Pixi timeout at launch

matterhorn103 · November 5, 2025, 3:52pm

Hi, can we maybe try the Pixi setup steps during launch fewer times? Currently, it’s not working for me, which isn’t necessarily the end of the world, but each failed attempt takes a good 5 seconds and Avogadro seems to attempt it 12 times, meaning launch takes a whole minute

The error I’m getting is the following, by the way:

"/app/bin/obabel"  found:  "/app/bin/obabel: Open Babel 3.1.1 -- Nov 11 2011 -- 11:11:11"
Using manifest in "/home/matt/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro"
QProcess: Destroyed while process ("/app/bin/pixi") is still running.
Using manifest in "/home/matt/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro"
QProcess: Destroyed while process ("/app/bin/pixi") is still running.
Using manifest in "/home/matt/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro"
QProcess: Destroyed while process ("/app/bin/pixi") is still running.
Using manifest in "/home/matt/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro"
QProcess: Destroyed while process ("/app/bin/pixi") is still running.
Using manifest in "/home/matt/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro"
QProcess: Destroyed while process ("/app/bin/pixi") is still running.
Using manifest in "/home/matt/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro"
QProcess: Destroyed while process ("/app/bin/pixi") is still running.
Using manifest in "/home/matt/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro"
QProcess: Destroyed while process ("/app/bin/pixi") is still running.
Using manifest in "/home/matt/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro"
QProcess: Destroyed while process ("/app/bin/pixi") is still running.
Using manifest in "/home/matt/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro"
QProcess: Destroyed while process ("/app/bin/pixi") is still running.
Using manifest in "/home/matt/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro"
QProcess: Destroyed while process ("/app/bin/pixi") is still running.
Using manifest in "/home/matt/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro"
QProcess: Destroyed while process ("/app/bin/pixi") is still running.
Using manifest in "/home/matt/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro"
QProcess: Destroyed while process ("/app/bin/pixi") is still running.
qt.network.http2: stream 1 error: "Connection closed"
qt.network.http2: stream 1 finished with error: "HTTP/2 protocol error"

The AppImage does something similar, but it prints:

QProcess: Destroyed while process ("/home/matt/.local/bin/pixi") is still running.
QProcess: Destroyed while process ("/home/matt/.local/bin/pixi") is still running.
QProcess: Destroyed while process ("/home/matt/.local/bin/pixi") is still running.
QProcess: Destroyed while process ("/home/matt/.local/bin/pixi") is still running.
QProcess: Destroyed while process ("/home/matt/.local/bin/pixi") is still running.
QProcess: Destroyed while process ("/home/matt/.local/bin/pixi") is still running.
QProcess: Destroyed while process ("/home/matt/.local/bin/pixi") is still running.
QProcess: Destroyed while process ("/home/matt/.local/bin/pixi") is still running.
QProcess: Destroyed while process ("/home/matt/.local/bin/pixi") is still running.
QProcess: Destroyed while process ("/home/matt/.local/bin/pixi") is still running.
QProcess: Destroyed while process ("/home/matt/.local/bin/pixi") is still running.
QProcess: Destroyed while process ("/home/matt/.local/bin/pixi") is still running.
QProcess: Destroyed while process ("/home/matt/.local/bin/pixi") is still running.
QProcess: Destroyed while process ("/home/matt/.local/bin/pixi") is still running.
QProcess: Destroyed while process ("/home/matt/.local/bin/pixi") is still running.
QProcess: Destroyed while process ("/home/matt/.local/bin/pixi") is still running.
QProcess: Destroyed while process ("/home/matt/.local/bin/pixi") is still running.
QProcess: Destroyed while process ("/home/matt/.local/bin/pixi") is still running.
QProcess: Destroyed while process ("/home/matt/.local/bin/pixi") is still running.
QProcess: Destroyed while process ("/home/matt/.local/bin/pixi") is still running.
QProcess: Destroyed while process ("/home/matt/.local/bin/pixi") is still running.
QProcess: Destroyed while process ("/home/matt/.local/bin/pixi") is still running.
QProcess: Destroyed while process ("/home/matt/.local/bin/pixi") is still running.
QProcess: Destroyed while process ("/home/matt/.local/bin/pixi") is still running.
QProcess: Destroyed while process ("/home/matt/.local/bin/pixi") is still running.
QProcess: Destroyed while process ("/home/matt/.local/bin/pixi") is still running.
QProcess: Destroyed while process ("/home/matt/.local/bin/pixi") is still running.
QProcess: Destroyed while process ("/home/matt/.local/bin/pixi") is still running.
QProcess: Destroyed while process ("/home/matt/.local/bin/pixi") is still running.
QProcess: Destroyed while process ("/home/matt/.local/bin/pixi") is still running.
QProcess: Destroyed while process ("/home/matt/.local/bin/pixi") is still running.
QProcess: Destroyed while process ("/home/matt/.local/bin/pixi") is still running.
QProcess: Destroyed while process ("/home/matt/.local/bin/pixi") is still running.
QProcess: Destroyed while process ("/home/matt/.local/bin/pixi") is still running.
Using manifest in "/home/matt/.local/share/OpenChemistry/Avogadro"
QProcess: Destroyed while process ("/home/matt/.local/bin/pixi") is still running.
Using manifest in "/home/matt/.local/share/OpenChemistry/Avogadro"
QProcess: Destroyed while process ("/home/matt/.local/bin/pixi") is still running.
Using manifest in "/home/matt/.local/share/OpenChemistry/Avogadro"
QProcess: Destroyed while process ("/home/matt/.local/bin/pixi") is still running.
Using manifest in "/home/matt/.local/share/OpenChemistry/Avogadro"
QProcess: Destroyed while process ("/home/matt/.local/bin/pixi") is still running.
Using manifest in "/home/matt/.local/share/OpenChemistry/Avogadro"
QProcess: Destroyed while process ("/home/matt/.local/bin/pixi") is still running.
Using manifest in "/home/matt/.local/share/OpenChemistry/Avogadro"
...

and actually takes even longer, so it’s not just the Flatpak, but given there hasn’t been a deluge of complaints on Linux I’m assuming it’s some problem with my system that I need to work out.

It’s more the excessive launch time that’s the imminent problem in my view though.

ghutchis · November 5, 2025, 4:01pm

I think the bigger question might be why is it failing?

matterhorn103 · November 5, 2025, 4:49pm

Sure, but there will always be some situations that lead to it failing, and I’m suggesting that when that situation arises taking a minute to launch should be avoided, because unless launched via the terminal it just looks like Avogadro is unresponsive.

As to the actual problem, I’ll do some investigation.

ghutchis · November 5, 2025, 5:27pm

Set AVO_PYTHON_SCRIPT_DEBUG=TRUE when running and all the m_debug statements will start showing up.

ghutchis · November 6, 2025, 8:48pm

Any progress on this?

I understand the complaint, but I’m less sure on how to address it systematically. I guess in principle, in the scriptloader.cpp code, which gets the list of scripts and queries them for names, it could check for multiple repeated timeouts and quit?

But that seems like it’s just masking the underlying cause.

matterhorn103 · November 7, 2025, 2:18am

No, not yet, I’ve been working nights. Next week I’ll have more chance.

I guess I was kind of assuming that the reason for the repeated errors was because somewhere in the code it’s hard-coded to keep trying a certain number of times if the first attempt fails?

ghutchis · November 7, 2025, 2:25am

No, there are no “retries.” It tries to run the script. If it fails, it goes to the next one.

If it’s taking around a minute, that’s because 5 second timeout multiplied by 11 input generator scripts = 55 seconds.

I guess what I could do in the scriptloader code is to check if multiple scripts with the same directory are returning errors, it can just give up on that directory. But again, that doesn’t solve the root cause.

matterhorn103 · November 7, 2025, 2:43am

Ah, I see. I think ideally, if the issue is that Pixi is failing, the Python scripts would just be disabled and none of the scripts would be run at all. But yeah, I’ll see if I can work out what’s going on.

matterhorn103 · November 11, 2025, 12:58pm

Running the Flatpak:

>>> flatpak run --env=AVO_PYTHON_SCRIPT_DEBUG=TRUE org.openchemistry.Avogadro2
Avogadroapp version:  1.102.1
Avogadrolibs version:  1.102.1
Qt version:  6.9.3
qt.core.qobject.connect: QObject::connect(QObject, Unknown): invalid nullptr parameter
SSL version:  "OpenSSL 3.3.5 30 Sep 2025"
Using locale:  "en_GB"
AvogadroApp Translation  "en_GB"  loaded  "/app/bin/../share/avogadro2/i18n/"
AvogadroLibs Translation  "en_GB"  loaded  "/app/bin/../share/avogadro2/i18n/"
 registering obmm plugins
"/app/bin/obabel"  found:  "/app/bin/obabel: Open Babel 3.1.1 -- Nov 11 2011 -- 11:11:11"
Using manifest in "/home/matt/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro"
Executing "/app/bin/pixi" "run --manifest-path /home/matt/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro python /app/lib64/avogadro2/scripts/inputGenerators/dalton.py --debug --display-name --lang en_GB" < ""
QProcess: Destroyed while process ("/app/bin/pixi") is still running.
"Cannot load script /app/lib64/avogadro2/scripts/inputGenerators/dalton.py"
Using manifest in "/home/matt/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro"
Executing "/app/bin/pixi" "run --manifest-path /home/matt/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro python /app/lib64/avogadro2/scripts/inputGenerators/gamessuk.py --debug --display-name --lang en_GB" < ""
QProcess: Destroyed while process ("/app/bin/pixi") is still running.
"Cannot load script /app/lib64/avogadro2/scripts/inputGenerators/gamessuk.py"
Using manifest in "/home/matt/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro"
Executing "/app/bin/pixi" "run --manifest-path /home/matt/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro python /app/lib64/avogadro2/scripts/inputGenerators/gaussian.py --debug --display-name --lang en_GB" < ""
QProcess: Destroyed while process ("/app/bin/pixi") is still running.
"Cannot load script /app/lib64/avogadro2/scripts/inputGenerators/gaussian.py"
Using manifest in "/home/matt/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro"
Executing "/app/bin/pixi" "run --manifest-path /home/matt/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro python /app/lib64/avogadro2/scripts/inputGenerators/molpro.py --debug --display-name --lang en_GB" < ""
QProcess: Destroyed while process ("/app/bin/pixi") is still running.
"Cannot load script /app/lib64/avogadro2/scripts/inputGenerators/molpro.py"
Using manifest in "/home/matt/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro"
Executing "/app/bin/pixi" "run --manifest-path /home/matt/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro python /app/lib64/avogadro2/scripts/inputGenerators/mopac.py --debug --display-name --lang en_GB" < ""
QProcess: Destroyed while process ("/app/bin/pixi") is still running.
"Cannot load script /app/lib64/avogadro2/scripts/inputGenerators/mopac.py"
Using manifest in "/home/matt/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro"
Executing "/app/bin/pixi" "run --manifest-path /home/matt/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro python /app/lib64/avogadro2/scripts/inputGenerators/nwchem.py --debug --display-name --lang en_GB" < ""
QProcess: Destroyed while process ("/app/bin/pixi") is still running.
"Cannot load script /app/lib64/avogadro2/scripts/inputGenerators/nwchem.py"
Using manifest in "/home/matt/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro"
Executing "/app/bin/pixi" "run --manifest-path /home/matt/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro python /app/lib64/avogadro2/scripts/inputGenerators/orca.py --debug --display-name --lang en_GB" < ""
QProcess: Destroyed while process ("/app/bin/pixi") is still running.
"Cannot load script /app/lib64/avogadro2/scripts/inputGenerators/orca.py"
Using manifest in "/home/matt/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro"
Executing "/app/bin/pixi" "run --manifest-path /home/matt/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro python /app/lib64/avogadro2/scripts/inputGenerators/psi4.py --debug --display-name --lang en_GB" < ""
QProcess: Destroyed while process ("/app/bin/pixi") is still running.
"Cannot load script /app/lib64/avogadro2/scripts/inputGenerators/psi4.py"
Using manifest in "/home/matt/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro"
Executing "/app/bin/pixi" "run --manifest-path /home/matt/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro python /app/lib64/avogadro2/scripts/inputGenerators/pyscf.py --debug --display-name --lang en_GB" < ""
QProcess: Destroyed while process ("/app/bin/pixi") is still running.
"Cannot load script /app/lib64/avogadro2/scripts/inputGenerators/pyscf.py"
Using manifest in "/home/matt/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro"
Executing "/app/bin/pixi" "run --manifest-path /home/matt/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro python /app/lib64/avogadro2/scripts/inputGenerators/qchem.py --debug --display-name --lang en_GB" < ""
QProcess: Destroyed while process ("/app/bin/pixi") is still running.
"Cannot load script /app/lib64/avogadro2/scripts/inputGenerators/qchem.py"
Using manifest in "/home/matt/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro"
Executing "/app/bin/pixi" "run --manifest-path /home/matt/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro python /app/lib64/avogadro2/scripts/inputGenerators/terachem.py --debug --display-name --lang en_GB" < ""
QProcess: Destroyed while process ("/app/bin/pixi") is still running.
"Cannot load script /app/lib64/avogadro2/scripts/inputGenerators/terachem.py"
Using manifest in "/home/matt/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro"
Executing "/app/bin/pixi" "run --manifest-path /home/matt/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro python /app/lib64/avogadro2/scripts/formatScripts/zyx.py --debug --display-name --lang en_GB" < ""
QProcess: Destroyed while process ("/app/bin/pixi") is still running.
"Cannot load script /app/lib64/avogadro2/scripts/formatScripts/zyx.py"
qt.network.http2: stream 1 error: "Connection closed"
qt.network.http2: stream 1 finished with error: "HTTP/2 protocol error"
Open Babel formats ready:  144
Setting default format to cjson.

Running the AppImage produces essentially the same:

>>> AVO_PYTHON_SCRIPT_DEBUG=TRUE ./Downloads/Avogadro2-x86_64.AppImage
Avogadroapp version:  1.102.1
Avogadrolibs version:  1.102.1
Qt version:  6.8.3
qt.core.qobject.connect: QObject::connect(QObject, Unknown): invalid nullptr parameter
SSL version:  "OpenSSL 3.0.2 15 Mar 2022"
qt.qpa.plugin: Could not find the Qt platform plugin "wayland" in ""
Using locale:  "en_GB"
AvogadroApp Translation  "en_GB"  loaded  "/tmp/.mount_AvogadLv6p7D/usr/bin/../share/avogadro2/i18n/"
AvogadroLibs Translation  "en_GB"  loaded  "/tmp/.mount_AvogadLv6p7D/usr/bin/../share/avogadro2/i18n/"
 registering GPL plugins
"/tmp/.mount_AvogadLv6p7D/usr/bin/obabel"  found:  "/tmp/.mount_AvogadLv6p7D/usr/bin/obabel: Open Babel 3.1.1 -- Oct 27 2025 -- 16:26:17"
Using manifest in "/home/matt/.local/share/OpenChemistry/Avogadro"
Executing "/home/matt/.local/bin/pixi" "run --manifest-path /home/matt/.local/share/OpenChemistry/Avogadro python /tmp/.mount_AvogadLv6p7D/usr/lib/avogadro2/scripts/inputGenerators/dalton.py --debug --display-name --lang en_GB" < ""
QProcess: Destroyed while process ("/home/matt/.local/bin/pixi") is still running.
"Cannot load script /tmp/.mount_AvogadLv6p7D/usr/lib/avogadro2/scripts/inputGenerators/dalton.py"
Using manifest in "/home/matt/.local/share/OpenChemistry/Avogadro"
Executing "/home/matt/.local/bin/pixi" "run --manifest-path /home/matt/.local/share/OpenChemistry/Avogadro python /tmp/.mount_AvogadLv6p7D/usr/lib/avogadro2/scripts/inputGenerators/gamessuk.py --debug --display-name --lang en_GB" < ""
QProcess: Destroyed while process ("/home/matt/.local/bin/pixi") is still running.
"Cannot load script /tmp/.mount_AvogadLv6p7D/usr/lib/avogadro2/scripts/inputGenerators/gamessuk.py"
Using manifest in "/home/matt/.local/share/OpenChemistry/Avogadro"
Executing "/home/matt/.local/bin/pixi" "run --manifest-path /home/matt/.local/share/OpenChemistry/Avogadro python /tmp/.mount_AvogadLv6p7D/usr/lib/avogadro2/scripts/inputGenerators/gaussian.py --debug --display-name --lang en_GB" < ""
QProcess: Destroyed while process ("/home/matt/.local/bin/pixi") is still running.
"Cannot load script /tmp/.mount_AvogadLv6p7D/usr/lib/avogadro2/scripts/inputGenerators/gaussian.py"
Using manifest in "/home/matt/.local/share/OpenChemistry/Avogadro"
Executing "/home/matt/.local/bin/pixi" "run --manifest-path /home/matt/.local/share/OpenChemistry/Avogadro python /tmp/.mount_AvogadLv6p7D/usr/lib/avogadro2/scripts/inputGenerators/molpro.py --debug --display-name --lang en_GB" < ""
QProcess: Destroyed while process ("/home/matt/.local/bin/pixi") is still running.
"Cannot load script /tmp/.mount_AvogadLv6p7D/usr/lib/avogadro2/scripts/inputGenerators/molpro.py"
Using manifest in "/home/matt/.local/share/OpenChemistry/Avogadro"
Executing "/home/matt/.local/bin/pixi" "run --manifest-path /home/matt/.local/share/OpenChemistry/Avogadro python /tmp/.mount_AvogadLv6p7D/usr/lib/avogadro2/scripts/inputGenerators/mopac.py --debug --display-name --lang en_GB" < ""
QProcess: Destroyed while process ("/home/matt/.local/bin/pixi") is still running.
"Cannot load script /tmp/.mount_AvogadLv6p7D/usr/lib/avogadro2/scripts/inputGenerators/mopac.py"
Using manifest in "/home/matt/.local/share/OpenChemistry/Avogadro"
Executing "/home/matt/.local/bin/pixi" "run --manifest-path /home/matt/.local/share/OpenChemistry/Avogadro python /tmp/.mount_AvogadLv6p7D/usr/lib/avogadro2/scripts/inputGenerators/nwchem.py --debug --display-name --lang en_GB" < ""
QProcess: Destroyed while process ("/home/matt/.local/bin/pixi") is still running.
"Cannot load script /tmp/.mount_AvogadLv6p7D/usr/lib/avogadro2/scripts/inputGenerators/nwchem.py"
Using manifest in "/home/matt/.local/share/OpenChemistry/Avogadro"
Executing "/home/matt/.local/bin/pixi" "run --manifest-path /home/matt/.local/share/OpenChemistry/Avogadro python /tmp/.mount_AvogadLv6p7D/usr/lib/avogadro2/scripts/inputGenerators/orca.py --debug --display-name --lang en_GB" < ""
QProcess: Destroyed while process ("/home/matt/.local/bin/pixi") is still running.
"Cannot load script /tmp/.mount_AvogadLv6p7D/usr/lib/avogadro2/scripts/inputGenerators/orca.py"
Using manifest in "/home/matt/.local/share/OpenChemistry/Avogadro"
Executing "/home/matt/.local/bin/pixi" "run --manifest-path /home/matt/.local/share/OpenChemistry/Avogadro python /tmp/.mount_AvogadLv6p7D/usr/lib/avogadro2/scripts/inputGenerators/psi4.py --debug --display-name --lang en_GB" < ""
QProcess: Destroyed while process ("/home/matt/.local/bin/pixi") is still running.
"Cannot load script /tmp/.mount_AvogadLv6p7D/usr/lib/avogadro2/scripts/inputGenerators/psi4.py"
Using manifest in "/home/matt/.local/share/OpenChemistry/Avogadro"
Executing "/home/matt/.local/bin/pixi" "run --manifest-path /home/matt/.local/share/OpenChemistry/Avogadro python /tmp/.mount_AvogadLv6p7D/usr/lib/avogadro2/scripts/inputGenerators/pyscf.py --debug --display-name --lang en_GB" < ""
QProcess: Destroyed while process ("/home/matt/.local/bin/pixi") is still running.
"Cannot load script /tmp/.mount_AvogadLv6p7D/usr/lib/avogadro2/scripts/inputGenerators/pyscf.py"
Using manifest in "/home/matt/.local/share/OpenChemistry/Avogadro"
Executing "/home/matt/.local/bin/pixi" "run --manifest-path /home/matt/.local/share/OpenChemistry/Avogadro python /tmp/.mount_AvogadLv6p7D/usr/lib/avogadro2/scripts/inputGenerators/qchem.py --debug --display-name --lang en_GB" < ""
QProcess: Destroyed while process ("/home/matt/.local/bin/pixi") is still running.
"Cannot load script /tmp/.mount_AvogadLv6p7D/usr/lib/avogadro2/scripts/inputGenerators/qchem.py"
Using manifest in "/home/matt/.local/share/OpenChemistry/Avogadro"
Executing "/home/matt/.local/bin/pixi" "run --manifest-path /home/matt/.local/share/OpenChemistry/Avogadro python /tmp/.mount_AvogadLv6p7D/usr/lib/avogadro2/scripts/inputGenerators/terachem.py --debug --display-name --lang en_GB" < ""
QProcess: Destroyed while process ("/home/matt/.local/bin/pixi") is still running.
"Cannot load script /tmp/.mount_AvogadLv6p7D/usr/lib/avogadro2/scripts/inputGenerators/terachem.py"
Using manifest in "/home/matt/.local/share/OpenChemistry/Avogadro"
Executing "/home/matt/.local/bin/pixi" "run --manifest-path /home/matt/.local/share/OpenChemistry/Avogadro python /tmp/.mount_AvogadLv6p7D/usr/lib/avogadro2/scripts/formatScripts/zyx.py --debug --display-name --lang en_GB" < ""
QProcess: Destroyed while process ("/home/matt/.local/bin/pixi") is still running.
"Cannot load script /tmp/.mount_AvogadLv6p7D/usr/lib/avogadro2/scripts/formatScripts/zyx.py"
qt.network.http2: stream 1 finished with error: "Connection closed"
Open Babel formats ready:  145
Setting default format to cjson.

I wondered if using python rather than python3 was the issue (it isn’t) so to test it I ran a bash shell within the Flatpak sandbox:

>>> flatpak run --command=bash org.openchemistry.Avogadro2
[📦 org.openchemistry.Avogadro2 ~]$ pixi run python
Error:   × could not find pixi.toml or pyproject.toml with tool.pixi at directory /home/matt

[📦 org.openchemistry.Avogadro2 ~]$ cd .var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro/
[📦 org.openchemistry.Avogadro2 Avogadro]$ ls
pyproject.toml
[📦 org.openchemistry.Avogadro2 Avogadro]$ pixi run python
Python 3.14.0 | packaged by conda-forge | (main, Oct 22 2025, 23:24:08) [GCC 14.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
Could not open PYTHONSTARTUP
FileNotFoundError: [Errno 2] No such file or directory: '/etc/pythonstart'
>>> exit()
[📦 org.openchemistry.Avogadro2 Avogadro]$ ls
pixi.lock  pyproject.toml

Note that before the interpreter ran, Pixi spent a while resolving the environment and downloading the necessary pieces, including Python.

When I run the Flatpak after doing that, the output looks more like success:

>>> flatpak run --env=AVO_PYTHON_SCRIPT_DEBUG=TRUE org.openchemistry.Avogadro2
Avogadroapp version:  1.102.1
Avogadrolibs version:  1.102.1
Qt version:  6.9.3
qt.core.qobject.connect: QObject::connect(QObject, Unknown): invalid nullptr parameter
SSL version:  "OpenSSL 3.3.5 30 Sep 2025"
Using locale:  "en_GB"
AvogadroApp Translation  "en_GB"  loaded  "/app/bin/../share/avogadro2/i18n/"
AvogadroLibs Translation  "en_GB"  loaded  "/app/bin/../share/avogadro2/i18n/"
 registering obmm plugins
"/app/bin/obabel"  found:  "/app/bin/obabel: Open Babel 3.1.1 -- Nov 11 2011 -- 11:11:11"
Using manifest in "/home/matt/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro"
Executing "/app/bin/pixi" "run --manifest-path /home/matt/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro python /app/lib64/avogadro2/scripts/inputGenerators/dalton.py --debug --display-name --lang en_GB" < ""
Output: "DALTON\n"
Using manifest in "/home/matt/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro"
Executing "/app/bin/pixi" "run --manifest-path /home/matt/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro python /app/lib64/avogadro2/scripts/inputGenerators/gamessuk.py --debug --display-name --lang en_GB" < ""
Output: "GAMESS-UK\n"
Using manifest in "/home/matt/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro"
Executing "/app/bin/pixi" "run --manifest-path /home/matt/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro python /app/lib64/avogadro2/scripts/inputGenerators/gaussian.py --debug --display-name --lang en_GB" < ""
Output: "Gaussian\n"
Using manifest in "/home/matt/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro"
Executing "/app/bin/pixi" "run --manifest-path /home/matt/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro python /app/lib64/avogadro2/scripts/inputGenerators/molpro.py --debug --display-name --lang en_GB" < ""
Output: "MOLPRO\n"
Using manifest in "/home/matt/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro"
Executing "/app/bin/pixi" "run --manifest-path /home/matt/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro python /app/lib64/avogadro2/scripts/inputGenerators/mopac.py --debug --display-name --lang en_GB" < ""
Output: "MOPAC\n"
Using manifest in "/home/matt/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro"
Executing "/app/bin/pixi" "run --manifest-path /home/matt/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro python /app/lib64/avogadro2/scripts/inputGenerators/nwchem.py --debug --display-name --lang en_GB" < ""
Output: "NWChem\n"
Using manifest in "/home/matt/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro"
Executing "/app/bin/pixi" "run --manifest-path /home/matt/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro python /app/lib64/avogadro2/scripts/inputGenerators/orca.py --debug --display-name --lang en_GB" < ""
Output: "ORCA\n"
Using manifest in "/home/matt/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro"
Executing "/app/bin/pixi" "run --manifest-path /home/matt/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro python /app/lib64/avogadro2/scripts/inputGenerators/psi4.py --debug --display-name --lang en_GB" < ""
Output: "Psi\n"
Using manifest in "/home/matt/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro"
Executing "/app/bin/pixi" "run --manifest-path /home/matt/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro python /app/lib64/avogadro2/scripts/inputGenerators/pyscf.py --debug --display-name --lang en_GB" < ""
Output: "PYSCF\n"
Using manifest in "/home/matt/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro"
Executing "/app/bin/pixi" "run --manifest-path /home/matt/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro python /app/lib64/avogadro2/scripts/inputGenerators/qchem.py --debug --display-name --lang en_GB" < ""
Output: "Q-Chem\n"
Using manifest in "/home/matt/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro"
Executing "/app/bin/pixi" "run --manifest-path /home/matt/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro python /app/lib64/avogadro2/scripts/inputGenerators/terachem.py --debug --display-name --lang en_GB" < ""
Output: "TeraChem\n"
Using manifest in "/home/matt/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro"
Executing "/app/bin/pixi" "run --manifest-path /home/matt/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro python /app/lib64/avogadro2/scripts/formatScripts/zyx.py --debug --display-name --lang en_GB" < ""
"Cannot load script /app/lib64/avogadro2/scripts/formatScripts/zyx.py"
Open Babel formats ready:  144
Setting default format to cjson.
current version is newer than latest release

and while still not exactly instant, launch is much much faster.