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This paper proposes an innovative force-directed parallel algorithm, FDPrior, to solve the multilayer partitioning problem of 3DICs. The growing scale and multi-layered structure of the 3DIC technology make it computational expensive for EDA tools to achieve optimization goals. Exploiting the algorithmic parallelism on multi-core architectures becomes the key to attain scalable runtime. By adopting the N-body simulation scheme and novel techniques to reduce synchronization overhead, FDPrior successfully exposes the massive parallelism on the multi-core GPGPU architecture. The objective is to minimize the total number of Through Silicon Vias (TSVs) while meeting the area constraint for each layer. The experimental results on ISPD98 benchmark show that FDPrior outperforms the conventional FM algorithm by achieving in average 5.0X better TSVs and up to 247.3X runtime speedup. Compared with PP3D, a parallel 3DIC partitioning algorithm, FDPrior achieves 6.7X better TSVS with 3.3 X runtime enhancement.