CEAZ: Accelerating Parallel I/O via Hardware-Algorithm Co-Design of Efficient and Adaptive Lossy Compression

As supercomputers continue to grow to exascale, the amount of data that needs to be saved or transmitted is exploding. To this end, many previous works have studied using error-bounded lossy compressors to reduce the data size and improve the I/O performance. However, little work has been done for effectively offloading lossy compression onto FPGA-based SmartNICs to reduce the compression overhead. In this paper, we propose a hardware-algorithm co-design of efficient and adaptive lossy compressor for scientific data on FPGAs (called CEAZ) to accelerate parallel I/O. Our contribution is fourfold: (1) We propose an efficient Huffman coding approach that can adaptively update Huffman codewords online based on codewords generated offline (from a variety of representative scientific datasets). (2) We derive a theoretical analysis to support a precise control of compression ratio under an error-bounded compression mode, enabling accurate offline Huffman codewords generation. This also helps us create a fixed-ratio compression mode for consistent throughput. (3) We develop an efficient compression pipeline by adopting cuSZ's dual-quantization algorithm to our hardware use case. (4) We evaluate CEAZ on five real-world datasets with both a single FPGA board and 128 nodes from Bridges-2 supercomputer. Experiments show that CEAZ outperforms the second-best FPGA-based lossy compressor by 2X of throughput and 9.6X of compression ratio. It also improves MPI_File_write and MPI_Gather throughputs by up to 25.8X and 24.8X, respectively.Comment: 14 pages, 17 figures, 8 table

Interpolation of Scientific Image Databases

This paper explores how recent convolutional neural network (CNN)-based techniques can be used to interpolate images inside scientific image databases. These databases are frequently used for the interactive visualization of large-scale simulations, where images correspond to samples of the parameter space (e.g., timesteps, isovalues, thresholds, etc.) and the visualization space (e.g., camera locations, clipping planes, etc.). These databases can be browsed post hoc along the sampling axis to emulate real-time interaction with large-scale datasets. However, the resulting databases are limited to their contained images, i.e., the sampling points. In this paper, we explore how efficiently and accurately CNN-based techniques can derive new images by interpolating database elements. We demonstrate on several real-world examples that the size of databases can be further reduced by dropping samples that can be interpolated post hoc with an acceptable error, which we measure qualitatively and quantitatively

Ultrafast Error-Bounded Lossy Compression for Scientific Datasets

Today\u27s 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

Toward smart and efficient scientific data management

Scientific research generates vast amounts of data, and the scale of data has significantly increased with advancements in scientific applications. To manage this data effectively, lossy data compression techniques are necessary to reduce storage and transmission costs. Nevertheless, the use of lossy compression introduces uncertainties related to its performance. This dissertation aims to answer key questions surrounding lossy data compression, such as how the performance changes, how much reduction can be achieved, and how to optimize these techniques for modern scientific data management workflows. One of the major challenges in adopting lossy compression techniques is the trade-off between data accuracy and compression performance, particularly the compression ratio. This trade-off is not well understood, leading to a trial-and-error approach in selecting appropriate setups. To address this, the dissertation analyzes and estimates the compression performance of two modern lossy compressors, SZ and ZFP, on HPC datasets at various error bounds. By predicting compression ratios based on intrinsic metrics collected under a given base error bound, the effectiveness of the estimation scheme is confirmed through evaluations using real HPC datasets. Furthermore, as scientific simulations scale up on HPC systems, the disparity between computation and input/output (I/O) becomes a significant challenge. To overcome this, error-bounded lossy compression has emerged as a solution to bridge the gap between computation and I/O. Nonetheless, the lack of understanding of compression performance hinders the wider adoption of lossy compression. The dissertation aims to address this challenge by examining the complex interaction between data, error bounds, and compression algorithms, providing insights into compression performance and its implications for scientific production. Lastly, the dissertation addresses the performance limitations of progressive data retrieval frameworks for post-hoc data analytics on full-resolution scientific simulation data. Existing frameworks suffer from over-pessimistic error control theory, leading to fetching more data than necessary for recomposition, resulting in additional I/O overhead. To enhance the performance of progressive retrieval, deep neural networks are leveraged to optimize the error control mechanism, reducing unnecessary data fetching and improving overall efficiency. By tackling these challenges and providing insights, this dissertation contributes to the advancement of scientific data management, lossy data compression techniques, and HPC progressive data retrieval frameworks. The findings and methodologies presented pave the way for more efficient and effective management of large-scale scientific data, facilitating enhanced scientific research and discovery. In future research, this dissertation highlights the importance of investigating the impact of lossy data compression on downstream analysis. On the one hand, more data reduction can be achieved under scenarios like image visualization where the error tolerance is very high, leading to less I/O and communication overhead. On the other hand, post-hoc calculations based on physical properties after compression may lead to misinterpretation, as the statistical information of such properties might be compromised during compression. Therefore, a comprehensive understanding of the impact of lossy data compression on each specific scenario is vital to ensure accurate analysis and interpretation of results

Visuelle Analyse großer Partikeldaten

Partikelsimulationen sind eine bewährte und weit verbreitete numerische Methode in der Forschung und Technik. Beispielsweise werden Partikelsimulationen zur Erforschung der Kraftstoffzerstäubung in Flugzeugturbinen eingesetzt. Auch die Entstehung des Universums wird durch die Simulation von dunkler Materiepartikeln untersucht. Die hierbei produzierten Datenmengen sind immens. So enthalten aktuelle Simulationen Billionen von Partikeln, die sich über die Zeit bewegen und miteinander interagieren. Die Visualisierung bietet ein großes Potenzial zur Exploration, Validation und Analyse wissenschaftlicher Datensätze sowie der zugrundeliegenden Modelle. Allerdings liegt der Fokus meist auf strukturierten Daten mit einer regulären Topologie. Im Gegensatz hierzu bewegen sich Partikel frei durch Raum und Zeit. Diese Betrachtungsweise ist aus der Physik als das lagrange Bezugssystem bekannt. Zwar können Partikel aus dem lagrangen in ein reguläres eulersches Bezugssystem, wie beispielsweise in ein uniformes Gitter, konvertiert werden. Dies ist bei einer großen Menge an Partikeln jedoch mit einem erheblichen Aufwand verbunden. Darüber hinaus führt diese Konversion meist zu einem Verlust der Präzision bei gleichzeitig erhöhtem Speicherverbrauch. Im Rahmen dieser Dissertation werde ich neue Visualisierungstechniken erforschen, welche speziell auf der lagrangen Sichtweise basieren. Diese ermöglichen eine effiziente und effektive visuelle Analyse großer Partikeldaten

Optimizing Error-Bounded Lossy Compression for Three-Dimensional Adaptive Mesh Refinement Simulations

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. However, little work has been done to improve error-bounded lossy compression for Adaptive Mesh Refinement (AMR) simulation data. Unlike the previous work that only leverages 1D compression, in this work, we propose to leverage high-dimensional (e.g., 3D) compression for each refinement level of AMR data. To remove the data redundancy across different levels, we propose three pre-process strategies and adaptively use them based on the data characteristics. Experiments on seven AMR datasets from a real-world large-scale AMR simulation demonstrate that our proposed approach can improve the compression ratio by up to 3.3X under the same data distortion, compared to the state-of-the-art method. In addition, we leverage the flexibility of our approach to tune the error bound for each level, which achieves much lower data distortion on two application-specific metrics.Comment: 13 pages, 17 figures, 3 tables, accepted by ACM HPDC 202

Approachable Error Bounded Lossy Compression

Compression is commonly used in HPC applications to move and store data. Traditional lossless compression, however, does not provide adequate compression of floating point data often found in scientific codes. Recently, researchers and scientists have turned to lossy compression techniques that approximate the original data rather than reproduce it in order to achieve desired levels of compression. Typical lossy compressors do not bound the errors introduced into the data, leading to the development of error bounded lossy compressors (EBLC). These tools provide the desired levels of compression as mathematical guarantees on the errors introduced. However, the current state of EBLC leaves much to be desired. The existing EBLC all have different interfaces requiring codes to be changed to adopt new techniques; EBLC have many more configuration options than their predecessors, making them more difficult to use; and EBLC typically bound quantities like point wise errors rather than higher level metrics such as spectra, p-values, or test statistics that scientists typically use. My dissertation aims to provide a uniform interface to compression and to develop tools to allow application scientists to understand and apply EBLC. This dissertation proposal presents three groups of work: LibPressio, a standard interface for compression and analysis; FRaZ/LibPressio-Opt frameworks for the automated configuration of compressors using LibPressio; and work on tools for analyzing errors in particular domains