Bug 420604

Summary: Kalzium crashed when measuring water molecule
Product: [Applications] kalzium Reporter: luca.cremonesi
Component: generalAssignee: Kalzium Developers <kalzium>
Status: RESOLVED UPSTREAM    
Severity: crash Keywords: drkonqi
Priority: NOR    
Version First Reported In: unspecified   
Target Milestone: ---   
Platform: Arch Linux   
OS: Linux   
Latest Commit: Version Fixed/Implemented In:
Sentry Crash Report:

Description luca.cremonesi 2020-04-26 07:07:53 UTC 
Application: kalzium (19.12.3)

Qt Version: 5.14.2
Frameworks Version: 5.69.0
Operating System: Linux 5.6.4-arch1-1 x86_64
Windowing system: X11
Distribution: "Arch Linux"

-- Information about the crash:
- What I was doing when the application crashed:
1) I loaded a water molecule in the Molecular Editor.
2) I switched to the Measure tab.
3) I left-clicked on a hydrogen atom.

-- Backtrace:
Application: Kalzium (kalzium), signal: Aborted
Using host libthread_db library "/usr/lib/libthread_db.so.1".
[Current thread is 1 (Thread 0x7fe13b857b00 (LWP 22253))]

Thread 19 (Thread 0x7fe0e77fe700 (LWP 22570)):
#0  0x00007fe1426e5abf in poll () at /usr/lib/libc.so.6
#1  0x00007fe10caf9c14 in  () at /usr/lib/libpulse.so.0
#2  0x00007fe10cb07059 in pa_mainloop_poll () at /usr/lib/libpulse.so.0
#3  0x00007fe10cb11301 in pa_mainloop_iterate () at /usr/lib/libpulse.so.0
#4  0x00007fe10cb113b1 in pa_mainloop_run () at /usr/lib/libpulse.so.0
#5  0x00007fe10cb0161e in  () at /usr/lib/libpulse.so.0
#6  0x00007fe10ca28d1c in  () at /usr/lib/pulseaudio/libpulsecommon-13.0.so
#7  0x00007fe1425d846f in start_thread () at /usr/lib/libpthread.so.0
#8  0x00007fe1426f03d3 in clone () at /usr/lib/libc.so.6

Thread 18 (Thread 0x7fe0e7fff700 (LWP 22294)):
#0  0x00007fe1426e14fc in read () at /usr/lib/libc.so.6
#1  0x00007fe14005d8c0 in  () at /usr/lib/libglib-2.0.so.0
#2  0x00007fe1400acd01 in g_main_context_check () at /usr/lib/libglib-2.0.so.0
#3  0x00007fe1400ae448 in  () at /usr/lib/libglib-2.0.so.0
#4  0x00007fe1400ae571 in g_main_context_iteration () at /usr/lib/libglib-2.0.so.0
#5  0x00007fe142de58ac in QEventDispatcherGlib::processEvents(QFlags<QEventLoop::ProcessEventsFlag>) () at /usr/lib/libQt5Core.so.5
#6  0x00007fe142d8c05c in QEventLoop::exec(QFlags<QEventLoop::ProcessEventsFlag>) () at /usr/lib/libQt5Core.so.5
#7  0x00007fe142bb0c62 in QThread::exec() () at /usr/lib/libQt5Core.so.5
#8  0x00007fe142bb1dd6 in  () at /usr/lib/libQt5Core.so.5
#9  0x00007fe1425d846f in start_thread () at /usr/lib/libpthread.so.0
#10 0x00007fe1426f03d3 in clone () at /usr/lib/libc.so.6

Thread 17 (Thread 0x7fe0f55b6700 (LWP 22293)):
#0  0x00007fe1426e5abf in poll () at /usr/lib/libc.so.6
#1  0x00007fe1400ae4a0 in  () at /usr/lib/libglib-2.0.so.0
#2  0x00007fe1400ae571 in g_main_context_iteration () at /usr/lib/libglib-2.0.so.0
#3  0x00007fe142de58ac in QEventDispatcherGlib::processEvents(QFlags<QEventLoop::ProcessEventsFlag>) () at /usr/lib/libQt5Core.so.5
#4  0x00007fe142d8c05c in QEventLoop::exec(QFlags<QEventLoop::ProcessEventsFlag>) () at /usr/lib/libQt5Core.so.5
#5  0x00007fe142bb0c62 in QThread::exec() () at /usr/lib/libQt5Core.so.5
#6  0x00007fe142bb1dd6 in  () at /usr/lib/libQt5Core.so.5
#7  0x00007fe1425d846f in start_thread () at /usr/lib/libpthread.so.0
#8  0x00007fe1426f03d3 in clone () at /usr/lib/libc.so.6

Thread 16 (Thread 0x7fe0f6b60700 (LWP 22270)):
#0  0x00007fe1425decf5 in pthread_cond_wait@@GLIBC_2.3.2 () at /usr/lib/libpthread.so.0
#1  0x00007fe1315f91cc in  () at /usr/lib/dri/radeonsi_dri.so
#2  0x00007fe1315f8dc8 in  () at /usr/lib/dri/radeonsi_dri.so
#3  0x00007fe1425d846f in start_thread () at /usr/lib/libpthread.so.0
#4  0x00007fe1426f03d3 in clone () at /usr/lib/libc.so.6

Thread 15 (Thread 0x7fe0f7361700 (LWP 22269)):
#0  0x00007fe1425decf5 in pthread_cond_wait@@GLIBC_2.3.2 () at /usr/lib/libpthread.so.0
#1  0x00007fe1315f91cc in  () at /usr/lib/dri/radeonsi_dri.so
#2  0x00007fe1315f8dc8 in  () at /usr/lib/dri/radeonsi_dri.so
#3  0x00007fe1425d846f in start_thread () at /usr/lib/libpthread.so.0
#4  0x00007fe1426f03d3 in clone () at /usr/lib/libc.so.6

Thread 14 (Thread 0x7fe0f7b62700 (LWP 22268)):
#0  0x00007fe1425decf5 in pthread_cond_wait@@GLIBC_2.3.2 () at /usr/lib/libpthread.so.0
#1  0x00007fe1315f91cc in  () at /usr/lib/dri/radeonsi_dri.so
#2  0x00007fe1315f8dc8 in  () at /usr/lib/dri/radeonsi_dri.so
#3  0x00007fe1425d846f in start_thread () at /usr/lib/libpthread.so.0
#4  0x00007fe1426f03d3 in clone () at /usr/lib/libc.so.6

Thread 13 (Thread 0x7fe10e7fc700 (LWP 22266)):
#0  0x00007fe1425decf5 in pthread_cond_wait@@GLIBC_2.3.2 () at /usr/lib/libpthread.so.0
#1  0x00007fe1315f91cc in  () at /usr/lib/dri/radeonsi_dri.so
#2  0x00007fe1315f8dc8 in  () at /usr/lib/dri/radeonsi_dri.so
#3  0x00007fe1425d846f in start_thread () at /usr/lib/libpthread.so.0
#4  0x00007fe1426f03d3 in clone () at /usr/lib/libc.so.6

Thread 12 (Thread 0x7fe10effd700 (LWP 22265)):
#0  0x00007fe1425decf5 in pthread_cond_wait@@GLIBC_2.3.2 () at /usr/lib/libpthread.so.0
#1  0x00007fe1315f91cc in  () at /usr/lib/dri/radeonsi_dri.so
#2  0x00007fe1315f8dc8 in  () at /usr/lib/dri/radeonsi_dri.so
#3  0x00007fe1425d846f in start_thread () at /usr/lib/libpthread.so.0
#4  0x00007fe1426f03d3 in clone () at /usr/lib/libc.so.6

Thread 11 (Thread 0x7fe10f7fe700 (LWP 22264)):
#0  0x00007fe1425decf5 in pthread_cond_wait@@GLIBC_2.3.2 () at /usr/lib/libpthread.so.0
#1  0x00007fe1315f91cc in  () at /usr/lib/dri/radeonsi_dri.so
#2  0x00007fe1315f8dc8 in  () at /usr/lib/dri/radeonsi_dri.so
#3  0x00007fe1425d846f in start_thread () at /usr/lib/libpthread.so.0
#4  0x00007fe1426f03d3 in clone () at /usr/lib/libc.so.6

Thread 10 (Thread 0x7fe10ffff700 (LWP 22263)):
#0  0x00007fe1425decf5 in pthread_cond_wait@@GLIBC_2.3.2 () at /usr/lib/libpthread.so.0
#1  0x00007fe1315f91cc in  () at /usr/lib/dri/radeonsi_dri.so
#2  0x00007fe1315f8dc8 in  () at /usr/lib/dri/radeonsi_dri.so
#3  0x00007fe1425d846f in start_thread () at /usr/lib/libpthread.so.0
#4  0x00007fe1426f03d3 in clone () at /usr/lib/libc.so.6

Thread 9 (Thread 0x7fe124bd1700 (LWP 22262)):
#0  0x00007fe1425decf5 in pthread_cond_wait@@GLIBC_2.3.2 () at /usr/lib/libpthread.so.0
#1  0x00007fe1315f91cc in  () at /usr/lib/dri/radeonsi_dri.so
#2  0x00007fe1315f8dc8 in  () at /usr/lib/dri/radeonsi_dri.so
#3  0x00007fe1425d846f in start_thread () at /usr/lib/libpthread.so.0
#4  0x00007fe1426f03d3 in clone () at /usr/lib/libc.so.6

Thread 8 (Thread 0x7fe1253d2700 (LWP 22261)):
#0  0x00007fe1425decf5 in pthread_cond_wait@@GLIBC_2.3.2 () at /usr/lib/libpthread.so.0
#1  0x00007fe1315f91cc in  () at /usr/lib/dri/radeonsi_dri.so
#2  0x00007fe1315f8dc8 in  () at /usr/lib/dri/radeonsi_dri.so
#3  0x00007fe1425d846f in start_thread () at /usr/lib/libpthread.so.0
#4  0x00007fe1426f03d3 in clone () at /usr/lib/libc.so.6

Thread 7 (Thread 0x7fe125bd3700 (LWP 22260)):
#0  0x00007fe1425decf5 in pthread_cond_wait@@GLIBC_2.3.2 () at /usr/lib/libpthread.so.0
#1  0x00007fe1315f91cc in  () at /usr/lib/dri/radeonsi_dri.so
#2  0x00007fe1315f8dc8 in  () at /usr/lib/dri/radeonsi_dri.so
#3  0x00007fe1425d846f in start_thread () at /usr/lib/libpthread.so.0
#4  0x00007fe1426f03d3 in clone () at /usr/lib/libc.so.6

Thread 6 (Thread 0x7fe1263d4700 (LWP 22259)):
#0  0x00007fe1425decf5 in pthread_cond_wait@@GLIBC_2.3.2 () at /usr/lib/libpthread.so.0
#1  0x00007fe1315f91cc in  () at /usr/lib/dri/radeonsi_dri.so
#2  0x00007fe1315f8dc8 in  () at /usr/lib/dri/radeonsi_dri.so
#3  0x00007fe1425d846f in start_thread () at /usr/lib/libpthread.so.0
#4  0x00007fe1426f03d3 in clone () at /usr/lib/libc.so.6

Thread 5 (Thread 0x7fe126bd5700 (LWP 22258)):
#0  0x00007fe1425decf5 in pthread_cond_wait@@GLIBC_2.3.2 () at /usr/lib/libpthread.so.0
#1  0x00007fe1315f91cc in  () at /usr/lib/dri/radeonsi_dri.so
#2  0x00007fe1315f8dc8 in  () at /usr/lib/dri/radeonsi_dri.so
#3  0x00007fe1425d846f in start_thread () at /usr/lib/libpthread.so.0
#4  0x00007fe1426f03d3 in clone () at /usr/lib/libc.so.6

Thread 4 (Thread 0x7fe130f3e700 (LWP 22257)):
#0  0x00007fe1425decf5 in pthread_cond_wait@@GLIBC_2.3.2 () at /usr/lib/libpthread.so.0
#1  0x00007fe1315f91cc in  () at /usr/lib/dri/radeonsi_dri.so
#2  0x00007fe1315f8dc8 in  () at /usr/lib/dri/radeonsi_dri.so
#3  0x00007fe1425d846f in start_thread () at /usr/lib/libpthread.so.0
#4  0x00007fe1426f03d3 in clone () at /usr/lib/libc.so.6

Thread 3 (Thread 0x7fe133fff700 (LWP 22256)):
#0  0x00007fe1426e5abf in poll () at /usr/lib/libc.so.6
#1  0x00007fe1400ae4a0 in  () at /usr/lib/libglib-2.0.so.0
#2  0x00007fe1400ae571 in g_main_context_iteration () at /usr/lib/libglib-2.0.so.0
#3  0x00007fe142de58ac in QEventDispatcherGlib::processEvents(QFlags<QEventLoop::ProcessEventsFlag>) () at /usr/lib/libQt5Core.so.5
#4  0x00007fe142d8c05c in QEventLoop::exec(QFlags<QEventLoop::ProcessEventsFlag>) () at /usr/lib/libQt5Core.so.5
#5  0x00007fe142bb0c62 in QThread::exec() () at /usr/lib/libQt5Core.so.5
#6  0x00007fe140c41b28 in  () at /usr/lib/libQt5DBus.so.5
#7  0x00007fe142bb1dd6 in  () at /usr/lib/libQt5Core.so.5
#8  0x00007fe1425d846f in start_thread () at /usr/lib/libpthread.so.0
#9  0x00007fe1426f03d3 in clone () at /usr/lib/libc.so.6

Thread 2 (Thread 0x7fe13a1ac700 (LWP 22255)):
#0  0x00007fe1426e5abf in poll () at /usr/lib/libc.so.6
#1  0x00007fe13e2ae63b in  () at /usr/lib/libxcb.so.1
#2  0x00007fe13e2b037b in xcb_wait_for_event () at /usr/lib/libxcb.so.1
#3  0x00007fe13ab17e01 in  () at /usr/lib/libQt5XcbQpa.so.5
#4  0x00007fe142bb1dd6 in  () at /usr/lib/libQt5Core.so.5
#5  0x00007fe1425d846f in start_thread () at /usr/lib/libpthread.so.0
#6  0x00007fe1426f03d3 in clone () at /usr/lib/libc.so.6

Thread 1 (Thread 0x7fe13b857b00 (LWP 22253)):
[KCrash Handler]
#6  0x00007fe14262cce5 in raise () at /usr/lib/libc.so.6
#7  0x00007fe142616857 in abort () at /usr/lib/libc.so.6
#8  0x00007fe142616727 in _nl_load_domain.cold () at /usr/lib/libc.so.6
#9  0x00007fe142625426 in  () at /usr/lib/libc.so.6
#10 0x00007fe144027f78 in  () at /usr/lib/libAvogadroCore.so.1
#11 0x00007fe1448eb572 in  () at /usr/lib/libAvogadroQtPlugins.so.1
#12 0x00007fe1448e8824 in  () at /usr/lib/libAvogadroQtPlugins.so.1
#13 0x00007fe144a5afa8 in Avogadro::QtOpenGL::GLWidget::updateScene() () at /usr/lib/libAvogadroQtOpenGL.so.1
#14 0x00007fe142dc2d10 in  () at /usr/lib/libQt5Core.so.5
#15 0x00007fe1448e8611 in  () at /usr/lib/libAvogadroQtPlugins.so.1
#16 0x00007fe144a5bd53 in Avogadro::QtOpenGL::GLWidget::mouseReleaseEvent(QMouseEvent*) () at /usr/lib/libAvogadroQtOpenGL.so.1
#17 0x00007fe14396c2ee in QWidget::event(QEvent*) () at /usr/lib/libQt5Widgets.so.5
#18 0x00007fe143928352 in QApplicationPrivate::notify_helper(QObject*, QEvent*) () at /usr/lib/libQt5Widgets.so.5
#19 0x00007fe143931a78 in QApplication::notify(QObject*, QEvent*) () at /usr/lib/libQt5Widgets.so.5
#20 0x00007fe142d8d4f2 in QCoreApplication::notifyInternal2(QObject*, QEvent*) () at /usr/lib/libQt5Core.so.5
#21 0x00007fe143930aeb in QApplicationPrivate::sendMouseEvent(QWidget*, QMouseEvent*, QWidget*, QWidget*, QWidget**, QPointer<QWidget>&, bool, bool) () at /usr/lib/libQt5Widgets.so.5
#22 0x00007fe143987b21 in  () at /usr/lib/libQt5Widgets.so.5
#23 0x00007fe14398aaa4 in  () at /usr/lib/libQt5Widgets.so.5
#24 0x00007fe143928352 in QApplicationPrivate::notify_helper(QObject*, QEvent*) () at /usr/lib/libQt5Widgets.so.5
#25 0x00007fe143931829 in QApplication::notify(QObject*, QEvent*) () at /usr/lib/libQt5Widgets.so.5
#26 0x00007fe142d8d4f2 in QCoreApplication::notifyInternal2(QObject*, QEvent*) () at /usr/lib/libQt5Core.so.5
#27 0x00007fe1431552a4 in QGuiApplicationPrivate::processMouseEvent(QWindowSystemInterfacePrivate::MouseEvent*) () at /usr/lib/libQt5Gui.so.5
#28 0x00007fe1431569b6 in QGuiApplicationPrivate::processWindowSystemEvent(QWindowSystemInterfacePrivate::WindowSystemEvent*) () at /usr/lib/libQt5Gui.so.5
#29 0x00007fe14312ec5c in QWindowSystemInterface::sendWindowSystemEvents(QFlags<QEventLoop::ProcessEventsFlag>) () at /usr/lib/libQt5Gui.so.5
#30 0x00007fe13ab18e2c in  () at /usr/lib/libQt5XcbQpa.so.5
#31 0x00007fe1400ac6be in g_main_context_dispatch () at /usr/lib/libglib-2.0.so.0
#32 0x00007fe1400ae531 in  () at /usr/lib/libglib-2.0.so.0
#33 0x00007fe1400ae571 in g_main_context_iteration () at /usr/lib/libglib-2.0.so.0
#34 0x00007fe142de5890 in QEventDispatcherGlib::processEvents(QFlags<QEventLoop::ProcessEventsFlag>) () at /usr/lib/libQt5Core.so.5
#35 0x00007fe142d8c05c in QEventLoop::exec(QFlags<QEventLoop::ProcessEventsFlag>) () at /usr/lib/libQt5Core.so.5
#36 0x00007fe142d94066 in QCoreApplication::exec() () at /usr/lib/libQt5Core.so.5
#37 0x000055e1d7b74654 in  ()
#38 0x00007fe142618023 in __libc_start_main () at /usr/lib/libc.so.6
#39 0x000055e1d7b747de in  ()
[Inferior 1 (process 22253) detached]

Reported using DrKonqi
Comment 1 Christoph Feck 2020-05-14 13:14:15 UTC 
Crash is in libAvogadroCore. If this is reproducible, please install debug symbols and report this issue directly to avogadro developers via https://github.com/cryos/avogadro/issues
Comment 2 Christoph Feck 2020-05-14 13:15:38 UTC 
https://github.com/openchemistry/avogadrolibs