Hands-on: Creating a conda environment file and building a container using cotainr

Exercises on the course GitHub.

Q&A

1. I get the following error ValueError: Invalid command cmd='bash conda_installer.sh -b -s -p /opt/conda' passed to Singularity resulted in the FATAL error: FATAL: container creation failed: mount /appl->/appl error: while mounting /appl: destination /appl doesn't exist in container when running cotainr build python312.sif --system=lumi-c --conda-env=python312.yml

   • Try logging in and out of LUMI. I have feeling that you have too many conflicting variables/modules set.

   • (Christian) It looks like you are trying to build a container using cotainr while having the singularity-userfilesystems module loaded. Unfortunately, this doesn't currently work because you try to bind mount a path inside the container during the build that isn't already in the container directory tree which results on a FATAL error. It's a bug in cotainr.