Fill crystal crash

Development
1

Bugs item #2908845, was opened at 2009-12-04 15:03
Message generated for change (Tracker Item Submitted) made by nobody
You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=835077&aid=2908845&group_id=165310

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including the initial issue submission, for this request,
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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: fill crystal crash

Initial Comment:
trying to populate the entire cell of the attached cif file causes crash.

You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=835077&aid=2908845&group_id=165310

2

I’ve also noticed that the supercell builder seems to crash a lot –
possibly related?

On Fri, Dec 4, 2009 at 10:03 AM, SourceForge.net
noreply@sourceforge.net wrote:

Bugs item #2908845, was opened at 2009-12-04 15:03
Message generated for change (Tracker Item Submitted) made by nobody
You can respond by visiting:
Avogadro / Old Bugs / #440 fill crystal crash

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: None
Group: None
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Nobody/Anonymous (nobody)
Assigned to: Nobody/Anonymous (nobody)
Summary: fill crystal crash

Initial Comment:
trying to populate the entire cell of the attached cif file causes crash.

You can respond by visiting:
Avogadro / Old Bugs / #440 fill crystal crash

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3

On Dec 4, 2009, at 11:18 AM, David Lonie wrote:

I’ve also noticed that the supercell builder seems to crash a lot –
possibly related?

Yes, it’s possibly related. If you can get us a backtrace, that would be super helpful – there aren’t obvious crash points that I’ve found.

Thanks,
-Geoff

4

BT at end of email. Oddly, it has always crashed on the first try,
until I was running in gdb and then it took a few tries. Murphy’s Law
I suppose :slight_smile:

On Fri, Dec 4, 2009 at 11:49 AM, Geoffrey Hutchison
geoff.hutchison@gmail.com wrote:

On Dec 4, 2009, at 11:18 AM, David Lonie wrote:

I’ve also noticed that the supercell builder seems to crash a lot –
possibly related?

Yes, it’s possibly related. If you can get us a backtrace, that would be super helpful – there aren’t obvious crash points that I’ve found.

Thanks,
-Geoff

(gdb) bt
#0 0xb673943a in Avogadro::Molecule::OBMol (this=0x8711118) at
/home/dl/src/avogadro/libavogadro/src/molecule.cpp:1173
#1 0xb41bd076 in Avogadro::SuperCellExtension::fillCell
(this=0x82da880) at
/home/dl/src/avogadro/libavogadro/src/extensions/supercellextension.cpp:169
#2 0xb41c4cb8 in Avogadro::SuperCellExtension::qt_metacall
(this=0x82da880, _c=QMetaObject::InvokeMetaMethod, _id=0,
_a=0xbfffcf4c)
at /home/dl/src/avogadro/build/libavogadro/src/extensions/moc_supercellextension.cxx:66
#3 0xb6a768ac in QMetaObject::activate(QObject*, int, int, void**) ()
from /usr/lib/libQtCore.so.4
#4 0xb6a774e2 in QMetaObject::activate(QObject*, QMetaObject const*,
int, void**) () from /usr/lib/libQtCore.so.4
#5 0xb41c5355 in Avogadro::SuperCellDialog::fillCell (this=0x8253698)
at /home/dl/src/avogadro/build/libavogadro/src/extensions/moc_supercelldialog.cxx:95
#6 0xb41c39a1 in Avogadro::SuperCellDialog::fillCellClicked
(this=0x8253698) at
/home/dl/src/avogadro/libavogadro/src/extensions/supercelldialog.cpp:85
#7 0xb41c52a6 in Avogadro::SuperCellDialog::qt_metacall
(this=0x8253698, _c=QMetaObject::InvokeMetaMethod, _id=3,
_a=0xbfffd108)
at /home/dl/src/avogadro/build/libavogadro/src/extensions/moc_supercelldialog.cxx:77
#8 0xb6a768ac in QMetaObject::activate(QObject*, int, int, void**) ()
from /usr/lib/libQtCore.so.4
#9 0xb6a76cf8 in QMetaObject::activate(QObject*, QMetaObject const*,
int, int, void**) () from /usr/lib/libQtCore.so.4
#10 0xb765c231 in QAbstractButton::clicked(bool) () from /usr/lib/libQtGui.so.4
#11 0xb7387259 in ?? () from /usr/lib/libQtGui.so.4
#12 0xb7388eb4 in ?? () from /usr/lib/libQtGui.so.4
#13 0xb7389141 in QAbstractButton::mouseReleaseEvent(QMouseEvent*) ()
from /usr/lib/libQtGui.so.4
#14 0xb702fc52 in QWidget::event(QEvent*) () from /usr/lib/libQtGui.so.4
#15 0xb73870fe in QAbstractButton::event(QEvent*) () from /usr/lib/libQtGui.so.4
#16 0xb743087d in QPushButton::event(QEvent*) () from /usr/lib/libQtGui.so.4
#17 0xb6fdb3a4 in QApplicationPrivate::notify_helper(QObject*,
QEvent*) () from /usr/lib/libQtGui.so.4
#18 0xb6fe33d0 in QApplication::notify(QObject*, QEvent*) () from
/usr/lib/libQtGui.so.4
#19 0xb6a60e8b in QCoreApplication::notifyInternal(QObject*, QEvent*)
() from /usr/lib/libQtCore.so.4
#20 0xb6fe2393 in QApplicationPrivate::sendMouseEvent(QWidget*,
QMouseEvent*, QWidget*, QWidget*, QWidget**, QPointer&) ()
from /usr/lib/libQtGui.so.4
#21 0xb704fe84 in ?? () from /usr/lib/libQtGui.so.4
#22 0xb704f365 in QApplication::x11ProcessEvent(_XEvent*) () from
/usr/lib/libQtGui.so.4
#23 0xb7079a52 in ?? () from /usr/lib/libQtGui.so.4
#24 0xb6895328 in g_main_context_dispatch () from /usr/lib/libglib-2.0.so.0
#25 0xb6898ba0 in g_main_context_iterate () from /usr/lib/libglib-2.0.so.0
#26 0xb6898cd3 in g_main_context_iteration () from /usr/lib/libglib-2.0.so.0
#27 0xb6a8b5f5 in
QEventDispatcherGlib::processEvents(QFlagsQEventLoop::ProcessEventsFlag)
() from /usr/lib/libQtCore.so.4
#28 0xb7079185 in ?? () from /usr/lib/libQtGui.so.4
#29 0xb6a5f479 in
QEventLoop::processEvents(QFlagsQEventLoop::ProcessEventsFlag) ()
from /usr/lib/libQtCore.so.4
#30 0xb6a5f8ca in
QEventLoop::exec(QFlagsQEventLoop::ProcessEventsFlag) () from
/usr/lib/libQtCore.so.4
#31 0xb6a61d3f in QCoreApplication::exec() () from /usr/lib/libQtCore.so.4
#32 0xb6fdb227 in QApplication::exec() () from /usr/lib/libQtGui.so.4
#33 0x0806ade6 in main (argc=1, argv=0xbffff2a4) at
/home/dl/src/avogadro/avogadro/src/main.cpp:223

5

David Lonie wrote:

BT at end of email. Oddly, it has always crashed on the first try,
until I was running in gdb and then it took a few tries. Murphy’s Law
I suppose :slight_smile:

I exercised this code loads and didn’t get crashes. It is one of the big
reasons we got a journal cover - they were building the images from
their CIF files. I will see if I can reproduce this tomorrow, are you
running trunk, a branch or a release?

Marcus

7

#0 0xb673943a in Avogadro::Molecule::OBMol (this=0x8711118) at
/home/dl/src/avogadro/libavogadro/src/molecule.cpp:1173

For me, that corresponds to this line:

    QString atomLabel = residue->atomId(atomId);

I don’t know any reason that would crash, but adding a qDebug() statement before and after this statement would be very helpful.

Does your crystal contain any residue data at all?

-Geoff