Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Mac needs to set BABEL_LIBDIR #1753

Closed
ghutchis opened this issue Oct 28, 2024 · 11 comments
Closed

Mac needs to set BABEL_LIBDIR #1753

ghutchis opened this issue Oct 28, 2024 · 11 comments

Comments

@ghutchis
Copy link
Member

The current release seems to print a lot of errors about setting BABEL_LIBDIR
@matterhorn103
Copy link
Contributor

As does the beta branch of the Flatpak (I know you know this, but just to put it on the record).

@ghutchis
Copy link
Member Author

Can you figure out what part of the code is complaining? I should have made a better note - because it's not happening on my Macs anymore. 🙄

@matterhorn103
Copy link
Contributor

Classic haha. I can have a look.

@matterhorn103
Copy link
Contributor

Not looked into the code yet, but the error is shown during the launch process, where the full terminal output after flatpak run org.openchemistry.Avogadro2 is:

Using locale:  "en_GB"
AvogadroApp Translation  "en_GB"  loaded  "/app/bin/../share/avogadro2/i18n/"
AvogadroLibs Translation  "en_GB"  loaded  "/app/bin/../share/avogadro2/i18n/"
Extension plugins dynamically found… 47
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" "-L charges"
OBProcess::executeObabel: Running "/app/bin/obabel" "-V"
"/app/bin/obabel"  found:  "/app/bin/obabel: Open Babel 3.1.1 -- Nov 14 2024 -- 17:10:01"
"Checking for energy scripts in path /home/matt/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro/energy"
"Checking for energy scripts in path /app/share/OpenChemistry/Avogadro/energy"
"Checking for energy scripts in path /usr/share/OpenChemistry/Avogadro/energy"
"Checking for energy scripts in path /usr/share/runtime/share/OpenChemistry/Avogadro/energy"
"Checking for energy scripts in path /run/host/user-share/OpenChemistry/Avogadro/energy"
"Checking for energy scripts in path /run/host/share/OpenChemistry/Avogadro/energy"
"Checking for energy scripts in path /app/bin/../lib/avogadro2/scripts/energy"
"Cannot load script /app/lib/avogadro2/scripts/energy/ani2x.py"
"Cannot load script /app/lib/avogadro2/scripts/energy/gfn1.py"
"Cannot load script /app/lib/avogadro2/scripts/energy/gfn2.py"
"Cannot load script /app/lib/avogadro2/scripts/energy/gfnff.py"
 registering GPL plugins
==============================
*** Open Babel Error  in LoadAllPlugins
  Unable to find OpenBabel plugins. Try setting the BABEL_LIBDIR environment variable.
==============================
*** Open Babel Error  in LoadAllPlugins
  Unable to find OpenBabel plugins. Try setting the BABEL_LIBDIR environment variable.
==============================
*** Open Babel Error  in LoadAllPlugins
  Unable to find OpenBabel plugins. Try setting the BABEL_LIBDIR environment variable.
OBEnergy: method:  MMFF94
OBEnergy: method not found:  MMFF94
==============================
*** Open Babel Error  in LoadAllPlugins
  Unable to find OpenBabel plugins. Try setting the BABEL_LIBDIR environment variable.
forcefields is not a recognized plugin type. Those with instances of sub-types loaded are:
ops

==============================
*** Open Babel Error  in LoadAllPlugins
  Unable to find OpenBabel plugins. Try setting the BABEL_LIBDIR environment variable.
==============================
*** Open Babel Error  in LoadAllPlugins
  Unable to find OpenBabel plugins. Try setting the BABEL_LIBDIR environment variable.
==============================
*** Open Babel Error  in LoadAllPlugins
  Unable to find OpenBabel plugins. Try setting the BABEL_LIBDIR environment variable.
OBEnergy: method:  UFF
OBEnergy: method not found:  UFF
==============================
*** Open Babel Error  in LoadAllPlugins
  Unable to find OpenBabel plugins. Try setting the BABEL_LIBDIR environment variable.
forcefields is not a recognized plugin type. Those with instances of sub-types loaded are:
ops

==============================
*** Open Babel Error  in LoadAllPlugins
  Unable to find OpenBabel plugins. Try setting the BABEL_LIBDIR environment variable.
==============================
*** Open Babel Error  in LoadAllPlugins
  Unable to find OpenBabel plugins. Try setting the BABEL_LIBDIR environment variable.
==============================
*** Open Babel Error  in LoadAllPlugins
  Unable to find OpenBabel plugins. Try setting the BABEL_LIBDIR environment variable.
OBEnergy: method:  GAFF
OBEnergy: method not found:  GAFF
==============================
*** Open Babel Error  in LoadAllPlugins
  Unable to find OpenBabel plugins. Try setting the BABEL_LIBDIR environment variable.
forcefields is not a recognized plugin type. Those with instances of sub-types loaded are:
ops

"Checking for commands scripts in path /home/matt/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro/commands"
"Checking for commands scripts in path /app/share/OpenChemistry/Avogadro/commands"
"Checking for commands scripts in path /usr/share/OpenChemistry/Avogadro/commands"
"Checking for commands scripts in path /usr/share/runtime/share/OpenChemistry/Avogadro/commands"
"Checking for commands scripts in path /run/host/user-share/OpenChemistry/Avogadro/commands"
"Checking for commands scripts in path /run/host/share/OpenChemistry/Avogadro/commands"
"Checking for commands scripts in path /app/bin/../lib/avogadro2/scripts/commands"
"Checking for inputGenerators scripts in path /home/matt/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro/inputGenerators"
"Checking for inputGenerators scripts in path /app/share/OpenChemistry/Avogadro/inputGenerators"
"Checking for inputGenerators scripts in path /usr/share/OpenChemistry/Avogadro/inputGenerators"
"Checking for inputGenerators scripts in path /usr/share/runtime/share/OpenChemistry/Avogadro/inputGenerators"
"Checking for inputGenerators scripts in path /run/host/user-share/OpenChemistry/Avogadro/inputGenerators"
"Checking for inputGenerators scripts in path /run/host/share/OpenChemistry/Avogadro/inputGenerators"
"Checking for inputGenerators scripts in path /app/bin/../lib/avogadro2/scripts/inputGenerators"
"Checking for charges scripts in path /home/matt/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro/charges"
"Checking for charges scripts in path /app/share/OpenChemistry/Avogadro/charges"
"Checking for charges scripts in path /usr/share/OpenChemistry/Avogadro/charges"
"Checking for charges scripts in path /usr/share/runtime/share/OpenChemistry/Avogadro/charges"
"Checking for charges scripts in path /run/host/user-share/OpenChemistry/Avogadro/charges"
"Checking for charges scripts in path /run/host/share/OpenChemistry/Avogadro/charges"
"Checking for charges scripts in path /app/bin/../lib/avogadro2/scripts/charges"
"Cannot load script /app/lib/avogadro2/scripts/charges/antechamber.py"
"Cannot load script /app/lib/avogadro2/scripts/charges/xtb.py"
"Checking for formatScripts scripts in path /home/matt/.var/app/org.openchemistry.Avogadro2/data/OpenChemistry/Avogadro/formatScripts"
"Checking for formatScripts scripts in path /app/share/OpenChemistry/Avogadro/formatScripts"
"Checking for formatScripts scripts in path /usr/share/OpenChemistry/Avogadro/formatScripts"
"Checking for formatScripts scripts in path /usr/share/runtime/share/OpenChemistry/Avogadro/formatScripts"
"Checking for formatScripts scripts in path /run/host/user-share/OpenChemistry/Avogadro/formatScripts"
"Checking for formatScripts scripts in path /run/host/share/OpenChemistry/Avogadro/formatScripts"
"Checking for formatScripts scripts in path /app/bin/../lib/avogadro2/scripts/formatScripts"
==============================
*** Open Babel Error  in LoadAllPlugins
  Unable to find OpenBabel plugins. Try setting the BABEL_LIBDIR environment variable.
==============================
*** Open Babel Error  in LoadAllPlugins
  Unable to find OpenBabel plugins. Try setting the BABEL_LIBDIR environment variable.
==============================
*** Open Babel Error  in LoadAllPlugins
  Unable to find OpenBabel plugins. Try setting the BABEL_LIBDIR environment variable.
OBEnergy: method:  MMFF94
OBEnergy: method not found:  MMFF94
==============================
*** Open Babel Error  in LoadAllPlugins
  Unable to find OpenBabel plugins. Try setting the BABEL_LIBDIR environment variable.
forcefields is not a recognized plugin type. Those with instances of sub-types loaded are:
ops

Open Babel formats ready:  145
Setting default format to cjson.

Then each time "Optimize Geometry" is clicked the following is appended:

==============================
*** Open Babel Error  in LoadAllPlugins
  Unable to find OpenBabel plugins. Try setting the BABEL_LIBDIR environment variable.
==============================
*** Open Babel Error  in LoadAllPlugins
  Unable to find OpenBabel plugins. Try setting the BABEL_LIBDIR environment variable.
 initial  0  gradNorm:  0
 maxSteps 250  steps  125
 optimize  0 0  gradNorm:  0

@ghutchis
Copy link
Member Author

Okay that helps.

@ghutchis
Copy link
Member Author

Is this still a problem in the current Flatpak - I think I fixed it?

@matterhorn103
Copy link
Contributor

What do you mean by current Flatpak? By that I mean which commit would have fixed it?

@ghutchis
Copy link
Member Author

In principle, #1791 should do it

@matterhorn103
Copy link
Contributor

Ah ok. The beta branch is currently at a422606 for avogadrolibs. Let me check the most recent test build.

@matterhorn103
Copy link
Contributor

Yep, it's fixed! Nice one.

@matterhorn103
Copy link
Contributor

You'll be happy to know it also fixed https://discuss.avogadro.cc/t/cannot-get-chlorophyll/6402, in the Flatpak at least. :) I'll post in that thread to let the user know once the changes have made it through to the beta branch (should be by tomorrow morning).

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
2 participants
@ghutchis @matterhorn103