Scientific applications generate an unprecedented volume of data, overwhelming the network and file systems’ bandwidth and posing challenges for efficient and scalable data retrieval and analysis. Progressive data compression offers a promising solution by enabling on-demand retrieval at reduced size. However, existing progressive methods either fail to bound the errors in essential quantities of interest (QoIs) derived from raw data or suffer from suboptimal retrieval efficiency. In this work, we propose QProR, an efficient QoI-based progressive framework that optimizes progressive retrieval for target QoIs. Our key contributions include: (1) a systematic framework that integrates error-controlled lossy compressors with bitplane encoding while decoupling the two processes for high flexibility and adaptability; (2) a novel weighted bitplane encoding method which incorperates QoI knowledge into data refactoring to enhance retrieval efficiency; (3) an optimized retrieval strategy that accounts for the varying impacts of different variables on multivariate QoIs; (4) comprehensive evaluations using six real-world datasets from multiple scientific applications and thorough comparisons against state of the arts. Experimental results demonstrate that QProR achieves up to \(80.38\%\) reduction in the retrieval size under the same requested QoI error tolerance, when compared with the best-performing existing methods. When transferring 384 GB of scientific data to remote sites, QProR delivers up to 1.68 × speedup in the end-to-end data transfer performance.

Error-controlled lossy compressors have been widely used in scientific applications to reduce the unprecedented size of scientific data while keeping data distortion within a user-specified threshold. While they significantly mitigate the pressure for data storage and transmission, they prolong the time to access the data because decompression is required to transform the binary compressed data into meaningful floating-point numbers. This incurs noticeable overhead for common analytical operations on scientific data that extract or derive useful information, because the time cost of the operations could be much lower than that of decompression. In this work, we design an error-controlled lossy compression and analytical framework that features multi-stage decompression and homomorphic analytical operation algorithms on intermediate decompressed data for reduced data access latency. Our contributions are threefold. (1) We abstract a generic compression pipeline with partial decompression to multiple intermediate data representations and implement four instances based on state-of-the-art high-throughput scientific data compressors. (2) We carefully design homomorphic algorithms to enable direct operations on intermediate decompressed data for three types of analytical operations on scientific data. (3) We evaluate our approach using five real-world scientific datasets. Experimental evaluations demonstrate that our method achieves significant speedups when performing analytical operations on compressed scientific data across all three targeted analytical operation types.

In this paper, we present a novel compression framework, TFZ, that preserves the topology of 2D symmetric and asymmetric second-order tensor fields defined on flat triangular meshes. A tensor field assigns a tensor-a multi-dimensional array of numbers-to each point in space. Tensor fields, such as the stress and strain tensors, and the Riemann curvature tensor, are essential to both science and engineering. The topology of tensor fields captures the core structure of data, and is useful in various disciplines, such as graphics (for manipulating shapes and textures) and neuroscience (for analyzing brain structures from diffusion MRI). Lossy data compression may distort the topology of tensor fields, thus hindering downstream analysis and visualization tasks. TFZ ensures that certain topological features are preserved during lossy compression. Specifically, TFZ preserves degenerate points essential to the topology of symmetric tensor fields and retains eigenvector and eigenvalue graphs that represent the topology of asymmetric tensor fields. TFZ scans through each cell, preserving the local topology of each cell, and thereby ensuring certain global topological guarantees. We showcase the effectiveness of our framework in enhancing the lossy scientific data compressors SZ3 and SPERR.

Scientific applications are generating unprecedented volumes of data that overwhelm storage and transmission systems, posing significant challenges for the design of data management tools and scientific databases. Lossy compression has emerged as a promising strategy to address this problem, but most existing compressors fail to preserve the topology of scientific data, leading to inaccuracies in downstream analyses and potentially erroneous scientific conclusions. In this work, we present a methodology for fully preserving the topology, specifically, Morse-Smale complexes (MSCs), in lossy-compressed 2D and 3D scalar field data from scientific simulations. We generalize the edit-based strategy introduced in MSz [1] (a previous method that preserves only segmentations and cannot preserve saddles or separatrices) by extending the framework to the full MSCs, including all critical points and separatrices. Our approach corrects the MSCs in the decompressed output of any error-bounded lossy compressor (e.g., SZ3 or ZFP), referred to as the base compressor, using an iterative editing strategy that preserves all critical points and their connectivity via separatrices. During compression, we generate a sequence of quantized edits that are applied to the decompressed output, ensuring accurate preservation of topological features while maintaining the error within prescribed bounds. The strategy iteratively fixes critical points and separatrices in alternating steps until convergence is achieved in a finite number of iterations. To meet diverse application needs, our method offers flexible options (e.g., whether to preserve the geometry of separatrices) that balance compression efficiency with feature preservation. To reduce computation time, we leverage GPU parallelism to accelerate each component of the workflow. Experiments on multiple datasets demonstrate that our method achieves 100% preservation of Morse-Smale complexes.

Data compression is a powerful solution for addressing big data challenges in database and data management. In scientific data compression for vector fields, preserving topological information is essential for accurate analysis and visualization. The topological skeleton, a fundamental component of vector field topology, consists of critical points and their connectivity (i.e., separatrices). While previous work has focused on preserving critical points in error-controlled lossy compression, little attention has been given to preserving separatrices, which are equally important. In this work, we introduce TspSZ, an efficient error-bounded lossy compression framework designed to preserve both critical points and separatrices. Our key contributions are threefold. First, we propose TspSZ, a topological-skeleton-preserving lossy compression framework that integrates two algorithms, enabling existing critical-point-preserving compressors to also retain separatrices, significantly enhancing their topology preservation capabilities. Second, we optimize TspSZ for efficiency through tailored improvements and parallelization. Specifically, we introduce a new error control mechanism to achieve high compression ratios and implement a shared-memory parallelization strategy to boost compression throughput. Third, we evaluate TspSZ against state-of-the-art lossy and lossless compressors using four real-world scientific datasets. Experimental results show that TspSZ achieves compression ratios of up to 7.7× while effectively preserving the topological skeleton, ensuring efficient storage and transmission of scientific data without compromising topological integrity.

The rapid growth in scientific data generation is outpacing advancements in computing systems necessary for efficient storage, transfer, and analysis, particularly in the context of exascale computing. With the deployment of first-generation exascale computing systems and next-generation experimental facilities, this gap is widening and necessitates effective data reduction techniques to manage enormous data volumes. Over the past decade, various data reduction methods, including lossless compression, error-controlled lossy compression, and data refactoring, have been developed to accelerate I/O in scientific workflows. Despite significant reductions in data volume, these methods introduce considerable computational overhead, which can become the new bottleneck in data processing. To mitigate this, GPU-accelerated data reduction algorithms have been introduced. However, challenges remain in their integration into exascale workflows, including limited portability across different GPU architectures, substantial memory transfer overhead, and reduced scalability on dense multi-GPU systems. To address these challenges, we propose HPDR, a high-performance and portable data reduction framework. HPDR is designed to enable the execution of state-of-the-art reduction algorithms across diverse processor architectures while reducing memory transfer overhead to 2.3 % of the original, resulting in up to$3.5 \times$faster throughput compared to existing solutions. It also achieves up to 96% of the theoretical speedup in multi-GPU settings. In addition, evaluations on accelerating I/O operations at scale up to 1,024 nodes of the Frontier supercomputer demonstrate that HPDR can achieve up to$103\ \text{TB} / \mathrm{s}$reduction throughput, providing up to$4 \times$acceleration in parallel I/O performance compared to existing data reduction routines. This work highlights the potential of HPDR to significantly enhance data reduction efficiency in exascale computing environments.

Large-scale scientific simulations produce unprecedented amounts of data using high-performance computing systems, leading to severe problems in data storage, I/O, and communication. To address the data movement challenge, errorcontrolled lossy compression has been proposed to significantly reduce the data size while retaining the data quality. Recently, interpolation-based compressors, including MGARD, SZ3, QoZ, and HPEZ, have stood out due to their efficiency in obtaining relatively high compression ratios with decent compression and decompression throughput. Nevertheless, these methods focus on data decorrelation in the compression pipeline yet overlook the correlation of the quantization indices generated after decorrelation. In this paper, we develop a generic framework that can use the correlation of quantization indices to significantly improve the compression ratios for state-of-the-art interpolation-based error-bounded lossy compressors. Our contributions are threefold: (1) We carefully characterized the quantization index array produced by the interpolation-based compressors and identified the unused correlation; (2) We designed a generic quantization index prediction method to exploit such correlation, which leads to improved compression ratio with only minor degradation in throughput; (3) We integrate our method into 4 state-of-theart interpolation-based compressors and evaluate them using 5 real-world datasets. Experimental results demonstrate that the proposed method improves the compression ratios of the base compressors by up to 95% while keeping the same quality. It also leads to 16% improvement in end-to-end data transfer performance under a parallel setting.

Today's scientific applications are producing vast amounts of data with cutting-edge high-performance computing systems and high-resolution instruments, causing severe problems in data transmission and storage. While error-controlled data compression is regarded as a direct way to solve the problem, most existing compressors are designed for data from structured meshes. In this work, we propose a generic framework to enable efficient error-controlled compression for scientific data from unstructured meshes. The contributions are four-fold: (1) We design a prediction-based framework with additional preprocessing stages to better incorporate mesh information. (2) We propose three families of prediction methods for unstructured meshes and integrate them into the framework, which yields high prediction accuracy and thus significantly improves the compression ratios and quality. (3) We enhance our framework by enabling invalid node processing and feature preservation. (4) We evaluate our approaches using five datasets from real-world applications and compare them with state-of-the-art error-controlled lossy compressors. Experiments demonstrate that the proposed compression methods deliver up to$26.36 \times, 8.24 \times$, and$2.56 \times$compression ratios over existing compressors under the same error bound, Peak Signal-to-Noise Ratios, and critical point preservation levels, respectively. This leads to$1.63 \times$performance speedup in the end-to-end data transfer on Globus.

Over the last nearly 20 years, lossy compression has become an essential aspect of HPC applications’ data pipelines, allowing them to overcome limitations in storage capacity and bandwidth and, in some cases, increase computational throughput and capacity. However, with the adoption of lossy compression comes the requirement to assess and control the impact lossy compression has on scientific outcomes. In this work, we take a major step forward in describing the state of practice and by characterizing workloads. We examine applications’ needs and compressors’ capabilities across 9 different supercomputing application domains. We present 24 takeaways that provide best practices for applications, operational impacts for facilities achieving compressed data, and gaps in application needs not addressed by production compressors that point towards opportunities for future compression research.

Checkpoint/Restart (C/R) strategies are vital for fault tolerance in PDE-based scientific simulations, yet traditional checkpointing incurs significant I/O overhead. Lossy compression offers a scalable solution by reducing checkpoint data size, but conventional methods often lack control over physical invariants (e.g., energy), leading to instability such as oscillations or divergence in Partial Differential Equations (PDE) systems. This paper introduces a stability-preserving compression approach tailored for PDE simulations by explicitly controlling kinetic and potential energy perturbations to ensure stable restarts. Extensive experiments conducted across diverse PDE configurations demonstrate that our method maintains numerical stability with minimal error magnification—even across multiple checkpoint-restart cycles—outperforming state-of-the-art lossy compressors. Parallel evaluations on the Frontier supercomputer show up to 8.4× improvement in checkpoint write performance and 6.3× in read performance, while maintaining relative L2 errors ∼ 2e-6 throughout continued simulation. These results provide practical guidance for balancing compression accuracy, stability, and computational efficiency in large-scale PDE applications.

Scientific applications produce vast amounts of data, posing grand challenges in the underlying data management and analytic tasks. Progressive compression is a promising way to address this problem, as it allows for on-demand data retrieval with significantly reduced data movement cost. However, most existing progressive methods are designed for CPUs, leaving a gap for them to unleash the power of today’s heterogeneous computing systems with GPUs.In this work, we propose HP-MDR, a high-performance and portable data refactoring and progressive retrieval framework for GPUs. Our contributions are four-fold: (1) We carefully optimize the bitplane encoding and lossless encoding, two key stages in progressive methods, to achieve high performance on GPUs; (2) We propose pipeline optimization and incorporate it with data refactoring and progressive retrieval workflows to further enhance the performance for large data process; (3) We leverage our framework to enable high-performance data retrieval with guaranteed error control for common Quantities of Interest; (4) We evaluate HP-MDR and compare it with state of the arts using five real-world datasets. Experimental results demonstrate that HP-MDR delivers an average 13.68 × and 6.31 × throughput in data refactoring and progressive retrieval tasks, respectively. It also leads to 11.22 × throughput for recomposing required data representations under Quantity-of-Interest error control and 6.04 × performance for the corresponding end-to-end data retrieval, when compared with state-of-the-art solutions.

As high-performance computing architectures evolve, more scientific computing workflows are being deployed on advanced computing platforms such as GPUs. These workflows can produce raw data at extremely high throughputs, requiring urgent high-ratio and low-latency error-bounded data compression solutions. In this paper, we propose cuSZ-Hi, an optimized high-ratio GPU-based scientific error-bounded lossy compressor with a flexible, domain-irrelevant, and fully open-source framework design. Our novel contributions are: 1) We maximally optimize the parallelized interpolation-based data prediction scheme on GPUs, enabling the full functionalities of interpolation-based scientific data prediction that are adaptive to diverse data characteristics; 2) We thoroughly explore and investigate lossless data encoding techniques, then craft and incorporate the best-fit lossless encoding pipelines for maximizing the compression ratio of cuSZ-Hi; 3) We systematically evaluate cuSZ-Hi on benchmarking datasets together with representative baselines. Compared to existing state-of-the-art scientific lossy compressors, with comparative or better throughput than existing high-ratio scientific error-bounded lossy compressors on GPUs, cuSZ-Hi can achieve up to 249% compression ratio improvement under the same error bound, and up to 215% compression ratio improvement under the same decompression data PSNR.

Many scientific applications opt for particles instead of meshes as their basic primitives to model complex systems composed of billions of discrete entities. Such applications span a diverse array of scientific domains, including molecular dynamics, cosmology, computational fluid dynamics, and geology. The scale of the particles in those scientific applications increases substantially thanks to the ever-increasing computational power in high-performance computing (HPC) platforms. However, the actual gains from such increases are often undercut by obstacles in data management systems related to data storage, transfer, and processing. Lossy compression has been widely recognized as a promising solution to enhance scientific data management systems regarding such challenges, although most existing compression solutions are tailored for Cartesian grids and thus have sub-optimal results on discrete particle data. In this paper, we introduce LCP, an innovative lossy compressor designed for particle datasets, offering superior compression quality and higher speed than existing compression solutions. Specifically, our contribution is threefold. (1) We propose LCP-S, an error-bound aware block-wise spatial compressor to efficiently reduce particle data size while satisfying the pre-defined error criteria. This approach is universally applicable to particle data across various domains, eliminating the need for reliance on specific application domain characteristics. (2) We develop LCP, a hybrid compression solution for multi-frame particle data, featuring dynamic method selection and parameter optimization. It aims to maximize compression effectiveness while preserving data quality as much as possible by utilizing both spatial and temporal domains. (3) We evaluate our solution alongside eight state-of-the-art alternatives on eight real-world particle datasets from seven distinct domains. The results demonstrate that our solution achieves up to 104% improvement in compression ratios and up to 593% increase in speed compared to the second-best option, under the same error criteria.

Error-bounded lossy compression has been widely adopted in many scientific domains because it can address the challenges in storing, transferring, and analyzing unprecedented amounts of scientific data. However, general error-bounded lossy compressors may fail to meet additional quality requirements for downstream analysis, a.k.a. Quantities of Interest (QoIs). This may lead to uncertainties and even misinterpretations in scientific discoveries, significantly limiting the use of lossy compression in practice. In this paper, we propose QPET, a novel, versatile, and portable framework for QoI-preserving error-bounded lossy compression, which overcomes the challenges of modeling diverse QoIs by leveraging numerical strategies. QPET features (1) high portability to multiple existing lossy compressors, (2) versatile preservation to most differentiable univariate and multivariate QoIs, and (3) significant compression improvements in QoI-preservation tasks. Experiments with six real-world datasets demonstrate that integrating QPET into state-of-the-art error-bounded lossy compressors can gain 2x to 10x compression speedups of existing QoI-preserving error-bounded lossy compression solutions, up to 1000% compression ratio improvements to general-purpose compressors, and up to 133% compression ratio improvements to existing QoI-integrated scientific compressors.

Topological descriptors such as contour trees are widely utilized in scientific data analysis and visualization, with applications from materials science to climate simulations. It is desirable to preserve topological descriptors when data compression is part of the scientific workflow for these applications. However, classic error-bounded lossy compressors for volumetric data do not guarantee the preservation of topological descriptors, despite imposing strict pointwise error bounds. In this work, we introduce a general framework for augmenting any lossy compressor to preserve the topology of the data during compression. Specifically, our framework quantifies the adjustments (to the decompressed data) needed to preserve the contour tree and then employs a custom variable-precision encoding scheme to store these adjustments. We demonstrate the utility of our framework in augmenting classic compressors (such as SZ3, TTHRESH, and ZFP) and deep learning-based compressors (such as Neurcomp) with topological guarantees.

This research explores a novel paradigm for preserving topological segmentations in existing error-bounded lossy compressors. Today's lossy compressors rarely consider preserving topologies such as Morse-Smale complexes, and the discrepancies in topology between original and decompressed datasets could potentially result in erroneous interpretations or even incorrect scientific conclusions. In this paper, we focus on preserving Morse-Smale segmentations in 2D/3D piecewise linear scalar fields, targeting the precise reconstruction of minimum/maximum labels induced by the integral line of each vertex. The key is to derive a series of edits during compression time. These edits are applied to the decompressed data, leading to an accurate reconstruction of segmentations while keeping the error within the prescribed error bound. To this end, we develop a workflow to fi x ex trema an d in tegral lines alternatively until convergence within finite iterations. We accelerate each workflow component with shared-memory/GPU parallelism to make the performance practical for coupling with compressors. We demonstrate use cases with fluid dynamics, ocean, and cosmology application datasets with a significant acceleration with an NVIDIA A100 GPU.

This study investigates the optimization of an electrostatic sieve designed for lunar regolith beneficiation. Two parameters of the electrostatic sieve, 1) the voltage amplitude and 2) angle of inclination, were chosen as variables in the optimization process. Numerical simulations revealed that increasing voltage amplitude significantly enhances sieve performance over the sieve angle. However, optimal separation required careful voltage adjustment for specific sieve angles. A comprehensive dataset incorporating additional parameters was then created to train Machine Learning (ML) and Deep Learning (DL) models for further optimization. The ML/DL models were trained on a small subset of the original dataset to predict the yield. We showcase the benefits of leveraging DL techniques to improve the electrostatic sieve for regolith beneficiation via tailored evaluations. Our model, trained on lower-yield examples, accurately (92%) identifies parameter combinations that increase yields above 30%. It leads to a near-optimal yield with 10× reduction on runtime when compared with exhaustive simulations. This not only reduces the reliance on resource-intensive numerical simulations but also offers a rapid, validated approach to optimizing equipment for lunar mining operations.

Modeling the electric potential profile above the lunar surface is critical for understanding surface charging and interactions with the space environment. Traditional methods like Particle-in-Cell (PIC) simulations are highly accurate but computationally expensive. To address this, we propose a hybrid approach using a Multi-Layer Perceptron (MLP) architecture in both data-driven neural networks and Physics-Informed Neural Networks (PINNs). The PINN component incorporates physical laws directly into the training process, ensuring physical consistency, while the data-driven component captures complex patterns. This combination offers a significant reduction in computational cost compared to PIC methods while maintaining high modeling accuracy. Our results show that the proposed method effectively represents the electric potential profile above the lunar surface, even with limited data.

Data compression plays a key role in reducing storage and I/O costs. Traditional lossy methods primarily target data on rectilinear grids and cannot leverage the spatial coherence in unstructured mesh data, leading to suboptimal compression ratios. We present a multi-component, error-bounded compression framework designed to enhance the compression of floating-point unstructured mesh data, which is common in scientific applications. Our approach involves interpolating mesh data onto a rectilinear grid and then separately compressing the grid interpolation and the interpolation residuals. This method is general, independent of mesh types and typologies, and can be seamlessly integrated with existing lossy compressors for improved performance. We evaluated our framework across twelve variables from two synthetic datasets and two real-world simulation datasets. The results indicate that the multi-component framework consistently outperforms state-of-the-art lossy compressors on unstructured data, achieving, on average, a 2.3 − 3.5× improvement in compression ratios, with error bounds ranging from 1 × 10 the−6to 1×10−2. We further investigate impact of hyperparameters, such as grid spacing and error allocation, to deliver optimal compression ratios in diverse datasets.

Lossy compression has been employed to reduce the unprecedented amount of data produced by today's large-scale scientific simulations and high-resolution instruments. To avoid loss of critical information, state-of-the-art scientific lossy compressors provide error controls on relatively simple metrics such as absolute error bound. However, preserving these metrics does not translate to the preservation of topological features, such as critical points in vector fields. To address this problem, we investigate how to effectively preserve the sign of determinant in error-controlled lossy compression, as it is an important quantity of interest used for the robust detection of many topological features. Our contribution is three-fold. (1) We develop a generic theory to derive the allowable perturbation for one row of a matrix while preserving its sign of the determinant. As a practical use-case, we apply this theory to preserve critical points in vector fields because critical point detection can be reduced to the result of the point-in-simplex test that purely relies on the sign of determinants. (2) We optimize this algorithm with a speculative compression scheme to allow for high compression ratios and efficiently parallelize it in distributed environments. (3) We perform solid experiments with real-world datasets, demonstrating that our method achieves up to 440% improvements in compression ratios over state-of-the-art lossy compressors when all critical points need to be preserved. Using the parallelization strategies, our method delivers up to 1.25 x and 4.38 x performance speedup in data writing and reading compared with the vanilla approach without compression.

Benefiting from the cutting-edge supercomputers that support extremely large-scale scientific simulations, climate research has advanced significantly over the past decades. However, new critical challenges have arisen regarding efficiently storing and transferring large-scale climate data among distributed repositories and databases for post hoc analysis. In this paper, we develop CliZ, an efficient online error-controlled lossy compression method with optimized data prediction and encoding methods for climate datasets across various climate models. On the one hand, we explored how to take advantage of particular properties of the climate datasets (such as mask-map information, dimension permutation/fusion, and data periodicity pattern) to improve the data prediction accuracy. On the other hand, CliZ features a novel multi-Huffman encoding method, which can significantly improve the encoding efficiency. Therefore significantly improving compression ratios. We evaluated CliZ versus many other state-of-the-art error-controlled lossy compressors (including SZ3, ZFP, SPERR, and QoZ) based on multiple real-world climate datasets with different models. Experiments show that CliZ outperforms the second-best compressor (SZ3, SPERR, or QoZ1.1) on climate datasets by 20%-200% in compression ratio. CliZ can significantly reduce the data transfer cost between the two remote Globus endpoints by 32%-38%.

As network bandwidth struggles to keep up with rapidly growing computing capabilities, the efficiency of collective communication has become a critical challenge for exa-scale distributed and parallel applications. Traditional approaches directly utilize error-bounded lossy compression to accelerate collective computation operations, exposing unsatisfying performance due to the expensive decompression-operation-compression (DOC) workflow. To address this issue, we present a first-ever homomorphic compression-communication co-design, hZCCL, which enables operations to be performed directly on compressed data, saving the cost of time-consuming decompression and recompression. In addition to the co-design framework, we build a light-weight compressor, optimized specifically for multi-core CPU platforms. We also present a homomorphic compressor with a run-time heuristic to dynamically select efficient compression pipelines for reducing the cost of DOC handling. We evaluate $h \mathbf{Z C C L}$ with up to 512 nodes and across five application datasets. The experimental results demonstrate that our homomorphic compressor achieves a CPU throughput of up to $379.08 \mathrm{~GB} / \mathrm{s}$, surpassing the conventional DOC workflow by up to $36.53 \times$. Moreover, our $\boldsymbol{h Z C C L}$-accelerated collectives outperform two state-of-the-art baselines, delivering speedups of up to $2.12 \times$ and $6.77 \times$ compared to original MPI collectives in single-thread and multi-thread modes, respectively, while maintaining data accuracy.

The unprecedented amount of scientific data has introduced heavy pressure on the current data storage and transmission systems. Progressive compression has been proposed to mitigate this problem, which offers data access with on-demand precision. However, existing approaches only consider precision control on primary data, leaving uncertainties on the quantities of interest (QoIs) derived from it. In this work, we present a progressive data retrieval framework with guaranteed error control on derivable QoIs. Our contributions are three-fold. (1) We carefully derive the theories to strictly control QoI errors during progressive retrieval. Our theory is generic and can be applied to any QoIs that can be composited by the basis of derivable QoIs proved in the paper. (2) We design and develop a generic progressive retrieval framework based on the proposed theories, and optimize it by exploring feasible progressive representations. (3) We evaluate our framework using five real-world datasets with a diverse set of QoIs. Experiments demonstrate that our framework can faithfully respect any user-specified QoI error bounds in the evaluated applications. This leads to over $2.02 \times$ performance gain in data transfer tasks compared to transferring the primary data while guaranteeing a QoI error that is less than 1E-5.

Abstract We explore an error‐bounded lossy compression approach for reducing scientific data associated with 2D/3D unstructured meshes. While existing lossy compressors offer a high compression ratio with bounded error for regular grid data, methodologies tailored for unstructured mesh data are lacking; for example, one can compress nodal data as 1D arrays, neglecting the spatial coherency of the mesh nodes. Inspired by the SZ compressor, which predicts and quantizes values in a multidimensional array, we dynamically reorganize nodal data into sequences. Each sequence starts with a seed cell; based on a predefined traversal order, the next cell is added to the sequence if the current cell can predict and quantize the nodal data in the next cell with the given error bound. As a result, one can efficiently compress the quantized nodal data in each sequence until all mesh nodes are traversed. This paper also introduces a suite of novel error metrics, namely continuous mean squared error (CMSE) and continuous peak signal‐to‐noise ratio (CPSNR), to assess compression results for unstructured mesh data. The continuous error metrics are defined by integrating the error function on all cells, providing objective statistics across nonuniformly distributed nodes/cells in the mesh. We evaluate our methods with several scientific simulations ranging from ocean‐climate models and computational fluid dynamics simulations with both traditional and continuous error metrics. We demonstrated superior compression ratios and quality than existing lossy compressors.

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.

Existing error-bounded lossy compression techniques control the pointwise error during compression to guarantee the integrity of the decompressed data. However, they typically do not explicitly preserve the topological features in data. When performing post hoc analysis with decompressed data using topological methods, preserving topology in the compression process to obtain topologically consistent and correct scientific insights is desirable. In this paper, we introduce TopoSZ, an error-bounded lossy compression method that preserves the topological features in 2D and 3D scalar fields. Specifically, we aim to preserve the types and locations of local extrema as well as the level set relations among critical points captured by contour trees in the decompressed data. The main idea is to derive topological constraints from contour-tree-induced segmentation from the data domain, and incorporate such constraints with a customized error-controlled quantization strategy from the SZ compressor (version 1.4). Our method allows users to control the pointwise error and the loss of topological features during the compression process with a global error bound and a persistence threshold.

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.

Scientific discoveries are increasingly constrained by limited storage space and I/O capacities. For time-series simulations and experiments, their data often need to be decimated over timesteps to accommodate storage and I/O limitations. In this paper, we propose a technique that addresses storage costs while improving post-analysis accuracy through spatiotemporal adaptive, error-controlled lossy compression. We investigate the trade-off between data precision and temporal output rates, revealing that reducing data precision and increasing timestep frequency lead to more accurate analysis outcomes. Additionally, we integrate spatiotemporal feature detection with data compression and demonstrate that performing adaptive error-bounded compression in higher dimensional space enables greater compression ratios, leveraging the error propagation theory of a transformation-based compressor. To evaluate our approach, we conduct experiments using the well-known E3SM climate simulation code and apply our method to compress variables used for cyclone tracking. Our results show a significant reduction in storage size while enhancing the quality of cyclone tracking analysis, both quantitatively and qualitatively, in comparison to the prevalent timestep decimation approach. Compared to three state-of-the-art lossy compressors lacking feature preservation capabilities, our adaptive compression framework improves perfectly matched cases in TC tracking by 26.4-51.3% at medium compression ratios and by 77.3-571.1% at large compression ratios, with a merely 5–11% computational overhead.

Today's scientific high-performance computing (HPC) applications are often running on large-scale environments, producing extremely large volumes of data that need to be compressed effectively for efficient storage or data transfer. Error-bounded lossy compression is arguably the most efficient way to this end, because it can get very high compression ratios while controlling the data distortion strictly based on user requirements for compression errors. However, error-bounded lossy compressors may have serious artifact issues in situations with relatively large error bound or high compression ratios, which is highly undesirable to users. In this paper, we compre-hensively characterize the artifacts for multiple state-of-the-art error-bounded lossy compressors (including SZ-1.4, SZ-2.1, SZ-3.0, FPZIP, ZFP, MGARD) and provide an in-depth analysis for the root cause of these artifacts. We summarize the artifact issue into three types and also develop an efficient artifact detection algorithm for each type of artifact. We finally evaluate our artifact detection methods using four scientific datasets, which demonstrates that the proposed methods are able to detect artifact issues under linear time complexity.

In modern science, big data plays an increasingly important role. Many scientific applications, such as running simulations on supercomputers or conducting experiments on advanced instruments, produce huge amount of data at unprecedented speed. Analyzing and understanding such big data is the key for scientists to make scientific breakthroughs. However, data might become unavailable for scientists to access when outages or maintenance of the storage system occur, which severely hinders scientific discovery. To improve the data availability, data duplication and erasure coding (EC) are often used. But as the scientific data gets larger, using these two methods can cause considerable storage and network overhead.

Today's large-scale scientific applications running on high-performance computing (HPC) systems generate vast data volumes. Thus, data compression is becoming a critical technique to mitigate the storage burden and data-movement cost. However, existing lossy compressors for scientific data cannot achieve a high compression ratio and throughput simultaneously, hindering their adoption in many applications requiring fast compression, such as in-memory compression. To this end, in this work, we develop a fast and high- ratio error-bounded lossy compressor on GPUs for scientific data (called FZ-GPU). Specifically, we first design a new compression pipeline that consists of fully parallelized quantization, bitshuffle, and our newly designed fast encoding. Then, we propose a series of deep architectural optimizations for each kernel in the pipeline to take full advantage of CUDA architectures. We propose a warp-level optimization to avoid data conflicts for bit-wise operations in bitshuffle, maximize shared memory utilization, and eliminate unnecessary data movements by fusing different compression kernels. Finally, we evaluate FZ-GPU on two NVIDIA GPUs (i.e., A100 and RTX A4000) using six representative scientific datasets from SDRBench. Results on the A100 GPU show that FZ-GPU achieves an average speedup of 4.2× over cuSZ and an average speedup of 37.0× over a multi-threaded CPU implementation of our algorithm under the same error bound. FZ-GPU also achieves an average speedup of 2.3× and an average compression ratio improvement of 2.0× over cuZFP under the same data distortion.

As the disparity between compute and I/O on high-performance computing systems has continued to widen, it has become increasingly difficult to perform post-hoc data analytics on full-resolution scientific simulation data due to the high I/O cost. Error-bounded data decomposition and progressive data retrieval framework has recently been developed to address such a challenge by performing data decomposition before storage and reading only part of the decomposed data when necessary. However, the performance of the progressive retrieval framework has been suffering from the over-pessimistic error control theory, such that the achieved maximum error of recomposed data is significantly lower than the required error. Therefore, more data than required is fetched for recomposition, incurring additional I/O overhead. In order to tackle this issue, we propose a DNN-based progressive retrieval framework that can better identify the minimum amount of data to be retrieved. Our contributions are as follows: 1) We provide an in-depth investigation of the recently developed progressive retrieval framework; 2) We propose two designs of prediction models (named D-MGARD and E-MGARD) to estimate the amount of retrieved data size based on error bounds. 3) We evaluate our proposed solutions using scientific datasets generated by real-world simulations from two domains. Evaluation results demonstrate the effectiveness of our solution in accurately predicting the amount of retrieval data size, as well as the advantages of our solution over the traditional approach to reducing the I/O overhead. Based on our evaluation, our solution is shown to read significantly less data (5% - 40% with D-MGARD, 20% - 80% with E-MGARD).

Error-bounded lossy compression has been effective to resolve the big scientific data issue because it has a great potential to significantly reduce the data volume while allowing users to control data distortion based on specified error bounds. However, none of the existing error-bounded lossy compressors can always obtain the best compression quality because of the diverse characteristics of different datasets. In this paper, we develop FAZ, a flexible and adaptive error-bounded lossy compression framework, which projects a fairly high capability of adapting to diverse datasets. FAZ can always keep the compression quality at the best level compared with other state-of-the-art compressors for different datasets. We perform a comprehensive evaluation using 6 real-world scientific applications and 6 other state-of-the-art error-bounded lossy compressors. Experiments show that compared with the other existing lossy compressors, FAZ can improve the compression ratio by up to 120%, 190%, and 75% when setting the same error bound, the same PSNR and the same SSIM, respectively.

One-sided dense matrix decompositions (e.g., Cholesky, LU, and QR) are the key components in scientific computing in many different fields. Although their design has been highly optimized for modern processors, they still consume a considerable amount of energy. As CPU-GPU heterogeneous systems are commonly used for matrix decompositions, in this work, we aim to further improve the energy saving of onesided matrix decompositions on CPU-GPU heterogeneous systems. We first build an Algorithm-Based Fault Tolerance protected overclocking technique (ABFT-OC) to enable us to exploit reliable overclocking for key matrix decomposition operations. Then, we design an energy-saving matrix decomposition framework, Bi-directional Slack Reclamation (BSR), that can intelligently combine the capability provided by ABFT-OC and DVFS to maximize energy saving and maintain performance and reliability. Experiments show that BSR is able to save up to 11.7% more energy compared with the current best energy saving optimization approach with no performance degradation and up to 14.1% Energy×Delay2 reduction. Also, BSR enables the Pareto efficient performance-energy trade-off, which is able to provide up to 1.43× performance improvement without costing extra energy.

Today's scientific simulations require a significant reduction of data volume because of extremely large amounts of data they produce and the limited I/O bandwidth and storage space. Error-bounded lossy compression has been considered one of the most effective solutions to the above problem. In practice, however, the best-fit compression method often needs to be customized or optimized in particular because of diverse characteristics in different datasets and various user requirements on the compression quality and performance. In this paper, we address this issue with a novel modular, composable compression framework named SZ3. Our contributions are four-folds. (1) We develop SZ3 which features an innovative modular abstraction for the prediction-based compression framework, such that compression modules can be plugged in easily to create new compressors based on characteristics of data and user requirements. (2) We create a new compression pipeline by SZ3 for GAMESS data, which significantly improves the compression ratios over state-of-the-art compressors. (3) We develop an adaptive compression pipeline by SZ3 for APS data with minimal efforts, which leads to the best rate-distortion among all existing error-bounded lossy compressors for any bit-rate. (4) We compare the sustainability of SZ3 with leading error-bounded prediction-based compressors, and then demonstrate the necessity of diverse pipelines by integrating and evaluating several compression pipelines on diverse scientific datasets from multiple disciplines. Experiments show that SZ3 incurs very limited overhead in compressor integration and our customized compression pipelines lead to up to 20% improvement in compression ratios under the same data distortion, when compared with the best existing approach.

The objective of this work is to develop error-bounded lossy compression methods to preserve topological features in 2D and 3D vector fields. Specifically, we explore the preservation of critical points in piecewise linear and bilinear vector fields. We define the preservation of critical points as, without any false positive, false negative, or false type in the decompressed data, (1) keeping each critical point in its original cell and (2) retaining the type of each critical point (e.g., saddle and attracting node). The key to our method is to adapt a vertex-wise error bound for each grid point and to compress input data together with the error bound field using a modified lossy compressor. Our compression algorithm can be also embarrassingly parallelized for large data handling and in situ processing. We benchmark our method by comparing it with existing lossy compressors in terms of false positive/negative/type rates, compression ratio, and various vector field visualizations with several scientific applications.

We present the first GPU-based parallel algorithm to efficiently update vertex coloring on large dynamic networks. For single GPU, we introduce the concept of loosely maintained vertex color update that reduces computation and memory requirements. For multiple GPUs, in distributed environments, we propose priority-based ordering of vertices to reduce the communication time. We prove the correctness of our algorithms and experimentally demonstrate that for graphs of over 16 million vertices and over 134 million edges on a single GPU, our dynamic algorithm is as much as 20x faster than state-of-the-art algorithm on static graphs. For larger graphs with over 130 million vertices and over 260 million edges, our distributed implementation with 8 GPUs produces updated color assignments within 160 milliseconds. In all cases, the proposed parallel algorithms produce comparable or fewer colors than state-of-the-art algorithms.

Today's scientific high-performance computing applications and advanced instruments are producing vast volumes of data across a wide range of domains, which impose a serious burden on data transfer and storage. Error-bounded lossy compression has been developed and widely used in the scientific community because it not only can significantly reduce the data volumes but also can strictly control the data distortion based on the user-specified error bound. Existing lossy compressors, however, cannot offer ultrafast compression speed, which is highly demanded by numerous applications or use cases (such as in-memory compression and online instrument data compression). In this paper, we propose a novel ultrafast error-bounded lossy compressor that can obtain fairly high compression performance on both CPUs and GPUs and with reasonably high compression ratios. The key contributions are threefold. (1) We propose a generic error-bounded lossy compression framework---called SZx---that achieves ultrafast performance through its novel design comprising only lightweight operations such as bitwise and addition/subtraction operations, while still keeping a high compression ratio. (2) We implement SZx on both CPUs and GPUs and optimize the performance according to their architectures. (3) We perform a comprehensive evaluation with six real-world production-level scientific datasets on both CPUs and GPUs. Experiments show that SZx is 2~16x faster than the second-fastest existing error-bounded lossy compressor (either SZ or ZFP) on CPUs and GPUs, with respect to both compression and decompression.

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.

With ever-increasing execution scale of the high performance computing (HPC) applications, vast amount of data are being produced by scientific research every day. Error-bounded lossy compression has been considered a very promising solution to address the big-data issue for scientific applications, because it can significantly reduce the data volume with low time cost meanwhile allowing users to control the compression errors with a specified error bound. The existing error-bounded lossy compressors, however, are all developed based on inflexible designs or compression pipelines, which cannot adapt to diverse compression quality requirements/metrics favored by different application users. In this paper, we propose a novel dynamic quality metric oriented error-bounded lossy compression frame-work, namely QoZ. The detailed contribution is three fold. (1) We design a novel highly-parameterized multi-level interpolation-based data predictor, which can significantly improve the overall compression quality with the same compressed size. (2) We design the error bounded lossy compression framework QoZ based on the adaptive predictor, which can auto-tune the critical parameters and optimize the compression result according to user-specified quality metrics during online compression. (3) We evaluate QoZ carefully by comparing its compression quality with multiple state-of-the-arts on various real-world scientific application datasets. Experiments show that, compared with the second best lossy compressor, QoZ can achieve up to 70% compression ratio improvement under the same error bound, up to 150% compression ratio improvement under the same PSNR, or up to 270% compression ratio improvement under the same SSIM.

The increase of computer processing speed is significantly outpacing improvements in network and storage bandwidth, leading to the big data challenge in modern science, where scientific applications can quickly generate much more data than that can be transferred and stored. As a result, big scientific data must be reduced by a few orders of magnitude while the accuracy of the reduced data needs to be guaranteed for further scientific explorations. Moreover, scientists are often interested in some specific spatial/temporal regions in their data, where higher accuracy is required. The locations of the regions requiring high accuracy can sometimes be prescribed based on application knowledge, while other times they must be estimated based on general spatial/temporal variation. In this paper, we develop a novel multilevel approach which allows users to impose region-wise compression error bounds. Our method utilizes the byproduct of a multilevel compressor to detect regions where details are rich and we provide the theoretical underpinning for region-wise error control. With spatially varying precision preservation, our approach can achieve significantly higher compression ratios than single-error bounded compression approaches and control errors in the regions of interest.

Today's scientific simulations and instruments are producing a large amount of data, leading to difficulties in storing, transmitting, and analyzing these data. While error-controlled lossy compressors are effective in significantly reducing data volumes and efficiently developing databases for multiple scientific applications, they mainly support error controls on raw data, which leaves a significant gap between the data and user's downstream analysis. This may cause unqualified uncertainties in the outcomes of the analysis, a.k.a quantities of interest (QoIs), which are the major concerns of users in adopting lossy compression in practice. In this paper, we propose rigorous mathematical theories to preserve four families of QoIs that are widely used in scientific analysis during lossy compression along with practical implementations. Specifically, we first develop the error control theory for univariate QoIs which are essential for computing physical properties such as kinetic energy, followed by multivariate QoIs that are more commonly used in real-world applications. The proposed method is integrated into a state-of-the-art compression framework in a modular fashion, which could easily adapt to new QoIs and new compression algorithms. Experiments on real-world datasets demonstrate that the proposed method provides faithful error control on important QoIs including kinetic energy, regional average, and isosurface without trials and errors, while offering compression ratios that are up to 4X of the compression ratios provided by state-of-the-art compressors.

Nowadays, data reduction is becoming increasingly important in dealing with the large amounts of scientific data. Existing multilevel compression algorithms offer a promising way to manage scientific data at scale, but may suffer from relatively low performance and reduction quality. In this paper, we propose MGARD+, a multilevel data reduction and refactoring framework drawing on previous multilevel methods, to achieve high-performance data decomposition and high-quality error-bounded lossy compression. Our contributions are four-fold: 1) We propose to leverage a level-wise coefficient quantization method, which uses different error tolerances to quantize the multilevel coefficients. 2) We propose an adaptive decomposition method which treats the multilevel decomposition as a preconditioner and terminates the decomposition process at an appropriate level. 3) We leverage a set of algorithmic optimization strategies to significantly improve the performance of multilevel decomposition/recomposition. 4) We evaluate our proposed method using four real-world scientific datasets and compare with several state-of-the-art lossy compressors. Experiments demonstrate that our optimizations improve the decomposition/recomposition performance of the existing multilevel method by up to$70 \times$, and the proposed compression method can improve compression ratio by up to$2 \times$compared with other state-of-the-art error-bounded lossy compressors under the same level of data distortion.

The applications being developed within the U.S. Exascale Computing Project (ECP) to run on imminent Exascale computers will generate scientific results with unprecedented fidelity and record turn-around time. Many of these codes are based on particle-mesh methods and use advanced algorithms, especially dynamic load-balancing and mesh-refinement, to achieve high performance on Exascale machines. Yet, as such algorithms improve parallel application efficiency, they raise new challenges for I/O logic due to their irregular and dynamic data distributions. Thus, while the enormous data rates of Exascale simulations already challenge existing file system write strategies, the need for efficient read and processing of generated data introduces additional constraints on the data layout strategies that can be used when writing data to secondary storage. We review these I/O challenges and introduce two online data layout reorganization approaches for achieving good tradeoffs between read and write performance. We demonstrate the benefits of using these two approaches for the ECP particle-in-cell simulation WarpX, which serves as a motif for a large class of important Exascale applications. We show that by understanding application I/O patterns and carefully designing data layouts we can increase read performance by more than 80 percent.

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.

Error-bounded lossy compression is becoming an indispensable technique for the success of today’s scientific projects with vast volumes of data produced during the simulations or instrument data acquisitions. Not only can it significantly reduce data size, but it also can control the compression errors based on user-specified error bounds. Autoencoder (AE) models have been widely used in image compression, but few AE-based compression approaches support error-bounding features, which are highly required by scientific applications. To address this issue, we explore using convolutional autoencoders to improve error-bounded lossy compression for scientific data, with the following three key contributions. (1) We provide an in-depth investigation of the characteristics of various autoencoder models and develop an error-bounded autoencoder-based framework in terms of the SZ model. (2) We optimize the compression quality for main stages in our designed AE-based error-bounded compression framework, fine-tuning the block sizes and latent sizes and also optimizing the compression efficiency of latent vectors. (3) We evaluate our proposed solution using five real-world scientific datasets and comparing them with six other related works. Experiments show that our solution exhibits a very competitive compression quality from among all the compressors in our tests. In absolute terms, it can obtain a much better compression quality (100% $\sim$ 800% improvement in compression ratio with the same data distortion) compared with SZ2.1 and ZFP in cases with a high compression ratio.

Error-bounded lossy compression is a critical technique for significantly reducing scientific data volumes. With ever-emerging heterogeneous high-performance computing (HPC) architecture, GPU-accelerated error-bounded compressors (such as CUSZ and cuZFP) have been developed. However, they suffer from either low performance or low compression ratios. To this end, we propose CUSZ+ to target both high compression ratios and throughputs. We identify that data sparsity and data smoothness are key factors for high compression throughputs. Our key contributions in this work are fourfold: (1) We propose an efficient compression workflow to adaptively perform run-length encoding and/or variable-length encoding. (2) We derive Lorenzo reconstruction in decompression as multidimensional partial-sum computation and propose a fine-grained Lorenzo reconstruction algorithm for GPU architectures. (3) We carefully optimize each of CUSZ kernels by leveraging state-of-the-art CUDA parallel primitives. (4) We evaluate CU SZ+ using seven real-world HPC application datasets on V100 and A100 GPUs. Experiments show CUSZ+ improves the compression throughputs and ratios by up to 18.4× and 5.3×, respectively, over CUSZ on the tested datasets.

Rapid growth in scientific data and a widening gap between computational speed and I/O bandwidth make it increasingly infeasible to store and share all data produced by scientific simulations. Instead, we need methods for reducing data volumes: ideally, methods that can scale data volumes adaptively so as to enable negotiation of performance and fidelity tradeoffs in different situations. Multigrid-based hierarchical data representations hold promise as a solution to this problem, allowing for flexible conversion between different fidelities so that, for example, data can be created at high fidelity and then transferred or stored at lower fidelity via logically simple and mathematically sound operations. However, the effective use of such representations has been hindered until now by the relatively high costs of creating, accessing, reducing, and otherwise operating on such representations. We describe here highly optimized data refactoring kernels for GPU accelerators that enable efficient creation and manipulation of data in multigrid-based hierarchical forms. We demonstrate that our optimized design can achieve up to 250 TB/s aggregated data refactoring throughput-83% of theoretical peak-on 1024 nodes of the Summit supercomputer. We showcase our optimized design by applying it to a large-scale scientific visualization workflow and the MGARD lossy compression software.

Today's high-performance computing (HPC) applications are producing vast volumes of data, which are challenging to store and transfer efficiently during the execution, such that data compression is becoming a critical technique to mitigate the storage burden and data movement cost. Huffman coding is arguably the most efficient Entropy coding algorithm in information theory, such that it could be found as a fundamental step in many modern compression algorithms such as DEFLATE. On the other hand, today's HPC applications are more and more relying on the accelerators such as GPU on supercomputers, while Huffman encoding suffers from low throughput on GPUs, resulting in a significant bottleneck in the entire data processing. In this paper, we propose and implement an efficient Huffman encoding approach based on modern GPU architectures, which addresses two key challenges: (1) how to parallelize the entire Huffman encoding algorithm, including codebook construction, and (2) how to fully utilize the high memory-bandwidth feature of modern GPU architectures. The detailed contribution is fourfold. (1) We develop an efficient parallel codebook construction on GPUs that scales effectively with the number of input symbols. (2) We propose a novel reduction based encoding scheme that can efficiently merge the codewords on GPUs. (3) We optimize the overall GPU performance by leveraging the state-of-the-art CUDA APIs such as Cooperative Groups. (4) We evaluate our Huffman encoder thoroughly using six real-world application datasets on two advanced GPUs and compare with our implemented multithreaded Huffman encoder. Experiments show that our solution can improve the encoding throughput by up to 5.0× and 6.8× on NVIDIA RTX 5000 and V100, respectively, over the state-of-the-art GPU Huffman encoder, and by up to 3.3× over the multithread encoder on two 28-core Xeon Platinum 8280 CPUs.

Extreme-scale simulations and high-resolution instruments have been generating an increasing amount of data, which poses significant challenges to not only data storage during the run, but also post-processing where data will be repeatedly retrieved and analyzed for a long period of time. The challenges in satisfying a wide range of post-hoc analysis needs while minimizing the I/O overhead caused by inappropriate and/or excessive data retrieval should never be left unmanaged. In this paper, we propose a data refactoring, compressing, and retrieval framework capable of 1) fine-grained data refactoring with regard to precision; 2) incrementally retrieving and recomposing the data in terms of various error bounds; and 3) adaptively retrieving data in multi-precision and multi-resolution with respect to different analysis. With the progressive data re-composition and the adaptable retrieval algorithms, our framework significantly reduces the amount of data retrieved when multiple incremental precision are requested and/or the downstream analysis time when coarse resolution is used. Experiments show that the amount of data retrieved under the same progressively requested error bound using our framework is 64% less than that using state-of-the-art single-error-bounded approaches. Parallel experiments with up to 1, 024 cores and ~ 600 GB data in total show that our approach yields 1.36× and 2.52× performance over existing approaches in writing to and reading from persistent storage systems, respectively.

Today's exa-scale scientific applications or advanced instruments are producing vast volumes of data, which need to be shared/transferred through the network/devices with relatively low bandwidth (e.g., data sharing on WAN or transferring from edge devices to supercomputers). Lossy compression is one of the candidate strategies to address the big data issue. However, little work was done to make it resilient against silent errors, which may happen during the stage of compression or data transferring. In this paper, we propose a resilient error-bounded lossy compressor based on the SZ compression framework. Specifically, we design a new independent-block-wise model that decomposes the entire dataset into many independent sub-blocks to compress. Then, we design and implement a series of error detection/correction strategies elaboratively for each stage of SZ. Our method is arguably the first algorithm-based fault tolerance (ABFT) solution for lossy compression. Our proposed solution incurs negligible execution overhead in the fault-free situation. Upon soft errors happening, it ensures decompressed data strictly bounded within user's requirement with a very limited degradation of compression ratio and low overhead.

Convolutional neural networks (CNNs) are becoming more and more important for solving challenging and critical problems in many fields. CNN inference applications have been deployed in safety-critical systems, which may suffer from soft errors caused by high-energy particles, high temperature, or abnormal voltage. Of critical importance is ensuring the stability of the CNN inference process against soft errors. Traditional fault tolerance methods are not suitable for CNN inference because error-correcting code is unable to protect computational components, instruction duplication techniques incur high overhead, and existing algorithm-based fault tolerance (ABFT) techniques cannot protect all convolution implementations. In this article, we focus on how to protect the CNN inference process against soft errors as efficiently as possible, with the following three contributions. (1) We propose several systematic ABFTschemes based on checksum techniques and analyze their fault protection ability and runtime thoroughly. Unlike traditional ABFT based on matrix-matrix multiplication, our schemes support any convolution implementations. (2) We design a novel workflow integrating all the proposed schemes to obtain a high detection/correction ability with limited total runtime overhead. (3) We perform our evaluation using ImageNet with well-known CNN models including AlexNet, VGG-19, ResNet-18, and YOLOv2. Experimental results demonstrate that our implementation can handle soft errors with very limited runtime overhead (4%~8% in both error-free and error-injected situations).

We present the Feature Tracking Kit (FTK), a framework that simplifies, scales, and delivers various feature-tracking algorithms for scientific data. The key of FTK is our simplicial spacetime meshing scheme that generalizes both regular and unstructured spatial meshes to spacetime while tessellating spacetime mesh elements into simplices. The benefits of using simplicial spacetime meshes include (1) reducing ambiguity cases for feature extraction and tracking, (2) simplifying the handling of degeneracies using symbolic perturbations, and (3) enabling scalable and parallel processing. The use of simplicial spacetime meshing simplifies and improves the implementation of several feature-tracking algorithms for critical points, quantum vortices, and isosurfaces. As a software framework, FTK provides end users with VTK/ParaView filters, Python bindings, a command line interface, and programming interfaces for feature-tracking applications. We demonstrate use cases as well as scalability studies through both synthetic data and scientific applications including tokamak, fluid dynamics, and superconductivity simulations. We also conduct end-to-end performance studies on the Summit supercomputer. FTK is open sourced under the MIT license: https://github.com/hguo/ftk.

Error-bounded lossy compression is a state-of-the-art data reduction technique for HPC applications because it not only significantly reduces storage overhead but also can retain high fidelity for postanalysis. Because supercomputers and HPC applications are becoming heterogeneous using accelerator-based architectures, in particular GPUs, several development teams have recently released GPU versions of their lossy compressors. However, existing state-of-the-art GPU-based lossy compressors suffer from either low compression and decompression throughput or low compression quality. In this paper, we present an optimized GPU version, cuSZ, for one of the best error-bounded lossy compressors-SZ. To the best of our knowledge, cuSZ is the first error-bounded lossy compressor on GPUs for scientific data. Our contributions are fourfold. (1) We propose a dual-quantization scheme to entirely remove the data dependency in the prediction step of SZ such that this step can be performed very efficiently on GPUs. (2) We develop an efficient customized Huffman coding for the SZ compressor on GPUs. (3) We implement cuSZ using CUDA and optimize its performance by improving the utilization of GPU memory bandwidth. (4) We evaluate our cuSZ on five real-world HPC application datasets from the Scientific Data Reduction Benchmarks and compare it with other state-of-the-art methods on both CPUs and GPUs. Experiments show that our cuSZ improves SZ's compression throughput by up to 370.1x and 13.1x, respectively, over the production version running on single and multiple CPU cores, respectively, while getting the same quality of reconstructed data. It also improves the compression ratio by up to 3.48x on the tested data compared with another state-of-the-art GPU supported lossy compressor.

The objective of this work is to develop error-bounded lossy compression methods to preserve topological features in 2D and 3D vector fields. Specifically, we explore the preservation of critical points in piecewise linear vector fields. We define the preservation of critical points as, without any false positive, false negative, or false type change in the decompressed data, (1) keeping each critical point in its original cell and (2) retaining the type of each critical point (e.g., saddle and attracting node). The key to our method is to adapt a vertex-wise error bound for each grid point and to compress input data together with the error bound field using a modified lossy compressor. Our compression algorithm can be also embarrassingly parallelized for large data handling and in situ processing. We benchmark our method by comparing it with existing lossy compressors in terms of false positive/negative/type rates, compression ratio, and various vector field visualizations with several scientific applications.

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.

Data reduction techniques have been widely demanded and used by large-scale high performance computing (HPC) applications because of vast volumes of data to be produced and stored for post-analysis. Due to very limited compression ratios of lossless compressors, error-bounded lossy compression has become an indispensable part in many HPC applications nowadays, because it can significantly reduce science data volume with user-acceptable data distortion. Since the large-scale HPC applications equipped with lossy compression techniques always need to deal with vast volume of data, soft errors or silent data corruptions (SDC) are non-negligible. Although SDC detection techniques have been studied for years, no studies were performed toward the HPC applications with lossy compression, leaving a significant gap between these applications and confidence of execution results. To fill this gap, this paper proposes a couple of SDC detection strategies for scientific simulations with lossy compression. Experimental results on 4 widely used scientific simulation datasets show promising detection ability could be still obtained with two popular lossy compressors. Our parallel experiments with up to 1,024 cores confirm that the time overheads could be limited within 7.9%.

Today's extreme-scale high-performance computing (HPC) applications are producing volumes of data too large to save or transfer because of limited storage space and I/O bandwidth. Error-bounded lossy compression has been commonly known as one of the best solutions to the big science data issue, because it can significantly reduce the data volume with strictly controlled data distortion based on user requirements. In this work, we develop an adaptive parameter optimization algorithm integrated with a series of optimization strategies for SZ, a state-of-the-art prediction-based compression model. Our contribution is threefold. (1) We exploit effective strategies by using 2nd-order regression and 2nd-order Lorenzo predictors to improve the prediction accuracy significantly for SZ, thus substantially improving the overall compression quality. (2) We design an efficient approach selecting the best-fit parameter setting, by conducting a comprehensive priori compression quality analysis and exploiting an efficient online controlling mechanism. (3) We evaluate the compression quality and performance on a supercomputer with 4,096 cores, as compared with other state-of-the-art error-bounded lossy compressors. Experiments with multiple real-world HPC simulations datasets show that our solution can improve the compression ratio up to 46% compared with the second-best compressor. Moreover, the parallel I/O performance is improved by up to 40% thanks to the significant reduction of data size.

Error-bounded lossy compression is critical to the success of extreme-scale scientific research because of ever-increasing volumes of data produced by today's high-performance computing (HPC) applications. Not only can error-controlled lossy compressors significantly reduce the I/O and storage burden but they can retain high data fidelity for post analysis. Existing state-of-the-art lossy compressors, however, generally suffer from relatively low compression and decompression throughput (up to hundreds of megabytes per second on a single CPU core), which considerably restrict the adoption of lossy compression by many HPC applications especially those with a fairly high data production rate. In this paper, we propose a highly efficient lossy compression approach based on field programmable gate arrays (FPGAs) under the state-of-the-art lossy compression model SZ. Our contributions are fourfold. (1) We adopt a wavefront memory layout to alleviate the data dependency during the prediction for higher-dimensional predictors, such as the Lorenzo predictor. (2) We propose a co-design framework named waveSZ based on the wavefront memory layout and the characteristics of SZ algorithm and carefully implement it by using high-level synthesis. (3) We propose a hardware-algorithm co-optimization method to improve the performance. (4) We evaluate our proposed waveSZ on three real-world HPC simulation datasets from the Scientific Data Reduction Benchmarks and compare it with other state-of-the-art methods on both CPUs and FPGAs. Experiments show that our waveSZ can improve SZ's compression throughput by 6.9X ~ 8.7X over the production version running on a state-of-the-art CPU and improve the compression ratio and throughput by 2.1X and 5.8X on average, respectively, compared with the state-of-the-art FPGA design.

Because of the ever-increasing data being produced by today's high performance computing (HPC) scientific simulations, I/O performance is becoming a significant bottleneck for their executions. An efficient error-controlled lossy compressor is a promising solution to significantly reduce data writing time for scientific simulations running on supercomputers. In this paper, we explore how to optimize the data dumping performance for scientific simulation by leveraging error-bounded lossy compression techniques. The contributions of the paper are threefold. (1) We propose a novel I/O performance profiling model that can effectively represent the I/O performance with different execution scales and data sizes, and optimize the estimation accuracy of data dumping performance using least square method. (2) We develop an adaptive lossy compression framework that can select the bestfit compressor (between two leading lossy compressors SZ and ZFP) with optimized parameter settings with respect to overall data dumping performance. (3) We evaluate our adaptive lossy compression framework with up to 32k cores on a supercomputer facilitated with fast I/O systems and using real-world scientific simulation datasets. Experiments show that our solution can mostly always lead the data dumping performance to the optimal level with very accurate selection of the bestfit lossy compressor and settings. The data dumping performance can be improved by up to 27% at different scales.

Today's deep neural networks (DNNs) are becoming deeper and wider because of increasing demand on the analysis quality and more and more complex applications to resolve. The wide and deep DNNs, however, require large amounts of resources (such as memory, storage, and I/O), significantly restricting their utilization on resource-constrained platforms. Although some DNN simplification methods (such as weight quantization) have been proposed to address this issue, they suffer from either low compression ratios or high compression errors, which may introduce an expensive fine-tuning overhead (i.e., a costly retraining process for the target inference accuracy). In this paper, we propose DeepSZ: an accuracy-loss expected neural network compression framework, which involves four key steps: network pruning, error bound assessment, optimization for error bound configuration, and compressed model generation, featuring a high compression ratio and low encoding time. The contribution is threefold. (1)We develop an adaptive approach to select the feasible error bounds for each layer. (2) We build a model to estimate the overall loss of inference accuracy based on the inference accuracy degradation caused by individual decompressed layers. (3) We develop an efficient optimization algorithm to determine the best-fit configuration of error bounds in order to maximize the compression ratio under the user-set inference accuracy constraint. Experiments show that DeepSZ can compress AlexNet and VGG-16 on the ImageNet dataset by a compression ratio of 46× and 116×, respectively, and compress LeNet-300-100 and LeNet-5 on the MNIST dataset by a compression ratio of 57× and 56×, respectively, with only up to 0.3% loss of inference accuracy. Compared with other state-of-the-art methods, DeepSZ can improve the compression ratio by up to 1.43×, the DNN encoding performance by up to 4.0× with four V100 GPUs, and the decoding performance by up to 6.2×.

Linear algebra operations have been widely used in big data analytics and scientific computations. Many works have been done on optimizing linear algebra operations on GPUs with regular-shaped input. However, few works are focusing on fully utilizing GPU resources when the input is not regular-shaped. Current optimizations lack of considering fully utilizing the memory bandwidth and computing power, therefore they could only achieve sub-optimal performance. In this paper, we propose a performant tall-and-skinny matrix-matrix multiplication algorithm on GPUs - TSM2. It focuses on optimizing linear algebra operation with none regular-shaped input. We implement the proposed algorithm and test on three different Nvidia GPU micro-architectures: Kepler, Maxwell, and Pascal. Experiments show that our TSM2 speedups the computation by 1.1x - 3x, improves memory bandwidth utilization by 8% - 47.6%, and improves computing power utilization by 7% - 37.3% comparing to the current state-of-the-art works. We replace the original matrix operations in K-means and Algorithm-Bases Fault Tolerance (ABFT) with TSM2 and achieve up to 1.89x and 1.90x speed up.

Introspective sorting is a ubiquitous sorting algorithm which underlies many large scale distributed systems. Hardware-mediated soft errors can result in comparison and memory errors, and thus cause introsort to generate incorrect output, which in turn disrupts systems built upon introsort; hence, it is critical to incorporate fault tolerance capability within introsort. This paper proposes the first theoretically-sound, practical fault tolerant introsort with negligible overhead: FT-iSort. To tolerate comparison errors, we use minimal TMR protection via exploiting the properties of the effects of soft errors on introsort. This algorithm-based selective protection incurs far less overhead than naïve TMR protection designed to protect an entire application. To tolerate memory errors that escape DRAM error correcting code, we propose XOR-based re-execution. We incorporate our fault tolerance method into the well-known parallel sorting implementation HykSort, and we find that fault tolerant HykSort incurs negligible overhead and obtains nearly the same scalability as unprotected HykSort.

With the ever-increasing volumes of data produced by today's large-scale scientific simulations, error-bounded lossy compression techniques have become critical: not only can they significantly reduce the data size but they also can retain high data fidelity for postanalysis. In this paper, we design a strategy to improve the compression quality significantly based on an optimized, hybrid prediction model. Our contribution is fourfold. (1) We propose a novel, transform-based predictor and optimize its compression quality. (2) We significantly improve the coefficient-encoding efficiency for the data-fitting predictor. (3) We propose an adaptive framework that can select the best-fit predictor accurately for different datasets. (4) We evaluate our solution and several existing state-of-the-art lossy compressors by running real-world applications on a supercomputer with 8,192 cores. Experiments show that our adaptive compressor can improve the compression ratio by 112~165% compared with the second-best compressor. The parallel I/O performance is improved by about 100% because of the significantly reduced data size. The total I/O time is reduced by up to 60X with our compressor compared with the original I/O time.

An effective data compressor is becoming increasingly critical to today's scientific research, and many lossy compressors are developed in the context of absolute error bounds. Based on physical/chemical definitions of simulation fields or multiresolution demand, however, many scientific applications need to compress the data with a pointwise relative error bound (i.e., the smaller the data value, the smaller the compression error to tolerate). To this end, we propose two optimized lossy compression strategies under a state-of-the-art three-staged compression framework (prediction + quantization + entropy-encoding). The first strategy (called block-based strategy) splits the data set into many small blocks and computes an absolute error bound for each block, so it is particularly suitable for the data with relatively high consecutiveness in space. The second strategy (called multi-threshold-based strategy) splits the whole value range into multiple groups with exponentially increasing thresholds and performs the compression in each group separately, which is particularly suitable for the data with a relatively large value range and spiky value changes. We implement the two strategies rigorously and evaluate them comprehensively by using two scientific applications which both require lossy compression with point-wise relative error bound. Experiments show that the two strategies exhibit the best compression qualities on different types of data sets respectively. The compression ratio of our lossy compressor is higher than that of other state-of-the-art compressors by 17.2-618 percent on the climate simulation data and 30-210 percent on the N-body simulation data, with the same relative error bound and without degradation of the overall visualization effect of the entire data.

With ever-increasing volumes of scientific data produced by high-performance computing 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 two leading BSD licensed open source C/C++ libraries for compressed floating-point arrays that support high throughput read and write random access. However, their performance is not consistent across different data sets and across different fields of some data sets, which raises the need for an automatic online (during compression) selection between SZ and ZFP, with 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 percent with the same level of data distortion because of very accurate selection (around 99 percent) of the bestfit compressor, with little overhead (less than 7 percent in the experiments).

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.

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 10-10absolute precision based on user's requirement.

Because of the ever-increasing execution scale of scientific applications, how to store the extremely large volume of data efficiently is becoming a serious issue. A significant reduction of the scientific data size can effectively mitigate the I/O burden and save considerable storage space. Since lossless compressors suffer from limited compression ratios, error-controlled lossy compressors have been studied for years. Existing error-controlled lossy compressors, however, focus mainly on absolute error bounds, which cannot meet users' diverse demands such as pointwise relative error bounds. Although some of the state-of-the-art lossy compressors support pointwise relative error bound, the compression ratios are generally low because of the limitation in their designs and possible spiky data changes in local data regions. In this work, we propose a novel, efficient approach to perform compression based on the pointwise relative error bound with higher compression ratios than existing solutions provide. Our contribution is threefold. (1) We propose a novel transformation scheme that can transfer the pointwise relative-error-bounded compression problem to an absolute-error-bounded compression issue. We also analyze the practical properties of our transformation scheme both theoretically and experimentally. (2) We implement the proposed technique in two of the most popular absolute-error-bounded lossy compressors, SZ and ZFP. (3) We evaluate our solution using multiple real-world application data across different scientific domains on a supercomputer with up to 4,096 cores and 12 TB of data. Experiments show that our solution achieves over 1.38X dumping and 1.31X loading performance over the second-best lossy compressor, respectively.

Error-controlled lossy compression has been studied for years because of extremely large volumes of data being produced by today's scientific simulations. None of existing lossy compressors, however, allow users to fix the peak signal-to-noise ratio (PSNR) during compression, although PSNR has been considered as one of the most significant indicators to assess compression quality. In this paper, we propose a novel technique providing a fixed-PSNR lossy compression for scientific data sets. We implement our proposed method based on the SZ lossy compression framework and release the code as an open-source toolkit. We evaluate our fixed-PSNR compressor on three realworld high-performance computing data sets. Experiments show that our solution has a high accuracy in controlling PSNR, with an average deviation of 0.1 ~ 5.0 dB on the tested data sets.

Iterative methods are commonly used approaches to solve large, sparse linear systems, which are fundamental operations for many modern scientific simulations. When the large-scale iterative methods are running with a large number of ranks in parallel, they have to checkpoint the dynamic variables periodically in case of unavoidable fail-stop errors, requiring fast I/O systems and large storage space. To this end, significantly reducing the checkpointing overhead is critical to improving the overall performance of iterative methods. Our contribution is fourfold. (1) We propose a novel lossy checkpointing scheme that can significantly improve the checkpointing performance of iterative methods by leveraging lossy compressors. (2) We formulate a lossy checkpointing performance model and derive theoretically an upper bound for the extra number of iterations caused by the distortion of data in lossy checkpoints, in order to guarantee the performance improvement under the lossy checkpointing scheme. (3) We analyze the impact of lossy checkpointing (i.e., extra number of iterations caused by lossy checkpointing files) for multiple types of iterative methods. (4) We evaluate the lossy checkpointing scheme with optimal checkpointing intervals on a high-performance computing environment with 2,048 cores, using a well-known scientific computation package PETSc and a state-of-the-art checkpoint/restart toolkit. Experiments show that our optimized lossy checkpointing scheme can significantly reduce the fault tolerance overhead for iterative methods by 23%∼70% compared with traditional checkpointing and 20%∼58% compared with lossless-compressed checkpointing, in the presence of system failures.

In this paper, we propose BeeFlow - an in situ analysis enabled workflow management system across multiple platforms using Docker containers. BeeFlow can support both traditional workflows as well as workflows with in situ analysis. BeeFlow leverages Docker containers to provide a portable, flexible, and reproducible workflow management system across HPC and cloud platforms. We showcase how current in situ visualization workflows can apply BeeFlow with DOE production codes VPIC and Flecsale.

This paper presents an algorithm based fault tolerance method to harden three two-sided matrix factorizations against soft errors: reduction to Hessenberg form, tridiagonal form, and bidiagonal form. These two sided factorizations are usually the prerequisites to computing eigenvalues/eigenvectors and singular value decomposition. Algorithm based fault tolerance has been shown to work on three main one-sided matrix factorizations: LU, Cholesky, and QR, but extending it to cover two sided factorizations is non-trivial because there are no obvious \textit{offline, problem} specific maintenance of checksums. We thus develop an \textit{online, algorithm} specific checksum scheme and show how to systematically adapt the two sided factorization algorithms used in LAPACK and ScaLAPACK packages to introduce the algorithm based fault tolerance.

While many algorithm-based fault tolerance (ABFT) schemes have been proposed to detect soft errors offline in the fast Fourier transform (FFT) after computation finishes, none of the existing ABFT schemes detect soft errors online before the computation finishes. This paper presents an online ABFT scheme for FFT so that soft errors can be detected online and the corrupted computation can be terminated in a much more timely manner. We also extend our scheme to tolerate both arithmetic errors and memory errors, develop strategies to reduce its fault tolerance overhead and improve its numerical stability and fault coverage, and finally incorporate it into the widely used FFTW library - one of the today's fastest FFT software implementations. Experimental results demonstrate that: (1) the proposed online ABFT scheme introduces much lower overhead than the existing offline ABFT schemes; (2) it detects errors in a much more timely manner; and (3) it also has higher numerical stability and better fault coverage.

Emerging high-performance computing platforms, with large component counts and lower power margins, are anticipated to be more susceptible to soft errors in both logic circuits and memory subsystems. We present an online algorithm-based fault tolerance (ABFT) approach to efficiently detect and recover soft errors for general iterative methods. We design a novel checksum-based encoding scheme for matrix-vector multiplication that is resilient to both arithmetic and memory errors. Our design decouples the checksum updating process from the actual computation, and allows adaptive checksum overhead control. Building on this new encoding mechanism, we propose two online ABFT designs that can effectively recover from errors when combined with a checkpoint/rollback scheme. These designs are capable of addressing scenarios under different error rates. Our ABFT approaches apply to a wide range of iterative solvers that primarily rely on matrix-vector multiplication and vector linear operations. We evaluate our designs through comprehensive analytical and empirical analysis. Experimental evaluation on the Stampede supercomputer demonstrates the low performance overheads incurred by our two ABFT schemes for preconditioned CG (0.4% and 2.2%) and preconditioned BiCGSTAB (1.0% and 4.0%) for the largest SPD matrix from UFL Sparse Matrix Collection. The evaluation also demonstrates the flexibility and effectiveness of our proposed designs for detecting and recovering various types of soft errors in general iterative methods.

Algorithm based fault tolerance (ABFT) attracts renewed interest for its extremely low overhead and good scalability. However the fault model used to design ABFT has been either abstract, simplistic, or both, leaving a gap between what occurs at the architecture level and what the algorithm expects. As the fault model is the deciding factor in choosing an effective checksum scheme, the resulting ABFT techniques have seen limited impact in practice. In this paper we seek to close the gap by directly using a comprehensive architectural fault model and devise a comprehensive ABFT scheme that can tolerate multiple architectural faults of various kinds. We implement the new ABFT scheme into high performance linpack (HPL) to demonstrate the feasibility in large scale high performance benchmark. We conduct architectural fault injection experiments and large scale experiments to empirically validate its fault tolerance and demonstrate the overhead of error handling, respectively.

Extensive researches have been done on developing and optimizing algorithm-based fault tolerance (ABFT) schemes for systolic arrays and general purpose microprocessors. However, little has been done on developing and optimizing ABFT schemes for heterogeneous systems with GPU accelerators. While existing ABFT schemes can correct computing errors like 1+1=3, we find that many memory storage errors can not be corrected by existing ABFT schemes. In this paper, we first develop a new ABFT scheme for Cholesky decomposition that can correct both computing errors and storage errors at the same time, and then develop several optimization techniques to reduce the fault tolerance overhead of ABFT for heterogeneous systems with GPU accelerators. Experimental results demonstrate that our fault tolerant Cholesky decomposition is able to correct both computing errors and storage errors in the middle of the computation and can achieve better performance than the state-of-the-art vendor provided version Cholesky decomposition library routine in CULA R18.

While many linear algebra libraries have been developed to optimize their performance, no linear algebra library considers their energy efficiency at the library design time. In this paper, we present GreenLA - an energy efficient linear algebra software package that leverages linear algebra algorithmic characteristics to maximize energy savings with negligible overhead. GreenLA is (1) energy efficient: it saves up to several times more energy than the best existing energy saving approaches that do not modify library source codes; (2) high performance: its performance is comparable to the highly optimized linear algebra library MAGMA; and (3) transparent to applications: with the same programming interface, existing MAGMA users do not need to modify their source codes to benefit from GreenLA. Experimental results demonstrate that GreenLA is able to save up to three times more energy than the best existing energy saving approaches while delivering similar performance compared to the state-of-the-art linear algebra library MAGMA.