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 .