Flatpak: Do Molequeue need network access?

I tried the latest avogadro flatpak on vm, it worked, it should work now.

I tried the latest flatpak installation for Avogadro2. Unfortunately, once again, the “submit calculation” feature did not work, even though I had first started MoleQueue.

Here is my terminal output:

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(base) rjrich@rjr-av2:~$ flatpak run org.openchemistry.Avogadro2
Gtk-Message: 18:58:52.411: Failed to load module “xapp-gtk3-module”
Qt: Session management error: Authentication Rejected, reason : None of the authentication protocols specified are supported and host-based authentication failed
Locale: “en_US”
translation success
“/usr/translations”
translation success
Extension plugins dynamically found… 31
Checking for “commands” scripts in “/home/rjrich/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro/commands”
Checking for “commands” scripts in “/app/share/OpenChemistry/Avogadro/commands”
Checking for “commands” scripts in “/usr/share/OpenChemistry/Avogadro/commands”
Checking for “commands” scripts in “/usr/share/runtime/share/OpenChemistry/Avogadro/commands”
Checking for “commands” scripts in “/run/host/share/OpenChemistry/Avogadro/commands”
Checking for “commands” scripts in “/app/bin/…/lib/avogadro2/scripts/commands”
OBProcess::executeObabel: Running “/app/bin/obabel” “-L formats read”
OBProcess::executeObabel: Running “/app/bin/obabel” “-L formats write”
OBProcess::executeObabel: Running “/app/bin/obabel” “-L forcefields”
OBProcess::executeObabel: Running “/app/bin/obabel” “-V”
“/app/bin/obabel” found: “/app/bin/obabel: Open Babel 3.1.0 – Apr 30 2021 – 16:05:29”
Checking for “inputGenerators” scripts in “/home/rjrich/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro/inputGenerators”
Checking for “inputGenerators” scripts in “/app/share/OpenChemistry/Avogadro/inputGenerators”
Checking for “inputGenerators” scripts in “/usr/share/OpenChemistry/Avogadro/inputGenerators”
Checking for “inputGenerators” scripts in “/usr/share/runtime/share/OpenChemistry/Avogadro/inputGenerators”
Checking for “inputGenerators” scripts in “/run/host/share/OpenChemistry/Avogadro/inputGenerators”
Checking for “inputGenerators” scripts in “/app/bin/…/lib/avogadro2/scripts/inputGenerators”
ScriptLoader::queryProgramName: Unable to retrieve program name for “/home/rjrich/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro/inputGenerators/generators.cmake” ; “Error running script ‘/home/rjrich/anaconda3/bin/python /home/rjrich/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro/inputGenerators/generators.cmake --display-name --lang en_US’: Abnormal exit status 1 (Unknown error.: Unknown error)\n\nOutput:\n File “/home/rjrich/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro/inputGenerators/generators.cmake”, line 3\n dalton.py\n ^\nSyntaxError: invalid syntax\n”
ScriptLoader::queryProgramName: Unable to retrieve program name for “/home/rjrich/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro/inputGenerators/LICENSE” ; “Error running script ‘/home/rjrich/anaconda3/bin/python /home/rjrich/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro/inputGenerators/LICENSE --display-name --lang en_US’: Abnormal exit status 1 (Unknown error.: Unknown error)\n\nOutput:\n File “/home/rjrich/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro/inputGenerators/LICENSE”, line 1\n Copyright (c) 2011-2018, Kitware, Inc.\n ^\nSyntaxError: invalid syntax\n”
ScriptLoader::queryProgramName: Unable to retrieve program name for “/home/rjrich/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro/inputGenerators/README.md” ; “Error running script ‘/home/rjrich/anaconda3/bin/python /home/rjrich/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro/inputGenerators/README.md --display-name --lang en_US’: Abnormal exit status 1 (Unknown error.: Unknown error)\n\nOutput:\n File “/home/rjrich/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro/inputGenerators/README.md”, line 1\n Avogadro 2 Python Input Generators\n ^\nSyntaxError: invalid syntax\n”
Checking for “formatScripts” scripts in “/home/rjrich/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro/formatScripts”
Checking for “formatScripts” scripts in “/app/share/OpenChemistry/Avogadro/formatScripts”
Checking for “formatScripts” scripts in “/usr/share/OpenChemistry/Avogadro/formatScripts”
Checking for “formatScripts” scripts in “/usr/share/runtime/share/OpenChemistry/Avogadro/formatScripts”
Checking for “formatScripts” scripts in “/run/host/share/OpenChemistry/Avogadro/formatScripts”
Checking for “formatScripts” scripts in “/app/bin/…/lib/avogadro2/scripts/formatScripts”
“Navigator” added
“Editor” added
“Selection” added
“Manipulator” added
“BondCentric” added
“MeasureTool” added
“PlayerTool” added
OBProcess::executeObabel: Running “/app/bin/obabel” “-icml -ocml --minimize --noh --log --ff GAFF”

(base) rjrich@rjr-av2:~ (base) rjrich@rjr-av2:~ flatpak run org.openchemistry.Avogadro2
Gtk-Message: 19:01:15.330: Failed to load module “xapp-gtk3-module”
Qt: Session management error: Authentication Rejected, reason : None of the authentication protocols specified are supported and host-based authentication failed
Locale: “en_US”
translation success
“/usr/translations”
translation success
Extension plugins dynamically found… 31
Checking for “commands” scripts in “/home/rjrich/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro/commands”
Checking for “commands” scripts in “/app/share/OpenChemistry/Avogadro/commands”
Checking for “commands” scripts in “/usr/share/OpenChemistry/Avogadro/commands”
Checking for “commands” scripts in “/usr/share/runtime/share/OpenChemistry/Avogadro/commands”
Checking for “commands” scripts in “/run/host/share/OpenChemistry/Avogadro/commands”
Checking for “commands” scripts in “/app/bin/…/lib/avogadro2/scripts/commands”
OBProcess::executeObabel: Running “/app/bin/obabel” “-L formats read”
OBProcess::executeObabel: Running “/app/bin/obabel” “-L formats write”
OBProcess::executeObabel: Running “/app/bin/obabel” “-L forcefields”
OBProcess::executeObabel: Running “/app/bin/obabel” “-V”
“/app/bin/obabel” found: “/app/bin/obabel: Open Babel 3.1.0 – Apr 30 2021 – 16:05:29”
Checking for “inputGenerators” scripts in “/home/rjrich/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro/inputGenerators”
Checking for “inputGenerators” scripts in “/app/share/OpenChemistry/Avogadro/inputGenerators”
Checking for “inputGenerators” scripts in “/usr/share/OpenChemistry/Avogadro/inputGenerators”
Checking for “inputGenerators” scripts in “/usr/share/runtime/share/OpenChemistry/Avogadro/inputGenerators”
Checking for “inputGenerators” scripts in “/run/host/share/OpenChemistry/Avogadro/inputGenerators”
Checking for “inputGenerators” scripts in “/app/bin/…/lib/avogadro2/scripts/inputGenerators”
ScriptLoader::queryProgramName: Unable to retrieve program name for “/home/rjrich/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro/inputGenerators/generators.cmake” ; “Error running script ‘/home/rjrich/anaconda3/bin/python /home/rjrich/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro/inputGenerators/generators.cmake --display-name --lang en_US’: Abnormal exit status 1 (Unknown error.: Unknown error)\n\nOutput:\n File “/home/rjrich/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro/inputGenerators/generators.cmake”, line 3\n dalton.py\n ^\nSyntaxError: invalid syntax\n”
ScriptLoader::queryProgramName: Unable to retrieve program name for “/home/rjrich/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro/inputGenerators/LICENSE” ; “Error running script ‘/home/rjrich/anaconda3/bin/python /home/rjrich/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro/inputGenerators/LICENSE --display-name --lang en_US’: Abnormal exit status 1 (Unknown error.: Unknown error)\n\nOutput:\n File “/home/rjrich/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro/inputGenerators/LICENSE”, line 1\n Copyright (c) 2011-2018, Kitware, Inc.\n ^\nSyntaxError: invalid syntax\n”
ScriptLoader::queryProgramName: Unable to retrieve program name for “/home/rjrich/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro/inputGenerators/README.md” ; “Error running script ‘/home/rjrich/anaconda3/bin/python /home/rjrich/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro/inputGenerators/README.md --display-name --lang en_US’: Abnormal exit status 1 (Unknown error.: Unknown error)\n\nOutput:\n File “/home/rjrich/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro/inputGenerators/README.md”, line 1\n Avogadro 2 Python Input Generators\n ^\nSyntaxError: invalid syntax\n”
Checking for “formatScripts” scripts in “/home/rjrich/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro/formatScripts”
Checking for “formatScripts” scripts in “/app/share/OpenChemistry/Avogadro/formatScripts”
Checking for “formatScripts” scripts in “/usr/share/OpenChemistry/Avogadro/formatScripts”
Checking for “formatScripts” scripts in “/usr/share/runtime/share/OpenChemistry/Avogadro/formatScripts”
Checking for “formatScripts” scripts in “/run/host/share/OpenChemistry/Avogadro/formatScripts”
Checking for “formatScripts” scripts in “/app/bin/…/lib/avogadro2/scripts/formatScripts”
“Navigator” added
“Editor” added
“Selection” added
“Manipulator” added
“BondCentric” added
“MeasureTool” added
“PlayerTool” added

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I also noticed that geometry optimization with OpenBabel did not work:

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OBProcess::executeObabel: Running “/app/bin/obabel” “-icml -ocml --minimize --noh --log --crit 1e-06 --ff UFF --steps 2500 --rvdw 10 --rele 10 --freq 10”
MDL: “”
Process encountered an error, and did not execute correctly.
Exit code: 6
Exit status: QProcess::CrashExit
Exit output: “”
MDL: “”
“Error: value must be object for key ‘Title’.”

=====

That is really strange, I try Avogadro Flatpak on Ubuntu 21.04 VM, I use openbabel optimize geometry and molequeue just fine.

What is your Flatpak version? Run this command.

flatpak --version

If you have old version which Ubuntu ship, which Mint also inherit, you would need to try update it first.
https://flatpak.org/setup/Ubuntu/

Did you install Avogadro as user or system? Run this to see list of applications and see “Installation” column. Or perhaps you have multiple Avogadro2 installation, try remove them and install it again as user.

flatpak list

What sandbox permission on your Avogadro installation have?

flatpak info --show-permissions org.openchemistry.Avogadro2

Mine look like this.

[Context]
shared=network;ipc;
sockets=x11;wayland;fallback-x11;
devices=dri;
filesystems=!home;xdg-config/kdeglobals:ro;

[Session Bus Policy]
com.canonical.AppMenu.Registrar=talk
org.kde.StatusNotifierWatcher=talk
org.freedesktop.Notifications=talk
org.freedesktop.DBus=talk

[System Bus Policy]
org.freedesktop.DBus.Proprieties=talk
org.freedesktop.DBus=talk

Thanks for the tips. Indeed, my flatpak is an older version and probably ought to be updated. Nevertheless, given that I have working versions of Avogadro2 and Molequeue generated by compiling from source code, I think I will continue to use these and put the flatpak version aside for the time being.

Now I need to consult the documentation for Molequeue to enable me to set up properly the links to quantum chemistry applications.

Best wishes for the continued successful refinement of your flatpak packages!

Alright, thank for the test anyway.