Running Forcefield sometimes crashes Avogadro

[cryos]

Program received signal SIGSEGV, Segmentation fault.
[Switching to Thread -1226713392 (LWP 399)]
0xb7d934ab in OpenBabel::OBAtom::GetVector (this=0x8ac86dc) at atom.cpp:345
345 _v.Set((__c)[_cidx],(__c)[_cidx+1],(*_c)[_cidx+2]);
Current language: auto; currently c++
(gdb) bt
#0 0xb7d934ab in OpenBabel::OBAtom::GetVector (this=0x8ac86dc) at atom.cpp:345
#1 0xb725fe6a in Avogadro::Atom::pos () from /home/kde4/build/avo/libavogadro/src/libavogadro.so.0
#2 0xb6937605 in Avogadro::ClickMeasureTool::paint () from /home/kde4/build/avo/libavogadro/src/tools/libclickmeasuretool.so
#3 0xb725b980 in Avogadro::GLWidget::render () from /home/kde4/build/avo/libavogadro/src/libavogadro.so.0
#4 0xb725ad74 in Avogadro::GLWidget::paintGL () from /home/kde4/build/avo/libavogadro/src/libavogadro.so.0
#5 0xb725acac in Avogadro::GLWidget::paintEvent () from /home/kde4/build/avo/libavogadro/src/libavogadro.so.0
#6 0xb77b38c5 in QWidget::event () from /usr//lib/libQtGui.so.4
#7 0xb7d2d906 in QGLWidget::event () from /usr//lib/libQtOpenGL.so.4
#8 0xb725ac2a in Avogadro::GLWidget::event () from /home/kde4/build/avo/libavogadro/src/libavogadro.so.0
#9 0xb776fe10 in QApplicationPrivate::notify_helper () from /usr//lib/libQtGui.so.4
#10 0xb7775fee in QApplication::notify () from /usr//lib/libQtGui.so.4
#11 0xb73b79ab in QCoreApplication::notifyInternal () from /usr//lib/libQtCore.so.4
#12 0xb77bbdae in qt_sendSpontaneousEvent () from /usr//lib/libQtGui.so.4
#13 0xb78cd20e in QWidgetPrivate::drawWidget () from /usr//lib/libQtGui.so.4
#14 0xb78ce5b9 in QWidget::repaint () from /usr//lib/libQtGui.so.4
#15 0xb78ce7bf in qt_syncBackingStore () from /usr//lib/libQtGui.so.4
#16 0xb77b37a2 in QWidget::event () from /usr//lib/libQtGui.so.4
#17 0xb7d2d906 in QGLWidget::event () from /usr//lib/libQtOpenGL.so.4
#18 0xb725ac2a in Avogadro::GLWidget::event () from /home/kde4/build/avo/libavogadro/src/libavogadro.so.0
#19 0xb776fe10 in QApplicationPrivate::notify_helper () from /usr//lib/libQtGui.so.4
#20 0xb7775fee in QApplication::notify () from /usr//lib/libQtGui.so.4
#21 0xb73b79ab in QCoreApplication::notifyInternal () from /usr//lib/libQtCore.so.4
#22 0xb73b8d45 in QCoreApplicationPrivate::sendPostedEvents () from /usr//lib/libQtCore.so.4
#23 0xb73b8ffd in QCoreApplication::sendPostedEvents () from /usr//lib/libQtCore.so.4
#24 0xb73d8c3b in postEventSourceDispatch () from /usr//lib/libQtCore.so.4
#25 0xb6e90de2 in g_main_context_dispatch () from /opt/gnome/lib/libglib-2.0.so.0
#26 0xb6e93e1f in g_main_context_prepare () from /opt/gnome/lib/libglib-2.0.so.0
#27 0xb6e94385 in g_main_context_iteration () from /opt/gnome/lib/libglib-2.0.so.0
#28 0xb73d92e8 in QEventDispatcherGlib::processEvents () from /usr//lib/libQtCore.so.4
#29 0xb77e80b5 in QGuiEventDispatcherGlib::processEvents () from /usr//lib/libQtGui.so.4
#30 0xb73b6ee8 in QEventLoop::processEvents () from /usr//lib/libQtCore.so.4
#31 0xb73b6ffc in QEventLoop::exec () from /usr//lib/libQtCore.so.4
#32 0xb73b90b8 in QCoreApplication::exec () from /usr//lib/libQtCore.so.4
#33 0xb776f527 in QApplication::exec () from /usr//lib/libQtGui.so.4
#34 0x0807e6bf in main ()

Reported by: @cniehaus

[cryos]

Logged In: YES
user_id=684210
Originator: YES

I played around with Avo forcefield feature (GHemical). I managed to crash it by playing around. But I didn't get a proper backtrace.

So I started Avo in gdb and played around again. No crash until I opened the file ethyl_propanoate.cml.

Original comment by: @cniehaus

[cryos]

Logged In: YES
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Originator: YES

This is OB 2.2-trunk (today) and Avo trunk (today)

Original comment by: @cniehaus

[cryos]

Logged In: YES
user_id=684210
Originator: YES

It seems this doesn't have anything to do with forcefields. This time I didn't use any forcefield-stuff but just played around. The backtrace seems to be the same.

I also used another molecule this time (lineloin.cml)...

Program received signal SIGSEGV, Segmentation fault.
[Switching to Thread -1225808176 (LWP 22161)]
0xb7e704ab in OpenBabel::OBAtom::GetVector (this=0x812679c) at atom.cpp:345
345 _v.Set((__c)[_cidx],(__c)[_cidx+1],(*_c)[_cidx+2]);
Current language: auto; currently c++
(gdb) bt
#0 0xb7e704ab in OpenBabel::OBAtom::GetVector (this=0x812679c) at atom.cpp:345
#1 0xb733ce6a in Avogadro::Atom::pos () from /home/kde4/build/avo/libavogadro/src/libavogadro.so.0
#2 0xb6a1444b in Avogadro::ClickMeasureTool::paint ()
from /home/kde4/build/avo/libavogadro/src/tools/libclickmeasuretool.so
#3 0xb7338980 in Avogadro::GLWidget::render () from /home/kde4/build/avo/libavogadro/src/libavogadro.so.0
#4 0xb7337d74 in Avogadro::GLWidget::paintGL () from /home/kde4/build/avo/libavogadro/src/libavogadro.so.0
#5 0xb7337cac in Avogadro::GLWidget::paintEvent () from /home/kde4/build/avo/libavogadro/src/libavogadro.so.0
#6 0xb78908c5 in QWidget::event () from /usr//lib/libQtGui.so.4
#7 0xb7e0a906 in QGLWidget::event () from /usr//lib/libQtOpenGL.so.4
#8 0xb7337c2a in Avogadro::GLWidget::event () from /home/kde4/build/avo/libavogadro/src/libavogadro.so.0
#9 0xb784ce10 in QApplicationPrivate::notify_helper () from /usr//lib/libQtGui.so.4
#10 0xb7852fee in QApplication::notify () from /usr//lib/libQtGui.so.4
#11 0xb74949ab in QCoreApplication::notifyInternal () from /usr//lib/libQtCore.so.4
#12 0xb7898dae in qt_sendSpontaneousEvent () from /usr//lib/libQtGui.so.4
#13 0xb79aa20e in QWidgetPrivate::drawWidget () from /usr//lib/libQtGui.so.4
#14 0xb79ab5b9 in QWidget::repaint () from /usr//lib/libQtGui.so.4
#15 0xb79ab85f in qt_syncBackingStore () from /usr//lib/libQtGui.so.4
#16 0xb79ab8b0 in qt_syncBackingStore () from /usr//lib/libQtGui.so.4
#17 0xb78979f3 in QETWidget::translatePaintEvent () from /usr//lib/libQtGui.so.4
#18 0xb78a1e8c in QApplication::x11ProcessEvent () from /usr//lib/libQtGui.so.4
#19 0xb78c52cb in x11EventSourceDispatch () from /usr//lib/libQtGui.so.4
#20 0xb6f6dde2 in g_main_context_dispatch () from /opt/gnome/lib/libglib-2.0.so.0
#21 0xb6f70e1f in g_main_context_prepare () from /opt/gnome/lib/libglib-2.0.so.0
#22 0xb6f71385 in g_main_context_iteration () from /opt/gnome/lib/libglib-2.0.so.0
#23 0xb74b62e8 in QEventDispatcherGlib::processEvents () from /usr//lib/libQtCore.so.4
#24 0xb78c50b5 in QGuiEventDispatcherGlib::processEvents () from /usr//lib/libQtGui.so.4
#25 0xb7493ee8 in QEventLoop::processEvents () from /usr//lib/libQtCore.so.4
#26 0xb7493ffc in QEventLoop::exec () from /usr//lib/libQtCore.so.4
#27 0xb74960b8 in QCoreApplication::exec () from /usr//lib/libQtCore.so.4
#28 0xb784c527 in QApplication::exec () from /usr//lib/libQtGui.so.4
#29 0x0807e6bf in main ()

Original comment by: @cniehaus

[cryos]

Logged In: YES
user_id=684210
Originator: YES

Today I tried hard to crash Avogadro, using latest OB and latest Avogadro. It simply works (tm) now.

Original comment by: @cniehaus