Some embodiments provide a method for manufacturing a programmable system in package. The method divides a system into sets of operations. For each set of operations, the method identifies several integrated circuits ("IC's") for performing the set of operations. The method packages several of identified IC's into a single IC package. The several identified IC's includes at least one configurable IC. In some embodiments, the configurable IC is a reconfigurable IC that can reconfigure more than once during run time. In some of these embodiments, the reconfigurable IC can be reconfigured at a first clock rate that is faster than the clock rates of one or more of the other IC's in the PSiP. The first clock rate is faster than the clock rate of all of the other IC's in the PSiP in some embodiments.