Abstract: Various approaches for controlling a circuit implemented on an integrated circuit device having programmable logic. According to one approach a hierarchy of directories and files are maintained in a virtual file system that is registered with an operating system. The directories and files are associated with resources of the programmable logic. Each file represents a respective data set of configuration data for an associated one of the resources, and at least one of the files is a clock control file that is associated with a clock control circuit on the integrated circuit. A first value is stored in the clock control circuit of the programmable logic in response to invocation of an operating system file access command that references the clock control file and specifies the first value. Advancement of a clock signal on the programmable logic is controlled in response to the first value stored in the clock control circuit.