Avogadro Suddenly Stopped Working

General Discussion Support
1

Environment Information

Avogadro version: 1.2.0-1+deb9u1
Operating system and version: Debian Stretch (x86_64)

Expected Behavior Open normally.

Actual Behavior Failed to open:

Script started on Wed 01 Aug 2018 08:45:31 AM EDT
root@AbNormal:/home/comp# avogadro
Qt: Session management error: Authentication Rejected, reason : None of the authentication protocols specified are supported and host-based authentication failed
"Avogadro version: 1.2.0 Git:
LibAvogadro version: 1.2.0 Git: "
Locale: “en_US”
Libavogadro translations not found.
System has OpenGL support.
About to test OpenGL capabilities.
OpenGL capabilities found:
Double Buffering.
Direct Rendering.
Antialiasing.
Loading plugins: “/usr/bin/…/lib/avogadro/1_2”
Searching for plugins in “/usr/lib/avogadro/1_2”
Searching for plugins in “/usr/lib/avogadro/1_2/colors”
Searching for plugins in “/usr/lib/avogadro/1_2/engines”
Searching for plugins in “/usr/lib/avogadro/1_2/extensions”
Searching for plugins in “/usr/lib/avogadro/1_2/tools”
Loading plugins: “/root/.avogadro/1_2/plugins”
*** stack smashing detected ***: avogadro terminated
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x70bfb)[0x2b2ae2b13bfb]
/lib/x86_64-linux-gnu/libc.so.6(__fortify_fail+0x37)[0x2b2ae2b9c1f7]
/lib/x86_64-linux-gnu/libc.so.6(__fortify_fail+0x0)[0x2b2ae2b9c1c0]
/usr/lib/avogadro/1_2/extensions/forcefieldextension.so(+0xd036)[0x2b2af4e40036]
======= Memory map: ========
2b2ae2875000-2b2ae287b000 rw-p 00000000 00:00 0
2b2ae287b000-2b2ae289e000 r-xp 00000000 08:01 7078548 /lib/x86_64-linux-gnu/ld-2.24.so
2b2ae289e000-2b2ae28a2000 rw-p 00000000 00:00 0
2b2ae28a3000-2b2ae28aa000 r–s 00000000 08:01 27820611 /usr/lib/x86_64-linux-gnu/gconv/gconv-modules.cache
2b2ae28ab000-2b2ae28c9000 r–s 00000000 08:01 23082396 /var/cache/fontconfig/467c019e582ee353435ea5c21d137ef6-le64.cache-4
2b2ae28cb000-2b2ae28cc000 r–s 00000000 08:01 23084746 /var/cache/fontconfig/e0aa53bcfa504e64f87823c16bc01eb6-le64.cache-4
2b2ae28d3000-2b2ae28d6000 r–s 00000000 08:01 23084739 /var/cache/fontconfig/16326683038b281783a0ef8c680e3a10-le64.cache-4
2b2ae28db000-2b2ae28dc000 r–s 00000000 08:01 23071735 /var/cache/fontconfig

–>more of the same
<…cut…>

Aborted
root@AbNormal:/home/comp# De[Kexit

Script done on Wed 01 Aug 2018 08:45:49 AM EDT

Reinstallation after purge of avogadro gave the same result.
Please upload files if appropriate here (or via file-sharing service like Dropbox or Pastebin)

2

root@AbNormal:/home/comp# avogadro
Qt: Session management error: Authentication Rejected, reason : None of the authentication protocols specified are supported and host-based authentication failed

I don’t know what changed, but that’s what I’d look into… Has anything changed in your Qt or X11 configuration?

There’s no authentication at all in Avogadro. Now it’s possible from your backtrace that it has something to do with force fields, but I’d start first with whether you can start a Qt session.

3

Thank you for the quick reply. Unfortunately, although I’ve been using computers for quite a while (my first exposure to programming was with FORTRAN in the early 1960’s and I have used Linux since the early days of Slackware) I am definitely not a OS or lib type of person. I’m an Organic Chemist.

As far as I know, nothing has changed inthe Qt or X11 configuration. How do I go about doing what you suggest?

I have attached the complete run.log to this email (it was too long for the discussion group web site).  I thought it might tell you something, it certainly doesn't tell me anything.  I have also attached the /etc/Xsession file.

Thanks in advance for any further help you may be able to give me.
4

I’d recommend asking on a Debian or Ubuntu support forum, e.g.

Attachments are removed by the forum, so I don’t have your “complete run.log” - perhaps you could put it on https://pastebin.com instead?

5

I uploaded the run log to Pastebin(u/n: stephenmolnar).