Segfault on launch

General Discussion Support
1

I believe this to be a bug with Avogadro

Environment Information

Avogadro version: 1.99 compiled
Operating system and version: OpenSUSE Tumbleweed 20240216

Expected Behavior

Actual Behavior

Seg fault during launch.

Steps to Reproduce

Nightly AppImage seems to launch just fine.

But compiling from source results in a broken binary. As well as avogadrolibs I made sure avogadroapp, avogadro-i18n and avogadrodata were up to date and still got the same result.

Traceback with gdb:

(gdb) bt
#0  0x00007ffff5639af0 in vtable for __cxxabiv1::__si_class_type_info () at /lib64/libstdc++.so.6
#1  0x0000000000421583 in Avogadro::setDefaultViews(Avogadro::QtGui::MultiViewWidget*) (viewWidget=0xadbfe0)
    at ~/avo/openchemistry/avogadroapp/avogadro/mainwindow.cpp:583
#2  0x0000000000421b43 in Avogadro::MainWindow::setMolecule(Avogadro::QtGui::Molecule*)
    (this=0x7fffffffd860, mol=0xdce820) at ~/avo/openchemistry/avogadroapp/avogadro/mainwindow.cpp:635
#3  0x00000000004213b0 in Avogadro::MainWindow::newMolecule() (this=0x7fffffffd860)
    at ~/avo/openchemistry/avogadroapp/avogadro/mainwindow.cpp:559
#4  0x000000000041f44e in Avogadro::MainWindow::MainWindow(QStringList const&, bool)
    (this=0x7fffffffd860, fileNames=..., disableSettings=false)
    at ~/avo/openchemistry/avogadroapp/avogadro/mainwindow.cpp:314
#5  0x000000000041c636 in main(int, char**) (argc=1, argv=0x7fffffffdf28)
    at ~/avo/openchemistry/avogadroapp/avogadro/avogadro.cpp:311

Any ideas? Anyone else getting the same?

2

What do you mean by “broken binary”?

Are you sure you’re using HEAD?

3

Broken as in doesn’t launch. Exits with error code 139 and:

...
"Checking for formatScripts scripts in path /usr/share/OpenChemistry/Avogadro/formatScripts"
"Checking for formatScripts scripts in path ~/avo/qt5/prefix/bin/../lib64/avogadro2/scripts/formatScripts"
fish: Job 1, 'avogadro2' terminated by signal SIGSEGV (Address boundary error)

Yep, I am in sync with the master branches of my forks which are in turn up to date with the master branches of openchemistry/avogadrolibs and openchemistry/avogadroapp.

4

I’d suggest starting up in gdb avogadro2 starting with run and then bt when you get the crash.

5

Yes, I did that, see my original post :slight_smile:

6

I see the back trace, but it doesn’t make sense. This suggests a pointer issue, but it’s not obvious that anything particularly changed.

Can you “make clean” or “ninja clean” and rebuild?

7

Sadly didn’t help :frowning:

I thought it might be related to system libraries/updates but updating Tumbleweed didn’t change anything so probably not a bug there.

8

Seems to have fixed itself :man_shrugging:

9

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