2022Wang Thunder

Citation

Wang, Zhao / Ruan, Huabin / Yang, Guangwen / Li, Xueming. Parallelizing the cryo-EM structure determination in THUNDER using GPU cluster. 2022. Engineering Reports. p. e12601

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.

Links

https://onlinelibrary.wiley.com/doi/full/10.1002/eng2.12601