MARIANE: Using MApReduce in HPC environments

MapReduce is increasingly becoming a popular programming model. However, the widely used implementation, Apache Hadoop, uses the Hadoop Distributed File System (HDFS), which is currently not directly applicable to a majority of existing HPC environments such as Teragrid and NERSC that support other distributed file systems. On such resourceful High Performance Computing (HPC) infrastructures, the MapReduce model can rarely make use of full resources, as special circumstances must be created for its adoption, or simply limited resources must be isolated to the same end. This paper not only presents a MapReduce implementation directly suitable for such environments, but also exposes the design choices for better performance gains in those settings. By leveraging inherent distributed file systems’ functions, and abstracting them away from its MapReduce framework, MARIANE (MApReduce Implementation Adapted for HPC Environments) not only allows for the use of the model in an expanding number of HPC environments, but also shows better performance in such settings. This paper identifies the components and trade-offs necessary for this model, and quantifies the performance gains exhibited by our approach in HPC environments over Apache Hadoop in a data intensive setting at the National Energy Research Scientific Computing Center (NERSC).     

Cloud computing paradigms for pleasingly parallel biomedical applications

Cloud computing offers exciting new approaches for scientific computing that leverage major commercial players’ hardware and software investments in large‐scale data centers. Loosely coupled problems are very important in many scientific fields, and with the ongoing move towards data‐intensive computing, they are on the rise. There exist several different approaches to leveraging clouds and cloud‐oriented data processing frameworks to perform pleasingly parallel (also called embarrassingly parallel) computations. In this paper, we present three pleasingly parallel biomedical applications: (i) assembly of genome fragments; (ii) sequence alignment and similarity search; and (iii) dimension reduction in the analysis of chemical structures, which are implemented utilizing a cloud infrastructure service‐based utility computing models of Amazon Web Services ( http://Amazon.com Inc., Seattle, WA, USA) and Microsoft Windows Azure (Microsoft Corp., Redmond, WA, USA) as well as utilizing MapReduce‐based data processing frameworks Apache Hadoop (Apache Software Foundation, Los Angeles, CA, USA) and Microsoft DryadLINQ. We review and compare each of these frameworks, performing a comparative study among them based on performance, cost, and usability. High latency, eventually consistent cloud infrastructure service‐based frameworks that rely on off‐the‐node cloud storage were able to exhibit performance efficiencies and scalability comparable to the MapReduce‐based frameworks with local disk‐based storage for the applications considered. In this paper, we also analyze variations in cost among the different platform choices (e.g., Elastic Compute Cloud instance types), highlighting the importance of selecting an appropriate platform based on the nature of the computation. Copyright © 2011 John Wiley & Sons, Ltd.     

Governing energy consumption in Hadoop through CPU frequency scaling: An analysis

With increasingly inexpensive storage and growing processing power, the cloud has rapidly become the environment of choice to store and analyze data for a variety of applications. Most large-scale data computations in the cloud heavily rely on the MapReduce paradigm and on its Hadoop implementation. Nevertheless, this exponential growth in popularity has significantly impacted power consumption in cloud infrastructures. In this paper, we focus on MapReduce processing and we investigate the impact of dynamically scaling the frequency of compute nodes on the performance and energy consumption of a Hadoop cluster. To this end, a series of experiments are conducted to explore the implications of Dynamic Voltage and Frequency Scaling (DVFS) settings on power consumption in Hadoop clusters. By enabling various existing DVFS governors (i.e., performance, powersave, ondemand, conservative and userspace) in a Hadoop cluster, we observe significant variation in performance and power consumption across different applications: the different DVFS settings are only sub-optimal for several representative MapReduce applications. Furthermore, our results reveal that the current CPU governors do not exactly reflect their design goal and may even become ineffective to manage the power consumption in Hadoop clusters. This study aims at providing a clearer understanding of the interplay between performance and power management in Hadoop clusters and therefore offers useful insight into designing power-aware techniques for Hadoop systems.     

iMapReduce: A Distributed Computing Framework for Iterative Computation

Iterative computation is pervasive in many applications such as data mining, web ranking, graph analysis, online social network analysis, and so on. These iterative applications typically involve massive data sets containing millions or billions of data records. This poses demand of distributed computing frameworks for processing massive data sets on a cluster of machines. MapReduce is an example of such a framework. However, MapReduce lacks built-in support for iterative process that requires to parse data sets iteratively. Besides specifying MapReduce jobs, users have to write a driver program that submits a series of jobs and performs convergence testing at the client. This paper presents iMapReduce, a distributed framework that supports iterative processing. iMapReduce allows users to specify the iterative computation with the separated map and reduce functions, and provides the support of automatic iterative processing within a single job. More importantly, iMapReduce significantly improves the performance of iterative implementations by (1) reducing the overhead of creating new MapReduce jobs repeatedly, (2) eliminating the shuffling of static data, and (3) allowing asynchronous execution of map tasks. We implement an iMapReduce prototype based on Apache Hadoop, and show that iMapReduce can achieve up to 5 times speedup over Hadoop for implementing iterative algorithms.     

SLA-aware energy-efficient scheduling scheme for Hadoop YARN

Apache Hadoop becomes ubiquitous for cloud computing which provides resources as services for multi-tenant applications. YARN (a.k.a. MapReduce 2.0) is one of the key features in the second-generation Hadoop, which provides resource management and scheduling for large-scale MapReduce environments. Two enormous challenges in the YARN scheduler are the abilities to automatically tailor and control resource allocations to different jobs for achieving their Service Level Agreements (SLAs), and minimize energy consumption of the overall cloud computing system. In this work, we propose an SLA-aware energy-efficient scheduling scheme which allocates appropriate amount of resources to MapReduce applications with YARN architecture. In our task scheduling policy, We consider the data locality information to save the MapReduce network traffic. Furthermore, the slack time between the actual execution time of completed tasks and expected completion time of the application is utilized to improve the energy-efficiency of the system. An online userspace governor-based dynamic voltage and frequency scaling (DVFS) scheme is designed in the YARN per-application ApplicationMaster to dynamically change the CPU frequency for upcoming tasks given the slack time from previous completed tasks. Experimental evaluation shows that our proposed scheme outperforms the existing MapReduce scheduling policies in terms of both resource ultization and energy-efficiency.     

Mapreduce performance model for Hadoop 2.x

MapReduce is a popular programming model for distributed processing of large data sets. Apache Hadoop is one of the most common open-source implementations of such paradigm. Performance analysis of concurrent job executions has been recognized as a challenging problem, at the same time, that may provide reasonably accurate job response time estimation at significantly lower cost than experimental evaluation of real setups. In this paper, we tackle the challenge of defining MapReduce performance model for Hadoop 2.x. While there are several efficient approaches for modeling the performance of MapReduce workloads in Hadoop 1.x, they could not be applied to Hadoop 2.x due to fundamental architectural changes and dynamic resource allocation in Hadoop 2.x. Thus, the proposed solution is based on an existing performance model for Hadoop 1.x, but taking into consideration architectural changes and capturing the execution flow of a MapReduce job by using queuing network model. This way, the cost model reflects the intra-job synchronization constraints that occur due the contention at shared resources. The accuracy of our solution is validated via comparison of our model estimates against measurements in a real Hadoop 2.x setup.     

MapReduce:新型的分布式并行计算编程模型

MapReduce是Google提出的分布式并行计算编程模型,用于大规模数据的并行处理。Ma-pReduce模型受函数式编程语言的启发,将大规模数据处理作业拆分成若干个可独立运行的Map任务,分配到不同的机器上去执行,生成某种格式的中间文件,再由若干个Reduce任务合并这些中间文件获得最后的输出文件。用户在使用MapReduce模型进行大规模数据处理时,可以将主要精力放在如何编写Map和Reduce函数上,其它并行计算中的复杂问题诸如分布式文件系统、工作调度、容错、机器间通信等都交给MapReduce系统处理,在很大程度上降低了整个编程难度。MapReduce日益成为云计算平台的主流编程模型。Apache Hadoop项目提供开源的MapReduce系统还有待进一步完善。     

Hadoop系统map阶段的排序性能分析与优化

MapReduce计算框架已被广泛用于大规模数据分析的应用。虽然它具有弹性的可扩展性和细粒度的容错系统,然而性能却并不令人满意。MapReduce可以通过分配更多的计算节点来实现更好的性能,但是,这种做法并不符合成本效益。用户渴望MapReduce在提供弹性的可扩展性和细密度容错的同时,可以具有更高的计算效率。该文提出了一种动态优化map阶段排序性能的方法,并进行了测试,测试结果表明,该方法能够提升MapReduce的基准测试性能。     

MapReduce Workload Modeling with Statistical Approach

Large-scale data-intensive cloud computing with the MapReduce framework is becoming pervasive for the core business of many academic, government, and industrial organizations. Hadoop, a state-of-the-art open source project, is by far the most successful realization of MapReduce framework. While MapReduce is easy- to-use, efficient and reliable for data-intensive computations, the excessive configuration parameters in Hadoop impose unexpected challenges on running various workloads with a Hadoop cluster effectively. Consequently, developers who have less experience with the Hadoop configuration system may devote a significant effort to write an application with poor performance, either because they have no idea how these configurations would influence the performance, or because they are not even aware that these configurations exist. There is a pressing need for comprehensive analysis and performance modeling to ease MapReduce application development and guide performance optimization under different Hadoop configurations. In this paper, we propose a statistical analysis approach to identify the relationships among workload characteristics, Hadoop configurations and workload performance. We apply principal component analysis and cluster analysis to 45 different metrics, which derive relationships between workload characteristics and corresponding performance under different Hadoop configurations. Regression models are also constructed that attempt to predict the performance of various workloads under different Hadoop configurations. Several non-intuitive relationships between workload characteristics and performance are revealed through our analysis and the experimental results demonstrate that our regression models accurately predict the performance of MapReduce workloads under different Hadoop configurations.     

CloudFlow: A data-aware programming model for cloud workflow applications on modern HPC systems

Traditional High-Performance Computing (HPC) based big-data applications are usually constrained by having to move large amount of data to compute facilities for real-time processing purpose. Modern HPC systems, represented by High-Throughput Computing (HTC) and Many-Task Computing (MTC) platforms, on the other hand, intend to achieve the long-held dream of moving compute to data instead. This kind of data-aware scheduling, typically represented by Hadoop MapReduce, has been successfully implemented in its Map Phase, whereby each Map Task is sent out to the compute node where the corresponding input data chunk is located. However, Hadoop MapReduce limits itself to a one-map-to-one-reduce framework, leading to difficulties for handling complex logics, such as pipelines or workflows. Meanwhile, it lacks built-in support and optimization when the input datasets are shared among multiple applications and/or jobs. The performance can be improved significantly when the knowledge of the shared and frequently accessed data is taken into scheduling decisions.To enhance the capability of managing workflow in modern HPC system, this paper presents CloudFlow, a Hadoop MapReduce based programming model for cloud workflow applications. CloudFlow is built on top of MapReduce, which is proposed not only being data aware, but also shared-data aware. It identifies the most frequently shared data, from both task-level and job-level, replicates them to each compute node for data locality purposes. It also supports user-defined multiple Map- and Reduce functions, allowing users to orchestrate the required data-flow logic. Mathematically, we prove the correctness of the whole scheduling framework by performing theoretical analysis. Further more, experimental evaluation also shows that the execution runtime speedup exceeds 4X compared to traditional MapReduce implementation with a manageable time overhead.     

基于最小生成树的大规模数据分类模型及其MapReduce实现

数据的快速增长,为我们提供了更多的信息,然而,也对传统信息获取技术提出了挑战。这篇论文提出了MCMM算法,它是基于MapReduce的大规模数据分类模型的最小生成树（MST）的算法。它可以看做是介于传统的KNN方法和基于聚类分类方法之间的模型,旨在克服这两种方法的不足并能处理大规模的数据。在这一模型中,训练集作为有权重的无向完全图来处理。顶点是对象,两点之间边的权重是对象间的距离。这一距离,不同于欧几里得距离,它是一个特定的距离度量。这样,可以找到图中最小生成树集,其中,图中每棵树代表一个类。为了降低时间复杂度,提取了每棵树中最具代表性的点来代表该树。这些压缩了的点集,可以通过计算无标签对象和它们之间的距离,来进行分类。MCMM模型基于MapReduce实现并且部署在Hadoop平台。该模型可扩展处理大规模的数据,是因为Hadoop支持数据密集分布应用,并且这些应用可以和数以千计的节点和数据一起运作。另外,MapReduce 和Hadoop能在由商品机组成的集群上很好的运行。MCMM模型使用云平台并且通过使用MapReduce 和Hadoop进行云计算是有益处的。实验采用的数据集包括从UCI数据库得到的真实数据和一些模拟数据,实验使用了4000个集群。实验表明,MCMM模型在精确度和扩展性上优于KNN和其他一些经常使用的基础分类方法。     

Adapting scientific computing problems to clouds using MapReduce

Cloud computing, with its promise of virtually infinite resources, seems to suit well in solving resource greedy scientific computing problems. To study this, we established a scientific computing cloud (SciCloud) project and environment on our internal clusters. The main goal of the project is to study the scope of establishing private clouds at the universities. With these clouds, students and researchers can efficiently use the already existing resources of university computer networks, in solving computationally intensive scientific, mathematical, and academic problems. However, to be able to run the scientific computing applications on the cloud infrastructure, the applications must be reduced to frameworks that can successfully exploit the cloud resources, like the MapReduce framework. This paper summarizes the challenges associated with reducing iterative algorithms to the MapReduce model. Algorithms used by scientific computing are divided into different classes by how they can be adapted to the MapReduce model; examples from each such class are reduced to the MapReduce model and their performance is measured and analyzed. The study mainly focuses on the Hadoop MapReduce framework but also compares it to an alternative MapReduce framework called Twister, which is specifically designed for iterative algorithms. The analysis shows that Hadoop MapReduce has significant trouble with iterative problems while it suits well for embarrassingly parallel problems, and that Twister can handle iterative problems much more efficiently. This work shows how to adapt algorithms from each class into the MapReduce model, what affects the efficiency and scalability of algorithms in each class and allows us to judge which framework is more efficient for each of them, by mapping the advantages and disadvantages of the two frameworks. This study is of significant importance for scientific computing as it often uses complex iterative methods to solve critical problems and adapting such methods to cloud computing frameworks is not a trivial task.     

用于Hadoop2.x的MapReduce性能评估模型

基于MapReduce的程序被越来越多地应用于大型数据分析的应用中.Apache Hadoop是最常用的开源MapReduce模型之一.程序运行时间的缩短对于MapReduce程序以及所有数据处理应用而言至关重要,而能够准确估算MapReduce程序的执行时间是优化程序的重要环节.本文定义了一个在Hadoop2.x版本...     

不同MapReduce运行系统的性能测试与分析

随着云计算技术的发展,许多MapReduce运行系统被开发出来,如Hadoop、Phoenix和Twister等.直观上,Hadoop具有很强的可扩展性、稳定性,适合处理大规模离线应用;Phoenix具有运行速度快等优点,适合处理数据密集型任务;Twister是轻量级的迭代系统,非常适合迭代式的应用.不同的应用在不同的MapReduce运行系统中有着不同的性能.通过测试不同应用在这些运行系统上的性能,给出了实验比较和性能分析,从而为大数据处理时选择合适的并行编程模型提供依据.     

A case study of tuning MapReduce for efficient Bioinformatics in the cloud

The combination of the Hadoop MapReduce programming model and cloud computing allows biological scientists to analyze next-generation sequencing (NGS) data in a timely and cost-effective manner. Cloud computing platforms remove the burden of IT facility procurement and management from end users and provide ease of access to Hadoop clusters. However, biological scientists are still expected to choose appropriate Hadoop parameters for running their jobs. More importantly, the available Hadoop tuning guidelines are either obsolete or too general to capture the particular characteristics of bioinformatics applications. In this study, we aim to minimize the cloud computing cost spent on bioinformatics data analysis by optimizing the extracted significant Hadoop parameters. When using MapReduce-based bioinformatics tools in the cloud, the default settings often lead to resource underutilization and wasteful expenses. We choose k-mer counting, a representative application used in a large number of NGS data analysis tools, as our study case. Experimental results show that, with the fine-tuned parameters, we achieve a total of 4× speedup compared with the original performance (using the default settings). This paper presents an exemplary case for tuning MapReduce-based bioinformatics applications in the cloud, and documents the key parameters that could lead to significant performance benefits.     

Tuning small analytics on Big Data: Data partitioning and secondary indexes in the Hadoop ecosystem

In the recent years the problems of using generic storage (i.e., relational) techniques for very specific applications have been detected and outlined and, as a consequence, some alternatives to Relational DBMSs (e.g., HBase) have bloomed. Most of these alternatives sit on the cloud and benefit from cloud computing, which is nowadays a reality that helps us to save money by eliminating the hardware as well as software fixed costs and just pay per use. On top of this, specific querying frameworks to exploit the brute force in the cloud (e.g., MapReduce) have also been devised. The question arising next tries to clear out if this (rather naive) exploitation of the cloud is an alternative to tuning DBMSs or it still makes sense to consider other options when retrieving data from these settings.In this paper, we study the feasibility of solving OLAP queries with Hadoop (the Apache project implementing MapReduce) while benefiting from secondary indexes and partitioning in HBase. Our main contribution is the comparison of different access plans and the definition of criteria (i.e., cost estimation) to choose among them in terms of consumed resources (namely CPU, bandwidth and I/O).     

基于MapReduce的并行同态加密算法

根据云计算分布式的特点,并结合同态加密和Hadoop环境下MapReduce并行框架,提出了一种基于MapReduce计算框架的并行同态加密方案。实现了具体的并行同态加密算法,并对该方案的安全性和正确性进行了理论分析。同时,在16个核的计算集群中进行实验,数据加密的加速比可以达到13。实验结果表明,基于MapReduce的同态加密方案可以有效地减少数据的加密时间,有利于面向实时的应用。     

Profiling and evaluating hardware choices for MapReduce environments: An application-aware approach

The core business of many companies depends on the timely analysis of large quantities of new data. MapReduce clusters that routinely process petabytes of data represent a new entity in the evolving landscape of clouds and data centers. During the lifetime of a data center, old hardware needs to be eventually replaced by new hardware. The hardware selection process needs to be driven by performance objectives of the existing production workloads. In this work, we present a general framework, called Ariel, that automates system administrators’ efforts for evaluating different hardware choices and predicting completion times of MapReduce applications for their migration to a Hadoop cluster based on the new hardware. The proposed framework consists of two key components: (i) a set of microbenchmarks to profile the MapReduce processing pipeline on a given platform, and (ii) a regression-based model that establishes a performance relationship between the source and target platforms. Benchmarking and model derivation can be done using a small test cluster based on new hardware. However, the designed model can be used for predicting the jobs’ completion time on a large Hadoop cluster and be applied for its sizing to achieve desirable service level objectives (SLOs). We validate the effectiveness of the proposed approach using a set of twelve realistic MapReduce applications and three different hardware platforms. The evaluation study justifies our design choices and shows that the derived model accurately predicts performance of the test applications. The predicted completion times of eleven applications (out of twelve) are within 10% of the measured completion times on the target platforms.     

Cloud computing-based parallel genetic algorithm for gene selection in cancer classification

Cancer classification is one of the main steps during patient healing process. This fact enforces modern clinical researchers to use advanced bioinformatics methods for cancer classification. Cancer classification is usually performed using gene expression data gained in microarray experiment and advanced machine learning methods. Microarray experiment generates huge amount of data, and its processing via machine learning methods represents a big challenge. In this study, two-step classification paradigm which merges genetic algorithm feature selection and machine learning classifiers is utilized. Genetic algorithm is built in MapReduce programming spirit which makes this algorithm highly scalable for Hadoop cluster. In order to improve the performance of the proposed algorithm, it is extended into a parallel algorithm which process on microarray data in distributed manner using the Hadoop MapReduce framework. In this paper, the algorithm was tested on eleven GEMS data sets (9 tumors, 11 tumors, 14 tumors, brain tumor 1, lung cancer, brain tumor 2, leukemia 1, DLBCL, leukemia 2, SRBCT, and prostate tumor) and its accuracy reached 100% for less than 25 selected features. The proposed cloud computing-based MapReduce parallel genetic algorithm performed well on gene expression data. In addition, the scalability of the suggested algorithm is unlimited because of underlying Hadoop MapReduce platform. The presented results indicate that the proposed method can be effectively implemented for real-world microarray data in the cloud environment. In addition, the Hadoop MapReduce framework demonstrates substantial decrease in the computation time.

     

Map-Reduce在媒资系统数据收集中的应用

在传统媒体资源管理系统中,数据收集工作通常是基于C/S或B/S架构设计的,这对服务器的要求比较高。为了提高服务器的性能,传统的模式就是购买更高性能的服务器,然而,近几年出现的云计算也是一个很好解决办法。采用Apache公司的Hadoop Map-Reduce框架来实现数据收集功能,并通过实验,将数据收集工作在传统的单线程模式（传统实现模式）、Hadoop伪分布模式和全分布模式下所需时间进行比较,并对执行结果进行了分析。研究表明：使用Map-Reduce的这种云模式,确实可以缩短执行时间,以达到提高服务器端性能的目的。