Performance optimization and energy efficiency of big-data computing workflows

Next-generation e-science is producing colossal amounts of data, now frequently termed as Big Data, on the order of terabyte at present and petabyte or even exabyte in the predictable future. These scientific applications typically feature data-intensive workflows comprised of moldable parallel computing jobs, such as MapReduce, with intricate inter-job dependencies. The granularity of task partitioning in each moldable job of such big data workflows has a significant impact on workflow completion time, energy consumption, and financial cost if executed in clouds, which remains largely unexplored. This dissertation conducts an in-depth investigation into the properties of moldable jobs and provides an experiment-based validation of the performance model where the total workload of a moldable job increases along with the degree of parallelism. Furthermore, this dissertation conducts rigorous research on workflow execution dynamics in resource sharing environments and explores the interactions between workflow mapping and task scheduling on various computing platforms. A workflow optimization architecture is developed to seamlessly integrate three interrelated technical components, i.e., resource allocation, job mapping, and task scheduling. Cloud computing provides a cost-effective computing platform for big data workflows where moldable parallel computing models are widely applied to meet stringent performance requirements. Based on the moldable parallel computing performance model, a big-data workflow mapping model is constructed and a workflow mapping problem is formulated to minimize workflow makespan under a budget constraint in public clouds. This dissertation shows this problem to be strongly NP-complete and designs i) a fully polynomial-time approximation scheme for a special case with a pipeline-structured workflow executed on virtual machines of a single class, and ii) a heuristic for a generalized problem with an arbitrary directed acyclic graph-structured workflow executed on virtual machines of multiple classes. The performance superiority of the proposed solution is illustrated by extensive simulation-based results in Hadoop/YARN in comparison with existing workflow mapping models and algorithms. Considering that large-scale workflows for big data analytics have become a main consumer of energy in data centers, this dissertation also delves into the problem of static workflow mapping to minimize the dynamic energy consumption of a workflow request under a deadline constraint in Hadoop clusters, which is shown to be strongly NP-hard. A fully polynomial-time approximation scheme is designed for a special case with a pipeline-structured workflow on a homogeneous cluster and a heuristic is designed for the generalized problem with an arbitrary directed acyclic graph-structured workflow on a heterogeneous cluster. This problem is further extended to a dynamic version with deadline-constrained MapReduce workflows to minimize dynamic energy consumption in Hadoop clusters. This dissertation proposes a semi-dynamic online scheduling algorithm based on adaptive task partitioning to reduce dynamic energy consumption while meeting performance requirements from a global perspective, and also develops corresponding system modules for algorithm implementation in the Hadoop ecosystem. The performance superiority of the proposed solutions in terms of dynamic energy saving and deadline missing rate is illustrated by extensive simulation results in comparison with existing algorithms, and further validated through real-life workflow implementation and experiments using the Oozie workflow engine in Hadoop/YARN systems

Performance optimization of big data computing workflows for batch and stream data processing in multi-clouds

Workflow techniques have been widely used as a major computing solution in many science domains. With the rapid deployment of cloud infrastructures around the globe and the economic benefits of cloud-based computing and storage services, an increasing number of scientific workflows have migrated or are in active transition to clouds. As the scale of scientific applications continues to grow, it is now common to deploy various data- and network-intensive computing workflows such as serial computing workflows, MapReduce/Spark-based workflows, and Storm-based stream data processing workflows in multi-cloud environments, where inter-cloud data transfer oftentimes plays a significant role in both workflow performance and financial cost. Rigorous mathematical models are constructed to analyze the intra- and inter-cloud execution process of scientific workflows and a class of budget-constrained workflow mapping problems are formulated to optimize the network performance of big data workflows in multi-cloud environments. Research shows that these problems are all NP-complete and a heuristic solution is designed for each that takes into consideration module execution, data transfer, and I/O operations. The performance superiority of the proposed solutions over existing methods are illustrated through extensive simulations and further verified by real-life workflow experiments deployed in public clouds

Scientific Workflows for Metabolic Flux Analysis

Metabolic engineering is a highly interdisciplinary research domain that interfaces biology, mathematics, computer science, and engineering. Metabolic flux analysis with carbon tracer experiments (13 C-MFA) is a particularly challenging metabolic engineering application that consists of several tightly interwoven building blocks such as modeling, simulation, and experimental design. While several general-purpose workflow solutions have emerged in recent years to support the realization of complex scientific applications, the transferability of these approaches are only partially applicable to 13C-MFA workflows. While problems in other research fields (e.g., bioinformatics) are primarily centered around scientific data processing, 13C-MFA workflows have more in common with business workflows. For instance, many bioinformatics workflows are designed to identify, compare, and annotate genomic sequences by "pipelining" them through standard tools like BLAST. Typically, the next workflow task in the pipeline can be automatically determined by the outcome of the previous step. Five computational challenges have been identified in the endeavor of conducting 13 C-MFA studies: organization of heterogeneous data, standardization of processes and the unification of tools and data, interactive workflow steering, distributed computing, and service orientation. The outcome of this thesis is a scientific workflow framework (SWF) that is custom-tailored for the specific requirements of 13 C-MFA applications. The proposed approach – namely, designing the SWF as a collection of loosely-coupled modules that are glued together with web services – alleviates the realization of 13C-MFA workflows by offering several features. By design, existing tools are integrated into the SWF using web service interfaces and foreign programming language bindings (e.g., Java or Python). Although the attributes "easy-to-use" and "general-purpose" are rarely associated with distributed computing software, the presented use cases show that the proposed Hadoop MapReduce framework eases the deployment of computationally demanding simulations on cloud and cluster computing resources. An important building block for allowing interactive researcher-driven workflows is the ability to track all data that is needed to understand and reproduce a workflow. The standardization of 13 C-MFA studies using a folder structure template and the corresponding services and web interfaces improves the exchange of information for a group of researchers. Finally, several auxiliary tools are developed in the course of this work to complement the SWF modules, i.e., ranging from simple helper scripts to visualization or data conversion programs. This solution distinguishes itself from other scientific workflow approaches by offering a system of loosely-coupled components that are flexibly arranged to match the typical requirements in the metabolic engineering domain. Being a modern and service-oriented software framework, new applications are easily composed by reusing existing components

Allocating MapReduce workflows with deadlines to heterogeneous servers in a cloud data center

[EN] Total profit is one of the most important factors to be considered from the perspective of resource providers. In this paper, an original MapReduce workflow scheduling with deadline and data locality is proposed to maximize total profit of resource providers. A new workflow conversion based on dynamic programming and ChainMap/ChainReduce is designed to decrease transmission times among MapReduce jobs of workflows. A new deadline division considering execution time, float time and job level is proposed to obtain better deadlines of MapReduce jobs in workflows. With the adapted replica strategy in MapReduce workflow, a new task scheduling is proposed to improve data locality which assigns tasks to servers with the earliest completion time in order to ensure resource providers obtain more profit. Experimental results show that the proposed heuristic results in larger total profit than other adopted algorithms.This work is supported by the National Key Research and Development Program of China (No. 2017YFB1400801), the National Natural Science Foundation of China (Nos. 61872077, 61832004) and Collaborative Innovation Center of Wireless Communications Technology. Rubén Ruiz is partly supported by the Spanish Ministry of Science, Innovation, and Universities, under the project ¿OPTEP-Port Terminal Operations Optimization¿ (No. RTI2018-094940-B-I00) financed with FEDER funds¿.Wang, J.; Li, X.; Ruiz García, R.; Xu, H.; Chu, D. (2020). Allocating MapReduce workflows with deadlines to heterogeneous servers in a cloud data center. Service Oriented Computing and Applications. 14(2):101-118. https://doi.org/10.1007/s11761-020-00290-1S101118142Zaharia M, Chowdhury M, Franklin M et al (2010) Spark: cluster computing with working sets. 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Scalable Architecture for Integrated Batch and Streaming Analysis of Big Data

Thesis (Ph.D.) - Indiana University, Computer Sciences, 2015As Big Data processing problems evolve, many modern applications demonstrate special characteristics. Data exists in the form of both large historical datasets and high-speed real-time streams, and many analysis pipelines require integrated parallel batch processing and stream processing. Despite the large size of the whole dataset, most analyses focus on specific subsets according to certain criteria. Correspondingly, integrated support for efficient queries and post- query analysis is required. To address the system-level requirements brought by such characteristics, this dissertation proposes a scalable architecture for integrated queries, batch analysis, and streaming analysis of Big Data in the cloud. We verify its effectiveness using a representative application domain - social media data analysis - and tackle related research challenges emerging from each module of the architecture by integrating and extending multiple state-of-the-art Big Data storage and processing systems. In the storage layer, we reveal that existing text indexing techniques do not work well for the unique queries of social data, which put constraints on both textual content and social context. To address this issue, we propose a flexible indexing framework over NoSQL databases to support fully customizable index structures, which can embed necessary social context information for efficient queries. The batch analysis module demonstrates that analysis workflows consist of multiple algorithms with different computation and communication patterns, which are suitable for different processing frameworks. To achieve efficient workflows, we build an integrated analysis stack based on YARN, and make novel use of customized indices in developing sophisticated analysis algorithms. In the streaming analysis module, the high-dimensional data representation of social media streams poses special challenges to the problem of parallel stream clustering. Due to the sparsity of the high-dimensional data, traditional synchronization method becomes expensive and severely impacts the scalability of the algorithm. Therefore, we design a novel strategy that broadcasts the incremental changes rather than the whole centroids of the clusters to achieve scalable parallel stream clustering algorithms. Performance tests using real applications show that our solutions for parallel data loading/indexing, queries, analysis tasks, and stream clustering all significantly outperform implementations using current state-of-the-art technologies