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The errors do not seem to result from the chain itself. There are very likely false namelist settings and/or compiler options.
You are downscaling from about 200km ( NCEP -RA) to 3km which is a factor of 67 !!!!!!! At least you need to perform a double nesting!
Regarding the compiler options: Please choose an option that stops the program in case of producing NaN. Your job already produces NaNs after the first few time steps but runs still on for the whole month producing always just NaNs.
It is very hard to help you from remote with so many mistakes. Do you plan to take part in the training course? I am sure that would be of valuable help for you.