We present a novel, Linear Programming (LP) based scheduling algorithm that exploits heterogeneous multi-core architectures such as CPUs and GPUs to accelerate a wide variety of proximity queries. To represent complicated performance relationships between heterogeneous architectures and different computations of proximity queries, we propose a simple, yet accurate model that measures the expected running time of these computations. Based on this model, we formulate an optimization problem that minimizes the largest time spent on computing resources, and propose a novel, iterative LP-based scheduling algorithm. Since our method is general, we are able to apply our method into various proximity queries that have different characteristics. Our method achieves an order of magnitude performance improvement by using four different GPUs and two hexa-core CPUs over using a hexa-core CPU only. Unlike prior scheduling methods, our method continually improves the performance, as we add more computing resources. Also, our method achieves much higher performance improvement compared with prior methods as heterogeneity of computing resources is increased. We also show that our method provides results that are close to the performance provided by a conservative upper bound of the ideal throughput. These results demonstrate the efficiency and robustness of our algorithm that have not been achieved by prior methods.
山东省济南市章丘区文博路2号
齐鲁师范学院 genelibs生信实验室
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