Running openCARP tissue-level examples with opencarp-docker and Git Bash

Question

I ran into an issue when running the first tissue-level example with the opencarp-docker script on Windows, using Docker with the WSL 2 backend and Git Bash from Git for Windows as a shell.

In experiments/tutorials//02_EP_tissue/01_basic_usage, I ran:

opencarp-docker python3 run.py

and got the following error after the openCARP command was displayed:

*** Unrecognized keyword



*** Error reading parameters

Answer 1

This was due to the fact that when checking out files from the openCARP repository on Windows, Unix-style line endings were converted to Windows-style line endings.

It is apparently necessary that files passed to the docker executable contain Unix-style line endings.

Git configuration can be modified so that Git will not perform any conversion when checking out text files. When committing text files, CRLF (Windows-style) will be converted to LF (Unix-style):

git config --global core.autocrlf input

Comments

In order for this change to take effect, you should have to run inside the "experiments" directory:
git rm --cached -r . && git reset --hard