After running configure, all that is required to compile the code is to type make all in the top level directory /athena1.0 (within which the configure script is run). This automatically creates the directory athena1.0/bin, which will contain the executable, and runs make in the athena1.0/src directory to compile and link the code. The top-level Makefile in the /athena1.0 directory also contains other targets which may be of use to users listed in Table 3.
| TARGET | Comments |
| all | creates athena1.0/bin directory and compiles code |
| compile | compiles code |
| clean | removes .o files in athena1.0/src |
| help | prints help message |
| check | runs benchmark (see §8.1) |
Normally the Makefiles should never need to be edited by hand. However, since compiler options and flags are not currently controlled through configure in athena1.0, it is possible to edit the Makefile in the athena1.0/src directory to change compiler flags, for example, to improve optimization. For example, setting GNUFLAGS to a blank (``'') value will speed-up the code already.