On the Cray, there may be more than one available compiler, but they will all be called "ftn". Do you know which one you are using? Can you show "module list"? On our system, check out the "PrgEnv" module - I have PrgEnv-intel/4.2.34 currently loaded.
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fish2 1140% module avail PrgEnv
------------------------------- /opt/modulefiles -------------------------------
PrgEnv-cray/4.0.46 PrgEnv-intel/4.0.46
PrgEnv-cray/4.2.34(default) PrgEnv-intel/4.2.34(default)
PrgEnv-gnu/4.0.46 PrgEnv-pgi/4.0.46
PrgEnv-gnu/4.2.34(default) PrgEnv-pgi/4.2.34(default)
You can have any one of these loaded - but only one at a time.
Did you select "ftn" for the FORT variable in your build script/makefile?
So, now go into the Compilers directory. There is probably a Linux-ftn.mk file. If this is the trunk ROMS, it will say "CRAY FTN cross-compiler with Linux" at the top. If this is my branch, it will say "PGI Fortran compiler on Linux (on Cray)". Actually, the latter has the "-Mfree" in it. My local file on the Cray system has "-free" instead, which is what ifort wants. You need to know which compiler you are using in order to know which options to give it. Compare with the Linux-ifort.mk file in that Compilers directory. If you are using the actual Cray compiler, you might have to read the man page to find out how to tell it to use F90 free format.