id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 128 mmCIF reader crashes on 4ffh Tom Goddard Greg Couch "open mmcif:4ffh produces the following crash. Process: Chimera2 [27151] Path: /Users/USER/*/Chimera2.app/Contents/MacOS/Chimera2 Identifier: edu.ucsf.cgl.Chimera2 Version: 2.0.0 (2.0.0.0) Code Type: X86-64 (Native) Parent Process: bash [98806] Responsible: Emacs-10.7 [98780] User ID: 501 Date/Time: 2015-08-10 16:58:44.449 -0700 OS Version: Mac OS X 10.10.4 (14E46) Report Version: 11 Anonymous UUID: ADCA02F2-9A59-6574-CF8F-380125498A20 Time Awake Since Boot: 2300000 seconds Crashed Thread: 0 Dispatch queue: com.apple.main-thread Exception Type: EXC_BAD_ACCESS (SIGSEGV) Exception Codes: KERN_INVALID_ADDRESS at 0x00000000000001ec VM Regions Near 0x1ec: --> __TEXT 0000000101b20000-0000000101b21000 [ 4K] r-x/rwx SM=COW /Users/USER/*/Chimera2.app/Contents/bin/Chimera2 Application Specific Information: Performing @selector(controlAction:) from sender wxNSComboBox 0x7f87dd65ba70 Thread 0 Crashed:: Dispatch queue: com.apple.main-thread 0 libsystem_kernel.dylib 0x00007fff89016c82 __kill + 10 1 ??? 000000000000000000 0 + 0 2 _mmcif.so 0x000000010fc7fa87 readcif::CIFFile::internal_parse(bool) + 2727 3 _mmcif.so 0x000000010fc8194f readcif::CIFFile::process_stash() + 303 4 _mmcif.so 0x000000010fc808df readcif::CIFFile::internal_parse(bool) + 6399 5 _mmcif.so 0x000000010fc7ec7b readcif::CIFFile::parse(char const*) + 283 6 _mmcif.so 0x000000010fc7e682 readcif::CIFFile::parse_file(char const*) + 450 7 _mmcif.so 0x000000010fc6c84b mmcif::parse_mmCIF_file(char const*, _object*) + 43 8 _mmcif.so 0x000000010fc7d5b3 mmcif::_mmcif_parse_mmCIF_file(_object*, _object*, _object*) + 211 9 org.python.python 0x0000000101be5913 PyEval_EvalFrameEx + 21827 (ceval.c:4237) 10 org.python.python 0x0000000101be0267 PyEval_EvalCodeEx + 2567 (ceval.c:3588) 11 org.python.python 0x0000000101b5513d function_call + 381 (funcobject.c:632) 12 org.python.python 0x0000000101b2fbc7 PyObject_Call + 103 (abstract.c:2040) 13 org.python.python 0x0000000101be601f PyEval_EvalFrameEx + 23631 (ceval.c:4561) 14 org.python.python 0x0000000101be0267 PyEval_EvalCodeEx + 2567 (ceval.c:3588) 15 org.python.python 0x0000000101b5513d function_call + 381 (funcobject.c:632) 16 org.python.python 0x0000000101b2fbc7 PyObject_Call + 103 (abstract.c:2040) 17 org.python.python 0x0000000101be601f PyEval_EvalFrameEx + 23631 (ceval.c:4561) 18 org.python.python 0x0000000101be0267 PyEval_EvalCodeEx + 2567 (ceval.c:3588) 19 org.python.python 0x0000000101b5513d function_call + 381 (funcobject.c:632) 20 org.python.python 0x0000000101b2fbc7 PyObject_Call + 103 (abstract.c:2040) 21 org.python.python 0x0000000101be601f PyEval_EvalFrameEx + 23631 (ceval.c:4561) 22 org.python.python 0x0000000101be0267 PyEval_EvalCodeEx + 2567 (ceval.c:3588) 23 org.python.python 0x0000000101be902c fast_function + 316 (ceval.c:4348) 24 org.python.python 0x0000000101be5314 PyEval_EvalFrameEx + 20292 (ceval.c:4262) 25 org.python.python 0x0000000101be0267 PyEval_EvalCodeEx + 2567 (ceval.c:3588) 26 org.python.python 0x0000000101b5513d function_call + 381 (funcobject.c:632) 27 org.python.python 0x0000000101b2fbc7 PyObject_Call + 103 (abstract.c:2040) 28 org.python.python 0x0000000101be601f PyEval_EvalFrameEx + 23631 (ceval.c:4561) 29 org.python.python 0x0000000101be0267 PyEval_EvalCodeEx + 2567 (ceval.c:3588) 30 org.python.python 0x0000000101be902c fast_function + 316 (ceval.c:4348) 31 org.python.python 0x0000000101be5314 PyEval_EvalFrameEx + 20292 (ceval.c:4262) 32 org.python.python 0x0000000101be0267 PyEval_EvalCodeEx + 2567 (ceval.c:3588) 33 org.python.python 0x0000000101b5513d function_call + 381 (funcobject.c:632) 34 org.python.python 0x0000000101b2fbc7 PyObject_Call + 103 (abstract.c:2040) 35 org.python.python 0x0000000101b431bd method_call + 141 (classobject.c:347) 36 org.python.python 0x0000000101b2fbc7 PyObject_Call + 103 (abstract.c:2040) 37 org.python.python 0x0000000101be865d PyEval_CallObjectWithKeywords + 93 (ceval.c:4114) 38 _core.so 0x000000010413b1fc wxPyCallback::EventThunker(wxEvent&) + 284 (sip_corewxEvtHandler.cpp:70) 39 libwx_osx_cocoau-3.0.0.3.0.dylib 0x000000010517adba wxEvtHandler::SearchDynamicEventTable(wxEvent&) + 186 40 libwx_osx_cocoau-3.0.0.3.0.dylib 0x000000010517ab2b wxEvtHandler::ProcessEventLocally(wxEvent&) + 59 41 libwx_osx_cocoau-3.0.0.3.0.dylib 0x000000010517aa3e wxEvtHandler::ProcessEvent(wxEvent&) + 190 42 _core.so 0x000000010408e7ea sipwxComboBox::ProcessEvent(wxEvent&) + 154 (sip_corewxComboBox.cpp:439) 43 libwx_osx_cocoau-3.0.0.3.0.dylib 0x000000010517ae5f wxEvtHandler::SafelyProcessEvent(wxEvent&) + 15 44 libwx_osx_cocoau-3.0.0.3.0.dylib 0x000000010527df86 wxNSTextFieldControl::controlAction(NSView*, void*, void*) + 166 45 libsystem_trace.dylib 0x00007fff8c1aecd7 _os_activity_initiate + 75 46 com.apple.AppKit 0x00007fff895fdeb1 -[NSApplication sendAction:to:from:] + 452 47 com.apple.AppKit 0x00007fff89613946 -[NSControl sendAction:to:] + 86 48 com.apple.AppKit 0x00007fff896505df -[NSTextField textDidEndEditing:] + 853 49 com.apple.CoreFoundation 0x00007fff8ec6745c __CFNOTIFICATIONCENTER_IS_CALLING_OUT_TO_AN_OBSERVER__ + 12 50 com.apple.CoreFoundation 0x00007fff8eb57634 _CFXNotificationPost + 3140 51 com.apple.Foundation 0x00007fff8f59f9d1 -[NSNotificationCenter postNotificationName:object:userInfo:] + 66 52 com.apple.AppKit 0x00007fff8975b847 -[NSTextView(NSPrivate) _giveUpFirstResponder:] + 423 53 com.apple.AppKit 0x00007fff897d7812 -[NSTextView(NSKeyBindingCommands) insertNewline:] + 239 54 com.apple.AppKit 0x00007fff896a3ef1 -[NSTextView doCommandBySelector:] + 195 55 com.apple.AppKit 0x00007fff896a3e01 -[NSTextInputContext(NSInputContext_WithCompletion) doCommandBySelector:completionHandler:] + 118 56 com.apple.AppKit 0x00007fff89689c23 -[NSKeyBindingManager(NSKeyBindingManager_MultiClients) interpretEventAsCommand:forClient:] + 1899 57 com.apple.AppKit 0x00007fff89c50272 __61-[NSTextInputContext _handleEvent:options:completionHandler:]_block_invoke972 + 335 58 com.apple.AppKit 0x00007fff8968bbff -[NSTextInputContext(NSInputContext_WithCompletion) hasMarkedTextWithCompletionHandler:] + 76 59 com.apple.AppKit 0x00007fff896a3d03 __61-[NSTextInputContext _handleEvent:options:completionHandler:]_block_invoke_3 + 95 60 com.apple.AppKit 0x00007fff8969ced8 -[NSTextInputContext tryHandleEvent_HasMarkedText_withDispatchCondition:dispatchWork:continuation:] + 101 61 com.apple.AppKit 0x00007fff89c50074 __61-[NSTextInputContext _handleEvent:options:completionHandler:]_block_invoke960 + 321 62 com.apple.HIToolbox 0x00007fff88a6fd4f __TSMProcessRawKeyEventWithOptionsAndCompletionHandler_block_invoke_5 + 70 63 com.apple.HIToolbox 0x00007fff88a6ec45 ___ZL23DispatchEventToHandlersP14EventTargetRecP14OpaqueEventRefP14HandlerCallRec_block_invoke + 108 64 com.apple.AppKit 0x00007fff8968c606 __55-[NSTextInputContext handleTSMEvent:completionHandler:]_block_invoke174 + 2387 65 com.apple.AppKit 0x00007fff8968bbff -[NSTextInputContext(NSInputContext_WithCompletion) hasMarkedTextWithCompletionHandler:] + 76 66 com.apple.AppKit 0x00007fff8968bba0 __55-[NSTextInputContext handleTSMEvent:completionHandler:]_block_invoke_2 + 95 67 com.apple.AppKit 0x00007fff8968bb18 -[NSTextInputContext tryHandleTSMEvent_HasMarkedText_withDispatchCondition:dispatchWork:continuation:] + 101 68 com.apple.AppKit 0x00007fff8968b7d5 -[NSTextInputContext handleTSMEvent:completionHandler:] + 3122 69 com.apple.AppKit 0x00007fff8968ab2e _NSTSMEventHandler + 324 70 com.apple.HIToolbox 0x00007fff88a08b6c DispatchEventToHandlers(EventTargetRec*, OpaqueEventRef*, HandlerCallRec*) + 1260 71 com.apple.HIToolbox 0x00007fff88a07fae SendEventToEventTargetInternal(OpaqueEventRef*, OpaqueEventTargetRef*, HandlerCallRec*) + 386 72 com.apple.HIToolbox 0x00007fff88a07e22 SendEventToEventTargetWithOptions + 43 73 com.apple.HIToolbox 0x00007fff88a6c26c SendTSMEvent_WithCompletionHandler + 417 74 com.apple.HIToolbox 0x00007fff88a6c76c __SendUnicodeTextAEToUnicodeDoc_WithCompletionHandler_block_invoke + 400 75 com.apple.HIToolbox 0x00007fff88a6c5a6 __SendFilterTextEvent_WithCompletionHandler_block_invoke + 189 76 com.apple.HIToolbox 0x00007fff88a6c2c0 SendTSMEvent_WithCompletionHandler + 501 77 com.apple.HIToolbox 0x00007fff88a6c08f SendFilterTextEvent_WithCompletionHandler + 236 78 com.apple.HIToolbox 0x00007fff88a6bd51 SendUnicodeTextAEToUnicodeDoc_WithCompletionHandler + 295 79 com.apple.HIToolbox 0x00007fff88a6bae9 __utDeliverTSMEvent_WithCompletionHandler_block_invoke_2 + 296 80 com.apple.HIToolbox 0x00007fff88a6b988 __utDeliverTSMEvent_WithCompletionHandler_block_invoke + 437 81 com.apple.HIToolbox 0x00007fff88a6b7cd TSMKeyEvent_WithCompletionHandler + 701 82 com.apple.HIToolbox 0x00007fff88a6b4d0 __TSMProcessRawKeyEventWithOptionsAndCompletionHandler_block_invoke_4 + 251 83 com.apple.HIToolbox 0x00007fff88a6b386 __TSMProcessRawKeyEventWithOptionsAndCompletionHandler_block_invoke_3 + 330 84 com.apple.HIToolbox 0x00007fff88a6b112 __TSMProcessRawKeyEventWithOptionsAndCompletionHandler_block_invoke_2 + 259 85 com.apple.HIToolbox 0x00007fff88a6af25 __TSMProcessRawKeyEventWithOptionsAndCompletionHandler_block_invoke + 251 86 com.apple.HIToolbox 0x00007fff88a4f76f TSMProcessRawKeyEventWithOptionsAndCompletionHandler + 3068 87 com.apple.AppKit 0x00007fff89c4fe86 __61-[NSTextInputContext _handleEvent:options:completionHandler:]_block_invoke949 + 131 88 com.apple.AppKit 0x00007fff89689352 -[NSTextInputContext tryTSMProcessRawKeyEvent:dispatchCondition:setupForDispatch:furtherCondition:dispatchWork:continuation:] + 127 89 com.apple.AppKit 0x00007fff89689085 -[NSTextInputContext _handleEvent:options:completionHandler:] + 1266 90 com.apple.AppKit 0x00007fff89688b4e -[NSTextInputContext handleEvent:] + 109 91 com.apple.AppKit 0x00007fff89688a54 -[NSView interpretKeyEvents:] + 207 92 com.apple.AppKit 0x00007fff8968886a -[NSTextView keyDown:] + 695 93 libwx_osx_cocoau-3.0.0.3.0.dylib 0x000000010527aeee -[wxNSTextFieldEditor keyDown:] + 110 94 com.apple.AppKit 0x00007fff89b780fb -[NSWindow _reallySendEvent:isDelayedEvent:] + 5452 95 com.apple.AppKit 0x00007fff89509c86 -[NSWindow sendEvent:] + 470 96 libwx_osx_cocoau-3.0.0.3.0.dylib 0x00000001052737c6 -[wxNSWindow sendEvent:] + 118 97 com.apple.AppKit 0x00007fff895068b1 -[NSApplication sendEvent:] + 4199 98 libwx_osx_cocoau-3.0.0.3.0.dylib 0x0000000105188f36 -[wxNSApplication sendEvent:] + 134 99 com.apple.AppKit 0x00007fff8942fb68 -[NSApplication run] + 711 100 libwx_osx_cocoau-3.0.0.3.0.dylib 0x0000000105267ec3 wxGUIEventLoop::OSXDoRun() + 115 101 libwx_osx_cocoau-3.0.0.3.0.dylib 0x0000000105145c14 wxCFEventLoop::DoRun() + 52 102 libwx_osx_cocoau-3.0.0.3.0.dylib 0x0000000105070b45 wxEventLoopBase::Run() + 165 103 libwx_osx_cocoau-3.0.0.3.0.dylib 0x0000000105034ee1 wxAppConsoleBase::MainLoop() + 209 104 _core.so 0x00000001043b7ee5 wxPyApp::MainLoop() + 181 (sip_corewxPyApp.cpp:316) 105 _core.so 0x00000001043bb65d meth_wxPyApp_MainLoop(_object*, _object*) + 205 (sip_corewxPyApp.cpp:1794) 106 org.python.python 0x0000000101be5913 PyEval_EvalFrameEx + 21827 (ceval.c:4237) 107 org.python.python 0x0000000101be8fc2 fast_function + 210 (ceval.c:4334) 108 org.python.python 0x0000000101be5314 PyEval_EvalFrameEx + 20292 (ceval.c:4262) 109 org.python.python 0x0000000101be8fc2 fast_function + 210 (ceval.c:4334) 110 org.python.python 0x0000000101be5314 PyEval_EvalFrameEx + 20292 (ceval.c:4262) 111 org.python.python 0x0000000101be0267 PyEval_EvalCodeEx + 2567 (ceval.c:3588) 112 org.python.python 0x0000000101be902c fast_function + 316 (ceval.c:4348) 113 org.python.python 0x0000000101be5314 PyEval_EvalFrameEx + 20292 (ceval.c:4262) 114 org.python.python 0x0000000101be0267 PyEval_EvalCodeEx + 2567 (ceval.c:3588) 115 org.python.python 0x0000000101bdf84f PyEval_EvalCode + 63 (ceval.c:775) 116 org.python.python 0x0000000101bffab5 PyImport_ImportFrozenModuleObject + 469 (import.c:869) 117 org.python.python 0x0000000101bffba2 PyImport_ImportFrozenModule + 34 (import.c:1291) 118 org.python.python 0x0000000101bf945e Py_FrozenMain + 430 (frozenmain.c:84) 119 libdyld.dylib 0x00007fff831795c9 start + 1 Thread 1:: Dispatch queue: com.apple.libdispatch-manager 0 libsystem_kernel.dylib 0x00007fff89018232 kevent64 + 10 1 libdispatch.dylib 0x00007fff87692a6a _dispatch_mgr_thread + 52 Thread 2: 0 libsystem_kernel.dylib 0x00007fff8901794a __workq_kernreturn + 10 1 libsystem_pthread.dylib 0x00007fff8b89840d start_wqthread + 13 Thread 3: 0 libsystem_kernel.dylib 0x00007fff8901794a __workq_kernreturn + 10 1 libsystem_pthread.dylib 0x00007fff8b89840d start_wqthread + 13 Thread 4: 0 libsystem_kernel.dylib 0x00007fff8901794a __workq_kernreturn + 10 1 libsystem_pthread.dylib 0x00007fff8b89840d start_wqthread + 13 Thread 5: 0 libsystem_kernel.dylib 0x00007fff8901794a __workq_kernreturn + 10 1 libsystem_pthread.dylib 0x00007fff8b89840d start_wqthread + 13 Thread 6: 0 libsystem_kernel.dylib 0x00007fff890124de mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff8901164f mach_msg + 55 2 com.apple.CoreFoundation 0x00007fff8ebb9eb4 __CFRunLoopServiceMachPort + 212 3 com.apple.CoreFoundation 0x00007fff8ebb937b __CFRunLoopRun + 1371 4 com.apple.CoreFoundation 0x00007fff8ebb8bd8 CFRunLoopRunSpecific + 296 5 com.apple.AppKit 0x00007fff8950256b _NSEventThread + 137 6 libsystem_pthread.dylib 0x00007fff8b89a268 _pthread_body + 131 7 libsystem_pthread.dylib 0x00007fff8b89a1e5 _pthread_start + 176 8 libsystem_pthread.dylib 0x00007fff8b89841d thread_start + 13 Thread 7: 0 libsystem_kernel.dylib 0x00007fff8901794a __workq_kernreturn + 10 1 libsystem_pthread.dylib 0x00007fff8b89840d start_wqthread + 13 Thread 8: 0 libsystem_kernel.dylib 0x00007fff8901794a __workq_kernreturn + 10 1 libsystem_pthread.dylib 0x00007fff8b89840d start_wqthread + 13 Thread 9: 0 libsystem_kernel.dylib 0x00007fff8901794a __workq_kernreturn + 10 1 libsystem_pthread.dylib 0x00007fff8b89840d start_wqthread + 13 Thread 10: 0 libsystem_kernel.dylib 0x00007fff8901794a __workq_kernreturn + 10 1 libsystem_pthread.dylib 0x00007fff8b89840d start_wqthread + 13 Thread 11:: OGL Profiler 0 libsystem_kernel.dylib 0x00007fff890124de mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff8901164f mach_msg + 55 2 com.apple.opengl 0x00007fff912a0a79 glcDebugListener + 336 3 libsystem_pthread.dylib 0x00007fff8b89a268 _pthread_body + 131 4 libsystem_pthread.dylib 0x00007fff8b89a1e5 _pthread_start + 176 5 libsystem_pthread.dylib 0x00007fff8b89841d thread_start + 13 Thread 12:: JavaScriptCore::BlockFree 0 libsystem_kernel.dylib 0x00007fff89017136 __psynch_cvwait + 10 1 libc++.1.dylib 0x00007fff91715c95 std::__1::condition_variable::wait(std::__1::unique_lock&) + 47 2 com.apple.JavaScriptCore 0x00007fff8d64d544 JSC::BlockAllocator::blockFreeingThreadMain() + 228 3 com.apple.JavaScriptCore 0x00007fff8d642cff WTF::wtfThreadEntryPoint(void*) + 15 4 libsystem_pthread.dylib 0x00007fff8b89a268 _pthread_body + 131 5 libsystem_pthread.dylib 0x00007fff8b89a1e5 _pthread_start + 176 6 libsystem_pthread.dylib 0x00007fff8b89841d thread_start + 13 Thread 13:: JavaScriptCore::Marking 0 libsystem_kernel.dylib 0x00007fff89017136 __psynch_cvwait + 10 1 libc++.1.dylib 0x00007fff91715c95 std::__1::condition_variable::wait(std::__1::unique_lock&) + 47 2 com.apple.JavaScriptCore 0x00007fff8d64dadb JSC::GCThread::waitForNextPhase() + 171 3 com.apple.JavaScriptCore 0x00007fff8d64d938 JSC::GCThread::gcThreadMain() + 88 4 com.apple.JavaScriptCore 0x00007fff8d642cff WTF::wtfThreadEntryPoint(void*) + 15 5 libsystem_pthread.dylib 0x00007fff8b89a268 _pthread_body + 131 6 libsystem_pthread.dylib 0x00007fff8b89a1e5 _pthread_start + 176 7 libsystem_pthread.dylib 0x00007fff8b89841d thread_start + 13 Thread 14:: JavaScriptCore::Marking 0 libsystem_kernel.dylib 0x00007fff89017136 __psynch_cvwait + 10 1 libc++.1.dylib 0x00007fff91715c95 std::__1::condition_variable::wait(std::__1::unique_lock&) + 47 2 com.apple.JavaScriptCore 0x00007fff8d64dadb JSC::GCThread::waitForNextPhase() + 171 3 com.apple.JavaScriptCore 0x00007fff8d64d938 JSC::GCThread::gcThreadMain() + 88 4 com.apple.JavaScriptCore 0x00007fff8d642cff WTF::wtfThreadEntryPoint(void*) + 15 5 libsystem_pthread.dylib 0x00007fff8b89a268 _pthread_body + 131 6 libsystem_pthread.dylib 0x00007fff8b89a1e5 _pthread_start + 176 7 libsystem_pthread.dylib 0x00007fff8b89841d thread_start + 13 Thread 15:: JavaScriptCore::Marking 0 libsystem_kernel.dylib 0x00007fff89017136 __psynch_cvwait + 10 1 libc++.1.dylib 0x00007fff91715c95 std::__1::condition_variable::wait(std::__1::unique_lock&) + 47 2 com.apple.JavaScriptCore 0x00007fff8d64dadb JSC::GCThread::waitForNextPhase() + 171 3 com.apple.JavaScriptCore 0x00007fff8d64d938 JSC::GCThread::gcThreadMain() + 88 4 com.apple.JavaScriptCore 0x00007fff8d642cff WTF::wtfThreadEntryPoint(void*) + 15 5 libsystem_pthread.dylib 0x00007fff8b89a268 _pthread_body + 131 6 libsystem_pthread.dylib 0x00007fff8b89a1e5 _pthread_start + 176 7 libsystem_pthread.dylib 0x00007fff8b89841d thread_start + 13 Thread 16:: JavaScriptCore::Marking 0 libsystem_kernel.dylib 0x00007fff89017136 __psynch_cvwait + 10 1 libc++.1.dylib 0x00007fff91715c95 std::__1::condition_variable::wait(std::__1::unique_lock&) + 47 2 com.apple.JavaScriptCore 0x00007fff8d64dadb JSC::GCThread::waitForNextPhase() + 171 3 com.apple.JavaScriptCore 0x00007fff8d64d938 JSC::GCThread::gcThreadMain() + 88 4 com.apple.JavaScriptCore 0x00007fff8d642cff WTF::wtfThreadEntryPoint(void*) + 15 5 libsystem_pthread.dylib 0x00007fff8b89a268 _pthread_body + 131 6 libsystem_pthread.dylib 0x00007fff8b89a1e5 _pthread_start + 176 7 libsystem_pthread.dylib 0x00007fff8b89841d thread_start + 13 Thread 17:: JavaScriptCore::Marking 0 libsystem_kernel.dylib 0x00007fff89017136 __psynch_cvwait + 10 1 libc++.1.dylib 0x00007fff91715c95 std::__1::condition_variable::wait(std::__1::unique_lock&) + 47 2 com.apple.JavaScriptCore 0x00007fff8d64dadb JSC::GCThread::waitForNextPhase() + 171 3 com.apple.JavaScriptCore 0x00007fff8d64d938 JSC::GCThread::gcThreadMain() + 88 4 com.apple.JavaScriptCore 0x00007fff8d642cff WTF::wtfThreadEntryPoint(void*) + 15 5 libsystem_pthread.dylib 0x00007fff8b89a268 _pthread_body + 131 6 libsystem_pthread.dylib 0x00007fff8b89a1e5 _pthread_start + 176 7 libsystem_pthread.dylib 0x00007fff8b89841d thread_start + 13 Thread 18:: JavaScriptCore::Marking 0 libsystem_kernel.dylib 0x00007fff89017136 __psynch_cvwait + 10 1 libc++.1.dylib 0x00007fff91715c95 std::__1::condition_variable::wait(std::__1::unique_lock&) + 47 2 com.apple.JavaScriptCore 0x00007fff8d64dadb JSC::GCThread::waitForNextPhase() + 171 3 com.apple.JavaScriptCore 0x00007fff8d64d938 JSC::GCThread::gcThreadMain() + 88 4 com.apple.JavaScriptCore 0x00007fff8d642cff WTF::wtfThreadEntryPoint(void*) + 15 5 libsystem_pthread.dylib 0x00007fff8b89a268 _pthread_body + 131 6 libsystem_pthread.dylib 0x00007fff8b89a1e5 _pthread_start + 176 7 libsystem_pthread.dylib 0x00007fff8b89841d thread_start + 13 Thread 0 crashed with X86 Thread State (64-bit): rax: 0x0000000000000000 rbx: 0x0000000101ed4f48 rcx: 0x0000000101ed4aa8 rdx: 0x0000000000000000 rdi: 0x0000000000006a0f rsi: 0x000000000000000b rbp: 0x0000000101ed4ab0 rsp: 0x0000000101ed4aa8 r8: 0x0000000101ed4f48 r9: 0x00007f87e0837710 r10: 0x00007fff89018c22 r11: 0x0000000000000202 r12: 0x0000000000000023 r13: 0x0000000000000000 r14: 0x00000000000001ec r15: 0x00007fff5e0da008 rip: 0x00007fff89016c82 rfl: 0x0000000000000202 cr2: 0x0000000104315000 Logical CPU: 0 Error Code: 0x02000025 Trap Number: 133 Binary Images: 0x101b20000 - 0x101b20ff7 +edu.ucsf.cgl.Chimera2 (2.0.0 - 2.0.0.0) <73F8A8A6-F58F-3A9D-8AD0-972177C7A943> /Users/USER/*/Chimera2.app/Contents/MacOS/Chimera2 0x101b23000 - 0x101cb2ff7 +org.python.python (3.4.3, [c] 2001-2015 Python Software Foundation. - 3.4.3) /Users/USER/*/Chimera2.app/Contents/Library/Frameworks/Python.framework/Versions/3.4/Python 0x102066000 - 0x102068fff +time.so (0) <307B7F4F-645D-3C3D-BFEF-0A5C4F6D390A> /Users/USER/*/Chimera2.app/Contents/Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/lib-dynload/time.so 0x1020b0000 - 0x1020b1fff +_heapq.so (0) /Users/USER/*/Chimera2.app/Contents/Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/lib-dynload/_heapq.so 0x1021d6000 - 0x1021daff7 +_struct.so (0) <3D108042-4157-3FBA-B318-08C56E80698D> /Users/USER/*/Chimera2.app/Contents/Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/lib-dynload/_struct.so 0x102222000 - 0x102222fff +grp.so (0) /Users/USER/*/Chimera2.app/Contents/Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/lib-dynload/grp.so 0x102225000 - 0x102226ff7 +_bz2.so (0) /Users/USER/*/Chimera2.app/Contents/Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/lib-dynload/_bz2.so 0x10226a000 - 0x10226bfff +_posixsubprocess.so (0) /Users/USER/*/Chimera2.app/Contents/Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/lib-dynload/_posixsubprocess.so 0x10226f000 - 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/System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/CarbonCore.framework/Versions/A/CarbonCore 0x7fff8f4f9000 - 0x7fff8f4f9ff7 libunc.dylib (29) <5676F7EA-C1DF-329F-B006-D2C3022B7D70> /usr/lib/system/libunc.dylib 0x7fff8f518000 - 0x7fff8f58afff com.apple.framework.IOKit (2.0.2 - 1050.20.2) <09C0518C-90DF-3FC3-96D6-34D35F72C8EF> /System/Library/Frameworks/IOKit.framework/Versions/A/IOKit 0x7fff8f598000 - 0x7fff8f8c9fff com.apple.Foundation (6.9 - 1153.20) /System/Library/Frameworks/Foundation.framework/Versions/C/Foundation 0x7fff8f9e9000 - 0x7fff8fa02ff7 com.apple.CFOpenDirectory (10.10 - 187) <2BF2705E-2CC6-37E7-BD49-D4B4E01591E3> /System/Library/Frameworks/OpenDirectory.framework/Versions/A/Frameworks/CFOpenDirectory.framework/Versions/A/CFOpenDirectory 0x7fff8fa28000 - 0x7fff8fcf7ff3 com.apple.CoreImage (10.3.4) /System/Library/Frameworks/QuartzCore.framework/Versions/A/Frameworks/CoreImage.framework/Versions/A/CoreImage 0x7fff8fd01000 - 0x7fff90cc3ffb com.apple.WebCore (10600 - 10600.7.11) <930FAFBB-C906-3017-A62B-5AE3B404A168> /System/Library/Frameworks/WebKit.framework/Versions/A/Frameworks/WebCore.framework/Versions/A/WebCore 0x7fff90cc4000 - 0x7fff9109bfe7 com.apple.CoreAUC (211.1.0 - 211.1.0) <12645629-E065-388E-A6B5-094A240578CE> /System/Library/PrivateFrameworks/CoreAUC.framework/Versions/A/CoreAUC 0x7fff9109c000 - 0x7fff9118fff7 libJP2.dylib (1238) <008AE93E-FB7F-3217-8220-0C1A6BEBFE0F> /System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libJP2.dylib 0x7fff91190000 - 0x7fff91282fff libxml2.2.dylib (26) /usr/lib/libxml2.2.dylib 0x7fff9129f000 - 0x7fff912adff7 com.apple.opengl (11.1.2 - 11.1.2) <5F355713-4637-33CD-9CBA-4B4CA43FB0FE> /System/Library/Frameworks/OpenGL.framework/Versions/A/OpenGL 0x7fff91422000 - 0x7fff9142afff libMatch.1.dylib (24) /usr/lib/libMatch.1.dylib 0x7fff9142b000 - 0x7fff91465ffb com.apple.DebugSymbols (115 - 115) <6F03761D-7C3A-3C80-8031-AA1C1AD7C706> /System/Library/PrivateFrameworks/DebugSymbols.framework/Versions/A/DebugSymbols 0x7fff91466000 - 0x7fff914a7fff libGLU.dylib (11.1.2) <2BA52A8D-ED35-3D86-B2D6-41479969C96D> /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLU.dylib 0x7fff914a8000 - 0x7fff914b0fe7 libcldcpuengine.dylib (2.4.5) <6CC680F9-0D13-333B-B151-F0D9C631A1E5> /System/Library/Frameworks/OpenCL.framework/Versions/A/Libraries/libcldcpuengine.dylib 0x7fff914b1000 - 0x7fff914ddfff libsandbox.1.dylib (358.20.5) <931BB6B5-F207-344A-8596-F1D0BB910C9A> /usr/lib/libsandbox.1.dylib 0x7fff9150c000 - 0x7fff91598ff7 libsystem_c.dylib (1044.10.1) <86FBED7A-F2C8-3591-AD6F-486DD57E6B6A> /usr/lib/system/libsystem_c.dylib 0x7fff915c6000 - 0x7fff915ceffb libcopyfile.dylib (118.1.2) <0C68D3A6-ACDD-3EF3-991A-CC82C32AB836> /usr/lib/system/libcopyfile.dylib 0x7fff916ea000 - 0x7fff916efffb libheimdal-asn1.dylib (398.10.1) /usr/lib/libheimdal-asn1.dylib 0x7fff916f0000 - 0x7fff9170bff7 libCRFSuite.dylib (34) /usr/lib/libCRFSuite.dylib 0x7fff9170c000 - 0x7fff9170dfff libDiagnosticMessagesClient.dylib (100) <2EE8E436-5CDC-34C5-9959-5BA218D507FB> /usr/lib/libDiagnosticMessagesClient.dylib 0x7fff9170e000 - 0x7fff91762fff libc++.1.dylib (120) <1B9530FD-989B-3174-BB1C-BDC159501710> /usr/lib/libc++.1.dylib 0x7fff9179d000 - 0x7fff917c1ff7 com.apple.Sharing (328.17 - 328.17) /System/Library/PrivateFrameworks/Sharing.framework/Versions/A/Sharing 0x7fff917eb000 - 0x7fff91838ff7 com.apple.print.framework.PrintCore (10.3 - 451.1) /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/PrintCore.framework/Versions/A/PrintCore 0x7fff91839000 - 0x7fff91839fff libOpenScriptingUtil.dylib (162.2) /usr/lib/libOpenScriptingUtil.dylib 0x7fff9183a000 - 0x7fff9195eff7 com.apple.LaunchServices (644.56 - 644.56) <20AABB1C-9319-3E4D-A024-51B0DD5FCD3B> /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/LaunchServices.framework/Versions/A/LaunchServices 0x7fff9195f000 - 0x7fff919cbff3 com.apple.MMCS (1.3 - 327.5) /System/Library/PrivateFrameworks/MMCS.framework/Versions/A/MMCS 0x7fff919f4000 - 0x7fff91e47fc7 com.apple.vImage (8.0 - 8.0) <33BE7B31-72DB-3364-B37E-C322A32748C5> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vImage.framework/Versions/A/vImage 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: 2894104 thread_create: 0 thread_set_state: 0 VM Region Summary: ReadOnly portion of Libraries: Total=295.2M resident=158.8M(54%) swapped_out_or_unallocated=136.4M(46%) Writable regions: Total=1.2G written=51.6M(4%) resident=85.0M(7%) swapped_out=0K(0%) unallocated=1.1G(93%) REGION TYPE VIRTUAL =========== ======= Activity Tracing 2048K CG backing stores 5684K CG image 236K CG raster data 1872K CG shared images 368K CoreAnimation 52K CoreImage 8K CoreServices 1092K CoreUI image data 104K Dispatch continuations 16.0M Foundation 4K IOKit 10.4M JS JIT generated code 128.0M JS JIT generated code (reserved) 896.0M reserved VM address space (unallocated) JS garbage collector 1216K Kernel Alloc Once 8K MALLOC 124.8M MALLOC (admin) 32K MALLOC_LARGE (reserved) 256K reserved VM address space (unallocated) Memory Tag 242 12K OpenCL 16K STACK GUARD 72K Stack 72.7M VM_ALLOCATE 17.2M WebKit Malloc 1296K __DATA 34.6M __GLSLBUILTINS 2588K __IMAGE 528K __LINKEDIT 86.1M __TEXT 209.1M __UNICODE 552K mapped file 75.1M shared memory 4K =========== ======= TOTAL 1.6G TOTAL, minus reserved VM space 791.3M Model: iMac13,2, BootROM IM131.010A.B08, 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 (7.15.166.24.3) Bluetooth: Version 4.3.5f8 15969, 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: SpaceNavigator USB Device: Kinesis Keyboard Hub USB Device: Composite Device USB Device: Composite Device USB Device: Hub USB Device: FaceTime HD Camera (Built-in) USB Device: Hub USB Device: Hub USB Device: BRCM20702 Hub USB Device: Bluetooth USB Host Controller Thunderbolt Bus: iMac, Apple Inc., 23.4 " defect closed major Input/Output fixed all chimera