Once installed, cdisolver can be executed by the command

$ ./cdiSolver <filename> [-v]

The <filename> specifies the path to the input file that shall be read.
If the flag -v is set, then cdisolver will output additional information
about the communication between the main program and Mathematica. The
input files have to obey the following grammar in Table 6.2 of the master
thesis.
A specification consists of five parts. The first part declares a list of
variables that is going to be used in the parts below. Otherwise, it would
not be possible to differentiate between variables and constant function
symbols when parsing a file. The second part declares the rewrite rules of
the considered TRS. The third part declares the stub of the context-dependent
interpretation. The fourth part declares a list of pairs (a,b), which means
that the Delta-monotonicity constraint has to be checked for the function
symbol "a" and argument position "b". The optional fifth part of the input
file declares a list of terms. If a context-dependent interpretation which
induces termination can be constructed from the stub in the given input
file, then the upper bounds on the derivation height are computed for
these terms.