I think, if you are using the serial PETSc ILU, you should just use a MatOrdering, which can be done from the command line:
-pc_type ilu -pc_factor_mat_ordering_type rcm
which I tested on KSP ex2.
Matt
From the experience of 2D code, the GMRES solver with ILU works well (thematrix is asymmetric.)
Gong Ding