Clean up PME rank variables

Clean up PME rank variables

Clarified the naming of several PME rank count variables and added
a boolean to DDRankSetup that tells whether we use separate PME ranks.
Fixes several misuses of npmenodes, all of which did not cause issues
in pratice.

Todo: Remove npmenodes from t_commrec.

Change-Id: I03b4547c975e3ffa354b53b35abcd91b4f3f6b26