Makefile error CCTM_v54.exe doesn't appear

Looking at the error message in the third attachment you posted, it appears to be the same issue as the one encountered by the users in these threads (as a google search for “multiple definition of nf_put_var1_int64” will also reveal):

Error when install ioapi 3.2 with intel

[airs2m3] Error

Based on @cjcoats answers in those threads, the solution (as documented on the I/O API webpage appears to be to either build I/O API without netCDF4 support or to add the -DIOAPI_NCF4=1 preprocessor flag when building I/O API>