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Added by
Yuankun Fu
Publication date
2020
fields
Informatics Engineering
and research's language is
English
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This chapter introduces the state-of-the-art in the emerging area of combining High Performance Computing (HPC) with Big Data Analysis. To understand the new area, the chapter first surveys the existing approaches to integrating HPC with Big Data. Next, the chapter introduces several optimization solutions that focus on how to minimize the data transfer time from computation-intensive applications to analysis-intensive applications as well as minimizing the end-to-end time-to-solution. The solutions utilize SDN to adaptively use both high speed interconnect network and high performance parallel file systems to optimize the application performance. A computational framework called DataBroker is designed and developed to enable a tight integration of HPC with data analysis. Multiple types of experiments have been conducted to show different performance issues in both message passing and parallel file systems and to verify the effectiveness of the proposed research approaches.
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Several fundamental changes in technology indicate domain-specific hardware and software co-design is the only path left. In this context, architecture, system, data management, and machine learning communities pay greater attention to innovative big data and AI algorithms, architecture, and systems. Unfortunately, complexity, diversity, frequently-changed workloads, and rapid evolution of big data and AI systems raise great challenges. First, the traditional benchmarking methodology that creates a new benchmark or proxy for every possible workload is not scalable, or even impossible for Big Data and AI benchmarking. Second, it is prohibitively expensive to tailor the architecture to characteristics of one or more application or even a domain of applications. We consider each big data and AI workload as a pipeline of one or more classes of units of computation performed on different initial or intermediate data inputs, each class of which we call a data motif. On the basis of our previous work that identifies eight data motifs taking up most of the run time of a wide variety of big data and AI workloads, we propose a scalable benchmarking methodology that uses the combination of one or more data motifs---to represent diversity of big data and AI workloads. Following this methodology, we present a unified big data and AI benchmark suite---BigDataBench 4.0, publicly available from~url{http://prof.ict.ac.cn/BigDataBench}. This unified benchmark suite sheds new light on domain-specific hardware and software co-design: tailoring the system and architecture to characteristics of the unified eight data motifs other than one or more application case by case. Also, for the first time, we comprehensively characterize the CPU pipeline efficiency using the benchmarks of seven workload types in BigDataBench 4.0.
Network Traffic Monitoring and Analysis (NTMA) represents a key component for network management, especially to guarantee the correct operation of large-scale networks such as the Internet. As the complexity of Internet services and the volume of traffic continue to increase, it becomes difficult to design scalable NTMA applications. Applications such as traffic classification and policing require real-time and scalable approaches. Anomaly detection and security mechanisms require to quickly identify and react to unpredictable events while processing millions of heterogeneous events. At last, the system has to collect, store, and process massive sets of historical data for post-mortem analysis. Those are precisely the challenges faced by general big data approaches: Volume, Velocity, Variety, and Veracity. This survey brings together NTMA and big data. We catalog previous work on NTMA that adopt big data approaches to understand to what extent the potential of big data is being explored in NTMA. This survey mainly focuses on approaches and technologies to manage the big NTMA data, additionally briefly discussing big data analytics (e.g., machine learning) for the sake of NTMA. Finally, we provide guidelines for future work, discussing lessons learned, and research directions.
Principal component analysis (PCA) is not only a fundamental dimension reduction method, but is also a widely used network anomaly detection technique. Traditionally, PCA is performed in a centralized manner, which has poor scalability for large distributed systems, on account of the large network bandwidth cost required to gather the distributed state at a fusion center. Consequently, several recent works have proposed various distributed PCA algorithms aiming to reduce the communication overhead incurred by PCA without losing its inferential power. This paper evaluates the tradeoff between communication cost and solution quality of two distributed PCA algorithms on a real domain name system (DNS) query dataset from a large network. We also apply the distributed PCA algorithm in the area of network anomaly detection and demonstrate that the detection accuracy of both distributed PCA-based methods has little degradation in quality, yet achieves significant savings in communication bandwidth.
The management of security credentials (e.g., passwords, secret keys) for computational science workflows is a burden for scientists and information security officers. Problems with credentials (e.g., expiration, privilege mismatch) cause workflows to fail to fetch needed input data or store valuable scientific results, distracting scientists from their research by requiring them to diagnose the problems, re-run their computations, and wait longer for their results. In this paper, we introduce SciTokens, open source software to help scientists manage their security credentials more reliably and securely. We describe the SciTokens system architecture, design, and implementation addressing use cases from the Laser Interferometer Gravitational-Wave Observatory (LIGO) Scientific Collaboration and the Large Synoptic Survey Telescope (LSST) projects. We also present our integration with widely-used software that supports distributed scientific computing, including HTCondor, CVMFS, and XrootD. SciTokens uses IETF-standard OAuth tokens for capability-based secure access to remote scientific data. The access tokens convey the specific authorizations needed by the workflows, rather than general-purpose authentication impersonation credentials, to address the risks of scientific workflows running on distributed infrastructure including NSF resources (e.g., LIGO Data Grid, Open Science Grid, XSEDE) and public clouds (e.g., Amazon Web Services, Google Cloud, Microsoft Azure). By improving the interoperability and security of scientific workflows, SciTokens 1) enables use of distributed computing for scientific domains that require greater data protection and 2) enables use of more widely distributed computing resources by reducing the risk of credential abuse on remote systems.
Background: Metabolomics datasets are becoming increasingly large and complex, with multiple types of algorithms and workflows needed to process and analyse the data. A cloud infrastructure with portable software tools can provide much needed resources enabling faster processing of much larger datasets than would be possible at any individual lab. The PhenoMeNal project has developed such an infrastructure, allowing users to run analyses on local or commercial cloud platforms. We have examined the computational scaling behaviour of the PhenoMeNal platform using four different implementations across 1-1000 virtual CPUs using two common metabolomics tools. Results: Our results show that data which takes up to 4 days to process on a standard desktop computer can be processed in just 10 min on the largest cluster. Improved runtimes come at the cost of decreased efficiency, with all platforms falling below 80% efficiency above approximately 1/3 of the maximum number of vCPUs. An economic analysis revealed that running on large scale cloud platforms is cost effective compared to traditional desktop systems. Conclusions: Overall, cloud implementations of PhenoMeNal show excellent scalability for standard metabolomics computing tasks on a range of platforms, making them a compelling choice for research computing in metabolomics.
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