"graphviz/libgvplugin_pango.so.6" - file not found" missing dependency on WSL installations

[TaikiKato]

Topic

Kinetic Library Addition to RMG Training Data

Context

I couldn't work with "kinetics_library_to_training.ipynb" because of "error while loading shared libraries: libltdl.so.7" message.
I tried to work with "kinetics_library_to_training_tools.py" but I didn't find how to use it.

Question

How to use "kinetics_library_to_training_tools.py" ?

Installation Information

• OS : Windows 10, WSL, Ubuntu 18.04
• Installation method: Miniconda using & download from github files
• RMG version information:
  • RMG-Py: 3.1.0-59-g74b176a77
  • RMG-database: 3.0.0-206-g833577ec

kinetics_library_to_training_tools.txt
kinetics_library_to_training.txt

[amarkpayne]

Can you see what happens when you run sudo apt-get install libltdl7 in the Ubuntu terminal? Let us know what it says when you execute this command. I am curious if it installs for the first time or re-installs.

I just setup a fresh WSL instance on my computer using Ubuntu 20.04 and this library was already installed, so I don't know if this is an Ubuntu 18.04 thing

[TaikiKato]

Thank you for your kind reply.
I tried "sudo apt-get install libltdl7" and got some response (attached).

And I tried kinetics_library_to_training.ipynb again.
I found some errors in Step 2a.

sudo apt-get install libltdl7.txt

kinetics_library_to_training.txt

[amarkpayne]

Okay, so it looks like the first package I suggested was in fact missing, and installing it seemed to fix that issue.

The next error message you are getting relates to these lines in your notebook file:

Warning: Could not load \"/home/taiki-kato/miniconda3/envs/rmg_rms_dev_env/lib/graphviz/libgvplugin_pango.so.6\" - file not found\\nWarning: Could not load \"/home/taiki-kato/miniconda3/envs/rmg_rms_dev_env/lib/graphviz/libgvplugin_pango.so.6\" - file not found\\nWarning: Could not load \"/home/taiki-kato/miniconda3/envs/rmg_rms_dev_env/lib/graphviz/libgvplugin_pango.so.6\" - file not found\\nFormat: \"png\" not recognized. Use one of: bmp canon cmap cmapx cmapx_np dot eps fig gtk gv ico imap imap_np ismap jpe jpeg jpg pdf pic plain plain-ext png pov ps ps2 svg svgz tif tiff tk vml vmlz x11 xdot xdot1.2 xdot1.4 xlib\\n'\n",

I think this is related to the discussion at conda-forge/graphviz-feedstock#35.

Can you run the command conda install -c conda-forge xorg-libxau from within your RMG environment on the Ubuntu terminal? This dependency can also be installed at the OS level, but it would be better to add this to our conda environment if this works

[TaikiKato]

Thank you for your advice.
I tried "conda install -c conda-forge xorg-libxau" & it may be successful.

But, kinetics_library_to_training.ipynb gives still error at step 2a.
Could you please give me some more advices ?

conda install -c conda-forge xorg-libxau.txt

kinetics_library_to_training.txt

[amarkpayne]

Can you try sudo apt-get install libxau ?

[TaikiKato]

"sudo apt-get install libxau" may failed.

(rmg_rms_dev_env) taiki-kato@JP06856910:~$ sudo apt-get install libxau

Reading package lists... Done
Building dependency tree
Reading state information... Done
E: Unable to locate package libxau

(rmg_rms_dev_env) taiki-kato@JP06856910:~$

Is source installation more difficult than binary installation ?
Can I add kinetics library & family addition on binary installed rmg ?

[TaikiKato]

I found that I have the "kinetics_library_to_training.ipynb" working environment.
But, I don't know how to check the environment (binary install or source install ?)
Please teach me how to check the environment detail.

[amarkpayne]

Execute conda env list from within your rmg environment. If rmg and rmg-database are listed then you likely installed the binary.

If you have and RMG-Py folder that you cd into, then you have installed from source

[amarkpayne]

"sudo apt-get install libxau" may failed.

(rmg_rms_dev_env) taiki-kato@JP06856910:~$ sudo apt-get install libxau

Reading package lists... Done
Building dependency tree
Reading state information... Done
E: Unable to locate package libxau

(rmg_rms_dev_env) taiki-kato@JP06856910:~$

Is source installation more difficult than binary installation ?
Can I add kinetics library & family addition on binary installed rmg ?

Sorry, the package might be libxau6. sudo apt-get install libxau6. If your environment is working without this though then you are good

[TaikiKato]

Thank you for your answers.
May be, I have libxau6.

(base) taiki-kato@JP06856910:~$ sudo apt-get install libxau6

[sudo] password for taiki-kato:
Reading package lists... Done
Building dependency tree
Reading state information... Done
libxau6 is already the newest version (1:1.0.8-1ubuntu1).
libxau6 set to manually installed.
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.

(base) taiki-kato@JP06856910:~$

[TaikiKato]

Other worked rmg_env is on Redhat.
But, I forgot how to build it.
From your answer, I did source install on all rmg_envs
because I don't have rmg-database in "conda env list" outputs.

[amarkpayne]

I am working on reproducing this error on a fresh WSL install--I'll let you know how it goes.

In the meantime, can you execute the command sudo apt-get install libxrender1 in the Ubuntu terminal just in case and try re-running the notebook?

[TaikiKato]

Thank you very much.
May be, I had libxrender1.

(base) taiki-kato@JP06856910:~$ sudo apt-get install libxrender1

[sudo] password for taiki-kato:
Reading package lists... Done
Building dependency tree
Reading state information... Done
libxrender1 is already the newest version (1:0.9.10-1).
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.

(base) taiki-kato@JP06856910:~$