If you are using NMM or anything other than the standard install, make sure that you go to the geogrid directory, check to see where GEOGRID.TBL is linked to, default is to GEOGRID.TBL.ARW, which gave me a seg fault when using the NMM core.
Correct GEOGRID.TBL removes the segmentation fault,
Similary if you have the wrong METGRID.TBL you can get
WRF_DEBUG: NetCDF error: NetCDF: Index exceeds dimension bound
WRF_DEBUG: NetCDF error in wrf_io.F90, line 1044
ERROR: Couldn't open file ./geo_em.d01.nc for input.
linking the right METGRID.TBL fixed that for more. Note that I thought you used to be able to link the correct versions of these tables into the WPS directory and it would use them, this did not seem to be the case for me reciently, you have to go to the geogrid and metgrid directories and change the links there.
Hopet this helps someone