A system and method for executing previously created run time executables in a configurable processing element array is disclosed. In one embodiment, this system and method begins by identifying at least one subset of program code. The method may then generate at least one set of configuration memory contexts that replaces each of the at least one subsets of program code, the at least one set of configuration memory contexts emulating the at least one subset of program code. The method may then manipulate the at least one set of multiple context processing elements using the at least one set of configuration memory contexts. The method may then execute the plurality of threads of program code using the at least one set of multiple context processing elements.