Error-bounded lossy compression has been identified as a promising solution for significantly reducing scientific data volumes upon users' requirements on data distortion. For the existing scientific error-bounded lossy compressors, some of them (such as SPERR and FAZ) can reach fairly high compression ratios and some others (such as SZx, SZ, and ZFP) feature high compression speeds, but they rarely exhibit both high ratio and high speed meanwhile. In this paper, we propose HPEZ with newly-designed interpolations and quality-metric-driven auto-tuning, which features significantly improved compression quality upon the existing high-performance compressors, meanwhile being exceedingly faster than high-ratio compressors. The key contributions lie as follows: (1) We develop a series of advanced techniques such as interpolation re-ordering, multi-dimensional interpolation, and natural cubic splines to significantly improve compression qualities with interpolation-based data prediction. (2) The auto-tuning module in HPEZ has been carefully designed with novel strategies, including but not limited to block-wise interpolation tuning, dynamic dimension freezing, and Lorenzo tuning. (3) We thoroughly evaluate HPEZ compared with many other compressors on six real-world scientific datasets. Experiments show that HPEZ outperforms other high-performance error-bounded lossy compressors in compression ratio by up to 140% under the same error bound, and by up to 360% under the same PSNR. In parallel data transfer experiments on the distributed database, HPEZ achieves a significant performance gain with up to 40% time cost reduction over the second-best compressor.

To address the challenges raised by the data management of exascale scientific data, error-bounded lossy compression has been proposed and well-researched as a prominent solution. Among the existing works, a recent trend leverages wavelet transforms in the error-bounded lossy compression task to effectively capture long-term data correlations within the inputs. Applying those transforms as data preprocessors and decorrelators, wavelet-based lossy compressors have achieved optimized compression rate-distortion on several datasets. However, certain significant limitations of wavelet-based compressors have also been observed: On one hand, attributed to the high computational cost of wavelet transforms, wavelet-based compressors suffer from relatively low computational efficiencies compared to other state-of-the-art compressors. On the other hand, one certain type of wavelet transform cannot perform well on all variations of scientific data. Consequently, to further fine-tune the wavelet-based scientific data lossy compression, more in-depth and systematic research and analysis needs to be conducted. In this paper, based on the FAZ auto-tuning-based modular compression framework, we have integrated a great number of wavelet transforms into the framework and evaluated them with various real-world scientific datasets and fields. From the analysis of those evaluations and the comparison to existing state-of-the-art wavelet-based and non-wavelet-based error-bounded lossy compressors, we conclude and present several essential takeaways for designing and optimizing the wavelet-based scientific error-bounded lossy compressor.

The fast growth of computational power and scales of modern super-computing systems have raised great challenges for the management of exascale scientific data. To maintain the usability of scientific data, error-bound lossy compression is proposed and developed as an essential technique for the size reduction of scientific data with constrained data distortion. Among the diverse datasets generated by various scientific simulations, certain datasets cannot be effectively compressed by existing error-bounded lossy compressors with traditional techniques. The recent success of Artificial Intelligence has inspired several researchers to integrate neural networks into error-bounded lossy compressors. However, those works still suffer from limited compression ratios and/or extremely low efficiencies. To address those issues and improve the compression on the hard-to-compress datasets, in this paper, we propose SRNNSZ, which is a deep learning-based scientific error-bounded lossy compressor leveraging the hierarchical data grid expansion paradigm implemented by super-resolution neural networks. SRNN-SZ applies the most advanced super-resolution network HAT for its compression, which is free of time-costing per-data training. In experiments compared with various state-of-the-art compressors, SRNN-SZ achieves up to 75% compression ratio improvements under the same error bound and up to 80% compression ratio improvements under the same PSNR than the second-best compressor.

The K-means algorithm is one of the simplest and most universal clustering algorithms. Significant work has been carried out over several years to improve its performance in both academic and industrial applications. Researchers have optimized K-means not only on the algorithm level but also on the architecture level. Notably, GEMM, a rigorously studied matrix multiplication operation, has been used to speed up the Euclidean-distance calculations in the K-means algorithm. The Intel DAAL library currently provides a fast K-means implementation based on the Intel Math Kernel Library GEMM subroutine and low-level architecture information. However, in spite of utilizing the MKL GEMM subroutine and architecture properties, the performance of the state-of-the-art K-means implementation is still far from its hardware peak performance. This paper presents a faster fused-matrix K-means kernel that is superior to current K-means designs. Based on our experimental results, the fused matrix K-means kernel runs around 76% faster than the state-of-the-art Intel DAAL K-means algorithm and is able to achieve nearly double floating point performance on Intel x86-84 Ivy micro-architectures.

Feature selection is an important preprocessing step in data mining and pattern recognition. The neighborhood rough set (NRS) model is a widely-used rough set model for feature selection on continuous data. All currently known NRS models are defined on a distance metric — mostly the euclidean distance metric — which invalidates the NRS models in scenarios wherein the euclidean distance is ineffective, for example, while considering differing attribute weights. We first introduce the concept of space division of granular-rectangular, and then construct the neighborhood radius in our method by describing the relationship between child and parent spaces, which avoids the use of a distance metric and reduces the search space for the neighborhood radius. This greatly improves both the accuracy and efficiency of NRS. In addition, the upper and lower approximations of the granular-rectangular rough sets (GRRSs) comprise equivalence classes; this results in better performance of GRRS in knowledge representation compared with the traditional NRS. Experimental results on public benchmark datasets reveal that our method, GRRS, achieves higher accuracy than ten popular and state-of-the-art feature-selection methods, including two NRS algorithms. Moreover, GRRS outperforms the established NRS algorithms regarding efficiency, including the state-of-the-art NRS algorithm, GBNRS. All code has been released as an open libary called GRRS:https://github.com/syxiaa/GRRS.

Soft error, namely silent corruption of signal or datum in a computer system, cannot be caverlierly ignored as compute and communication density grow exponentially. Soft error detection has been studied in the context of enterprise computing, high-performance computing and more recently in convolutional neural networks related to autonomous driving.Deep learning recommendation systems (DLRMs) have by now become ubiquitous and serve billions of users per day. Nevertheless, DLRM-specific soft error detection methods are hitherto missing. To fill the gap, this paper presents the first set of soft-error detection methods for low-precision quantized-arithmetic operators in DLRM including general matrix multiplication (GEMM) and EmbeddingBag. A practical method must detect error and do so with low overhead lest reduced inference speed degrades user experience. Exploiting the characteristics of both quantized arithmetic and the operators, we achieved more than 95% detection accuracy for GEMM with an overhead below 20%. For EmbeddingBag, we achieved 99% effectiveness in significant-bit-flips detection with less than 10% of false positives, while keeping overhead below 26%.

Molecular dynamics (MD) has been widely used in today's 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 handing particle data beyond MD simulations.

Feature reduction is an important aspect of Big Data analytics on today’s ever-larger datasets. Rough sets are a classical method widely applied in attribute reduction. Most rough set algorithms use theprioridomain knowledge of a dataset to process continuous attributes through using a membership function. Neighborhood rough sets (NRS) replace the membership function with the concept of neighborhoods, allowing NRS to handle scenarios where noa prioriknowledge is available. However, the neighborhood radius of each object in NRS is fixed, and the optimization of the radius depends on grid searching. This diminishes both the efficiency and effectiveness, leading to a time complexity of not lower than$O(N^2)$O(N2). To resolve these limitations, granular ball neighborhood rough sets (GBNRS), a novel NRS method with time complexity$O(N)$O(N), is proposed. GBNRS adaptively generates a different neighborhood for each object, resulting in greater generality and flexibility in comparison to standard NRS methods. GBNRS is compared with the current state-of-the-art NRS method, FARNeMF, and find that GBNRS obtains both higher performance and higher classification accuracy on public benchmark datasets. All code has been released in the open source GBNRS library athttp://www.cquptshuyinxia.com/GBNRS.html.

In the past decades, various lossy compressors have been studied broadly due to the ever-increasing volume of data being produced by today’s scientific applications. SZ has been one of the best error-bounded lossy compressors ever raised, and it has a flexible framework that includes four adjustable steps: prediction, quantization, variable-length encoding, and lossless compression. In this paper, we improve the lossy compression performances of the SZ compression model by exploring different existing lossless compression techniques using the Squash data compression benchmark. Specifically, we first characterize the bytes outputted by the first three steps in SZ, then we investigate the best lossless compressor with different datasets and different error bounds. We perform our exploration by testing 8 widely used lossless compressors under different configurations together with SZ over five well-known scientific simulation datasets. Our experiments show that adopting the best-fit lossless compressor selected based on our analysis can improve the overall compression speed by up to 40% compared to the previous lossless compression technique used in SZ with the comparable quality of reconstructed data.

Today's scientific simulations are producing vast volumes of data that cannot be stored and transferred efficiently because of limited storage capacity, parallel I/O bandwidth, and network bandwidth. The situation is getting worse over time because of the ever-increasing gap between relatively slow data transfer speed and fast-growing computation power in modern supercomputers. Error-bounded lossy compression is becoming one of the most critical techniques for resolving the big scientific data issue, in that it can significantly reduce the scientific data volume while guaranteeing that the reconstructed data is valid for users because of its compression-error-bounding feature. In this paper, we present a novel error-bounded lossy compressor based on a state-of-the-art prediction-based compression framework. Our solution exhibits substantially better compression quality than all of the existing error-bounded lossy compressors, with comparable compression speed. Specifically, our contribution is threefold. (1) We provide an in-depth analysis of why the best-existing prediction-based lossy compressor can only minimally improve the compression quality. (2) We propose a dynamic spline interpolation approach with a series of optimization strategies that can significantly improve the data prediction accuracy, substantially improving the compression quality in turn. (3) We perform a thorough evaluation using six real-world scientific simulation datasets across different science domains to evaluate our solution vs. all other related works. Experiments show that the compression ratio of our solution is higher than that of the second-best lossy compressor by 20% 460% with the same error bound in most of the cases.

Efficient error-controlled lossy compressors are becoming critical to the success of today's large-scale scientific applications because of the ever-increasing volume of data produced by the applications. In the past decade, many lossless and lossy compressors have been developed with distinct design principles for different scientific datasets in largely diverse scientific domains. In order to support researchers and users assessing and comparing compressors in a fair and convenient way, we establish a standard compression assessment benchmark - Scientific Data Reduction Benchmark (SDRBench)1. SDRBench contains a vast variety of real-world scientific datasets across different domains, summarizes several critical compression quality evaluation metrics, and integrates many state-of-the-art lossy and lossless compressors. We demonstrate evaluation results using SDRBench and summarize six valuable takeaways that are helpful to the in-depth understanding of lossy compressors.

The existing noise detection methods required the classifiers or distance measurements or data overall distribution, and `curse of dimensionality' and other restrictions made them insufficiently effective in complex data, e.g., different attribute weights, high-dimensionality, containing feature noise, nonlinearity, etc. This is also the main reason that the existing noise filtering methods were not widely applied and formed an effective learning framework. To address this problem, we propose here a complete and efficient random forest method (CRF) specifically for the class noise detection by simulating the grid generation and expansion. The CRF is not based on distance measures or overall distribution or classifiers; besides, the voting mechanism makes it able to effectively process datasets containing feature noise. Furthermore, we introduce CRF based class noise filtering learning framework (CRF-NFL) and derive its mathematical model. The framework is then applied to many widely used classifiers including some state-of-the-art algorithms, e.g., k-means tree, GBDT, and XGBoost. Moreover, its parallelized is designed for large-scale data. The CRF-NFL show much better generalizability than the conventional classifiers and the relative density-based method, which is the most effective noise filtering method as far as we know. All research has formed an open source library, called CRF-NFL: http://www.cquptshuyinxia.com/CRF-NFL.html.

Variations in High Performance Computing (HPC) system software configurations mean that applications are typically configured and built for specific HPC environments. Building applications can require a significant investment of time and effort for application users and requires application users to have additional technical knowledge. Linux container technologies such as Docker and Charliecloud bring great benefits to the application development, build and deployment processes. While cloud platforms already widely support containers, HPC systems still have non-uniform support of container technologies. In this work, we propose a unified runtime framework - Build and Execution Environment (BEE) across both HPC and cloud platforms that allows users to run their containerized HPC applications across all supported platforms without modification. We design four BEE backends for four different classes of HPC or cloud platform so that together they cover the majority of mainstream computing platforms for HPC users. Evaluations show that BEE provides an easy-to-use unified user interface, execution environment, and comparable performance.

Today's N-body simulations are producing extremely large amounts of data. The Hardware/Hybrid Accelerated Cosmology Code (HACC), for example, may simulate trillions of particles, producing tens of petabytes of data to store in a parallel file system, according to the HACC users. In this paper, we design and implement an efficient, in situ error-bounded lossy compressor to significantly reduce the data size for N-body simulations. Not only can our compressor save significant storage space for N-body simulation researchers, but it can also improve the I/O performance considerably with limited memory and computation overhead. Our contribution is threefold. (1) We propose an efficient data compression model by leveraging the consecutiveness of the cosmological data in both space and time dimensions as well as the physical correlation across different fields. (2) We propose a lightweight, efficient alignment mechanism to align the disordered particles across adjacent snapshots in the simulation, which is a fundamental step in the whole compression procedure. We also optimize the compression quality by exploring best-fit data prediction strategies and optimizing the frequencies of the space-based compression vs. time-based compression. (3) We evaluate our compressor using both a cosmological simulation package and molecular dynamics simulation data-two major categories in the N-body simulation domain. Experiments show that under the same distortion of data, our solution produces up to 43% higher compression ratios on the velocity field and up to 300% higher on the position field than do other state-of-the-art compressors (including SZ, ZFP, NUMARCK, and decimation). With our compressor, the overall I/O time on HACC data is reduced by up to 20% compared with the second-best compressor.

Today's scientific simulations require a significant reduction of the data size because of extremely large volumes of data they produce and the limitation of storage bandwidth and space. If the compression is set to reach a high compression ratio, however, the reconstructed data are often distorted too much to tolerate. In this paper, we explore a new compression strategy that can effectively control the data distortion when significantly reducing the data size. The contribution is threefold. (1) We propose an adaptive compression framework to select either our improved Lorenzo prediction method or our optimized linear regression method dynamically in different regions of the dataset. (2) We explore how to select them accurately based on the data features in each block to obtain the best compression quality. (3) We analyze the effectiveness of our solution in details using four real-world scientific datasets with 100+ fields. Evaluation results confirm that our new adaptive solution can significantly improve the rate distortion for the lossy compression with fairly high compression ratios. The compression ratio of our compressor is 1.5X~8X as high as that of two other leading lossy compressors (SZ and ZFP) with the same peak single-to-noise ratio (PSNR), in the high-compression cases. Parallel experiments with 8,192 cores and 24 TB of data shows that our solution obtains 1.86X dumping performance and 1.95X loading performance compared with the second-best lossy compressor, respectively.

In situ lossy compression allowing user-controlled data loss can significantly reduce the I/O burden. For large-scale N-body simulations where only one snapshot can be compressed at a time, the lossy compression ratio is very limited because of the fairly low spatial coherence of the particle data. In this work, we assess the state-of-the-art single-snapshot lossy compression techniques of two common N-body simulation models: cosmology and molecular dynamics. We design a series of novel optimization techniques based on the two representative real-world N-body simulation codes. For molecular dynamics simulation, we propose three compression modes (i.e., best speed, best tradeoff, best compression mode) that can refine the tradeoff between the compression rate (a.k.a., speed/throughput) and ratio. For cosmology simulation, we identify that our improved SZ is the best lossy compressor with respect to both compression ratio and rate. Its compression ratio is higher than the second-best compressor by 11% with comparable compression rate. Experiments with up to 1024 cores on the Blues supercomputer at Argonne show that our proposed lossy compression method can reduce I/O time by 80% compared with writing data directly to a parallel file system and outperforms the second-best solution by 60%. Moreover, our proposed lossy compression methods have the best rate-distortion with reasonable compression errors on the tested N-body simulation data compared with state-of-the-art compressors.