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We describe the integrated power, area and thermal modeling framework in the Structural Simulation Toolkit (SST) for large-scale high performance computer simulation. It integrates various power and thermal modeling tools and computes run-time energy dissipation for core, network on chip, memory controller and shared cache. It also has functionality to update the leakage power as temperature changes. We illustrate the utilization of the framework by applying it to explore interconnect options in manycore systems with consideration of temperature variation and leakage feedback. We compare power, energy-delay-area product (EDAP), and energy-delay product (EDP) of four manycore configurations-1 core, 2 cores, 4 cores and 8 cores per cluster. Results from simulation with or without consideration of temperature variation both show that the 4-core per cluster configuration has the best EDAP and EDP. Even so, considering temperature variation increases total power dissipation. We demonstrate the importance of considering temperature variation in the design ow. With this power, area and thermal modeling capability, SST can be used for hardware/software co-design of future Exascale systems.