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The size of future high-performance SoC is such that the time-of-flight of wires connecting distant pins in the layout can be much higher than the clock period. In order to keep the frequency as high as possible, the wires may be pipelined. However, the insertion of flip-flops may alter the throughput of the system due to the presence of loops in the logic netlist. In this paper, we address the problem of floorplanning a large design where long interconnects are pipelined by inserting the throughput in the cost function of a tool based on simulated annealing. The results obtained on a series of benchmarks are then validated using a simple router that breaks long interconnects by suitably placing flip-flops along the wires.