Improve the Resolution and Parallel Performance of the Three-Dimensional Refine Algorithm in RELION Using CUDA and MPI

doi:10.1109/TCBB.2019.2929171

	Improve the Resolution and Parallel Performance of the Three-Dimensional Refine Algorithm in RELION Using CUDA and MPI
	Zhang, Jingrong 1; Wang, Zihao 1; Liu, Zhiyong 2; Zhang, Fa 2
	2021-03-01
发表期刊	IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
ISSN	1545-5963
卷号	18 期号:2 页码:583-595
摘要	In cryo-electron microscopy, RELION is a powerful tool for high-resolution reconstruction. Due to the complicated imaging procedure and the heterogeneity of particles, some of the selected particle images offer more disturbing information than others. However, in the current RELION, all these particle images are treated equally. In our work, we extend RELION's model with one scalar parameter to score the contribution of a particle depending on the error between the experimental particle and the corresponding reprojection. This scores down weight potentially poor particles, hence accelerating the convergence. Besides, by now there is no sophisticated memory management system for RELION, fragmentation on GPU will increase with iterations, eventually crashing the program. In our work, we designed the stack-based memory management system to guarantee the stability of RELION and to optimize the memory usage condition. Also, to reduce memory usage, we developed a customized compressed data structure for the memory-demanding weight array. In addition, to speed up the GPU version of RELION, we proposed two highly efficient parallel algorithms for weight calculation algorithm and weight selection algorithm. Experiments show that compared with RELION, the optimized three-dimensional refine algorithm can speed up the converge procedure, the memory system can avoid memory fragmentation, and a better speed-up ratio can be obtained.
关键词	Memory management Graphics processing units Arrays Statistical analysis Three-dimensional displays cryoEM RELION CUDA statistical method Top-k selection
DOI	10.1109/TCBB.2019.2929171
收录类别	SCI
语种	英语
资助项目	National Key Research and Development Program of China[2017YFA0504702] ; NSFC[U1611263] ; NSFC[U1611261] ; NSFC[61232001] ; NSFC[61472397] ; NSFC[61502455] ; NSFC[61672493] ; Special Program for Applied Research on Super Computation of the NSFC-Guangdong Joint Fund (the second phase)
WOS研究方向	Biochemistry & Molecular Biology ; Computer Science ; Mathematics
WOS类目	Biochemical Research Methods ; Computer Science, Interdisciplinary Applications ; Mathematics, Interdisciplinary Applications ; Statistics & Probability
WOS记录号	WOS:000639652100007
出版者	IEEE COMPUTER SOC
引用统计
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/17856
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Zhang, Fa
作者单位	1.Univ Chinese Acad Sci, Beijing 100039, Peoples R China 2.Chinese Acad Sci, Inst Comp Technol, High Performance Comp Res Ctr, Beijing 100190, Peoples R China
推荐引用方式 GB/T 7714	Zhang, Jingrong,Wang, Zihao,Liu, Zhiyong,et al. Improve the Resolution and Parallel Performance of the Three-Dimensional Refine Algorithm in RELION Using CUDA and MPI[J]. IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS,2021,18(2):583-595.
APA	Zhang, Jingrong,Wang, Zihao,Liu, Zhiyong,&Zhang, Fa.(2021).Improve the Resolution and Parallel Performance of the Three-Dimensional Refine Algorithm in RELION Using CUDA and MPI.IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS,18(2),583-595.
MLA	Zhang, Jingrong,et al."Improve the Resolution and Parallel Performance of the Three-Dimensional Refine Algorithm in RELION Using CUDA and MPI".IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 18.2(2021):583-595.