1. A method of using a computer to configure a programmable integrated circuit device with a user logic design, said method comprising: accepting into said computer a first user input defining said user logic design; accepting into said computer a second user input defining availability of multithreading for at least a portion said user logic design; determining, using said computer, a configuration of said programmable integrated circuit device having said user logic design; using said computer to multithread said at least a portion of said configuration based on said second user input; and using said computer to retime said multithreaded configuration.