Hello,
I tried to use Avogadro2 with Molequeue with Flatpak build on openSUSE that I have added to Flathub sometime ago.
https://flathub.org/apps/details/org.openchemistry.Avogadro2
I noticed that Molequeue does not work. When I tried using Quantum > Input Generators > GAMESS > Submit Calculations…
It said
Cannot connect to MoleQueue server. Please ensure that it is running and try again.
Molequeue is already include in Avogadro2 Flatpak, but not start by default.
Normally Avogadro can be start with,
flatpak run org.openchemistry.Avogadro2
But I need to get Molequeue to work, so I have to add extra option to allow some feature through sandbox in Flatpak.
To start molequeue, I use this command.
flatpak run --command=molequeue --talk-name=org.freedesktop.Notifications --talk-name=o
rg.kde.StatusNotifierWatcher --share=network org.openchemistry.Avogadro2
This part give Molequeue access to menu tray. (need to add this to Flathub)
–talk-name=org.freedesktop.Notifications --talk-name=org.kde.StatusNotifierWatcher
I assume that for Molequeue to talk to Avogadro2, it need some kind of network access.
So I add this in the command
–share=network
After starting Molequeue, I start Avogadro with this command.
flatpak run --talk-name=org.freedesktop.Notifications --talk-name=org.kde.StatusNotifie
rWatcher --share=network org.openchemistry.Avogadro2
Even with network access I got the same error.
Cannot connect to MoleQueue server. Please ensure that it is running and try again.
Avogadro command log.
flatpak run --talk-name=org.freedesktop.Notifications --talk-name=org.kde.StatusNotifie
rWatcher --share=network org.openchemistry.Avogadro2
Locale: “en_US”
translation success
“/usr/translations”
translation success
Extension plugins dynamically found… 31
Checking for “commands” scripts in “/home/kev/.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 21 2021 – 19:53:41”
Checking for “inputGenerators” scripts in “/home/kev/.var/app/org.openchemistry.Avogadro2/data/OpenChe
mistry/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/inputGenera
tors”
Checking for “inputGenerators” scripts in “/run/host/share/OpenChemistry/Avogadro/inputGenerators”
Checking for “inputGenerators” scripts in “/app/bin/…/lib/avogadro2/scripts/inputGenerators”
Checking for “formatScripts” scripts in “/home/kev/.var/app/org.openchemistry.Avogadro2/data/OpenChemi
stry/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”
ScriptLoader::queryProgramName: Unable to retrieve program name for “/app/lib/avogadro2/scripts/formatSc
ripts/cclibScript.py” ; “Error running script ‘/usr/bin/python3 /app/lib/avogadro2/scripts/formatScripts
/cclibScript.py --display-name --lang en_US’: Abnormal exit status 1 (Unknown error.: Unknown error)\n\n
Output:\nTraceback (most recent call last):\n File “/app/lib/avogadro2/scripts/formatScripts/cclibScri
pt.py”, line 22, in \n from cclib.io.ccio import ccopen\nModuleNotFoundError: No module name
d ‘cclib’\n”
“Navigator” added
“Editor” added
“Selection” added
“Manipulator” added
“BondCentric” added
“MeasureTool” added
“PlayerTool” added
Molequeue
flatpak run --command=molequeue --talk-name=org.freedesktop.Notifications --talk-name=org.kde.StatusNotifierWatcher --share=network org.openchemistry.Avogadro2
Checking for plugins in “/app/lib/molequeue/plugins”
(“LocalSocketServer.so”)
Loaded “LocalSocketServer.so” →
OBJECT MoleQueue::LocalSocketConnectionListenerFactory::unnamed
SIGNALS OUT
SIGNALS IN
MoleQueue::Logger::~Logger() – Cannot determine working directory.
MoleQueue::Logger::~Logger() – Cannot determine working directory.
I’m not sure if this is sandboxs access blocking Molequeue or something else, do you have some clue?
Thanks.