Menu

#604 Segfault in orbital extension

v_1.1.0
closed
OpenQube (3)
7
2016-04-26
2012-05-30
No

The attached file crashes Avogadro for me on startup when the orbital extension is activated. Note that it contains no MO information, just vibrations.

The backtrace is:

Program received signal SIGSEGV, Segmentation fault.
0x00007fffcf1bcc2b in ?? () from /usr/lib/avogadro/1_1/extensions/orbitalextension.so
(gdb) bt

0 0x00007fffcf1bcc2b in ?? () from /usr/lib/avogadro/1_1/extensions/orbitalextension.so

1 0x00007fffcf1b6ead in ?? () from /usr/lib/avogadro/1_1/extensions/orbitalextension.so

2 0x00007fffcf1b965b in ?? () from /usr/lib/avogadro/1_1/extensions/orbitalextension.so

3 0x00007fffcf1b9d90 in ?? () from /usr/lib/avogadro/1_1/extensions/orbitalextension.so

4 0x00007ffff5fd05b1 in Avogadro::Extension::qt_metacall(QMetaObject::Call, int, void**) () from /usr/lib/libavogadro.so.1

5 0x00007fffcf1c4805 in ?? () from /usr/lib/avogadro/1_1/extensions/orbitalextension.so

6 0x00007ffff67c62e6 in QMetaObject::activate(QObject, QMetaObject const, int, void**) () from /usr/lib/libQtCore.so.4

7 0x0000000000436b7d in ?? ()

8 0x0000000000446021 in ?? ()

9 0x00000000004462e7 in ?? ()

10 0x0000000000450308 in ?? ()

11 0x00007ffff67c62e6 in QMetaObject::activate(QObject, QMetaObject const, int, void**) () from /usr/lib/libQtCore.so.4

12 0x00007ffff5fd1534 in Avogadro::MoleculeFile::qt_metacall(QMetaObject::Call, int, void**) () from /usr/lib/libavogadro.so.1

13 0x00007ffff67c2e29 in QObject::event(QEvent*) () from /usr/lib/libQtCore.so.4

14 0x00007ffff6cc332c in QApplicationPrivate::notify_helper(QObject, QEvent) () from /usr/lib/libQtGui.so.4

15 0x00007ffff6cc980b in QApplication::notify(QObject, QEvent) () from /usr/lib/libQtGui.so.4

16 0x00007ffff67b309c in QCoreApplication::notifyInternal(QObject, QEvent) () from /usr/lib/libQtCore.so.4

17 0x00007ffff67b6744 in QCoreApplicationPrivate::sendPostedEvents(QObject, int, QThreadData) () from /usr/lib/libQtCore.so.4

18 0x00007ffff67dcb73 in ?? () from /usr/lib/libQtCore.so.4

19 0x00007ffff42016f2 in g_main_context_dispatch () from /lib/libglib-2.0.so.0

20 0x00007ffff4205568 in ?? () from /lib/libglib-2.0.so.0

21 0x00007ffff420571c in g_main_context_iteration () from /lib/libglib-2.0.so.0

22 0x00007ffff67dc6b3 in QEventDispatcherGlib::processEvents(QFlags<QEventLoop::ProcessEventsFlag>) () from /usr/lib/libQtCore.so.4

23 0x00007ffff6d7319e in ?? () from /usr/lib/libQtGui.so.4

24 0x00007ffff67b6b8f in QCoreApplication::processEvents(QFlags<QEventLoop::ProcessEventsFlag>) () from /usr/lib/libQtCore.so.4

25 0x000000000046196d in ?? ()

26 0x00007ffff7a9bc8d in __libc_start_main () from /lib/libc.so.6

27 0x0000000000420129 in _start ()

Discussion

  • Michael Banck

    Michael Banck - 2012-05-30

    methane.molden

     
  • Michael Banck

    Michael Banck - 2012-05-30

    Just to be clear, openbabel seems to read this one in fine.

     
  • Geoff Hutchison

    Geoff Hutchison - 2012-06-14

    This file seems to expose a bug in Open Babel's molden support as well. When I successfully open the file, I see only 2 hydrogen atoms!

    I submitted a patch to Gerrit which seems to fix the Avogadro side for me.
    http://review.source.kitware.com/#/t/814

     
  • Geoff Hutchison

    Geoff Hutchison - 2016-04-26
    • status: pending --> closed