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In this work, a 3D thermal model of a multicore system is developed to investigate the effects of hotspot, and placement of silicon die layers, on the thermal performance of a modern flip-chip package. In this regard, both the steady-state and transient heat transfer analysis has been performed on the 3D flip-chip package. Two different stacked die configurations were evaluated under different operating conditions. Through experimental simulations, we have found a configuration which has better thermal performance. The optimal placement solution is also provided based on the maximum temperature attained by the individual silicon dies. We have also provided the improvement that is required in the heat sink thermal resistance of a 3D system when compared to the single-die system.