Version: 1.9.91 (using KDE 4.0.0) Installed from: Mandriva RPMs OS: Linux When the file to load is chosen (double clicked 'Open' button clicked), kalzium crashes and causes signal 11 (SIGSEGV) Backtrace: Using host libthread_db library "/lib64/libthread_db.so.1". [Thread debugging using libthread_db enabled] [New Thread 47917707722272 (LWP 28320)] [KCrash handler] #5 0x00002b94aba11894 in OpenBabel::OBConversion::SetOutFormat () from /usr/lib64/libopenbabel.so.2 #6 0x00002b94aba118da in OpenBabel::OBConversion::SetInAndOutFormats () from /usr/lib64/libopenbabel.so.2 #7 0x00002b94abf38701 in OpenBabel2Wrapper::readMolecule () from /opt/kde4/lib64/libcompoundviewer.so.4 #8 0x0000000000447ab0 in MoleculeDialog::slotLoadMolecule () #9 0x0000000000447cbc in MoleculeDialog::qt_metacall () #10 0x00002b94b0c57582 in QMetaObject::activate () from /usr/lib/qt4/lib64/libQtCore.so.4 #11 0x00002b94ae5cbead in KDialog::slotButtonClicked () from /opt/kde4/lib64/libkdeui.so.5 #12 0x00002b94ae5cdcd5 in KDialog::qt_metacall () from /opt/kde4/lib64/libkdeui.so.5 #13 0x0000000000447c9d in MoleculeDialog::qt_metacall () #14 0x00002b94b0c57582 in QMetaObject::activate () from /usr/lib/qt4/lib64/libQtCore.so.4 #15 0x00002b94b0c5ab8e in QSignalMapper::mapped () from /usr/lib/qt4/lib64/libQtCore.so.4 #16 0x00002b94b0c5afda in QSignalMapper::map () from /usr/lib/qt4/lib64/libQtCore.so.4 #17 0x00002b94b0c5b49c in QSignalMapper::qt_metacall () from /usr/lib/qt4/lib64/libQtCore.so.4 #18 0x00002b94b0c57582 in QMetaObject::activate () from /usr/lib/qt4/lib64/libQtCore.so.4 #19 0x00002b94b07dfc77 in QAbstractButton::clicked () from /usr/lib/qt4/lib64/libQtGui.so.4 #20 0x00002b94b0601e7b in QAbstractButtonPrivate::emitClicked () from /usr/lib/qt4/lib64/libQtGui.so.4 #21 0x00002b94b0602c95 in QAbstractButtonPrivate::click () from /usr/lib/qt4/lib64/libQtGui.so.4 #22 0x00002b94b0602e91 in QAbstractButton::mouseReleaseEvent () from /usr/lib/qt4/lib64/libQtGui.so.4 #23 0x00002b94b03b7952 in QWidget::event () from /usr/lib/qt4/lib64/libQtGui.so.4 #24 0x00002b94b06020d0 in QAbstractButton::event () from /usr/lib/qt4/lib64/libQtGui.so.4 #25 0x00002b94b067c058 in QPushButton::event () from /usr/lib/qt4/lib64/libQtGui.so.4 #26 0x00002b94b03788ab in QApplicationPrivate::notify_helper () from /usr/lib/qt4/lib64/libQtGui.so.4 #27 0x00002b94b037ec4d in QApplication::notify () from /usr/lib/qt4/lib64/libQtGui.so.4 #28 0x00002b94ae6316fe in KApplication::notify () from /opt/kde4/lib64/libkdeui.so.5 #29 0x00002b94b0c47020 in QCoreApplication::notifyInternal () from /usr/lib/qt4/lib64/libQtCore.so.4 #30 0x00002b94b03c77c3 in QETWidget::translateMouseEvent () from /usr/lib/qt4/lib64/libQtGui.so.4 #31 0x00002b94b03c6842 in QApplication::x11ProcessEvent () from /usr/lib/qt4/lib64/libQtGui.so.4 #32 0x00002b94b03e7883 in KParts::Factory::metaObject () from /usr/lib/qt4/lib64/libQtGui.so.4 #33 0x00002b94b4bb9c24 in g_main_context_dispatch () from /usr/lib64/libglib-2.0.so.0 #34 0x00002b94b4bbcf1d in KParts::Factory::metaObject () from /usr/lib64/libglib-2.0.so.0 #35 0x00002b94b4bbd3ee in g_main_context_iteration () from /usr/lib64/libglib-2.0.so.0 #36 0x00002b94b0c65dd1 in QEventDispatcherGlib::processEvents () from /usr/lib/qt4/lib64/libQtCore.so.4 #37 0x00002b94b03e756f in QGuiEventDispatcherGlib::processEvents () from /usr/lib/qt4/lib64/libQtGui.so.4 #38 0x00002b94b0c465d8 in QEventLoop::processEvents () from /usr/lib/qt4/lib64/libQtCore.so.4 #39 0x00002b94b0c466ed in QEventLoop::exec () from /usr/lib/qt4/lib64/libQtCore.so.4 #40 0x00002b94b0c48d61 in QCoreApplication::exec () from /usr/lib/qt4/lib64/libQtCore.so.4 #41 0x0000000000455206 in ?? () #42 0x00002b94b3988ae4 in __libc_start_main () from /lib64/libc.so.6 #43 0x0000000000443cc9 in _start () #0 0x00002b94b3a01d20 in nanosleep () from /lib64/libc.so.6
Thank you for the report. Could you please specify the exact version of OpenBabel you are using? Is that a 64bit system?
Hm. We've already seen this issue many times before in Avogadro. In addition to what Carsten asked, please: 1) look for the directory containing the file named "cmlformat.so" on your hard drive (you can use 'slocate' or 'find'). 2) set the BABEL_LIBDIR environment variable to this directory Example: export BABEL_LIBDIR=/usr/lib/openbabel/2.1 if the file /usr/lib/openbabel/2.1/cmlformat.so exists. 3) rerun Kalzium if that works, you can set this variable permanently by e.g. editing your .bashrc.
Hm. Thinking more about it -- I don't think that what I suggested in #2 will work. Could you 1) still tell me whether cmlformat.so exists on your hard drive 2) install openbabel (the program -- the library you already have) and post here the output of "babel -Hcml"
Yes, I use a 64bit system. OpenBabel version is 2.1.1-1mdv2008.0 I cannot find the cmlformat.so file and "openbabel -Hcml" says: "Format type: cml was not recognized".
*** Bug 160104 has been marked as a duplicate of this bug. ***
Hello In the last couple of days we added a lot (a lot!) new stuff and fixes in the relevant code. Could you retry with KDE 4.1 as of today or later if this bug is still valid? I simply cannot reproduce here. Carsten
No, there is the same problem with the same error-message. I tried to use a Nvidia-card instead of a Ati-card Now I tried with the 4.1 unstable
Jan, The above discussion with Peter clearly shows that, at least in his case, the problem is caused by OpenBabel format plugins not being found. OpenBabel is the library we use to handle 80+ chemical file formats, and each format is handled by a separate plugin. Nothing to do with OpenGL and graphics cards. First check if this is also your problem: see comment #3. Then we can talk :)
This is basically a distibution issue (or because you selfcompiled). We kind of fixed it. If the OB install is incomplete (for example you have libopenbabel installed but not openbabel itself (eg. the "babel" tool)) you get a popup with this warning: "Cannot read the file format. Check your OpenBabel installation." This should prevent any such crashes.