Newbie. I believe this to be a bug with Avogadro. When I try to download ‘chlrophyll’ the program exits immediately with no message. Other compounds such as ‘vitamin a’ and ‘vitamin c’ work fine.
Environment Information
Avogadro version: 1.99
Operating system and version:
Distributor ID:
Ubuntu
Description:
Ubuntu 24.04.1 LTS
Release:
24.04
Codename:
noble
Expected Behavior
Success
Actual Behavior
Crash after seeing “Querying for chlorophyll”
Steps to Reproduce
File → Import → Download by Name
“chlorophyll”
Please upload files if appropriate here (or via file-sharing service like Dropbox or Pastebin)
I can confirm this, I get the exact same error with Flatpak as well.
Opening that SDF file causes the same error for me.
The AppImage also fails to load it when done via File > Import > Download by Name, but gives an SSL error:
qt.network.ssl: QSslSocket: cannot call unresolved function SSL_get_peer_certificate
Though I don’t think that’s relevant here.
Loading the SDF file with the AppImage works, but an error relating to Open Babel occurs and is reported, even though the molecule shows up in the view:
OBEnergy: method: UFF
==============================
*** Open Babel Error in ParseParamFile
Cannot open UFF.prm
==============================
*** Open Babel Error in SetTypes
Cannot open UFF.prm
Meanwhile the versions I have compiled from source (both Qt5 and Qt6) both successfully load chlorophyll, both from file and via File > Import > Download by Name, but in all cases report the following error:
Okay, then there’s some error in the Avogadro SDF parsing code. Good to know, since that’ll be easier to track.
That’s not relevant, because Avogadro is using it’s own SDF parser. But it’s good to know that there’s an issue with getting the Open Babel plugins loading.
Famous last words. Loading either from the network or from the SDF file itself works fine on my Ubuntu VM.
@matterhorn103 - would you be willing to run gdb avogadro2 to get a backtrace on the crash?
There are a bunch of possible [] calls and I don’t see anything obvious in the code. I can potentially create a debug pull request with a bunch of debugging print statements to help narrow it down, but gdb avogadro2 and then run and bt to get a backtrace is usually a big help because it shows the call trace and usually line numbers.
No, it’s threaded code. That’s just Avogadro generally saying “I was setting everything up and I can’t load Open Babel” … not that it was using Open Babel to read the file.
Well clearly I’m missing something … why would it print that message once for every time the file is loaded then? The error message only prints literally the moment that “Open” is clicked, not before (and plenty of other error messages are printed during the file browser usage on Qt5).
The response to bt is No stack. I’m afraid. Even after installing the vast majority of the debug packages from the openSUSE repos. Do I need to compile in debug mode? I thought that was the default, though.
What I get is:
❯❯❯ gdb ./qt5/prefix/bin/avogadro2
GNU gdb (GDB; openSUSE Tumbleweed) 14.2
Copyright (C) 2023 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.
Type "show copying" and "show warranty" for details.
This GDB was configured as "x86_64-suse-linux".
Type "show configuration" for configuration details.
For bug reporting instructions, please see:
<http://bugs.opensuse.org/>.
Find the GDB manual and other documentation resources online at:
<http://www.gnu.org/software/gdb/documentation/>.
For help, type "help".
Type "apropos word" to search for commands related to "word"...
Reading symbols from ./qt5/prefix/bin/avogadro2...
(gdb) run
Starting program: /home/matt/avo/qt5/prefix/bin/avogadro2
This GDB supports auto-downloading debuginfo from the following URLs:
<https://debuginfod.opensuse.org/>
Enable debuginfod for this session? (y or [n]) y
Debuginfod has been enabled.
To make this setting permanent, add 'set debuginfod enabled on' to .gdbinit.
Downloading separate debug info for /lib64/ld-linux-x86-64.so.2
Downloading separate debug info for system-supplied DSO at 0x7ffff7fc3000
Missing separate debuginfos, use: zypper install glibc-debuginfo-2.40-2.1.x86_64
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Using locale: "en_GB"
AvogadroApp Translation "en_GB" loaded "/home/matt/avo/qt5/prefix/bin/../share/avogadro2/i18n/"
AvogadroLibs Translation "en_GB" loaded "/home/matt/avo/qt5/prefix/bin/../share/avogadro2/i18n/"
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Extension plugins dynamically found… 42
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OBProcess::executeObabel: Running "/home/matt/avo/qt5/prefix/bin/obabel" "-L formats read"
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OBProcess::executeObabel: Running "/home/matt/avo/qt5/prefix/bin/obabel" "-L formats write"
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OBProcess::executeObabel: Running "/home/matt/avo/qt5/prefix/bin/obabel" "-L forcefields"
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OBProcess::executeObabel: Running "/home/matt/avo/qt5/prefix/bin/obabel" "-V"
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"/home/matt/avo/qt5/prefix/bin/obabel" found: "/home/matt/avo/qt5/prefix/bin/obabel: Open Babel 3.1.1 -- Oct 21 2024 -- 23:31:07"
"Checking for energy scripts in path /home/matt/.local/share/OpenChemistry/Avogadro/energy"
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registering obmm plugins
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Open Babel formats ready: 145
Setting default format to cjson.
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Error, Open Babel plugins directory not found.
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qt.qpa.wayland: Wayland does not support QWindow::requestActivate()
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[New process 7380]
[Inferior 1 (process 7380) exited normally]
Missing separate debuginfos, use: zypper install libKF5DBusAddons5-debuginfo-5.116.0-1.1.x86_64 libKF5GuiAddons5-debuginfo-5.116.0-1.2.x86_64 libQt5PrintSupport5-debuginfo-5.15.15+kde127-1.3.x86_64 libXfixes3-debuginfo-6.0.1-1.3.x86_64 libcanberra0-debuginfo-0.30-18.1.x86_64 libcurl4-debuginfo-8.10.1-1.1.x86_64 libdbusmenu-qt5-2-debuginfo-0.9.3+16.04.20160218-2.2.x86_64 libgbm1-debuginfo-24.1.7-391.1.x86_64 liblcms2-2-debuginfo-2.16-1.3.x86_64 libmng2-x86-64-v3-debuginfo-2.0.3-3.8.x86_64 libpciaccess0-debuginfo-0.18.1-1.2.x86_64 libplist-2_0-4-debuginfo-2.3.0-1.6.x86_64 libpsl5-debuginfo-0.21.5-1.2.x86_64 libpxbackend-1_0-debuginfo-0.5.9-1.1.x86_64 libqt5-qtimageformats-debuginfo-5.15.15+kde4-1.1.x86_64 libudev1-debuginfo-256.7-1.1.x86_64 libunistring5-debuginfo-1.3-1.1.x86_64 libvorbis0-x86-64-v3-debuginfo-1.3.7-5.1.x86_64 libvorbisfile3-x86-64-v3-debuginfo-1.3.7-5.1.x86_64 libwayland-server0-debuginfo-1.23.1-1.1.x86_64 libwebpmux3-debuginfo-1.4.0-1.1.x86_64 libxcb-dri2-0-debuginfo-1.17.0-1.1.x86_64 libxcb-keysyms1-debuginfo-0.4.1-1.4.x86_64 libxcb-randr0-debuginfo-1.17.0-1.1.x86_64 libxcb-sync1-debuginfo-1.17.0-1.1.x86_64 libxcb1-debuginfo-1.17.0-1.1.x86_64 libxshmfence1-debuginfo-1.3.2-1.4.x86_64 nss-mdns-debuginfo-0.15.1-1.5.x86_64 plasma6-integration-plugin-debuginfo-6.2.1-1.2.x86_64 systemd-debuginfo-256.7-1.1.x86_64
(gdb) bt
No stack.
This was produced by opening the program, loading once by name, closing the molecule, loading from file, closing the molecule again. It’s these snippets:
[New Thread 0x7fff910006c0 (LWP 7984)]
[Thread 0x7fff910006c0 (LWP 7984) exited]
Error, Open Babel plugins directory not found.
[Detaching after fork from child process 7985]
The default should be RelWithDebInfo which does some optimization but leaves in the debug symbols.
So it crashes in the debugger, but there’s no back trace?
I suspect that’s from checking file formats, but I’m not sure. OTOH if “load by name” works for most molecules, but not chlorophyll, it’s specific to that file parsing – which shouldn’t happen with Open Babel.
I’ll go make a branch with a bunch of debugging statements.
It doesn’t crash, the error is non-terminal, and the structure loads regardless. It’s only the AppImage that actually crashes. If you can whip up an AppImage that has debugging symbols, I can try running that in gdb?
This is a good point, I checked now and the same error appears with other molecules that do load successfully in the AppImage (from file at least, I can’t check the web lookup due to the SSL not working.)
So yeah, it’s not the Open Babel error that’s causing it to crash.
You said you were using Flatpak, so if you switch to getting your Flatpak from the beta branch you can get the fixes that way, see the instructions here. You’ll want to uninstall the stable Flatpak so they don’t conflict in your app drawer.
Dunno. I’ll look into it.