Mpi over ssh sounds like a bad idea. Typically hpc clusters have a highly optimized vendor libmpi. E.g. cray has an abi compatible libmpi.so to mpich, so you are likely better of replacing the libmpi.so in your container with the vendor version by mounting a bunch of paths from the host. That can be a hook like nvidia has for their gpu support. One container runtime that does this is Sarus: https://github.com/eth-cscs/sarus