Compiler settings are located in the two files env_mach_specific and Macros.$MACH. The env_mach_specific file is a shell script that sets various machine specific configure options such as modules and MPI or system environment variables. This script is run as part of every build or run step, and accounts for settings not included in the CCSM xml env files. The Macros.$MACH file contains the machine specific build options used in the CCSM Makefile. Both of these files are usually involved in defining build options, and the env_mach_specific file might also contain critical settings for the run phase.
If you are running at NCAR, env_mach_specific also contains variables to set up mass storage archiving. You need to modify these if you activate long-term archiving on the mass store.
You need to modify these files for user-defined machines during the process of porting CCSM to your machine.