On Thu, Oct 29, 2009 at 6:54 PM, Geoffrey Hutchison geoff.hutchison@gmail.com wrote:
Hi Gary!
Good to hear from you. I don’t know if you remember me from the Ratner group.
Of course I remember you. You were working on Ghemical back then, I
think, among other things. Congratulations on the 1.0.0 release of
avogadro! It gives me hope for computational chemists. 
Avogadro dumps core when it exits also. I ran it through valgrind, which shows several problems with the destructor for AutoOptTool, which is probably related to the AutoOptTool not getting initialized properly.
OK, if you can give us some more detail into the core dump and/or the valgrind messages, it would be really helpful. What compiler did you use?
gcc version 4.1.2 20080704 (Red Hat 4.1.2-44)
The valgrind error message that comes after File->Exit is
==12414== Process terminating with default action of signal 11
(SIGSEGV): dumping core
==12414== Access not within mapped region at address 0x1000003
==12414== at 0x4E9D3B7: QThread::exit(int) (qthread.h:130)
==12414== by 0x6524A98: Avogadro::AutoOptTool::~AutoOptTool() (in
/hafs8/ccm/opt/linux.ix86/src/avogadro-1.0.0/build/lib/autoopttool.so)
==12414== by 0x4FB17F0: QObjectPrivate::deleteChildren() (qobject.cpp:1838)
==12414== by 0x4429FFD: QWidget::~QWidget() (qwidget.cpp:1367)
==12414== by 0x48266D0: QMainWindow::~QMainWindow() (qmainwindow.cpp:331)
==12414== by 0x807ABD8: Avogadro::MainWindow::~MainWindow() (in
/hafs8/ccm/opt/linux.ix86/src/avogadro-1.0.0/build/bin/avogadro)
==12414== by 0x4FB07F4: qDeleteInEventHandler(QObject*) (qobject.cpp:3806)
==12414== by 0x4FB2122: QObject::event(QEvent*) (qobject.cpp:1085)
==12414== by 0x4434674: QWidget::event(QEvent*) (qwidget.cpp:7951)
==12414== by 0x482883E: QMainWindow::event(QEvent*) (qmainwindow.cpp:1399)
==12414== by 0x8081504: Avogadro::MainWindow::event(QEvent*) (in
/hafs8/ccm/opt/linux.ix86/src/avogadro-1.0.0/build/bin/avogadro)
==12414== by 0x43DA64E:
QApplicationPrivate::notify_helper(QObject*, QEvent*)
(qapplication.cpp:4065)
If you want I can send the whole file to you. There are other memory
leak errors associated with AutoOptTools. Where in the code is the
link made to the babel forcefields? I’m guessing the AutoOptTools
constructor points to it, and something is going wrong there.
Also, when you say that some buttons aren’t active, what’s active, and what’s not?
The pull-down that should list the available force fields and the
start button are grayed out and inactive.
It could be that I haven’t set up the code properly. I did set $BABEL_LIBDIR and $BABEL_DATADIR in my shell from which I’m running avogadro.
Well, if it compiles, that’s a good sign. What do you get if you run “babel -L forcefields”? What about if you use the “Optimize Geometry” command in the Extensions menu?
babel -L gives
Ghemical Ghemical force field.
MMFF94 MMFF94 force field.
MMFF94s MMFF94s force field.
UFF Universal Force Field.
The ‘Optimize Geomtry’ entry does not appear in the Extensions menu.
X Error: BadLength (poly request too large or internal Xlib length error) 16
Major opcode: 18 (X_ChangeProperty)
Resource id: 0x2a00020
These are probably an issue between X and your graphics driver.
Yes that sound right to me.
Thanks,
Gary