An embodiment of the invention includes a method of simulating a hybrid instruction processor and reconfigurable processor implemented algorithm which utilizes a runtime selectable emulation library that emulates a reconfigurable processor and its resources, and a control-data flow emulator that emulates the reconfigurable logic for the algorithm. Another embodiment of the invention includes a method of simulating a control-dataflow graph that includes building an internal representation of the control-dataflow graph that includes one or more dataflow code blocks, and simulating the control-dataflow graph as a sequence of code block dataflow executions, where control is passed from one code block to another code block based on the output value of the code block until EXIT is reached.