Rate-distortion Balanced Data Compression for Wireless Sensor Networks

This paper presents a data compression algorithm with error bound guarantee for wireless sensor networks (WSNs) using compressing neural networks. The proposed algorithm minimizes data congestion and reduces energy consumption by exploring spatio-temporal correlations among data samples. The adaptive rate-distortion feature balances the compressed data size (data rate) with the required error bound guarantee (distortion level). This compression relieves the strain on energy and bandwidth resources while collecting WSN data within tolerable error margins, thereby increasing the scale of WSNs. The algorithm is evaluated using real-world datasets and compared with conventional methods for temporal and spatial data compression. The experimental validation reveals that the proposed algorithm outperforms several existing WSN data compression methods in terms of compression efficiency and signal reconstruction. Moreover, an energy analysis shows that compressing the data can reduce the energy expenditure, and hence expand the service lifespan by several folds.Comment: arXiv admin note: text overlap with arXiv:1408.294

Optimizing Lossy Compression Rate-Distortion from Automatic Online Selection between SZ and ZFP

With ever-increasing volumes of scientific data produced by HPC applications, significantly reducing data size is critical because of limited capacity of storage space and potential bottlenecks on I/O or networks in writing/reading or transferring data. SZ and ZFP are the two leading lossy compressors available to compress scientific data sets. However, their performance is not consistent across different data sets and across different fields of some data sets: for some fields SZ provides better compression performance, while other fields are better compressed with ZFP. This situation raises the need for an automatic online (during compression) selection between SZ and ZFP, with a minimal overhead. In this paper, the automatic selection optimizes the rate-distortion, an important statistical quality metric based on the signal-to-noise ratio. To optimize for rate-distortion, we investigate the principles of SZ and ZFP. We then propose an efficient online, low-overhead selection algorithm that predicts the compression quality accurately for two compressors in early processing stages and selects the best-fit compressor for each data field. We implement the selection algorithm into an open-source library, and we evaluate the effectiveness of our proposed solution against plain SZ and ZFP in a parallel environment with 1,024 cores. Evaluation results on three data sets representing about 100 fields show that our selection algorithm improves the compression ratio up to 70% with the same level of data distortion because of very accurate selection (around 99%) of the best-fit compressor, with little overhead (less than 7% in the experiments).Comment: 14 pages, 9 figures, first revisio

MDZ: An Efficient Error-Bounded Lossy Compressor for Molecular Dynamics

Molecular dynamics (MD) has been widely used in today\u27s scientific research across multiple domains including materials science, biochemistry, biophysics, and structural biology. MD simulations can produce extremely large amounts of data in that each simulation could involve a large number of atoms (up to trillions) for a large number of timesteps (up to hundreds of millions). In this paper, we perform an in-depth analysis of a number of MD simulation datasets and then develop an efficient error-bounded lossy compressor that can significantly improve the compression ratios. The contributions are fourfold. (1) We characterize a number of MD datasets and summarize two commonly used execution models. (2) We develop an adaptive error-bounded lossy compression framework (called MDZ), which can optimize the compression for both execution models adaptively by taking advantage of their specific characteristics. (3) We compare our solution with six other state-of-the-art related works by using three MD simulation packages each with multiple configurations. Experiments show that our solution has up to 233 % higher compression ratios than the second-best lossy compressor in most cases. (4) We demonstrate that MDZ is fully capable of handling particle data beyond MD simulations

Toward Resilience and Data Reduction in Exascale Scientific Computing

Because of the ever-increasing execution scale, reliability and data management are becoming more and more important for scientific applications. On the one hand, exascale systems are anticipated to be more susceptible to soft errors ,e.g. silent data corruptions, due to the reduction in the size of transistors and the increase of the number of components. These errors will lead to corrupted results without warning, making the output of the computation untrustable. On the other hand, large volumes of highly variable data are produced by scientific computing with high velocity on exascale systems or advanced instruments, and the I/O time on storing these data is prohibitive due to the I/O bottleneck in parallel file systems. In this work, we leverage algorithm-based fault tolerance (ABFT) and error-bound lossy compression to tackle the two problems, in order to support efficient scientific computing on exascale systems.We propose an efficient fault tolerant scheme to tolerant soft errors in Fast Fourier Transform (FFT), one of the most important computation kernels widely used in scientific computing. Traditional redundancy approaches will at least double the execution time or resources, limiting the usage in practice because of the large overhead. Previous works on offline ABFT algorithms for FFT mitigate this problem by providing resilient FFT with lower overhead, but these algorithms fail to make progress in vulnerable environments with high error rates because they can only detect and correct errors after the whole computation finishes. We propose an online ABFT scheme for large-scale FFT inspired by the divide-and-conquer nature of the FFT computation. We devise fault tolerant schemes for both computational and memory errors in FFT, with both serial and parallel optimizations. Experimental results demonstrate that the proposed approach provides more timely error detection and recovery as well as better fault coverage with less overhead, compared to the offline ABFT algorithm.To alleviate the I/O bottleneck in the parallel file systems, we work on a prediction-based error-bounded lossy compressor to significantly reduce the size of scientific datasets while retaining the accuracy of the decompressed data, with adaptive prediction algorithms and compression models. We first propose a regression-based predictor for better prediction accuracy than traditional approaches under large error bounds, followed by an adaptive algorithm that dynamically selects between the traditional Lorenzo predictor and the proposed regression-based predictor, leading to very high compression ratios with little visual distortion. We further unify the prediction-based model and transform-baed model by using transform-based compressors as a predictor, with novel optimizations toward efficient coefficient encoding for both the two models. The proposed adaptive multi-algorithm design provides better compression ratios given the same distortion, significantly reducing storage requirements and I/O time.We further adapt the compression algorithms and compressors to different requirements and/or objectives in realistic scenarios. We leverage a logarithmic transform to precondition the data, which turns a relative-error-bound compression problem into an absolute-error-bound compression problem. This transform aligns two different error requirements while improving the compression quality, efficiently reducing the workload for compressor design. We also correlate the compression algorithm with system information to achieve better I/O performance compared to traditional single compressor deployment. These studies further improve the efficiency of lossy compression from the perspective of efficient I/O in the context of scientific simulation, making scientific applications running on exascale systems more efficient