A system and method configures a target processing entity having multiple processing elements to execute a graphical program. A first part of the graphical program is designated for execution by a first processing element, and a second part of the graphical program is designed for execution by a second processing element. A code generation system generates a single build file from the graphical program having an initialization section, suitable executable code sections for each processing element, and a communication section that supports communication between the two processing elements. The build file may be downloaded to, and run by the target processing entity to implement the graphical program at the target processing entity.