PaSTRI: Error-Bounded Lossy Compression for Two-Electron Integrals in Quantum Chemistry
PaSTRI: Error-Bounded Lossy Compression for Two-Electron Integrals in Quantum Chemistry
复制标题
PaSTRI：量子化学中双电子积分的误差有界有损压缩
DOI：
10.1109/cluster.2018.00013
复制
发表时间：
2018
期刊：
影响因子：
--
通讯作者：
F. Cappello
中科院分区：
文献类型：
--
作者：
A. M. Gok;S. Di;Y. Alexeev;Dingwen Tao;V. Mironov;Xin Liang;F. Cappello
在典型的并行量子化学模拟中，双电子排斥积分的计算是最关键和最耗时的步骤。这样的计算有大量的计算和存储需求，随着化学体系的大小，其规模为O(N^4)。压缩积分的数据并将其存储在磁盘上可以避免昂贵的重新计算，从而显著加快整体量子化学计算；但它需要快速的压缩算法。为此，我们开发了双电子斥力积分的模式缩放算法，并在数据压缩包SZ中实现了该算法。PaSTRI利用积分数据集中的潜在模式特征，并优化积分存储所需的适当位数的计算。我们使用量子化学程序GAMESS生成的积分数据集评估了PaSTRI。结果表明，在满足用户要求的同时，在保持10^-10绝对精度的情况下，以较低的开销获得了16.8的压缩比。
Computation of two-electron repulsion integrals is the critical and the most time-consuming step in a typical parallel quantum chemistry simulation. Such calculations have massive computing and storage requirements, which scale as O(N^4) with the size of a chemical system. Compressing the integral's data and storing it on disk can avoid costly recalculation, significantly speeding the overall quantum chemistry calculations; but it requires a fast compression algorithm. To this end, we developed PaSTRI (Pattern Scaling for Two-electron Repulsion Integrals) and implemented the algorithm in the data compression package SZ. PaSTRI leverages the latent pattern features in the integral dataset and optimizes the calculation of the appropriate number of bits required for the storage of the integral. We have evaluated PaSTRI using integral datasets generated by the quantum chemistry program GAMESS. The results show an excellent 16.8 compression ratio with low overhead, while maintaining 10^-10 absolute precision based on user's requirement.