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- W1498943610 abstract "In this paper, we introduce the GPU acceleration of dRMSD algorithm, used to compare different structures of a molecule. Comparing to multithreaded CPU implementation, we have reached 13.4× speedup in clustering and 62.7× speedup in 1∶1 dRMSD computation using mid-end GPU. The dRMSD computation exposes strong memory locality and thus is compute-bound. Along with conservative implementation using shared memory, we have decided to implement variants of the algorithm using GPU caches to maintain memory locality. Our implementation using cache reaches 96.5% and 91.6% of shared memory performance on Fermi and Maxwell, respectively. We have identified several performance pitfalls related to cache blocking in compute-bound codes and suggested optimization techniques to improve the performance." @default.
- W1498943610 created "2016-06-24" @default.
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- W1498943610 date "2015-07-01" @default.
- W1498943610 modified "2023-09-26" @default.
- W1498943610 title "Acceleration of dRMSD calculation and efficient usage of GPU caches" @default.
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- W1498943610 doi "https://doi.org/10.1109/hpcsim.2015.7237020" @default.
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