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Homogeneous manycore systems are emerging for tera-scale computation and typically utilize Network-on-Chip (NoC) as the communication scheme between embedded cores. Effective defect tolerance techniques are essential to improve the yield of such complex integrated circuits. We propose to achieve fault tolerance by employing redundancy at the core-level instead of at the microarchitecture level. When faulty cores exist on-chip in this architecture, however, the physical topologies of various manufactured chips can be significantly different. How to reconfigure the system with the most effective NoC topology is a relevant research problem. In this paper, we first show that this problem is an instance of a well known NP-complete problem. We then present novel solutions for the above problem, which not only maximize the performance of the on-chip communication scheme, but also provide a unified topology to Operating System and application software running on the processor. Experimental results show the effectiveness of the proposed techniques.