Large-scale Parallel Design for Cryo-EM Structure Determination on Heterogeneous Many-core Architectures

Liang Qiao, Hongkun Yu, Kunpeng Wang, Ruixin Sun, Wenlai Zhao, Haohuan Fu, Guangwen Yang

Abstract: Cryo-EM structure determination is the most important research area in structural biology. With the development of cryo-electron microscopy, the resolution has been enhanced significantly, which leads to the huge computation to reconstruct the biomolecule in recent years. In this paper, we present a large-scale parallel design for Cryo-EM structure determination on heterogeneous many-core architectures. A novel task parallel strategy is proposed to reduce the redundant computation and improve the scalability on large-scale systems. Further, We distribute the reconstruction model to each node and rearrange the data layout to achieve high parallel efficiency and reduce the memory footprint. The proposed comprehensive parallel design shows highly parallel efficiency and scalability on large-scale heterogeneous architectures, which could significantly accelerate the whole period of Cryo-EM structure determination process.