Update and clean up documentation

[sungeunchoi]

• Convert NOTES to markdown and make them a bit more general
• Add a README

[sungeunchoi]

A few general response to your general comments:

• I explained the srun/aprun thing in the inline comments.
• -N and --ntasks-per-node are not the same. That said, there is a type-o in one of the files that is from the original NOTES files. While we're at it, some of the srun->aprun mappings don't seem quite right. I will try to fix.
• Not all the programs can be run with the same number of nodes with the various constraints. There might be something we could do to get close, but the run script has the a definition of small, medium and large so I don't think it's worth doing right now.