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Register a new userExploring Autoencoder-based Error-bounded Compression for Scientific Data
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Added by
Jinyang Liu
Publication date
2021
fields
Informatics Engineering
and research's language is
English
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Error-bounded lossy compression is becoming an indispensable technique for the success of todays 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% ~ 800% improvement in compression ratio with the same data distortion) compared with SZ2.1 and ZFP in cases with a high compression ratio.
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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 cuSZ+ using seven real-world HPC application datasets on V100 and A100 GPUs. Experiments show cuSZ+ improves the compression throughputs and ratios by up to 18.4X and 5.3X, respectively, over cuSZ on the tested datasets.
Data management is becoming increasingly important in dealing with the large amounts of data produced by large-scale scientific simulations and instruments. 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 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 70X, and the proposed compression method can improve compression ratio by up to 2X compared with other state-of-the-art error-bounded lossy compressors under the same level of data distortion.
Training deep neural networks on large datasets containing high-dimensional data requires a large amount of computation. A solution to this problem is data-parallel distributed training, where a model is replicated into several computational nodes that have access to different chunks of the data. This approach, however, entails high communication rates and latency because of the computed gradients that need to be shared among nodes at every iteration. The problem becomes more pronounced in the case that there is wireless communication between the nodes (i.e. due to the limited network bandwidth). To address this problem, various compression methods have been proposed including sparsification, quantization, and entropy encoding of the gradients. Existing methods leverage the intra-node information redundancy, that is, they compress gradients at each node independently. In contrast, we advocate that the gradients across the nodes are correlated and propose methods to leverage this inter-node redundancy to improve compression efficiency. Depending on the node communication protocol (parameter server or ring-allreduce), we propose two instances of the LGC approach that we coin Learned Gradient Compression (LGC). Our methods exploit an autoencoder (i.e. trained during the first stages of the distributed training) to capture the common information that exists in the gradients of the distributed nodes. We have tested our LGC methods on the image classification and semantic segmentation tasks using different convolutional neural networks (ResNet50, ResNet101, PSPNet) and multiple datasets (ImageNet, Cifar10, CamVid). The ResNet101 model trained for image classification on Cifar10 achieved an accuracy of 93.57%, which is lower than the baseline distributed training with uncompressed gradients only by 0.18%.
This letter introduces a new denoiser that modifies the structure of denoising autoencoder (DAE), namely noise learning based DAE (nlDAE). The proposed nlDAE learns the noise of the input data. Then, the denoising is performed by subtracting the regenerated noise from the noisy input. Hence, nlDAE is more effective than DAE when the noise is simpler to regenerate than the original data. To validate the performance of nlDAE, we provide three case studies: signal restoration, symbol demodulation, and precise localization. Numerical results suggest that nlDAE requires smaller latent space dimension and smaller training dataset compared to DAE.
As parallel computing trends towards the exascale, scientific data produced by high-fidelity simulations are growing increasingly massive. For instance, a simulation on a three-dimensional spatial grid with 512 points per dimension that tracks 64 variables per grid point for 128 time steps yields 8~TB of data, assuming double precision. By viewing the data as a dense five-way tensor, we can compute a Tucker decomposition to find inherent low-dimensional multilinear structure, achieving compression ratios of up to 5000 on real-world data sets with negligible loss in accuracy. So that we can operate on such massive data, we present the first-ever distributed-memory parallel implementation for the Tucker decomposition, whose key computations correspond to parallel linear algebra operations, albeit with nonstandard data layouts. Our approach specifies a data distribution for tensors that avoids any tensor data redistribution, either locally or in parallel. We provide accompanying analysis of the computation and communication costs of the algorithms. To demonstrate the compression and accuracy of the method, we apply our approach to real-world data sets from combustion science simulations. We also provide detailed performance results, including parallel performance in both weak and strong scaling experiments.
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