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Three-dimensional integration has the potential to improve the communication latency and integration density of chip-level multiprocessors (CMPs). However, the stacked high-power density layers of 3D CMPs increase the importance and difficulty of thermal management. In this paper, we investigate the 3D CMP run-time thermal management problem and describe efficient management techniques. This paper makes the following main contributions: 1) It identifies and describes the critical concepts required for optimal thermal management, namely the methods by which heterogeneity in both workload power characteristics and processor core thermal characteristics should be exploited; and 2) it proposes an efficient proactive continuously engaged hardware and operating system thermal management technique governed by optimal thermal management polices. The proposed technique is evaluated using multiprogrammed and multithreaded benchmarks in an integrated power, performance, and temperature full-system simulation environment. We find that proactive power-thermal budgeting allows a 30% improvement in instruction throughput compared to a proactive thermal management approach that bases decisions only upon local information. The software components of the proposed thermal management technique have been implemented in the Linux 2.6.8 kernel. This source code will be publicly released. The analysis and technique developed in this paper provide a general solution for future 3D and 2D CMPs.