A compiler system that converts an application source program into an executable program according to a predetermined ISA executable by a general purpose processor. The processor includes a PEU that is programmable to execute a UDI. The compiler system includes a PEU programming tool that converts a functional description of a processing operation to be performed by the PEU of the processor into programming information for programming the PEU to perform the processing operation in response to the specified UDI. The compiler system includes a compiler that converts the application source program into the executable program, which includes an optimization routine that represents a portion of the application source program with the specified UDI and that inserts the UDI into the executable program, and that further inserts into the executable program a UDI load instruction that specifies the UDI and a location of the programming information in the executable program.