To alleviate bottlenecks in storing and accessing data on high-performance computing (HPC) systems, I/O libraries are enabling computation while data is in-transit, such as HDFS filters. For scientific applications that commonly use floating-point data, error-bounded lossy compression methods are a critical technique to significantly reduce the storage and bandwidth requirements. Thus far, deciding when and where to schedule in-transit data transformations, such as compression, has been outside the scope of I/O libraries. In this paper, we introduce Runway, a runtime framework that enables computation on in-transit data with an object storage abstraction. Runway is designed to be extensible to execute user-defined functions at runtime. In this effort, we focus on studying methods to offload data compression operations to available processing units based on latency and throughput. We compare the performance of running compression on multi-core CPUs, as well as offloading it to a GPU and a Data Processing Unit (DPU). We implement a state-of-the-art error-bounded lossy compression algorithm, SZ3, as a Runway function with a variant optimized for DPUs. We propose dynamic modeling to guide scheduling decisions for in-transit data compression. We evaluate Runway using four scientific datasets from the SDRBench benchmark suite on a the Perlmutter supercomputer at NERSC.
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Understanding and Modeling Lossy Compression Schemes on HPC Scientific Data
Scientific simulations generate large amounts of floating-point data, which are often not very compressible using the traditional reduction schemes, such as deduplication or lossless compression. The emergence of lossy floating-point compression holds promise to satisfy the data reduction demand from HPC applications; however, lossy compression has not been widely adopted in science production. We believe a fundamental reason is that there is a lack of understanding of the benefits, pitfalls, and performance of lossy compression on scientific data. In this paper, we conduct a comprehensive study on state-of- the-art lossy compression, including ZFP, SZ, and ISABELA, using real and representative HPC datasets. Our evaluation reveals the complex interplay between compressor design, data features and compression performance. The impact of reduced accuracy on data analytics is also examined through a case study of fusion blob detection, offering domain scientists with the insights of what to expect from fidelity loss. Furthermore, the trial and error approach to understanding compression performance involves substantial compute and storage overhead. To this end, we propose a sampling based estimation method that extrapolates the reduction ratio from data samples, to guide domain scientists to make more informed data reduction decisions.
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- NSF-PAR ID:
- 10065104
- Date Published:
- Journal Name:
- the 32nd IEEE International Parallel and Distributed Processing Symposium (IPDPS)
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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