Bugs item #2502050, was opened at 2009-01-12 18:16
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Category: None
Group: None
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Nobody/Anonymous (nobody)
Assigned to: Nobody/Anonymous (nobody)
Summary: AutoOpt after “Remove Hydrogens” Crashes
Initial Comment:
This is with the latest version from git.
Draw cyclohexane.
Run the auto-opt tool.
Stop auto-optimization.
Remove hydrogens
Move an atom (e.g., into boat form)
Start auto-optimize
-> Crash
Process: avogadro [17200]
Path: /Applications/Avogadro.app/Contents/MacOS/avogadro
Identifier: net.sourceforge
Version: (0.9.0)
Code Type: X86 (Native)
Parent Process: launchd [121]
Date/Time: 2009-01-12 13:13:56.658 -0500
OS Version: Mac OS X 10.5.6 (9G55)
Report Version: 6
Exception Type: EXC_BAD_ACCESS (SIGBUS)
Exception Codes: KERN_PROTECTION_FAILURE at 0x0000000000000020
Crashed Thread: 0
Thread 0 Crashed:
0 libopenbabel.3.dylib 0x0037edf0 OpenBabel::OBForceFieldUFF::SetupCalculations() + 9408
1 libopenbabel.3.dylib 0x002a3210 OpenBabel::OBForceField::Setup(OpenBabel::OBMol&) + 352 (forcefield.cpp:878)
2 libautoopttool.so 0x1db984d0 Avogadro::AutoOptThread::update() + 144 (autoopttool.cpp:513)
3 libautoopttool.so 0x1db9af23 Avogadro::AutoOptTool::timerEvent(QTimerEvent*) + 291 (autoopttool.cpp:427)
4 QtCore 0x005dddd8 QObject::event(QEvent*) + 424
5 QtGui 0x009ccc1f QApplicationPrivate::notify_helper(QObject*, QEvent*) + 191
6 QtGui 0x009ce90c QApplication::notify(QObject*, QEvent*) + 220
7 QtCore 0x005cbd01 QCoreApplication::notifyInternal(QObject*, QEvent*) + 145
8 QtGui 0x00a249d6 QApplicationPrivate::globalEventProcessor(OpaqueEventHandlerCallRef*, OpaqueEventRef*, void*) + 2374
9 com.apple.HIToolbox 0x90ba0143 DispatchEventToHandlers(EventTargetRec*, OpaqueEventRef*, HandlerCallRec*) + 1181
10 com.apple.HIToolbox 0x90b9f57d SendEventToEventTargetInternal(OpaqueEventRef*, OpaqueEventTargetRef*, HandlerCallRec*) + 405
11 com.apple.HIToolbox 0x90b9f3e2 SendEventToEventTargetWithOptions + 58
12 com.apple.HIToolbox 0x90bcdd54 ToolboxEventDispatcherHandler(OpaqueEventHandlerCallRef*, OpaqueEventRef*, void*) + 356
13 com.apple.HIToolbox 0x90ba04fc DispatchEventToHandlers(EventTargetRec*, OpaqueEventRef*, HandlerCallRec*) + 2134
14 com.apple.HIToolbox 0x90b9f57d SendEventToEventTargetInternal(OpaqueEventRef*, OpaqueEventTargetRef*, HandlerCallRec*) + 405
15 com.apple.HIToolbox 0x90bbbed2 SendEventToEventTarget + 52
16 QtGui 0x00a20521 qt_mac_send_event(QFlagsQEventLoop::ProcessEventsFlag, OpaqueEventRef*, OpaqueWindowPtr*) + 97
17 QtGui 0x00a2eb62 QEventDispatcherMac::processEvents(QFlagsQEventLoop::ProcessEventsFlag) + 658
18 QtCore 0x005cb2c1 QEventLoop::processEvents(QFlagsQEventLoop::ProcessEventsFlag) + 65
19 QtCore 0x005cb38d QEventLoop::exec(QFlagsQEventLoop::ProcessEventsFlag) + 157
20 QtCore 0x005cf331 QCoreApplication::exec() + 161
21 net.sourceforge 0x00014b6d main + 7325 (main.cpp:177)
22 net.sourceforge 0x000071db _start + 209
23 net.sourceforge 0x00007109 start + 41
Thread 1:
0 libSystem.B.dylib 0x9384f3ae __semwait_signal + 10
1 libSystem.B.dylib 0x93879d0d pthread_cond_wait$UNIX2003 + 73
2 libGLProgrammability.dylib 0x95335b32 glvmDoWork + 162
3 libSystem.B.dylib 0x93879095 _pthread_start + 321
4 libSystem.B.dylib 0x93878f52 thread_start + 34
Thread 2:
0 libSystem.B.dylib 0x9387f30a select$DARWIN_EXTSN$NOCANCEL + 10
1 QtCore 0x005f6f8b QEventDispatcherUNIX::select(int, fd_set*, fd_set*, fd_set*, timeval*) + 363
2 QtCore 0x005f7339 QEventDispatcherUNIXPrivate::doSelect(QFlagsQEventLoop::ProcessEventsFlag, timeval*) + 441
3 QtCore 0x005f849c QEventDispatcherUNIX::processEvents(QFlagsQEventLoop::ProcessEventsFlag) + 156
4 QtCore 0x005cb2c1 QEventLoop::processEvents(QFlagsQEventLoop::ProcessEventsFlag) + 65
5 QtCore 0x005cb38d QEventLoop::exec(QFlagsQEventLoop::ProcessEventsFlag) + 157
6 QtCore 0x004dde77 QThread::exec() + 87
7 QtCore 0x004e004b QThreadPrivate::start(void*) + 203
8 libSystem.B.dylib 0x93879095 _pthread_start + 321
9 libSystem.B.dylib 0x93878f52 thread_start + 34
Thread 0 crashed with X86 Thread State (32-bit):
eax: 0x00000002 ebx: 0x0037c93b ecx: 0x22be63c0 edx: 0x00000000
edi: 0x22bee440 esi: 0x004058c0 ebp: 0xbfffe7c8 esp: 0xbfffe080
ss: 0x0000001f efl: 0x00010297 eip: 0x0037edf0 cs: 0x00000017
ds: 0x0000001f es: 0x0000001f fs: 0x00000000 gs: 0x00000037
cr2: 0x00000020
You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=835077&aid=2502050&group_id=165310