As @cjcoats noted, it’s probably not so much the compiler as whether or not netcdf4 support was enabled when building the respective netcdf libraries. If the netcdf library used to compile WRF had netcdf4 support enabled, the wrfout files probably use the netcdf4 data format. If so, and if the netcdf library linked in when compiling MCIP did not enable netcdf4 support, these wrfout files would not be readable by that MCIP executable.
If this is the case, to solve the issue, either rebuild your copy of netcdf with netcdf4 support and then rebuiled i/o api and MCIP, or have your colleague convert the wrfout files back to “netCDF classic format” or “netCDF 64-bit format” by using his version of nccopy to do so, e.g. nccopy -k nc3 infile outfile or nccopy -k nc6 infile outfile - see the man pages for nccopy for further details.
To determine the data format of your wrfout files, use ncdump -k wrfout, the result will be
classic', 64-bit offset’,
netCDF-4', or netCDF-4 classic model’. Only the first two will be readable by any executable compiled with a netcdf library that did not have netcdf4 support enabled.