mD3DOCKxb: An Ultra-Scalable CPU-MIC Coordinated Virtual Screening Framework


Molecular docking is an important method in computational drug discovery. In large-scale virtual screening, millions of small drug-like molecules (chemical compounds) are compared against a designated target protein (receptor). Depending on the utilized docking algorithm for screening, this can take several weeks on conventional HPC systems. However, for certain applications including large-scale screening tasks for newly emerging infectious diseases such high runtimes can be highly prohibitive. In this paper, we investigate how the massively parallel neo-heterogeneous architecture of Tianhe-2 Supercomputer consisting of thousands of nodes comprising CPUs and MIC coprocessors that can efficiently be used for virtual screening tasks. Our proposed approach is based on a coordinated parallel framework called mD3DOCKxb in which CPUs collaborate with MICs to achieve high hardware utilization. mD3DOCKxb comprises a novel efficient communication engine for dynamic task scheduling and load balancing between nodes in order to reduce communication and I/O latency. This results in a highly scalable implementation with parallel efficiency of over 84% (strong scaling) when executing on 8,000 Tianhe-2 nodes comprising 192,000 CPU cores and 1,368,000 MIC cores.

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@article{Peng2017mD3DOCKxbAU, title={mD3DOCKxb: An Ultra-Scalable CPU-MIC Coordinated Virtual Screening Framework}, author={Shaoliang Peng and Xiaoyu Zhang and Shunyun Yang and Wenhe Su and Zhiqiang Zhang and Dong Dong and Kai Lu and Yutong Lu and Xiangke Liao and Bertil Schmidt and Weiliang Zhu and Kuan-Ching Li}, journal={2017 17th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGRID)}, year={2017}, pages={671-676} }