Use --allow-run-as-root flag only when in docker

[mcgibbon]

There are several scripts (especially tests) where we pass --allow-run-as-root to mpirun. We should detect whether we are running inside a docker container (maybe specifically our docker container, from some environment variable we set inside it) and only pass this flag when we're inside a container. This would prevent users from running tests as root in their main system where doing so might cause damage to their OS.

[ofuhrer]

It is standard practice to create a user inside a docker container to run MPI jobs afaik. Singularity and other HPC container runtimes do provide workarounds, though.

[mcgibbon]

Yeah, that might be a better fix.