Parallelizing the cryo‐EM structure determination in THUNDER using GPU cluster
Abstract Electron cryo‐microscopy (cryo‐EM) is a powerful tool utilized by biologists for understanding the mysteries of life. However, obtaining high‐resolution 3D reconstructions from innumerable noisy images of macromolecules is an extremely complicated task, involving massive image analysis and...
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| Format: | Article |
| Language: | English |
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Wiley
2025-01-01
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| Series: | Engineering Reports |
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| Online Access: | https://doi.org/10.1002/eng2.12601 |
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| _version_ | 1832576628175142912 |
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| author | Zhao Wang Huabin Ruan Guangwen Yang Xueming Li |
| author_facet | Zhao Wang Huabin Ruan Guangwen Yang Xueming Li |
| author_sort | Zhao Wang |
| collection | DOAJ |
| description | Abstract Electron cryo‐microscopy (cryo‐EM) is a powerful tool utilized by biologists for understanding the mysteries of life. However, obtaining high‐resolution 3D reconstructions from innumerable noisy images of macromolecules is an extremely complicated task, involving massive image analysis and calculation on a computing cluster. Although extensive efforts have been made for improving the computational efficiency, methods for completely utilizing the computing resources are still challenging for modern cryo‐EM programs. Here, we designed a new computing approach specialized for GPU to optimize and maximize the computing power of a single GPU, multiple GPU, and the GPU cluster, highlighted by a well‐designed cache structure and mixed computing precision of single‐precision and double‐precision. Our approaches achieved remarkable improvement in performance and linear scalability. At an identical cost of the hardware, three‐fold more speed‐up was achieved. The average parallel efficiency can increase up to 84% when multiple GPU configurations are parallelized. |
| format | Article |
| id | doaj-art-7dc2158ddd6b4bd1a5e3bed221fc08ad |
| institution | Kabale University |
| issn | 2577-8196 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | Engineering Reports |
| spelling | doaj-art-7dc2158ddd6b4bd1a5e3bed221fc08ad2025-01-31T00:22:48ZengWileyEngineering Reports2577-81962025-01-0171n/an/a10.1002/eng2.12601Parallelizing the cryo‐EM structure determination in THUNDER using GPU clusterZhao Wang0Huabin Ruan1Guangwen Yang2Xueming Li3Department of Computer Science and Technology Tsinghua University Beijing ChinaSchool of Life Sciences Tsinghua University Beijing ChinaDepartment of Computer Science and Technology Tsinghua University Beijing ChinaSchool of Life Sciences Tsinghua University Beijing ChinaAbstract Electron cryo‐microscopy (cryo‐EM) is a powerful tool utilized by biologists for understanding the mysteries of life. However, obtaining high‐resolution 3D reconstructions from innumerable noisy images of macromolecules is an extremely complicated task, involving massive image analysis and calculation on a computing cluster. Although extensive efforts have been made for improving the computational efficiency, methods for completely utilizing the computing resources are still challenging for modern cryo‐EM programs. Here, we designed a new computing approach specialized for GPU to optimize and maximize the computing power of a single GPU, multiple GPU, and the GPU cluster, highlighted by a well‐designed cache structure and mixed computing precision of single‐precision and double‐precision. Our approaches achieved remarkable improvement in performance and linear scalability. At an identical cost of the hardware, three‐fold more speed‐up was achieved. The average parallel efficiency can increase up to 84% when multiple GPU configurations are parallelized.https://doi.org/10.1002/eng2.126013D reconstructioncryo‐EMGPU optimization |
| spellingShingle | Zhao Wang Huabin Ruan Guangwen Yang Xueming Li Parallelizing the cryo‐EM structure determination in THUNDER using GPU cluster Engineering Reports 3D reconstruction cryo‐EM GPU optimization |
| title | Parallelizing the cryo‐EM structure determination in THUNDER using GPU cluster |
| title_full | Parallelizing the cryo‐EM structure determination in THUNDER using GPU cluster |
| title_fullStr | Parallelizing the cryo‐EM structure determination in THUNDER using GPU cluster |
| title_full_unstemmed | Parallelizing the cryo‐EM structure determination in THUNDER using GPU cluster |
| title_short | Parallelizing the cryo‐EM structure determination in THUNDER using GPU cluster |
| title_sort | parallelizing the cryo em structure determination in thunder using gpu cluster |
| topic | 3D reconstruction cryo‐EM GPU optimization |
| url | https://doi.org/10.1002/eng2.12601 |
| work_keys_str_mv | AT zhaowang parallelizingthecryoemstructuredeterminationinthunderusinggpucluster AT huabinruan parallelizingthecryoemstructuredeterminationinthunderusinggpucluster AT guangwenyang parallelizingthecryoemstructuredeterminationinthunderusinggpucluster AT xuemingli parallelizingthecryoemstructuredeterminationinthunderusinggpucluster |