Improve the Resolution and Parallel Performance of the Three-Dimensional Refine Algorithm in RELION Using CUDA and MPI
文献类型：期刊论文
| 作者 | Zhang, Jingrong2; Wang, Zihao2; Liu, Zhiyong1; Zhang, Fa1 |
| 刊名 | IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
 |
| 出版日期 | 2021-03-01 |
| 卷号 | 18期号:2页码:583-595 |
| 关键词 | Memory management Graphics processing units Arrays Statistical analysis Three-dimensional displays cryoEM RELION CUDA statistical method Top-k selection |
| ISSN号 | 1545-5963 |
| DOI | 10.1109/TCBB.2019.2929171 |
| 英文摘要 | 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. |
| 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 |
| 语种 | 英语 |
| WOS记录号 | WOS:000639652100007 |
| 出版者 | IEEE COMPUTER SOC |
| 源URL | [http://119.78.100.204/handle/2XEOYT63/17855]  |
| 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.Chinese Acad Sci, Inst Comp Technol, High Performance Comp Res Ctr, Beijing 100190, Peoples R China 2.Univ Chinese Acad Sci, Beijing 100039, 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. |
入库方式： OAI收割
来源：计算技术研究所
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