Artur,
So I think I figured out the problem. When I ran real.exe with your met_em* files, I also got the error, so I then created my own met_em* files with your intermediate files. When I did this, using your exact namelist.wps file, met_em files were created, but real.exe failed again. When I removed the 'process_only_bdy' parameter from the &metgrid namelist, the met_em* files that were created were able to be processed by real.exe. This namelist variable is something that should only be used if no interpolation of data is necessary, and therefore I don't think this option will work with your case. Try turning that off and seeing if that makes a difference.
Kelly
So I think I figured out the problem. When I ran real.exe with your met_em* files, I also got the error, so I then created my own met_em* files with your intermediate files. When I did this, using your exact namelist.wps file, met_em files were created, but real.exe failed again. When I removed the 'process_only_bdy' parameter from the &metgrid namelist, the met_em* files that were created were able to be processed by real.exe. This namelist variable is something that should only be used if no interpolation of data is necessary, and therefore I don't think this option will work with your case. Try turning that off and seeing if that makes a difference.
Kelly