Regarding input generators for a Linux (Linux Mint 20.1 Xfce) version of Avogadro2, I have managed to get this working using the Flatpak version and copying the input generator python scripts from another version of Avogadro to /home/user/openchemistry/avogadrogenerators. This enables me to generate QM input files and save them to disk.

Now that this is working, it would be good to be able to submit QM jobs directly from Avogadro, but when this is attempted, I get an error, "Cannot connect to MoleQueue".

Are there any updates regarding when this feature will be available in Avogadro and/or how it could be implemented by the end-user?

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    $\begingroup$ If Avogadro need a queue software tho run jobs, you will need to install one to manage them. $\endgroup$
    – Camps
    Apr 24, 2021 at 2:07
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    $\begingroup$ I'd suggest asking the creator of the Flatpak on the Avogadro discussion forum - he seems quite active. My guess is that you're not running MoleQueue, which is used to actually run programs or submit to clusters. $\endgroup$ Apr 24, 2021 at 4:24

1 Answer 1


I am the person who package Avogadro2 as Flatpak. Stumble upon this thread randomly. I was not aware about this issue when I just randomly clicking on things. Not Avogadro power user, just software packager.

Anyway, we are looking into that, but will probably take some time, since there is no detail error for us to work with at the moment.

I suspect that Flatpak sandboxing might prevent some communication between them, but even permitting many permissions, I still could not get it to work.

For now, suggest you compile from source. The Flatpak manifest (contain instructions for Flatpak builder to build Avogadro2 from source) should give you all info on what and how to install stuff. Here you can find it on GitHub.

You might also find interesting this thread on the Avogadro forum.

Sorry for the inconvenience.

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    $\begingroup$ Thanks for the advice. I have managed to compile Avogadro2 from source, and I now get a response from submitting a job by first starting MoleQueue. However, I was unable to compile Avogadro2 by including VTK and so I had to omit this feature. Now I need to familiarize myself with Avogadro2 and MoleQueue to be able to submit jobs directly to quantum chemistry programs. $\endgroup$ Apr 27, 2021 at 21:13

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