System and method for debugging a program intended for execution on a programmable hardware element (PHE) to perform a function. A first portion of the program is converted into a first hardware configuration program (HCP) deployable on the PHE, where a remaining portion is to be debugged by a user. The PHE is configured with the first HCP, and the program executed, including the PHE executing the first portion of the program, and the computer system executing the remaining portion, which is then analyzed and debugged in response to being executed, and user input received modifying the remaining portion to debug the remaining portion. The method is repeated, where in each iteration the first portion is a successively larger portion of the program. After being debugged, the program is converted into a second HCP deployable on the PHE to perform the function, and the PHE configured with the second HCP.