Supercomputers and non-RPM?
I would suggest you go over and subscribe at Beowulf.org. A tiny mailing list full of very bright people who've been doing supercomputing / HPC for 30 years or so. It was an accident that they started out with Red Hat packages to form Extreme Linux all those years ago: it's really not easy to build something from scratch but it is do-able. There are some supercomputing facilities running on Debian and Ubuntu, I think, and genomics sequencing is largely Ubuntu at the Wellcome Sanger Institute, for example.