[General] [All] Notebooks to work outside container - replace absolute paths

[mozhgan-kch]

At the moment, notebooks/makefiles (particularly HPC) contains fixed paths depending on the versions of the compiler and environment variables set inside the container. This causes issues if someone tries to run the material on bare metal.

These paths in cells should be independent of the container and ideally should work on any cluster by loading modules only. Many paths are absolutes and assume a specific container configuration. This needs fixing.