System and method for specifying and implementing relative hardware clocking in a high level programming language. User input specifying a program may be received. The program is specified for deployment to a programmable hardware element (PHE), and includes first and second code portions configured to communicate with each other during execution. The user input may further specify a rational ratio of respective execution rates for the first and second code portions. A hardware configuration program (HCP) implementing the specified program is automatically generated, including automatically determining a respective clock rate for at least one of the first and second code portions based on the rational ratio. The HCP may be deployable to the PHE, including implementing first and second clocks for controlling execution of the first and second code portions in accordance with the rational ratio and the automatically determined respective clock rate for the at least one code portion.