Does some of you know a mesh partitioner that assures non empty subdomains? For METIS, ParMETIS and Zoltan this is not the case.
I was having an issue with
Metis_PartMeshDual where if my number of processors was greater than (number of elements)/2 I would get processors that were given no elements. I believe this is what the OP means by a partition getting an "empty subdomain".
I found that the line
options[METIS_OPTION_PTYPE] = METIS_PTYPE_RB;
made it so that for all cases where the number of processors $\leq$ number of elements, every processor gets at least one element. I know this isn't terribly enlightening, but hopefully, it helps someone.