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Register a new userParallelizing Convergent Cross Mapping Using Apache Spark
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Added by
Bo Pu
Publication date
2019
fields
Informatics Engineering
and research's language is
English
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Identifying the causal relationships between subjects or variables remains an important problem across various scientific fields. This is particularly important but challenging in complex systems, such as those involving human behavior, sociotechnical contexts, and natural ecosystems. By exploiting state space reconstruction via lagged embedding of time series, convergent cross mapping (CCM) serves as an important method for addressing this problem. While powerful, CCM is computationally costly; moreover, CCM results are highly sensitive to several parameter values. While best practice entails exploring a range of parameter settings when assessing casual relationships, the resulting computational burden can raise barriers to practical use, especially for long time series exhibiting weak causal linkages. We demonstrate here several means of accelerating CCM by harnessing the distributed Apache Spark platform. We characterize and report on results of several experiments with parallelized solutions that demonstrate high scalability and a capacity for over an order of magnitude performance improvement for the baseline configuration. Such economies in computation time can speed learning and robust identification of causal drivers in complex systems.
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With the era of big data, an explosive amount of information is now available. This enormous increase of Big Data in both academia and industry requires large-scale data processing systems. A large body of research is behind optimizing Sparks performance to make it state of the art, a fast and general data processing system. Many science and engineering fields have advanced with Big Data analytics, such as Biology, finance, and transportation. Intelligent transportation systems (ITS) gain popularity and direct benefit from the richness of information. The objective is to improve the safety and management of transportation networks by reducing congestion and incidents. The first step toward the goal is better understanding, modeling, and detecting congestion across a network efficiently and effectively. In this study, we introduce an efficient congestion detection model. The underlying network consists of 3017 segments in I-35, I-80, I-29, and I-380 freeways with an overall length of 1570 miles and averaged (0.4-0.6) miles per segment. The result of congestion detection shows the proposed method is 90% accurate while has reduced computation time by 99.88%.
Experimental Particle Physics has been at the forefront of analyzing the worlds largest datasets for decades. The HEP community was among the first to develop suitable software and computing tools for this task. In recent times, new toolkits and systems for distributed data processing, collectively called Big Data technologies have emerged from industry and open source projects to support the analysis of Petabyte and Exabyte datasets in industry. While the principles of data analysis in HEP have not changed (filtering and transforming experiment-specific data formats), these new technologies use different approaches and tools, promising a fresh look at analysis of very large datasets that could potentially reduce the time-to-physics with increased interactivity. Moreover these new tools are typically actively developed by large communities, often profiting of industry resources, and under open source licensing. These factors result in a boost for adoption and maturity of the tools and for the communities supporting them, at the same time helping in reducing the cost of ownership for the end-users. In this talk, we are presenting studies of using Apache Spark for end user data analysis. We are studying the HEP analysis workflow separated into two thrusts: the reduction of centrally produced experiment datasets and the end-analysis up to the publication plot. Studying the first thrust, CMS is working together with CERN openlab and Intel on the CMS Big Data Reduction Facility. The goal is to reduce 1 PB of official CMS data to 1 TB of ntuple output for analysis. We are presenting the progress of this 2-year project with first results of scaling up Spark-based HEP analysis. Studying the second thrust, we are presenting studies on using Apache Spark for a CMS Dark Matter physics search, comparing Sparks feasibility, usability and performance to the ROOT-based analysis.
Distributed data processing ecosystems are widespread and their components are highly specialized, such that efficient interoperability is urgent. Recently, Apache Arrow was chosen by the community to serve as a format mediator, providing efficient in-memory data representation. Arrow enables efficient data movement between data processing and storage engines, significantly improving interoperability and overall performance. In this work, we design a new zero-cost data interoperability layer between Apache Spark and Arrow-based data sources through the Arrow Dataset API. Our novel data interface helps separate the computation (Spark) and data (Arrow) layers. This enables practitioners to seamlessly use Spark to access data from all Arrow Dataset API-enabled data sources and frameworks. To benefit our community, we open-source our work and show that consuming data through Apache Arrow is zero-cost: our novel data interface is either on-par or more performant than native Spark.
As dataset sizes increase, data analysis tasks in high performance computing (HPC) are increasingly dependent on sophisticated dataflows and out-of-core methods for efficient system utilization. In addition, as HPC systems grow, memory access and data sharing are becoming performance bottlenecks. Cloud computing employs a data processing paradigm typically built on a loosely connected group of low-cost computing nodes without relying upon shared storage and/or memory. Apache Spark is a popular engine for large-scale data analysis in the cloud, which we have successfully deployed via job submission scripts on production clusters. In this paper, we describe common parallel analysis dataflows for both Message Passing Interface (MPI) and cloud based applications. We developed an effective benchmark to measure the performance characteristics of these tasks using both types of systems, specifically comparing MPI/C-based analyses with Spark. The benchmark is a data processing pipeline representative of a typical analytics framework implemented using map-reduce. In the case of Spark, we also consider whether language plays a role by writing tests using both Python and Scala, a language built on the Java Virtual Machine (JVM). We include performance results from two large systems at Argonne National Laboratory including Theta, a Cray XC40 supercomputer on which our experiments run with 65,536 cores (1024 nodes with 64 cores each). The results of our experiments are discussed in the context of their applicability to future HPC architectures. Beyond understanding performance, our work demonstrates that technologies such as Spark, while typically aimed at multi-tenant cloud-based environments, show promise for data analysis needs in a traditional clustering/supercomputing environment.
We propose TRANSMUT-Spark, a tool that automates the mutation testing process of Big Data processing code within Spark programs. Apache Spark is an engine for Big Data Processing. It hides the complexity inherent to Big Data parallel and distributed programming and processing through built-in functions, underlying parallel processes, and data management strategies. Nonetheless, programmers must cleverly combine these functions within programs and guide the engine to use the right data management strategies to exploit the large number of computational resources required by Big Data processing and avoid substantial production losses. Many programming details in data processing code within Spark programs are prone to false statements that need to be correctly and automatically tested. This paper explores the application of mutation testing in Spark programs, a fault-based testing technique that relies on fault simulation to evaluate and design test sets. The paper introduces the TRANSMUT-Spark solution for testing Spark programs. TRANSMUT-Spark automates the most laborious steps of the process and fully executes the mutation testing process. The paper describes how the tool automates the mutants generation, test execution, and adequacy analysis phases of mutation testing with TRANSMUT-Spark. It also discusses the results of experiments that were carried out to validate the tool to argue its scope and limitations.
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