Scientific simulations on high-performance computing (HPC) systems can generate large amounts of floating-point data per run. To mitigate the data storage bottleneck and lower the data volume, it is common for floating-point compressors to be employed. As compared to lossless compressors, lossy compressors, such as SZ and ZFP, can reduce data volume more aggressively while maintaining the usefulness of the data. However, a reduction ratio of more than two orders of magnitude is almost impossible without seriously distorting the data. In deep learning, the autoencoder technique has shown great potential for data compression, in particular with images. Whether the autoencoder can deliver similar performance on scientific data, however, is unknown. In this article, we for the first time conduct a comprehensive study on the use of autoencoders to compress real-world scientific data and illustrate several key findings on using autoencoders for scientific data reduction. We implement an autoencoder-based compression prototype to reduce floating-point data. Our study shows that the out-of-the-box implementation needs to be further tuned in order to achieve high compression ratios and satisfactory error bounds. Our evaluation results show that, for most of the test datasets, the tuned autoencoder outperforms SZ by up to 4X, and ZFP by up to 50X in compression ratios, respectively. Our practices and lessons learned in this work can direct future optimizations for using autoencoders to compress scientific data.

With the scaling up of simulation-based scientific discovery on high-performance computing systems, the disparity between compute and I/O has increased, forcing domain scientists to save only a small amount of simulation data to persistent storage. This can result in the loss of essential physics fields that are needed for data analysis. While error-bounded lossy compression has made tremendous progress in bridging the gap between compute and I/O, the lack of understanding of compression performance remains a key hurdle to its wide adoption. In this work, we present zPerf, a statistical gray-box performance modeling approach for scientific lossy compression. Our contributions are threefold: 1) We develop zPerf to estimate the performance of lossy compression techniques, based on in-depth understanding and statistical modeling for data features and core compression metrics; 2) We demonstrate the in-detailed implementation of zPerf using two case studies, where we derive the performance modeling for SZ and ZFP, two leading lossy compressors; 3) We evaluate the effectiveness of zPerf on real-world datasets across various domains. Based on the evaluation, we demonstrate the efficacy of the zPerf performance model; 4) We further discuss three case studies where zPerf is applied to extrapolate the compression ratio of SZ and ZFP with alternative encoding schemes as well as ZFP with an alternative transform scheme. Through the case studies, we demonstrate the potential of zPerf for exploring the design space of lossy compression, which has hardly been studied in the literature.

As the storage overhead of high-performance computing (HPC) data reaches into the petabyte or even exabyte scale, it could be useful to find new methods of compressing such data. The compression autoencoder (CAE) has recently been proposed to compress HPC data with a very high compression ratio. However, this machine learning-based method suffers from the major drawback of lengthy training time. In this paper, we attempt to mitigate this problem by proposing a proportioning scheme to reduce the amount of data that is used for training relative to the amount of data to be compressed. We show that this method drastically reduces the training time without, in most cases, significantly increasing the error. We further explain how this scheme can even improve the accuracy of the CAE on certain datasets. Finally, we provide some guidance on how to determine a suitable proportion of the training dataset to use in order to train the CAE for a given dataset.

Nowadays, modern industry data centers have employed erasure codes to provide reliability for large amounts of data at a low cost. Although erasure codes provide optimal storage efficiency, they suffer from high repair costs compared to traditional three-way replication: when a data miss occurs in a data center, erasure codes would require high disk usage and network bandwidth consumption across nodes and racks to repair the failed data. In this paper, we propose RPR, a rack-aware pipeline repair scheme for erasure-coded distributed storage systems. RPR for the first time investigates the insights of the racks, and explores the connection between the node level and rack level to help improve the repair performance when a single failure or multiple failures occur in a data center. The evaluation results on several common RS code configurations show that, for single-block failures, our RPR scheme reduces the total repair time by up to 81.5% compared to the traditional RS code repair method and 50.2% compared to the state-of-the-art CAR algorithm. For multi-block failures, RPR reduces the total repair time and cross-rack data transfer traffic by up to 64.5% and 50%, respectively, over the traditional repair.

Nowadays erasure coding is one of the most significant techniques in cloud storage systems, which provides both quick parallel I/O processing and high capabilities of fault tolerance on massive data accesses. In these systems, triple disk failure tolerant arrays (3DFTs) is a typical configuration, which is supported by several classic erasure codes like Reed-Solomon (RS) codes, Local Reconstruction Codes (LRC), Minimum Storage Regeneration (MSR) codes, etc. For an online recovery process, the foreground application workloads and the background recovery workloads are handled simultaneously, which requires a comprehensive understanding on both two types of workload characteristics. Although several techniques have been proposed to accelerate the I/O requests of online recovery processes, they are typically unilateral due to the fact that the above two workloads are not combined together to achieve high cost-effective performance.To address this problem, we propose Erasure Codes Fusion (EC-Fusion), an efficient hybrid erasure coding framework in cloud storage systems. EC-Fusion is a combination of RS and MSR codes, which dynamically selects the appropriate code based on its properties. On one hand, for write-intensive application workloads or low risk on data loss in recovery workloads, EC-Fusion uses RS code to decrease the computational overhead and storage cost concurrently. On the other hand, for read-intensive or frequent reconstruction in workloads, MSR code is a proper choice. Therefore, a better overall application and recovery performance can be achieved in a cost-effective fashion. To demonstrate the effectiveness of EC-Fusion, several experiments are conducted in hadoop systems. The results show that, compared with the traditional hybrid erasure coding techniques, EC-Fusion accelerates the response time for application by up to 1.77×, and reduces the reconstruction time by up to 69.10%.

Scientific simulations on high-performance computing (HPC) systems generate vast amounts of floating-point data that need to be reduced in order to lower the storage and I/O cost. Lossy compressors trade data accuracy for reduction performance and have been demonstrated to be effective in reducing data volume. However, a key hurdle to wide adoption of lossy compressors is that the trade-off between data accuracy and compression performance, particularly the compression ratio, is not well understood. Consequently, domain scientists often need to exhaust many possible error bounds before they can figure out an appropriate setup. The current practice of using lossy compressors to reduce data volume is, therefore, through trial and error, which is not efficient for large datasets which take a tremendous amount of computational resources to compress. This paper aims to analyze and estimate the compression performance of lossy compressors on HPC datasets. In particular, we predict the compression ratios of two modern lossy compressors that achieve superior performance, SZ and ZFP, on HPC scientific datasets at various error bounds, based upon the compressors' intrinsic metrics collected under a given base error bound. We evaluate the estimation scheme using twenty real HPC datasets and the results confirm the effectiveness of our approach.

Nowadays, scientific simulations on high-performance computing (HPC) systems can generate large amounts of data (in the scale of terabytes or petabytes) per run. When this huge amount of HPC data is processed by machine learning applications, the training overhead will be significant. Typically, the training process for a neural network can take several hours to complete, if not longer. When machine learning is applied to HPC scientific data, the training time can take several days or even weeks. Transfer learning, an optimization usually used to save training time or achieve better performance, has potential for reducing this large training overhead. In this paper, we apply transfer learning to a machine learning HPC application. We find that transfer learning can reduce training time without, in most cases, significantly increasing the error. This indicates transfer learning can be very useful for working with HPC datasets in machine learning applications.

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.

In modern distributed storage systems, space efficiency and system reliability are two major concerns. As a result, contemporary storage systems often employ data deduplication and erasure coding to reduce the storage overhead and provide fault tolerance, respectively. However, little work has been done to explore the relationship between these two techniques. In this paper, we propose Reference-counter Aware Deduplication (RAD), which employs the features of deduplication into erasure coding to improve garbage collection performance when deletion occurs. RAD wisely encodes the data according to the reference counter, which is provided by the deduplication level and thus reduces the encoding overhead when garbage collection is conducted. Further, since the reference counter also represents the reliability levels of the data chunks, we additionally made some effort to explore the trade-offs between storage overhead and reliability level among different erasure codes. The experiment results show that RAD can effectively improve the GC performance by up to 24.8% and the reliability analysis shows that, with certain data features, RAD can provide both better reliability and better storage efficiency compared to the traditional Round- Robin placement.

Cloud file systems like Hadoop have become a norm for handling big data because of the easy scaling and distributed storage layout. However, these systems are susceptible to failures and data needs to be recovered when a failure is detected. During temporary failures, MapReduce jobs or file system clients perform degraded reads and satisfy the read request. We argue that lack of sharing of the recovered data during degraded reads and recovery of only the requested data block places a heavy strain on the system's network resources and increases the job execution time. To this end, we propose CoARC (Co-operative, Aggressive Recovery and Caching), which is a new data-recovery mechanism for unavailable data during degraded reads in distributed file systems. The main idea is to recover not only the data block that was requested but also other temporarily unavailable blocks in the same strip and cache them in a separate data node. We also propose an LRF (Least Recently Failed) cache replacement algorithm for such a kind of recovery caches. We also show that CoARC significantly reduces the network usage and job runtime in erasure coded Hadoop.