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In general it would be better to keep GEM output in RPN format to avoid "doubling" the output data. However, in some cases it can be useful to convert files in RPN format to NetCDF format or vice versa.
The tool with which one can do this is called cdf2rpn. You can find information about cdf2rpn under the following link: cdf2rpn - documentation
Running GEM
CRCM/GEM is installed on certain clusters of The Digital Research Alliance of Canada.
To learn how to run CRCM/GEM have a look at the wiki pages under: GEM-UQAM