To build the code:

A) Go to the top level menu and 
1) decide on the directory names.
2) run the script

B) Go deep into the Atmosphere build menu and 
1) set the choices for package, options etc in every case.
2) save the file in every case

C) Configure the Atmosphere genmake2 menu and run genmake2

D) Go up to the Atmosphere build menu, decide on the variables and 
run the script

E) Go deep into the Ocean build menu and 
1) set the choices for package, options etc in every case.
2) save the file in every case

F) Configure the Ocean genmake2 menu and run genmake2

G) Go up to the Ocean build menu, decide on the variables and 
run the script

B) Go deep into the Coupler build menu and 
1) set the choices for Parameters in every case.
2) save the file in every case

C) Configure the Coupler genmake2 menu and run genmake2

D) Go up to the Atmosphere Coupler menu, decide on the variables and 
run the script

To run the code:

A) Go deep into each menu and edit the data parameter files. Save them.

B) To to the top runtime menu, edit the options and run the script.

LEGEND current faux-pass:
a) Do not forget to remove the default PBS monitor from the options under Tools.