Engineering Papers⌕ Search

Engineering topics

Liu, Qing

Publications and source records attributed to Liu, Qing.

At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Error-controlled Progressive Retrieval of Scientific Data under Derivable Quantities of Interest

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× performance gain in data transfer tasks compared to transferring the primary data while guaranteeing a QoI error that is less than 1E-5.

Wu, Xuan↗
DOE OSTI2024

A General Framework for Error-controlled Unstructured Scientific Data Compression

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 −6 to 1×10−2. We further investigate impact of hyperparameters, such as grid spacing and error allocation, to deliver optimal compression ratios in diverse datasets.

Gong, Qian↗
DOE OSTI2023

RAPIDS: Reconciling Availability, Accuracy, and Performance in Managing Geo-Distributed Scientific Data

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.In this paper, we propose RAPIDS, a hybrid approach that combines the multigrid-based error-bounded lossy compression with erasure coding, to significantly reduce the storage and network overhead required for maintaining high data availability. Our experiments show that RAPIDS reduces the storage overhead by up to 7.5x and network overhead by up to 3x to achieve the same level of availability compared to the regular EC method. We improve RAPIDS by building two models to optimize the fault tolerance configurations and data gathering strategy. We demonstrate that RAPIDS significantly improves performance when running on many CPU cores in parallel or on GPUs.

Wan, Lipeng↗
DOE OSTI2023

Improving Progressive Retrieval for HPC Scientific Data using Deep Neural Network

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).

Wang, Jinzhen↗
DOE OSTI2023

zPerf: A Statistical Gray-Box Approach to Performance Modeling and Extrapolation for Scientific Lossy Compression

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. Here, 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.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

ornladios/ADIOS2

ADIOS 2: The Adaptable Input Output (I/O) System version 2 is an open-source framework that addresses scientific data management challenges, e.g. scalable parallel I/O, as we approach the exascale era in high-performance computing (HPC). ADIOS 2 bindings are available in C++, C, Fortran, Python and can be used on supercomputers, personal computers, and cloud systems running on Linux, macOS and Windows. ADIOS 2 has out-of-the-box support for MPI and serial environments.

ECP↗
DOE OSTI2021

Unbalanced Parallel I/O: An Often-Neglected Side Effect of Lossy Scientific Data Compression

Lossy compression techniques have demonstrated promising results in significantly reducing the scientific data size while guaranteeing the compression error bounds. However, one important yet often neglected side effect of lossy scientific data compression is its impact on the performance of parallel I/O. Our key observation is that the compressed data size is often highly skewed across processes in lossy scientific compression. To understand this behavior, we conduct extensive experiments where we apply three lossy compressors MGARD, ZFP, and SZ, which are specifically designed and optimized for scientific data, to three real-world scientific applications Gray-Scott simulation, WarpX, and XGC. Our analysis result demonstrates that the size of the compressed data is always skewed even if the original data is evenly decomposed among processes. Such skewness widely exists in different scientific applications using different compressors as long as the information density of the data varies across processes. We then systematically study how this side effect of lossy scientific data compression impacts the performance of parallel I/O. We observe that the skewness in the sizes of the compressed data often leads to I/O imbalance, which can significantly reduce the efficiency of I/O bandwidth utilization if not properly handled. In addition, writing data concurrently to a single shared file through MPI-IO library is more sensitive to the unbalanced I/O loads. Therefore, we believe our research community should pay more attention to the unbalanced parallel I/O caused by lossy scientific data compression.

Wang, Xinying↗
DOE OSTI2021

The Exascale Framework for High Fidelity coupled Simulations (EFFIS): Enabling whole device modeling in fusion science

We present the Exascale Framework for High Fidelity coupled Simulations (EFFIS), a workflow and code coupling framework developed as part of the Whole Device Modeling Application (WDMApp) in the Exascale Computing Project. EFFIS consists of a library, command line utilities, and a collection of run-time daemons. Together, these software products enable users to easily compose and execute workflows that include: strong or weak coupling, in situ (or offline) analysis/visualization/monitoring, command-and-control actions, remote dashboard integration, and more. We describe WDMApp physics coupling cases and computer science requirements that motivate the design of the EFFIS framework. Furthermore, we explain the essential enabling technology that EFFIS leverages: ADIOS for performant data movement, PerfStubs/TAU for performance monitoring, and an advanced COUPLER for transforming coupling data from its native format to the representation needed by another application. Finally, we demonstrate EFFIS using coupled multi-simulation WDMApp workflows and exemplify how the framework supports the project’s needs. We show that EFFIS and its associated services for data movement, visualization, and performance collection does not introduce appreciable overhead to the WDMApp workflow and that the resource-dominant application’s idle time while waiting for data is minimal.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Accelerating Multigrid-based Hierarchical Scientific Data Refactoring on GPUs

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.

Chen, Jieyang↗
DOE OSTI2021

Polymorphonuclear-MDSCs Facilitate Tumor Regrowth After Radiation by Suppressing CD8+ T Cells

Radiation therapy (RT) is widely used in the treatment of cancer. Unfortunately, RT alone is insufficient to control the disease in most cases, as regrowth after irradiation still occur. Thus, it would be meaningful to explore the underlying mechanism of tumor regrowth after irradiation. Myeloid-derived suppressor cells (MDSCs) contribute to the immunosuppressive tumor microenvironment and hinder the therapeutic efficacy of RT. However, it is unclear whether MDSCs-mediated immune suppression contributes to local relapse after irradiation. In this article, we tried to figure out how MDSCs sabotage the therapeutic effect of RT, and tried to determine the potential synergistic effect of combination between targeting MDSCs and RT.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2021

Accelerating Multigrid-based Hierarchical Scientific Data Refactoring on GPUs

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.

Data refactoring↗