa613a497 raise + 26
3 libsystem_platform.dylib 0x00007fffa6302bba _sigtramp + 26
4 ??? 000000000000000000 0 + 0
5 libsystem_c.dylib 0x00007fffa6189420 abort + 129
6 libmolc.dylib 0x000000010be03f20 Array_Updater::filter_array(tagPyArrayObject*, std::1::set<void*, std::1::less<void*>, std::1::allocator<void*> > const&) + 272
7 libmolc.dylib 0x000000010be03d7f Array_Updater::destructors_done(std::1::set<void*, std::1::less<void*>, std::1::allocator<void*> > const&) + 47
8 libatomstruct.dylib 0x000000010be2f84d atomstruct::DestructionCoordinator::finalizing_destruction(void*) + 701
9 libatomstruct.dylib 0x000000010be700c9 atomstruct::Ring::~Ring() + 25
10 libatomstruct.dylib 0x000000010be70e7d atomstruct::Structure::_calculate_rings(bool, unsigned int, std::1::set<atomstruct::Residue const*, std::__1::less<atomstruct::Residue const*>, std::1::allocator<atomstruct::Residue const*> >*) const + 3421
11 libatomstruct.dylib 0x000000010be7f329 atomstruct::Structure::rings(bool, unsigned int, std::1::set<atomstruct::Residue const*, std::__1::less<atomstruct::Residue const*>, std::1::allocator<atomstruct::Residue const*> >*) const + 121
12 libatomstruct.dylib 0x000000010be38338 atomstruct::AtomicStructure::_compute_atom_types() + 16584
13 libatomstruct.dylib 0x000000010be2c67b atomstruct::Atom::default_radius() const + 3547
14 libmolc.dylib 0x000000010bdecfe6 atom_radius + 54
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151 QtWidgets 0x000000010c9adc5a QWidget::event(QEvent*) + 4666
152 QtWidgets 0x000000010cab81f4 QLineEdit::event(QEvent*) + 628
153 QtWidgets 0x000000010ca7b3b3 QComboBox::keyPressEvent(QKeyEvent*) + 691
154 QtWidgets.so 0x000000010c61f48d meth_QComboBox_keyPressEvent(_object*, _object*) + 141
155 org.python.python 0x0000000109f64a2c _PyCFunction_FastCallDict + 172 (methodobject.c:234)
156 org.python.python 0x0000000109ff04e2 call_function + 466 (ceval.c:4788)
157 org.python.python 0x0000000109fed0a0 _PyEval_EvalFrameDefault + 27024 (ceval.c:3276)
158 org.python.python 0x0000000109ff134f _PyEval_EvalCodeWithName + 3503 (ceval.c:718)
159 org.python.python 0x0000000109ff1e5b _PyFunction_FastCallDict + 891 (ceval.c:5021)
160 org.python.python 0x0000000109f1bf48 _PyObject_FastCallDict + 360 (abstract.c:2295)
161 org.python.python 0x0000000109f1c065 _PyObject_Call_Prepend + 149 (abstract.c:2358)
162 org.python.python 0x0000000109f1bc95 PyObject_Call + 101 (abstract.c:2243)
163 sip.so 0x000000010d98c95d call_method + 85
164 sip.so 0x000000010d988c1d sip_api_call_procedure_method + 156
165 QtWidgets.so 0x000000010c523673 sipQComboBox::keyPressEvent(QKeyEvent*) + 115
166 QtWidgets 0x000000010c9adc5a QWidget::event(QEvent*) + 4666
167 QtWidgets 0x000000010ca7ad73 QComboBox::event(QEvent*) + 403
168 QtWidgets.so 0x000000010c522b6f sipQComboBox::event(QEvent*) + 191
169 QtWidgets 0x000000010c96c58d QApplicationPrivate::notify_helper(QObject*, QEvent*) + 269
170 QtWidgets 0x000000010c96e78b QApplication::notify(QObject*, QEvent*) + 4043
171 QtWidgets.so 0x000000010c53e2b7 sipQApplication::notify(QObject*, QEvent*) + 231
172 QtCore 0x000000010d5f8544 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 164
173 QtWidgets 0x000000010c9cca0f 0x10c95b000 + 465423
174 QtWidgets 0x000000010c96c58d QApplicationPrivate::notify_helper(QObject*, QEvent*) + 269
175 QtWidgets 0x000000010c96eed2 QApplication::notify(QObject*, QEvent*) + 5906
176 QtWidgets.so 0x000000010c53e2b7 sipQApplication::notify(QObject*, QEvent*) + 231
177 QtCore 0x000000010d5f8544 QCoreApplication::notifyInternal2(QObject*, QEvent*) + 164
178 QtGui 0x000000010cf47d13 QGuiApplicationPrivate::processKeyEvent(QWindowSystemInterfacePrivate::KeyEvent*) + 163
179 QtGui 0x000000010cf2e49b QWindowSystemInterface::sendWindowSystemEvents(QFlags<QEventLoop::ProcessEventsFlag>) + 155
180 QtGui 0x000000010cf2d54c QWindowSystemInterface::flushWindowSystemEvents(QFlags<QEventLoop::ProcessEventsFlag>) + 572
181 libqcocoa.dylib 0x00000001166d8ca3 0x1166b8000 + 134307
182 libqcocoa.dylib 0x00000001166d8dc8 0x1166b8000 + 134600
183 com.apple.AppKit 0x00007fff8ef19b34 -[NSWindow(NSEventRouting) _reallySendEvent:isDelayedEvent:] + 4086
184 com.apple.AppKit 0x00007fff8ef18772 -[NSWindow(NSEventRouting) sendEvent:] + 541
185 libqcocoa.dylib 0x00000001166c70e7 0x1166b8000 + 61671
186 libqcocoa.dylib 0x00000001166c69c8 0x1166b8000 + 59848
187 com.apple.AppKit 0x00007fff8eda1ed0 -[NSApplication(NSEvent) sendEvent:] + 4768
188 libqcocoa.dylib 0x00000001166e1d5e 0x1166b8000 + 171358
189 com.apple.AppKit 0x00007fff8e61d4b1 -[NSApplication run] + 1002
190 libqcocoa.dylib 0x00000001166de6bf 0x1166b8000 + 157375
191 QtCore 0x000000010d5f4781 QEventLoop::exec(QFlags<QEventLoop::ProcessEventsFlag>) + 401
192 QtCore 0x000000010d5f8bb5 QCoreApplication::exec() + 341
193 QtWidgets.so 0x000000010c62ca12 meth_QApplication_exec_(_object*, _object*) + 82
194 org.python.python 0x0000000109f64a2c _PyCFunction_FastCallDict + 172 (methodobject.c:234)
195 org.python.python 0x0000000109ff04e2 call_function + 466 (ceval.c:4788)
196 org.python.python 0x0000000109fed0a0 _PyEval_EvalFrameDefault + 27024 (ceval.c:3276)
197 org.python.python 0x0000000109ff1a2f fast_function + 495 (ceval.c:718)
198 org.python.python 0x0000000109ff04bd call_function + 429 (ceval.c:4809)
199 org.python.python 0x0000000109fed0a0 _PyEval_EvalFrameDefault + 27024 (ceval.c:3276)
200 org.python.python 0x0000000109ff134f _PyEval_EvalCodeWithName + 3503 (ceval.c:718)
201 org.python.python 0x0000000109ff1acb fast_function + 651 (ceval.c:4936)
202 org.python.python 0x0000000109ff04bd call_function + 429 (ceval.c:4809)
203 org.python.python 0x0000000109fed0a0 _PyEval_EvalFrameDefault + 27024 (ceval.c:3276)
204 org.python.python 0x0000000109ff134f _PyEval_EvalCodeWithName + 3503 (ceval.c:718)
205 org.python.python 0x0000000109fe6654 PyEval_EvalCode + 100 (ceval.c:695)
206 org.python.python 0x0000000109fe3f00 builtin_exec + 528 (bltinmodule.c:974)
207 org.python.python 0x0000000109f64a2c _PyCFunction_FastCallDict + 172 (methodobject.c:234)
208 org.python.python 0x0000000109ff04e2 call_function + 466 (ceval.c:4788)
209 org.python.python 0x0000000109fed0a0 _PyEval_EvalFrameDefault + 27024 (ceval.c:3276)
210 org.python.python 0x0000000109ff134f _PyEval_EvalCodeWithName + 3503 (ceval.c:718)
211 org.python.python 0x0000000109ff1acb fast_function + 651 (ceval.c:4936)
212 org.python.python 0x0000000109ff04bd call_function + 429 (ceval.c:4809)
213 org.python.python 0x0000000109fed0a0 _PyEval_EvalFrameDefault + 27024 (ceval.c:3276)
214 org.python.python 0x0000000109ff134f _PyEval_EvalCodeWithName + 3503 (ceval.c:718)
215 org.python.python 0x0000000109fe66c4 PyEval_EvalCodeEx + 100 (ceval.c:4140)
216 org.python.python 0x0000000109f443cd function_call + 381 (funcobject.c:604)
217 org.python.python 0x0000000109f1bc95 PyObject_Call + 101 (abstract.c:2243)
218 org.python.python 0x000000010a036563 RunModule + 147 (main.c:210)
219 org.python.python 0x000000010a035e03 Py_Main + 2563 (main.c:721)
220 edu.ucsf.cgl.ChimeraX 0x0000000109f05e16 main + 278
221 libdyld.dylib 0x00007fffa60f5255 start + 1

Thread 1:
0 libsystem_kernel.dylib 0x00007fffa62244e2 workq_kernreturn + 10
1 libsystem_pthread.dylib 0x00007fffa630c791 _pthread_wqthread + 1426
2 libsystem_pthread.dylib 0x00007fffa630c1ed start_wqthread + 13

Thread 2:
0 libsystem_kernel.dylib 0x00007fffa62244e2 workq_kernreturn + 10
1 libsystem_pthread.dylib 0x00007fffa630c791 _pthread_wqthread + 1426
2 libsystem_pthread.dylib 0x00007fffa630c1ed start_wqthread + 13

Thread 3:
0 libsystem_kernel.dylib 0x00007fffa62244e2 workq_kernreturn + 10
1 libsystem_pthread.dylib 0x00007fffa630c791 _pthread_wqthread + 1426
2 libsystem_pthread.dylib 0x00007fffa630c1ed start_wqthread + 13

Thread 4:
0 libsystem_kernel.dylib 0x00007fffa62244e2 workq_kernreturn + 10
1 libsystem_pthread.dylib 0x00007fffa630c791 _pthread_wqthread + 1426
2 libsystem_pthread.dylib 0x00007fffa630c1ed start_wqthread + 13

Thread 5:
0 libsystem_kernel.dylib 0x00007fffa62244e2 workq_kernreturn + 10
1 libsystem_pthread.dylib 0x00007fffa630c5fe _pthread_wqthread + 1023
2 libsystem_pthread.dylib 0x00007fffa630c1ed start_wqthread + 13

Thread 6:
0 libsystem_kernel.dylib 0x00007fffa62244e2 workq_kernreturn + 10
1 libsystem_pthread.dylib 0x00007fffa630c791 _pthread_wqthread + 1426
2 libsystem_pthread.dylib 0x00007fffa630c1ed start_wqthread + 13

Thread 7:: OGL Profiler
0 libsystem_kernel.dylib 0x00007fffa621c38a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fffa621b7d7 mach_msg + 55
2 com.apple.opengl 0x00007fff95b0cd35 glcDebugListener + 302
3 libsystem_pthread.dylib 0x00007fffa630caab _pthread_body + 180
4 libsystem_pthread.dylib 0x00007fffa630c9f7 _pthread_start + 286
5 libsystem_pthread.dylib 0x00007fffa630c1fd thread_start + 13

Thread 8:
0 libsystem_kernel.dylib 0x00007fffa62244e2 workq_kernreturn + 10
1 libsystem_pthread.dylib 0x00007fffa630c791 _pthread_wqthread + 1426
2 libsystem_pthread.dylib 0x00007fffa630c1ed start_wqthread + 13

Thread 9:
0 libsystem_kernel.dylib 0x00007fffa62244e2 workq_kernreturn + 10
1 libsystem_pthread.dylib 0x00007fffa630c791 _pthread_wqthread + 1426
2 libsystem_pthread.dylib 0x00007fffa630c1ed start_wqthread + 13

Thread 10:: com.apple.NSEventThread
0 libsystem_kernel.dylib 0x00007fffa621c38a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fffa621b7d7 mach_msg + 55
2 com.apple.CoreFoundation 0x00007fff90af8e84 CFRunLoopServiceMachPort + 212
3 com.apple.CoreFoundation 0x00007fff90af8301 CFRunLoopRun + 1361
4 com.apple.CoreFoundation 0x00007fff90af7b54 CFRunLoopRunSpecific + 420
5 com.apple.AppKit 0x00007fff8e775f92 _NSEventThread + 205
6 libsystem_pthread.dylib 0x00007fffa630caab _pthread_body + 180
7 libsystem_pthread.dylib 0x00007fffa630c9f7 _pthread_start + 286
8 libsystem_pthread.dylib 0x00007fffa630c1fd thread_start + 13

Thread 11:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fffa6225232 poll + 10
1 QtCore 0x000000010d64aa90 qt_safe_poll(pollfd*, unsigned int, timespec const*) + 544
2 QtCore 0x000000010d64bf75 QEventDispatcherUNIX::processEvents(QFlags<QEventLoop::ProcessEventsFlag>) + 885
3 QtCore 0x000000010d5f4781 QEventLoop::exec(QFlags<QEventLoop::ProcessEventsFlag>) + 401
4 QtWebEngineCore 0x000000010e1489da 0x10e12c000 + 117210
5 QtWebEngineCore 0x000000010f4239a1 0x10e12c000 + 19888545
6 QtWebEngineCore 0x000000010f441e1d 0x10e12c000 + 20012573
7 QtWebEngineCore 0x000000010f441f00 0x10e12c000 + 20012800
8 QtWebEngineCore 0x000000010f43dcc7 0x10e12c000 + 19995847
9 libsystem_pthread.dylib 0x00007fffa630caab _pthread_body + 180
10 libsystem_pthread.dylib 0x00007fffa630c9f7 _pthread_start + 286
11 libsystem_pthread.dylib 0x00007fffa630c1fd thread_start + 13

Thread 12:: DnsConfigService
0 libsystem_kernel.dylib 0x00007fffa6225232 poll + 10
1 QtWebEngineCore 0x000000010ee8962c 0x10e12c000 + 14013996
2 QtWebEngineCore 0x000000010ee884ad 0x10e12c000 + 14009517
3 QtWebEngineCore 0x000000010f3e7320 0x10e12c000 + 19641120
4 QtWebEngineCore 0x000000010f4239a1 0x10e12c000 + 19888545
5 QtWebEngineCore 0x000000010f441e1d 0x10e12c000 + 20012573
6 QtWebEngineCore 0x000000010f441f00 0x10e12c000 + 20012800
7 QtWebEngineCore 0x000000010f43dcc7 0x10e12c000 + 19995847
8 libsystem_pthread.dylib 0x00007fffa630caab _pthread_body + 180
9 libsystem_pthread.dylib 0x00007fffa630c9f7 _pthread_start + 286
10 libsystem_pthread.dylib 0x00007fffa630c1fd thread_start + 13

Thread 13:: WorkerPool/55607
0 libsystem_kernel.dylib 0x00007fffa6223c86 psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fffa630d9a3 _pthread_cond_wait + 769
2 QtWebEngineCore 0x000000010f430e0b 0x10e12c000 + 19942923
3 QtWebEngineCore 0x000000010f443baa 0x10e12c000 + 20020138
4 QtWebEngineCore 0x000000010f44400a 0x10e12c000 + 20021258
5 QtWebEngineCore 0x000000010f43dcc7 0x10e12c000 + 19995847
6 libsystem_pthread.dylib 0x00007fffa630caab _pthread_body + 180
7 libsystem_pthread.dylib 0x00007fffa630c9f7 _pthread_start + 286
8 libsystem_pthread.dylib 0x00007fffa630c1fd thread_start + 13

Thread 14:: WorkerPool/55355
0 libsystem_kernel.dylib 0x00007fffa6223c86 psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fffa630d9a3 _pthread_cond_wait + 769
2 QtWebEngineCore 0x000000010f430e0b 0x10e12c000 + 19942923
3 QtWebEngineCore 0x000000010f443baa 0x10e12c000 + 20020138
4 QtWebEngineCore 0x000000010f44400a 0x10e12c000 + 20021258
5 QtWebEngineCore 0x000000010f43dcc7 0x10e12c000 + 19995847
6 libsystem_pthread.dylib 0x00007fffa630caab _pthread_body + 180
7 libsystem_pthread.dylib 0x00007fffa630c9f7 _pthread_start + 286
8 libsystem_pthread.dylib 0x00007fffa630c1fd thread_start + 13

Thread 15:: Chrome_DBThread
0 libsystem_kernel.dylib 0x00007fffa621c38a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fffa621b7d7 mach_msg + 55
2 com.apple.CoreFoundation 0x00007fff90af8e84 CFRunLoopServiceMachPort + 212
3 com.apple.CoreFoundation 0x00007fff90af8301 CFRunLoopRun + 1361
4 com.apple.CoreFoundation 0x00007fff90af7b54 CFRunLoopRunSpecific + 420
5 QtWebEngineCore 0x000000010f3e819f 0x10e12c000 + 19644831
6 QtWebEngineCore 0x000000010f3e7c2c 0x10e12c000 + 19643436
7 QtWebEngineCore 0x000000010f4239a1 0x10e12c000 + 19888545
8 QtWebEngineCore 0x000000010f441e1d 0x10e12c000 + 20012573
9 QtWebEngineCore 0x000000010e603fe8 0x10e12c000 + 5079016
10 QtWebEngineCore 0x000000010e604407 0x10e12c000 + 5080071
11 QtWebEngineCore 0x000000010f441f00 0x10e12c000 + 20012800
12 QtWebEngineCore 0x000000010f43dcc7 0x10e12c000 + 19995847
13 libsystem_pthread.dylib 0x00007fffa630caab _pthread_body + 180
14 libsystem_pthread.dylib 0x00007fffa630c9f7 _pthread_start + 286
15 libsystem_pthread.dylib 0x00007fffa630c1fd thread_start + 13

Thread 16:: Chrome_FileThread
0 libsystem_kernel.dylib 0x00007fffa6225232 poll + 10
1 QtWebEngineCore 0x000000010ee8962c 0x10e12c000 + 14013996
2 QtWebEngineCore 0x000000010ee884ad 0x10e12c000 + 14009517
3 QtWebEngineCore 0x000000010f3e7308 0x10e12c000 + 19641096
4 QtWebEngineCore 0x000000010f4239a1 0x10e12c000 + 19888545
5 QtWebEngineCore 0x000000010f441e1d 0x10e12c000 + 20012573
6 QtWebEngineCore 0x000000010e604068 0x10e12c000 + 5079144
7 QtWebEngineCore 0x000000010e604417 0x10e12c000 + 5080087
8 QtWebEngineCore 0x000000010f441f00 0x10e12c000 + 20012800
9 QtWebEngineCore 0x000000010f43dcc7 0x10e12c000 + 19995847
10 libsystem_pthread.dylib 0x00007fffa630caab _pthread_body + 180
11 libsystem_pthread.dylib 0x00007fffa630c9f7 _pthread_start + 286
12 libsystem_pthread.dylib 0x00007fffa630c1fd thread_start + 13

Thread 17:: Chrome_FileUserBlockingThread
0 libsystem_kernel.dylib 0x00007fffa621c38a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fffa621b7d7 mach_msg + 55
2 com.apple.CoreFoundation 0x00007fff90af8e84 CFRunLoopServiceMachPort + 212
3 com.apple.CoreFoundation 0x00007fff90af8301 CFRunLoopRun + 1361
4 com.apple.CoreFoundation 0x00007fff90af7b54 CFRunLoopRunSpecific + 420
5 QtWebEngineCore 0x000000010f3e819f 0x10e12c000 + 19644831
6 QtWebEngineCore 0x000000010f3e7c2c 0x10e12c000 + 19643436
7 QtWebEngineCore 0x000000010f4239a1 0x10e12c000 + 19888545
8 QtWebEngineCore 0x000000010f441e1d 0x10e12c000 + 20012573
9 QtWebEngineCore 0x000000010e6040e8 0x10e12c000 + 5079272
10 QtWebEngineCore 0x000000010e604427 0x10e12c000 + 5080103
11 QtWebEngineCore 0x000000010f441f00 0x10e12c000 + 20012800
12 QtWebEngineCore 0x000000010f43dcc7 0x10e12c000 + 19995847
13 libsystem_pthread.dylib 0x00007fffa630caab _pthread_body + 180
14 libsystem_pthread.dylib 0x00007fffa630c9f7 _pthread_start + 286
15 libsystem_pthread.dylib 0x00007fffa630c1fd thread_start + 13

Thread 18:: Chrome_ProcessLauncherThread
0 libsystem_kernel.dylib 0x00007fffa621c38a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fffa621b7d7 mach_msg + 55
2 com.apple.CoreFoundation 0x00007fff90af8e84 CFRunLoopServiceMachPort + 212
3 com.apple.CoreFoundation 0x00007fff90af8301 CFRunLoopRun + 1361
4 com.apple.CoreFoundation 0x00007fff90af7b54 CFRunLoopRunSpecific + 420
5 QtWebEngineCore 0x000000010f3e819f 0x10e12c000 + 19644831
6 QtWebEngineCore 0x000000010f3e7c2c 0x10e12c000 + 19643436
7 QtWebEngineCore 0x000000010f4239a1 0x10e12c000 + 19888545
8 QtWebEngineCore 0x000000010f441e1d 0x10e12c000 + 20012573
9 QtWebEngineCore 0x000000010e604168 0x10e12c000 + 5079400
10 QtWebEngineCore 0x000000010e604434 0x10e12c000 + 5080116
11 QtWebEngineCore 0x000000010f441f00 0x10e12c000 + 20012800
12 QtWebEngineCore 0x000000010f43dcc7 0x10e12c000 + 19995847
13 libsystem_pthread.dylib 0x00007fffa630caab _pthread_body + 180
14 libsystem_pthread.dylib 0x00007fffa630c9f7 _pthread_start + 286
15 libsystem_pthread.dylib 0x00007fffa630c1fd thread_start + 13

Thread 19:: Chrome_CacheThread
0 libsystem_kernel.dylib 0x00007fffa621c38a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fffa621b7d7 mach_msg + 55
2 com.apple.CoreFoundation 0x00007fff90af8e84 CFRunLoopServiceMachPort + 212
3 com.apple.CoreFoundation 0x00007fff90af8301 CFRunLoopRun + 1361
4 com.apple.CoreFoundation 0x00007fff90af7b54 CFRunLoopRunSpecific + 420
5 QtWebEngineCore 0x000000010f3e819f 0x10e12c000 + 19644831
6 QtWebEngineCore 0x000000010f3e7c2c 0x10e12c000 + 19643436
7 QtWebEngineCore 0x000000010f4239a1 0x10e12c000 + 19888545
8 QtWebEngineCore 0x000000010f441e1d 0x10e12c000 + 20012573
9 QtWebEngineCore 0x000000010e6041e8 0x10e12c000 + 5079528
10 QtWebEngineCore 0x000000010e604441 0x10e12c000 + 5080129
11 QtWebEngineCore 0x000000010f441f00 0x10e12c000 + 20012800
12 QtWebEngineCore 0x000000010f43dcc7 0x10e12c000 + 19995847
13 libsystem_pthread.dylib 0x00007fffa630caab _pthread_body + 180
14 libsystem_pthread.dylib 0x00007fffa630c9f7 _pthread_start + 286
15 libsystem_pthread.dylib 0x00007fffa630c1fd thread_start + 13

Thread 20:: Chrome_IOThread
0 libsystem_kernel.dylib 0x00007fffa6225232 poll + 10
1 QtWebEngineCore 0x000000010ee8962c 0x10e12c000 + 14013996
2 QtWebEngineCore 0x000000010ee884ad 0x10e12c000 + 14009517
3 QtWebEngineCore 0x000000010f3e7308 0x10e12c000 + 19641096
4 QtWebEngineCore 0x000000010f4239a1 0x10e12c000 + 19888545
5 QtWebEngineCore 0x000000010f441e1d 0x10e12c000 + 20012573
6 QtWebEngineCore 0x000000010e604268 0x10e12c000 + 5079656
7 QtWebEngineCore 0x000000010e60444e 0x10e12c000 + 5080142
8 QtWebEngineCore 0x000000010f441f00 0x10e12c000 + 20012800
9 QtWebEngineCore 0x000000010f43dcc7 0x10e12c000 + 19995847
10 libsystem_pthread.dylib 0x00007fffa630caab _pthread_body + 180
11 libsystem_pthread.dylib 0x00007fffa630c9f7 _pthread_start + 286
12 libsystem_pthread.dylib 0x00007fffa630c1fd thread_start + 13

Thread 21:: IndexedDB
0 libsystem_kernel.dylib 0x00007fffa621c38a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fffa621b7d7 mach_msg + 55
2 com.apple.CoreFoundation 0x00007fff90af8e84 CFRunLoopServiceMachPort + 212
3 com.apple.CoreFoundation 0x00007fff90af8301 CFRunLoopRun + 1361
4 com.apple.CoreFoundation 0x00007fff90af7b54 CFRunLoopRunSpecific + 420
5 QtWebEngineCore 0x000000010f3e819f 0x10e12c000 + 19644831
6 QtWebEngineCore 0x000000010f3e7c2c 0x10e12c000 + 19643436
7 QtWebEngineCore 0x000000010f4239a1 0x10e12c000 + 19888545
8 QtWebEngineCore 0x000000010f441e1d 0x10e12c000 + 20012573
9 QtWebEngineCore 0x000000010f441f00 0x10e12c000 + 20012800
10 QtWebEngineCore 0x000000010f43dcc7 0x10e12c000 + 19995847
11 libsystem_pthread.dylib 0x00007fffa630caab _pthread_body + 180
12 libsystem_pthread.dylib 0x00007fffa630c9f7 _pthread_start + 286
13 libsystem_pthread.dylib 0x00007fffa630c1fd thread_start + 13

Thread 22:: CompositorTileWorker1/68099
0 libsystem_kernel.dylib 0x00007fffa6223c86 psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fffa630d96a _pthread_cond_wait + 712
2 QtWebEngineCore 0x0000000111166758 0x10e12c000 + 50571096
3 QtWebEngineCore 0x000000010f441683 0x10e12c000 + 20010627
4 QtWebEngineCore 0x000000010f4414c8 0x10e12c000 + 20010184
5 QtWebEngineCore 0x000000010f43dcc7 0x10e12c000 + 19995847
6 libsystem_pthread.dylib 0x00007fffa630caab _pthread_body + 180
7 libsystem_pthread.dylib 0x00007fffa630c9f7 _pthread_start + 286
8 libsystem_pthread.dylib 0x00007fffa630c1fd thread_start + 13

Thread 23:: AudioThread
0 libsystem_kernel.dylib 0x00007fffa621c38a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fffa621b7d7 mach_msg + 55
2 com.apple.CoreFoundation 0x00007fff90af8e84 CFRunLoopServiceMachPort + 212
3 com.apple.CoreFoundation 0x00007fff90af8301 CFRunLoopRun + 1361
4 com.apple.CoreFoundation 0x00007fff90af7b54 CFRunLoopRunSpecific + 420
5 QtWebEngineCore 0x000000010f3e819f 0x10e12c000 + 19644831
6 QtWebEngineCore 0x000000010f3e7c2c 0x10e12c000 + 19643436
7 QtWebEngineCore 0x000000010f4239a1 0x10e12c000 + 19888545
8 QtWebEngineCore 0x000000010f441e1d 0x10e12c000 + 20012573
9 QtWebEngineCore 0x000000010f441f00 0x10e12c000 + 20012800
10 QtWebEngineCore 0x000000010f43dcc7 0x10e12c000 + 19995847
11 libsystem_pthread.dylib 0x00007fffa630caab _pthread_body + 180
12 libsystem_pthread.dylib 0x00007fffa630c9f7 _pthread_start + 286
13 libsystem_pthread.dylib 0x00007fffa630c1fd thread_start + 13

Thread 24:: Chrome_InProcGpuThread
0 libsystem_kernel.dylib 0x00007fffa621c38a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fffa621b7d7 mach_msg + 55
2 com.apple.CoreFoundation 0x00007fff90af8e84 CFRunLoopServiceMachPort + 212
3 com.apple.CoreFoundation 0x00007fff90af8301 CFRunLoopRun + 1361
4 com.apple.CoreFoundation 0x00007fff90af7b54 CFRunLoopRunSpecific + 420
5 QtWebEngineCore 0x000000010f3e819f 0x10e12c000 + 19644831
6 QtWebEngineCore 0x000000010f3e7c2c 0x10e12c000 + 19643436
7 QtWebEngineCore 0x000000010f4239a1 0x10e12c000 + 19888545
8 QtWebEngineCore 0x000000010f441e1d 0x10e12c000 + 20012573
9 QtWebEngineCore 0x000000010f441f00 0x10e12c000 + 20012800
10 QtWebEngineCore 0x000000010f43dcc7 0x10e12c000 + 19995847
11 libsystem_pthread.dylib 0x00007fffa630caab _pthread_body + 180
12 libsystem_pthread.dylib 0x00007fffa630c9f7 _pthread_start + 286
13 libsystem_pthread.dylib 0x00007fffa630c1fd thread_start + 13

Thread 25:: BrowserBlockingWorker1/73987
0 libsystem_kernel.dylib 0x00007fffa6223c86 psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fffa630d96a _pthread_cond_wait + 712
2 QtWebEngineCore 0x000000010f43ed47 0x10e12c000 + 20000071
3 QtWebEngineCore 0x000000010f43e3dd 0x10e12c000 + 19997661
4 QtWebEngineCore 0x000000010f4414c8 0x10e12c000 + 20010184
5 QtWebEngineCore 0x000000010f43dcc7 0x10e12c000 + 19995847
6 libsystem_pthread.dylib 0x00007fffa630caab _pthread_body + 180
7 libsystem_pthread.dylib 0x00007fffa630c9f7 _pthread_start + 286
8 libsystem_pthread.dylib 0x00007fffa630c1fd thread_start + 13

Thread 26:: Chrome_ChildIOThread
0 libsystem_kernel.dylib 0x00007fffa6225232 poll + 10
1 QtWebEngineCore 0x000000010ee8962c 0x10e12c000 + 14013996
2 QtWebEngineCore 0x000000010ee884ad 0x10e12c000 + 14009517
3 QtWebEngineCore 0x000000010f3e7320 0x10e12c000 + 19641120
4 QtWebEngineCore 0x000000010f4239a1 0x10e12c000 + 19888545
5 QtWebEngineCore 0x000000010f441e1d 0x10e12c000 + 20012573
6 QtWebEngineCore 0x000000010f441f00 0x10e12c000 + 20012800
7 QtWebEngineCore 0x000000010f43dcc7 0x10e12c000 + 19995847
8 libsystem_pthread.dylib 0x00007fffa630caab _pthread_body + 180
9 libsystem_pthread.dylib 0x00007fffa630c9f7 _pthread_start + 286
10 libsystem_pthread.dylib 0x00007fffa630c1fd thread_start + 13

Thread 27:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fffa6225232 poll + 10
1 QtCore 0x000000010d64aa90 qt_safe_poll(pollfd*, unsigned int, timespec const*) + 544
2 QtCore 0x000000010d64bf75 QEventDispatcherUNIX::processEvents(QFlags<QEventLoop::ProcessEventsFlag>) + 885
3 QtCore 0x000000010d5f4781 QEventLoop::exec(QFlags<QEventLoop::ProcessEventsFlag>) + 401
4 QtWebEngineCore 0x000000010e1489da 0x10e12c000 + 117210
5 QtWebEngineCore 0x000000010f4239a1 0x10e12c000 + 19888545
6 QtWebEngineCore 0x000000010f441e1d 0x10e12c000 + 20012573
7 QtWebEngineCore 0x000000010f441f00 0x10e12c000 + 20012800
8 QtWebEngineCore 0x000000010f43dcc7 0x10e12c000 + 19995847
9 libsystem_pthread.dylib 0x00007fffa630caab _pthread_body + 180
10 libsystem_pthread.dylib 0x00007fffa630c9f7 _pthread_start + 286
11 libsystem_pthread.dylib 0x00007fffa630c1fd thread_start + 13

Thread 28:
0 libsystem_kernel.dylib 0x00007fffa62244e2 workq_kernreturn + 10
1 libsystem_pthread.dylib 0x00007fffa630c791 _pthread_wqthread + 1426
2 libsystem_pthread.dylib 0x00007fffa630c1ed start_wqthread + 13

Thread 29:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fffa6225232 poll + 10
1 QtCore 0x000000010d64aa90 qt_safe_poll(pollfd*, unsigned int, timespec const*) + 544
2 QtCore 0x000000010d64bf75 QEventDispatcherUNIX::processEvents(QFlags<QEventLoop::ProcessEventsFlag>) + 885
3 QtCore 0x000000010d5f4781 QEventLoop::exec(QFlags<QEventLoop::ProcessEventsFlag>) + 401
4 QtWebEngineCore 0x000000010e1489da 0x10e12c000 + 117210
5 QtWebEngineCore 0x000000010f4239a1 0x10e12c000 + 19888545
6 QtWebEngineCore 0x000000010f441e1d 0x10e12c000 + 20012573
7 QtWebEngineCore 0x000000010f441f00 0x10e12c000 + 20012800
8 QtWebEngineCore 0x000000010f43dcc7 0x10e12c000 + 19995847
9 libsystem_pthread.dylib 0x00007fffa630caab _pthread_body + 180
10 libsystem_pthread.dylib 0x00007fffa630c9f7 _pthread_start + 286
11 libsystem_pthread.dylib 0x00007fffa630c1fd thread_start + 13

Thread 30:: NetworkConfigWatcher
0 libsystem_kernel.dylib 0x00007fffa6225232 poll + 10
1 QtCore 0x000000010d64aa90 qt_safe_poll(pollfd*, unsigned int, timespec const*) + 544
2 QtCore 0x000000010d64bf75 QEventDispatcherUNIX::processEvents(QFlags<QEventLoop::ProcessEventsFlag>) + 885
3 QtCore 0x000000010d5f4781 QEventLoop::exec(QFlags<QEventLoop::ProcessEventsFlag>) + 401
4 QtWebEngineCore 0x000000010e1489da 0x10e12c000 + 117210
5 QtWebEngineCore 0x000000010f4239a1 0x10e12c000 + 19888545
6 QtWebEngineCore 0x000000010f441e1d 0x10e12c000 + 20012573
7 QtWebEngineCore 0x000000010f441f00 0x10e12c000 + 20012800
8 QtWebEngineCore 0x000000010f43dcc7 0x10e12c000 + 19995847
9 libsystem_pthread.dylib 0x00007fffa630caab _pthread_body + 180
10 libsystem_pthread.dylib 0x00007fffa630c9f7 _pthread_start + 286
11 libsystem_pthread.dylib 0x00007fffa630c1fd thread_start + 13

Thread 31:: BrowserBlockingWorker2/75643
0 libsystem_kernel.dylib 0x00007fffa6223c86 psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fffa630d96a _pthread_cond_wait + 712
2 QtWebEngineCore 0x000000010f43ed47 0x10e12c000 + 20000071
3 QtWebEngineCore 0x000000010f43e3dd 0x10e12c000 + 19997661
4 QtWebEngineCore 0x000000010f4414c8 0x10e12c000 + 20010184
5 QtWebEngineCore 0x000000010f43dcc7 0x10e12c000 + 19995847
6 libsystem_pthread.dylib 0x00007fffa630caab _pthread_body + 180
7 libsystem_pthread.dylib 0x00007fffa630c9f7 _pthread_start + 286
8 libsystem_pthread.dylib 0x00007fffa630c1fd thread_start + 13

Thread 32:
0 libsystem_kernel.dylib 0x00007fffa6223c86 psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fffa630d96a _pthread_cond_wait + 712
2 org.python.python 0x000000010a0327b4 PyThread_acquire_lock_timed + 244 (thread_pthread.h:506)
3 org.python.python 0x000000010a039174 acquire_timed + 116 (_threadmodule.c:68)
4 org.python.python 0x000000010a038ed0 lock_PyThread_acquire_lock + 48 (_threadmodule.c:151)
5 org.python.python 0x0000000109f64b4d _PyCFunction_FastCallDict + 461 (methodobject.c:234)
6 org.python.python 0x0000000109ff04e2 call_function + 466 (ceval.c:4788)
7 org.python.python 0x0000000109fed0a0 _PyEval_EvalFrameDefault + 27024 (ceval.c:3276)
8 org.python.python 0x0000000109ff134f _PyEval_EvalCodeWithName + 3503 (ceval.c:718)
9 org.python.python 0x0000000109ff1acb fast_function + 651 (ceval.c:4936)
10 org.python.python 0x0000000109ff04bd call_function + 429 (ceval.c:4809)
11 org.python.python 0x0000000109fed0a0 _PyEval_EvalFrameDefault + 27024 (ceval.c:3276)
12 org.python.python 0x0000000109ff134f _PyEval_EvalCodeWithName + 3503 (ceval.c:718)
13 org.python.python 0x0000000109ff1acb fast_function + 651 (ceval.c:4936)
14 org.python.python 0x0000000109ff04bd call_function + 429 (ceval.c:4809)
15 org.python.python 0x0000000109fed0a0 _PyEval_EvalFrameDefault + 27024 (ceval.c:3276)
16 org.python.python 0x0000000109ff1a2f fast_function + 495 (ceval.c:718)
17 org.python.python 0x0000000109ff04bd call_function + 429 (ceval.c:4809)
18 org.python.python 0x0000000109fed0a0 _PyEval_EvalFrameDefault + 27024 (ceval.c:3276)
19 org.python.python 0x0000000109ff1a2f fast_function + 495 (ceval.c:718)
20 org.python.python 0x0000000109ff04bd call_function + 429 (ceval.c:4809)
21 org.python.python 0x0000000109fed0a0 _PyEval_EvalFrameDefault + 27024 (ceval.c:3276)
22 org.python.python 0x0000000109ff1cf6 _PyFunction_FastCallDict + 534 (ceval.c:718)
23 org.python.python 0x0000000109f1bf48 _PyObject_FastCallDict + 360 (abstract.c:2295)
24 org.python.python 0x0000000109f1c065 _PyObject_Call_Prepend + 149 (abstract.c:2358)
25 org.python.python 0x0000000109f1bc95 PyObject_Call + 101 (abstract.c:2243)
26 org.python.python 0x000000010a039a76 t_bootstrap + 70 (_threadmodule.c:1000)
27 libsystem_pthread.dylib 0x00007fffa630caab _pthread_body + 180
28 libsystem_pthread.dylib 0x00007fffa630c9f7 _pthread_start + 286
29 libsystem_pthread.dylib 0x00007fffa630c1fd thread_start + 13

Thread 0 crashed with X86 Thread State (64-bit):

rax: 0x0000000000000000 rbx: 0x0000000000000006 rcx: 0x000000010a325a58 rdx: 0x0000000000000000
rdi: 0x0000000000000307 rsi: 0x0000000000000006 rbp: 0x000000010a325a80 rsp: 0x000000010a325a58

r8: 0x000000010a325f48 r9: 0x00007fffaef21040 r10: 0x0000000008000000 r11: 0x0000000000000206

r12: 0x000000012ecac000 r13: 0x00007fff55cf1318 r14: 0x00007fffaef3d3c0 r15: 0x0000000000000001
rip: 0x00007fffa6223dd6 rfl: 0x0000000000000206 cr2: 0x000000010a0d07c8

Logical CPU: 0
Error Code: 0x02000148
Trap Number: 133

Binary Images:

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0x7fffa515a000 - 0x7fffa524cff7 libiconv.2.dylib (50) <42125B35-81D7-3FC4-9475-A26DBE10884D> /usr/lib/libiconv.2.dylib
0x7fffa524d000 - 0x7fffa5472ffb libicucore.A.dylib (57149.0.1) <6B5FDA93-AA88-318F-9608-C2A33D602EC7> /usr/lib/libicucore.A.dylib
0x7fffa5478000 - 0x7fffa5479fff liblangid.dylib (126) <3F4530C9-8BE1-3AA7-9A82-98694D240866> /usr/lib/liblangid.dylib
0x7fffa547a000 - 0x7fffa5493ffb liblzma.5.dylib (10) <44BD0279-99DD-36B5-8A6E-C11432E2098D> /usr/lib/liblzma.5.dylib
0x7fffa5494000 - 0x7fffa54aaff7 libmarisa.dylib (5) <2183D484-032D-3DE5-8984-3A14006E034E> /usr/lib/libmarisa.dylib
0x7fffa54ab000 - 0x7fffa5752ff7 libmecabra.dylib (744.5) <EF046855-CB9C-32D8-B2F1-C85B526E386F> /usr/lib/libmecabra.dylib
0x7fffa5785000 - 0x7fffa57feff7 libnetwork.dylib (856.30.16) <66C6E4D6-B39C-3309-80C1-CBBE170DDD51> /usr/lib/libnetwork.dylib
0x7fffa57ff000 - 0x7fffa5bd4127 libobjc.A.dylib (706) <47104A1B-13E8-369F-BC36-27FF465809FD> /usr/lib/libobjc.A.dylib
0x7fffa5bd7000 - 0x7fffa5bdbfff libpam.2.dylib (21.30.1) <71EB0D88-DE84-3C8D-A2C5-58AA282BC5BC> /usr/lib/libpam.2.dylib
0x7fffa5bdc000 - 0x7fffa5c0cff7 libpcap.A.dylib (67) <450DB888-2C0C-3085-A5F1-69324DFE902C> /usr/lib/libpcap.A.dylib
0x7fffa5c2a000 - 0x7fffa5c46ffb libresolv.9.dylib (64) <A244AE4C-00B0-396C-98FF-97FE4DB3DA30> /usr/lib/libresolv.9.dylib
0x7fffa5c47000 - 0x7fffa5c80fff libsandbox.1.dylib (592.31.1) <F87604AB-C47D-327D-B56A-54600C26B3B6> /usr/lib/libsandbox.1.dylib
0x7fffa5c94000 - 0x7fffa5c95ff3 libspindump.dylib (230.3) <59FAC445-F8FB-3881-A69A-FD0E98100E19> /usr/lib/libspindump.dylib
0x7fffa5c96000 - 0x7fffa5dd7fff libsqlite3.dylib (253) <AECBC92F-FF00-3369-8ECB-AE053B3578B8> /usr/lib/libsqlite3.dylib
0x7fffa5dfa000 - 0x7fffa5e32ff3 libssl.0.9.8.dylib (64.30.2) <6E690FB1-A581-3027-93B3-060D9D497A27> /usr/lib/libssl.0.9.8.dylib
0x7fffa5ecc000 - 0x7fffa5ed9fff libxar.1.dylib (357) <58BFB84B-66FE-3299-AA3D-BBA178ADEE39> /usr/lib/libxar.1.dylib
0x7fffa5edd000 - 0x7fffa5fccffb libxml2.2.dylib (30.11) <E12AF929-0FA5-3214-840F-C81E6AC9F36E> /usr/lib/libxml2.2.dylib
0x7fffa5fcd000 - 0x7fffa5ff6fff libxslt.1.dylib (15.8) <FFF5DD45-F544-34B2-BE3C-DB877DC60081> /usr/lib/libxslt.1.dylib
0x7fffa5ff7000 - 0x7fffa6008ff3 libz.1.dylib (67) <46E3FFA2-4328-327A-8D34-A03E20BFFB8E> /usr/lib/libz.1.dylib
0x7fffa6017000 - 0x7fffa601bff7 libcache.dylib (79) <0C8092D3-600F-3ADD-A036-F225B6CDCA43> /usr/lib/system/libcache.dylib
0x7fffa601c000 - 0x7fffa6027ff7 libcommonCrypto.dylib (60092.30.2) <B16E29B6-EC8D-3A8F-9A89-DD9CF35F7C4B> /usr/lib/system/libcommonCrypto.dylib
0x7fffa6028000 - 0x7fffa602ffff libcompiler_rt.dylib (62) <E992E8D9-037C-3454-A366-A25E4D31D6BB> /usr/lib/system/libcompiler_rt.dylib
0x7fffa6030000 - 0x7fffa6038fff libcopyfile.dylib (138) <64E285D9-5485-333B-AEE7-8B0C8FB9275F> /usr/lib/system/libcopyfile.dylib
0x7fffa6039000 - 0x7fffa60bcfdf libcorecrypto.dylib (442.30.20) <2074B932-FD79-30A9-8E90-AF25C49F2AF1> /usr/lib/system/libcorecrypto.dylib
0x7fffa60bd000 - 0x7fffa60effff libdispatch.dylib (703.30.5) <EA0CC14E-D559-3802-B4B2-0E8C7579AAC4> /usr/lib/system/libdispatch.dylib
0x7fffa60f0000 - 0x7fffa60f5ff3 libdyld.dylib (421.2) <E5A2414F-2480-3BB2-BE94-176119A80876> /usr/lib/system/libdyld.dylib
0x7fffa60f6000 - 0x7fffa60f6ffb libkeymgr.dylib (28) <1A318923-1200-3B06-B432-5007D82F195D> /usr/lib/system/libkeymgr.dylib
0x7fffa60f7000 - 0x7fffa6103ffb libkxld.dylib (3789.31.2) <524D7C3D-73EB-3F62-ADB1-9DFBACB95924> /usr/lib/system/libkxld.dylib
0x7fffa6104000 - 0x7fffa6104fff liblaunch.dylib (972.30.7) <15FACC21-079A-3BDF-9AFB-4253EFDEB587> /usr/lib/system/liblaunch.dylib
0x7fffa6105000 - 0x7fffa610afff libmacho.dylib (894) <A2F38EC1-C37C-3B93-B0E4-36B07C177F8C> /usr/lib/system/libmacho.dylib
0x7fffa610b000 - 0x7fffa610dff3 libquarantine.dylib (85) <C1D7749F-5F5F-3BB9-BEFC-1F0B9DA941FD> /usr/lib/system/libquarantine.dylib
0x7fffa610e000 - 0x7fffa610fffb libremovefile.dylib (45) <CD42974E-BE0B-39FC-9BFC-8A7540A04DC6> /usr/lib/system/libremovefile.dylib
0x7fffa6110000 - 0x7fffa6128ff7 libsystem_asl.dylib (349.30.2) <EFAC72D7-CB13-3DF7-ADF3-EC6635C6F1EA> /usr/lib/system/libsystem_asl.dylib
0x7fffa6129000 - 0x7fffa6129ff7 libsystem_blocks.dylib (67) <B8C3701D-5A91-3D35-999D-2DC8D5393525> /usr/lib/system/libsystem_blocks.dylib
0x7fffa612a000 - 0x7fffa61b7fef libsystem_c.dylib (1158.30.7) <2F881962-03CB-3B9D-A782-D98C1BBA4E3D> /usr/lib/system/libsystem_c.dylib
0x7fffa61b8000 - 0x7fffa61bbffb libsystem_configuration.dylib (888.30.2) <4FE3983C-E4ED-3939-A578-03AD29C99788> /usr/lib/system/libsystem_configuration.dylib
0x7fffa61bc000 - 0x7fffa61bffff libsystem_coreservices.dylib (41.4) <1A572B9E-0C47-320F-8C64-7990D0A5FB5A> /usr/lib/system/libsystem_coreservices.dylib
0x7fffa61c0000 - 0x7fffa61d8ff3 libsystem_coretls.dylib (121.31.1) <4676F06D-274D-31BE-B61C-4D7A4AEF4858> /usr/lib/system/libsystem_coretls.dylib
0x7fffa61d9000 - 0x7fffa61dffff libsystem_dnssd.dylib (765.30.11) <DC708D84-ED7D-3936-B996-A67C66B8DDAA> /usr/lib/system/libsystem_dnssd.dylib
0x7fffa61e0000 - 0x7fffa6209ff7 libsystem_info.dylib (503.30.1) <9ED9121C-F111-3FAD-BC2F-C95DEE1C9362> /usr/lib/system/libsystem_info.dylib
0x7fffa620a000 - 0x7fffa622cff7 libsystem_kernel.dylib (3789.31.2) <FCEEBBD4-DF66-34D8-A32F-4F8C8E814E40> /usr/lib/system/libsystem_kernel.dylib
0x7fffa622d000 - 0x7fffa6274fe7 libsystem_m.dylib (3121.4) <266DB92B-A86F-3691-80FB-1B26AD73CFF3> /usr/lib/system/libsystem_m.dylib
0x7fffa6275000 - 0x7fffa6293ff7 libsystem_malloc.dylib (116.30.3) <F40DEE3B-386A-3529-A3F7-98117ED55BF4> /usr/lib/system/libsystem_malloc.dylib
0x7fffa6294000 - 0x7fffa62ebffb libsystem_network.dylib (856.30.16) <4AE368E9-605D-379D-B04C-2AC7455B8250> /usr/lib/system/libsystem_network.dylib
0x7fffa62ec000 - 0x7fffa62f5ff3 libsystem_networkextension.dylib (563.30.15) <EB020B0C-7DF0-3EEF-8E3C-15DA3C01D687> /usr/lib/system/libsystem_networkextension.dylib
0x7fffa62f6000 - 0x7fffa62ffff3 libsystem_notify.dylib (165.20.1) <E7FD3A7C-DD07-36E2-9FA4-7561F9F114DA> /usr/lib/system/libsystem_notify.dylib
0x7fffa6300000 - 0x7fffa6308fe7 libsystem_platform.dylib (126.1.2) <3CA06D4E-C00A-36DE-AA65-3A390097D1F6> /usr/lib/system/libsystem_platform.dylib
0x7fffa6309000 - 0x7fffa6313ff7 libsystem_pthread.dylib (218.30.1) <C869ED7C-BE29-3532-8E69-3A8DA1447EDC> /usr/lib/system/libsystem_pthread.dylib
0x7fffa6314000 - 0x7fffa6317ff7 libsystem_sandbox.dylib (592.31.1) <7BBFDF96-293F-3DD9-B3A4-7C168280B441> /usr/lib/system/libsystem_sandbox.dylib
0x7fffa6318000 - 0x7fffa6319fff libsystem_secinit.dylib (24) <5C1F1E47-0F7D-3E25-8DEB-D9DB1F902281> /usr/lib/system/libsystem_secinit.dylib
0x7fffa631a000 - 0x7fffa6321fff libsystem_symptoms.dylib (532.30.6) <5D990CF5-B58F-39F7-B375-99B4EC62CFBD> /usr/lib/system/libsystem_symptoms.dylib
0x7fffa6322000 - 0x7fffa6342ff7 libsystem_trace.dylib (518.30.7) <5BD4ECD4-75CA-38EA-AF5C-B481C15955F8> /usr/lib/system/libsystem_trace.dylib
0x7fffa6343000 - 0x7fffa6348ffb libunwind.dylib (35.3) <9F7C2AD8-A9A7-3DE4-828D-B0F0F166AAA0> /usr/lib/system/libunwind.dylib
0x7fffa6349000 - 0x7fffa6372ff7 libxpc.dylib (972.30.7) <65E41BB6-EBD5-3D93-B0BE-B190CEE4DD93> /usr/lib/system/libxpc.dylib

External Modification Summary:

Calls made by other processes targeting this process:

task_for_pid: 2
thread_create: 0
thread_set_state: 0

Calls made by this process:

task_for_pid: 0
thread_create: 0
thread_set_state: 0

Calls made by all processes on this machine:

task_for_pid: 7567112
thread_create: 0
thread_set_state: 0

VM Region Summary:
ReadOnly portion of Libraries: Total=452.7M resident=0K(0%) swapped_out_or_unallocated=452.7M(100%)
Writable regions: Total=579.4M written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=579.4M(100%)

VIRTUAL REGION

REGION TYPE SIZE COUNT (non-coalesced)
=========== ======= =======
Accelerate framework 128K 2
Activity Tracing 256K 2
CG backing stores 10.1M 8
CG image 36K 8
CoreAnimation 76K 11
CoreUI image data 936K 9
CoreUI image file 180K 4
Dispatch continuations 16.0M 2
Foundation 4K 2
Kernel Alloc Once 8K 2
MALLOC 447.5M 79
MALLOC guard page 48K 10
MALLOC_LARGE (reserved) 5184K 3 reserved VM address space (unallocated)
Memory Tag 242 12K 2
OpenGL GLSL 256K 4
STACK GUARD 128K 33
Stack 29.1M 34
Stack Guard 55.7M 2
VM_ALLOCATE 53.2M 108
DATA 45.6M 373
GLSLBUILTINS 2588K 2
IMAGE 528K 2
LINKEDIT 125.0M 104
TEXT 327.7M 356
UNICODE 556K 2
mapped file 69.6M 22
shared memory 16.4M 12
=========== ======= =======
TOTAL 1.2G 1171
TOTAL, minus reserved VM space 1.2G 1171

Model: iMac13,2, BootROM IM131.010A.B0A, 4 processors, Intel Core i7, 3.4 GHz, 32 GB, SMC 2.11f16
Graphics: NVIDIA GeForce GTX 680MX, NVIDIA GeForce GTX 680MX, PCIe, 2048 MB
Memory Module: BANK 0/DIMM0, 8 GB, DDR3, 1600 MHz, 0x85F7, 0x483634314755363747313630304700000000
Memory Module: BANK 1/DIMM0, 8 GB, DDR3, 1600 MHz, 0x85F7, 0x483634314755363747313630304700000000
Memory Module: BANK 0/DIMM1, 8 GB, DDR3, 1600 MHz, 0x85F7, 0x483634314755363747313630304700000000
Memory Module: BANK 1/DIMM1, 8 GB, DDR3, 1600 MHz, 0x85F7, 0x483634314755363747313630304700000000
AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0xF4), Broadcom BCM43xx 1.0 (7.21.171.68.1a4)
Bluetooth: Version 5.0.2f4, 3 services, 27 devices, 1 incoming serial ports
Network Service: Ethernet, Ethernet, en0
Network Service: Wi-Fi, AirPort, en1
Serial ATA Device: APPLE HDD ST3000DM001, 3 TB
Serial ATA Device: APPLE SSD SM128E, 121.33 GB
USB Device: USB 2.0 Bus
USB Device: Hub
USB Device: FaceTime HD Camera (Built-in)
USB Device: USB 2.0 Bus
USB Device: Hub
USB Device: Hub
USB Device: BRCM20702 Hub
USB Device: Bluetooth USB Host Controller
USB Device: USB 3.0 Bus
USB Device: BUP Fast HDD
USB Device: Portable SSD T3
USB Device: My Passport 25E2
USB Device: Advantage2 Keyboard
Thunderbolt Bus: iMac, Apple Inc., 23.4

[Tom Goddard]

Will need to rename attached exosome.cif to exosome.ihm to open.

Before the spurious atom deletion it appears that 3 or 4 copies of mmcif 4ifd are opened and likely they have many atoms deleted (from all but one chain for each copy). Those earlier atom deletions may be related to this bug.

[Tom Goddard]

Grrrr... This bug only happens when ChimeraX is started from the shell

ChimeraX.app/Contents/MacOS/ChimeraX

If it is started by clicking the icon it works correctly. I spent the last 2 hours trying to debug why matchmaker gives the wrong alignment for two structures and just figured out that it only happens if ChimeraX is started from a shell, not if it is started from clicking the icon. Possibly it is finding the wrong dynamic libraries when started from the shell. I tried starting in /tmp, same bug. Even running with environment variables cleared with

env -i PATH="" ChimeraX.app/Contents/MacOS/ChimeraX

still results in matchmaker errors. Probably should try getting a Mac crash dump and see what dynamic libraries are being used.

[Tom Goddard]

Sending an abort signal to ChimeraX started on command-line which exhibited wrong matchmaker gives a Mac crash dump that only references dynamic libraries from the app and system locations. I'm completely baffled.

[Tom Goddard]

Running a March 24, 2017 daily build from a shell and matchmaker exhibits the same misalignment bug.

[Eric Pettersen]

Is this the right ticket for this matchmaker bug?  It is somehow also related to mistakenly deleting atoms when they shouldn’t be?

—Eric

[Eric Pettersen]

Fixed. Needed to clear destruction-batcher variables earlier to clear the way for recursive destruction from destruction observers.