Methods to Improve Applicability and Efficiency of Distributed Data-Centric Compute Frameworks

The success of modern applications depends on the insights they collect from their data repositories. Data repositories for such applications currently exceed exabytes and are rapidly increasing in size, as they collect data from varied sources - web applications, mobile phones, sensors and other connected devices. Distributed storage and data-centric compute frameworks have been invented to store and analyze these large datasets. This dissertation focuses on extending the applicability and improving the efficiency of distributed data-centric compute frameworks

Risk Intelligence: Making Profit from Uncertainty in Data Processing System

In extreme scale data processing systems, fault tolerance is an essential and indispensable part. Proactive fault tolerance scheme (such as the speculative execution in MapReduce framework) is introduced to dramatically improve the response time of job executions when the failure becomes a norm rather than an exception. Efficient proactive fault tolerance schemes require precise knowledge on the task executions, which has been an open challenge for decades. To well address the issue, in this paper we design and implement RiskI, a profile-based prediction algorithm in conjunction with a riskaware task assignment algorithm, to accelerate task executions, taking the uncertainty nature of tasks into account. Our design demonstrates that the nature uncertainty brings not only great challenges, but also new opportunities. With a careful design, we can benefit from such uncertainties. We implement the idea in Hadoop 0.21.0 systems and the experimental results show that, compared with the traditional LATE algorithm, the response time can be improved by 46% with the same system throughput

Low latency fast data computation scheme for map reduce based clusters

MapReduce based clusters is an emerging paradigm for big data analytics to scale up and speed up the big data classification, investigation, and processing of the huge volumes, massive and complex data sets. One of the fundamental issues of processing the data in MapReduce clusters is to deal with resource heterogeneity, especially when there is data inter-dependency among the tasks. Secondly, MapReduce runs a job in many phases; the intermediate data traffic and its migration time become a major bottleneck for the computation of jobs which produces a huge intermediate data in the shuffle phase. Further, encountering factors to monitor the critical issue of straggling is necessary because it produces unnecessary delays and poses a serious constraint on the overall performance of the system. Thus, this research aims to provide a low latency fast data computation scheme which introduces three algorithms to handle interdependent task computation among heterogeneous resources, reducing intermediate data traffic with its migration time and monitoring and modelling job straggling factors. This research has developed a Low Latency and Computational Cost based Tasks Scheduling (LLCC-TS) algorithm of interdependent tasks on heterogeneous resources by encountering priority to provide cost-effective resource utilization and reduced makespan. Furthermore, an Aggregation and Partition based Accelerated Intermediate Data Migration (APAIDM) algorithm has been presented to reduce the intermediate data traffic and data migration time in the shuffle phase by using aggregators and custom partitioner. Moreover, MapReduce Total Execution Time Prediction (MTETP) scheme for MapReduce job computation with inclusion of the factors which affect the job computation time has been produced using machine learning technique (linear regression) in order to monitor the job straggling and minimize the latency. LLCCTS algorithm has 66.13%, 22.23%, 43.53%, and 44.74% performance improvement rate over FIFO, improved max-min, SJF and MOS algorithms respectively for makespan time of scheduling of interdependent tasks. The AP-AIDM algorithm scored 66.62% and 48.4% performance improvements in reducing the data migration time over hash basic and conventional aggregation algorithms, respectively. Moreover, an MTETP technique shows the performance improvement in predicting the total job execution time with 20.42% accuracy than the improved HP technique. Thus, the combination of the three algorithms mentioned above provides a low latency fast data computation scheme for MapReduce based clusters

Efficient processing of similarity queries with applications

Today, a myriad of data sources, from the Internet to business operations to scientific instruments, produce large and different types of data. Many application scenarios, e.g., marketing analysis, sensor networks, and medical and biological applications, call for identifying and processing similarities in big data. As a result, it is imperative to develop new similarity query processing approaches and systems that scale from low dimensional data to high dimensional data, from single machine to clusters of hundreds of machines, and from disk-based to memory-based processing. This dissertation introduces and studies several similarity-aware query operators, analyzes and optimizes their performance. The first contribution of this dissertation is an SQL-based Similarity Group-by operator (SGB, for short) that extends the semantics of the standard SQL Group-by operator to group data with similar but not necessarily equal values. We realize these SGB operators by extending the Standard SQL Group-by and introduce two new SGB operators for multi-dimensional data. We implement and test the new SGB operators and their algorithms inside an open-source centralized database server (PostgreSQL). In the second contribution of this dissertation, we study how to efficiently process Hamming-distance-based similarity queries (Hamming-distance select and Hamming-distance join) that are crucial to many applications. We introduce a new index, termed the HA-Index, that speeds up distance comparisons and eliminates redundancies when performing the two flavors of Hamming distance range queries (namely, the selects and joins). In the third and last contribution of this dissertation, we develop a system for similarity query processing and optimization in an in-memory and distributed setup for big spatial data. We propose a query scheduler and a distributed query optimizer that use a new cost model to optimize the cost of similarity query processing in this in-memory distributed setup. The scheduler and query optimizer generates query execution plans that minimize the effect of query skew. The query scheduler employs new spatial indexing techniques based on bloom filters to forward queries to the appropriate local sites. The proposed query processing and optimization techniques are prototyped inside Spark, a distributed main-memory computation system

High Performance Computing for DNA Sequence Alignment and Assembly

Recent advances in DNA sequencing technology have dramatically increased the scale and scope of DNA sequencing. These data are used for a wide variety of important biological analyzes, including genome sequencing, comparative genomics, transcriptome analysis, and personalized medicine but are complicated by the volume and complexity of the data involved. Given the massive size of these datasets, computational biology must draw on the advances of high performance computing. Two fundamental computations in computational biology are read alignment and genome assembly. Read alignment maps short DNA sequences to a reference genome to discover conserved and polymorphic regions of the genome. Genome assembly computes the sequence of a genome from many short DNA sequences. Both computations benefit from recent advances in high performance computing to efficiently process the huge datasets involved, including using highly parallel graphics processing units (GPUs) as high performance desktop processors, and using the MapReduce framework coupled with cloud computing to parallelize computation to large compute grids. This dissertation demonstrates how these technologies can be used to accelerate these computations by orders of magnitude, and have the potential to make otherwise infeasible computations practical

Performance Improvement of Distributed Computing Framework and Scientific Big Data Analysis

Analysis of Big data to gain better insights has been the focus of researchers in the recent past. Traditional desktop computers or database management systems may not be suitable for efficient and timely analysis, due to the requirement of massive parallel processing. Distributed computing frameworks are being explored as a viable solution. For example, Google proposed MapReduce, which is becoming a de facto computing architecture for Big data solutions. However, scheduling in MapReduce is coarse grained and remains as a challenge for improvement. Related with MapReduce scheduler when configured over distributed clusters, we identify two issues: data locality disruption and random assignment of non-local map tasks. We propose a network aware scheduler to extend the existing rack awareness. The tasks are scheduled in the order of node, rack and any other rack within the same cluster to achieve cluster level data locality. The issue of random assignment non-local map tasks is handled by enhancing the scheduler to consider the network parameters, such as delay, bandwidth and packet loss between remote clusters. As part of Big data analysis at computational biology, we consider two major data intensive applications: indexing genome sequences and de Novo assembly. Both of these applications deal with the massive amount data generated from DNA sequencers. We developed a scalable algorithm to construct sub-trees of a suffix tree in parallel to address huge memory requirements needed for indexing the human genome. For the de Novo assembly, we propose Parallel Giraph based Assembler (PGA) to address the challenges associated with the assembly of large genomes over commodity hardware. PGA uses the de Bruijn graph to represent the data generated from sequencers. Huge memory demands and performance expectations are addressed by developing parallel algorithms based on the distributed graph-processing framework, Apache Giraph

Optimizations for Energy-Aware, High-Performance and Reliable Distributed Storage Systems

With the decreasing cost and wide-spread use of commodity hard drives, it has become possible to create very large-scale storage systems with less expense. However, as we approach exabyte-scale storage systems, maintaining important features such as energy-efficiency, performance, reliability and usability became increasingly difficult. Despite the decreasing cost of storage systems, the energy consumption of these systems still needs to be addressed in order to retain cost-effectiveness. Any improvements in a storage system can be outweighed by high energy costs. On the other hand, large-scale storage systems can benefit more from the object storage features for improved performance and usability. One area of concern is metadata performance bottleneck of applications reading large directories or creating a large number of files. Similarly, computation on big data where data needs to be transferred between compute and storage clusters adversely affects I/O performance. As the storage systems become more complex and larger, transferring data between remote compute and storage tiers becomes impractical. Furthermore, storage systems implement reliability typically at the file system or client level. This approach might not always be practical in terms of performance. Lastly, object storage features are usually tailored to specific use cases that makes it harder to use them in various contexts. In this thesis, we are presenting several approaches to enhance energy-efficiency, performance, reliability and usability of large-scale storage systems. To begin with, we improve the energy-efficiency of storage systems by moving I/O load to a subset of the storage nodes with energy-aware node allocation methods and turn off the unused nodes, while preserving load balance on demand. To address the metadata performance issue associated with large creates and directory reads, we represent directories with object storage collections and implement lazy creation of objects. Similarly, in-situ computation on large-scale data is enabled by using object storage features to integrate a computational framework with the existing object storage layer to eliminate the need to transfer data between compute and storage silos for better performance. We then present parity-based redundancy using object storage features to achieve reliability with less performance impact. Finally, unified storage brings together the object storage features to meet the needs of distinct use cases; such as cloud storage, big data or high-performance computing to alleviate the unnecessary fragmentation of storage resources. We evaluate each proposed approach thoroughly and validate their effectiveness in terms of improving energy-efficiency, performance, reliability and usability of a large-scale storage system

Efficient processing of large-scale spatio-temporal data

Millionen Geräte, wie z.B. Mobiltelefone, Autos und Umweltsensoren senden ihre Positionen zusammen mit einem Zeitstempel und weiteren Nutzdaten an einen Server zu verschiedenen Analysezwecken. Die Positionsinformationen und übertragenen Ereignisinformationen werden als Punkte oder Polygone dargestellt. Eine weitere Art räumlicher Daten sind Rasterdaten, die zum Beispiel von Kameras und Sensoren produziert werden. Diese großen räumlich-zeitlichen Datenmengen können nur auf skalierbaren Plattformen wie Hadoop und Apache Spark verarbeitet werden, die jedoch z.B. die Nachbarschaftsinformation nicht ausnutzen können - was die Ausführung bestimmter Anfragen praktisch unmöglich macht. Die wiederholten Ausführungen der Analyseprogramme während ihrer Entwicklung und durch verschiedene Nutzer resultieren in langen Ausführungszeiten und hohen Kosten für gemietete Ressourcen, die durch die Wiederverwendung von Zwischenergebnissen reduziert werden können. Diese Arbeit beschäftigt sich mit den beiden oben beschriebenen Herausforderungen. Wir präsentieren zunächst das STARK Framework für die Verarbeitung räumlich-zeitlicher Vektor- und Rasterdaten in Apache Spark. Wir identifizieren verschiedene Algorithmen für Operatoren und analysieren, wie diese von den Eigenschaften der zugrundeliegenden Plattform profitieren können. Weiterhin wird untersucht, wie Indexe in der verteilten und parallelen Umgebung realisiert werden können. Außerdem vergleichen wir Partitionierungsmethoden, die unterschiedlich gut mit ungleichmäßiger Datenverteilung und der Größe der Datenmenge umgehen können und präsentieren einen Ansatz um die auf Operatorebene zu verarbeitende Datenmenge frühzeitig zu reduzieren. Um die Ausführungszeit von Programmen zu verkürzen, stellen wir einen Ansatz zur transparenten Materialisierung von Zwischenergebnissen vor. Dieser Ansatz benutzt ein Entscheidungsmodell, welches auf den tatsächlichen Operatorkosten basiert. In der Evaluierung vergleichen wir die verschiedenen Implementierungs- sowie Konfigurationsmöglichkeiten in STARK und identifizieren Szenarien wann Partitionierung und Indexierung eingesetzt werden sollten. Außerdem vergleichen wir STARK mit verwandten Systemen. Im zweiten Teil der Evaluierung zeigen wir, dass die transparente Wiederverwendung der materialisierten Zwischenergebnisse die Ausführungszeit der Programme signifikant verringern kann.Millions of location-aware devices, such as mobile phones, cars, and environmental sensors constantly report their positions often in combination with a timestamp to a server for different kinds of analyses. While the location information of the devices and reported events is represented as points and polygons, raster data is another type of spatial data, which is for example produced by cameras and sensors. This Big spatio-temporal Data needs to be processed on scalable platforms, such as Hadoop and Apache Spark, which, however, are unaware of, e.g., spatial neighborhood, what makes them practically impossible to use for this kind of data. The repeated executions of the programs during development and by different users result in long execution times and potentially high costs in rented clusters, which can be reduced by reusing commonly computed intermediate results. Within this thesis, we tackle the two challenges described above. First, we present the STARK framework for processing spatio-temporal vector and raster data on the Apache Spark stack. For operators, we identify several possible algorithms and study how they can benefit from the underlying platform's properties. We further investigate how indexes can be realized in the distributed and parallel architecture of Big Data processing engines and compare methods for data partitioning, which perform differently well with respect to data skew and data set size. Furthermore, an approach to reduce the amount of data to process at operator level is presented. In order to reduce the execution times, we introduce an approach to transparently recycle intermediate results of dataflow programs, based on operator costs. To compute the costs, we instrument the programs with profiling code to gather the execution time and result size of the operators. In the evaluation, we first compare the various implementation and configuration possibilities in STARK and identify scenarios when and how partitioning and indexing should be applied. We further compare STARK to related systems and show that we can achieve significantly better execution times, not only when exploiting existing partitioning information. In the second part of the evaluation, we show that with the transparent cost-based materialization and recycling of intermediate results, the execution times of programs can be reduced significantly

Dependable mapreduce in a cloud-of-clouds

Tese de doutoramento, Informática (Engenharia Informática), Universidade de Lisboa, Faculdade de Ciências, 2017MapReduce is a simple and elegant programming model suitable for loosely coupled parallelization problems—problems that can be decomposed into subproblems. Hadoop MapReduce has become the most popular framework for performing large-scale computation on off-the-shelf clusters, and it is widely used to process these problems in a parallel and distributed fashion. This framework is highly scalable, can deal efficiently with large volumes of unstructured data, and it is a platform for many other applications. However, the framework has limitations concerning dependability. Namely, it is solely prepared to tolerate crash faults by re-executing tasks in case of failure, and to detect file corruptions using file checksums. Unfortunately, there is evidence that arbitrary faults do occur and can affect the correctness of MapReduce execution. Although such Byzantine faults are considered to be rare, particular MapReduce applications are critical and intolerant to this type of fault. Furthermore, typical MapReduce implementations are constrained to a single cloud environment. This is a problem as there is increasing evidence of outages on major cloud offerings, raising concerns about the dependence on a single cloud. In this thesis, I propose techniques to improve the dependability of MapReduce systems. The proposed solutions allow MapReduce to scale out computations to a multi-cloud environment, or cloud of-clouds, to tolerate arbitrary and malicious faults and cloud outages. The proposals have three important properties: they increase the dependability of MapReduce by tolerating the faults mentioned above; they require minimal or no modifications to users’ applications; and they achieve this increased level of fault tolerance at reasonable cost. To achieve these goals, I introduce three key ideas: minimizing the required replication; applying context-based job scheduling based on cloud and network conditions; and performing fine-grained replication. I evaluated all proposed solutions in real testbed environments running typical MapReduce applications. The results demonstrate interesting trade-offs concerning resilience and performance when compared to traditional methods. The fundamental conclusion is that the cost introduced by our solutions is small, and thus deemed acceptable for many critical applications.O MapReduce é um modelo de programação adequado para processar grandes volumes de dados em paralelo, executando um conjunto de tarefas independentes, e combinando os resultados parciais na solução final. OHadoop MapReduce é uma plataforma popular para processar grandes quantidades de dados de forma paralela e distribuída. Do ponto de vista da confiabilidade, a plataforma está preparada exclusivamente para tolerar faltas de paragem, re-executando tarefas, e detectar corrupções de ficheiros usando somas de verificação. Esta é uma importante limitação dado haver evidência de que faltas arbitrárias ocorrem e podem afetar a execução do MapReduce. Embora estas faltas Bizantinas sejam raras, certas aplicações de MapReduce são críticas e não toleram faltas deste tipo. Além disso, o número de ocorrências de interrupções em infraestruturas da nuvem tem vindo a aumentar ao longo dos anos, levantando preocupações sobre a dependência dos clientes num fornecedor único de serviços de nuvem. Nesta tese proponho várias técnicas para melhorar a confiabilidade do sistema MapReduce. As soluções propostas permitem processar tarefas MapReduce num ambiente de múltiplas nuvens para tolerar faltas arbitrárias, maliciosas e faltas de paragem nas nuvens. Estas soluções oferecem três importantes propriedades: toleram os tipos de faltas mencionadas; não exigem modificações às aplicações dos clientes; alcançam esta tolerância a faltas a um custo razoável. Estas técnicas são baseadas nas seguintes ideias: minimizar a replicação, desenvolver algoritmos de escalonamento para o MapReduce baseados nas condições da nuvem e da rede, e criar um sistema de tolerância a faltas com granularidade fina no que respeita à replicação. Avaliei as minhas propostas em ambientes de teste real com aplicações comuns do MapReduce, que me permite demonstrar compromissos interessantes em termos de resiliência e desempenho, quando comparados com métodos tradicionais. Em particular, os resultados mostram que o custo introduzido pelas soluções são aceitáveis para muitas aplicações críticas