Understanding Spark System Performance for Image Processing in a Heterogeneous Commodity Cluster

In recent years, Apache Spark has seen a widespread adoption in industries and institutions due to its cache mechanism for faster Big Data analytics. However, the speed advantage Spark provides, especially in a heterogeneous cluster environment, is not obtainable out-of-the-box; it requires the right combination of configuration parameters from the myriads of parameters provided by Spark developers. Recognizing this challenge, this thesis undertakes a study to provide insight on Spark performance particularly, regarding the impact of choice parameter settings. These are parameters that are critical to fast job completion and effective utilization of resources. To this end, the study focuses on two specific example applications namely, flowerCounter and imageClustering, for processing still image datasets of Canola plants collected during the Summer of 2016 from selected plot fields using timelapse cameras in a heterogeneous Spark-clustered environments. These applications were of initial interest to the Plant Phenotyping and Imaging Research Centre (P2IRC) at the University of Saskatchewan. The P2IRC is responsible for developing systems that will aid fast analysis of large-scale seed breeding to ensure global food security. The flowerCounter application estimates the count of flowers from the images while the imageClustering application clusters images based on physical plant attributes. Two clusters are used for the experiments: a 12-node and 3-node cluster (including a master node), with Hadoop Distributed File System (HDFS) as the storage medium for the image datasets. Experiments with the two case study applications demonstrate that increasing the number of tasks does not always speed-up job processing due to increased communication overheads. Findings from other experiments show that numerous tasks with one core per executor and small allocated memory limits parallelism within an executor and result in inefficient use of cluster resources. Executors with large CPU and memory, on the other hand, do not speed-up analytics due to processing delays and threads concurrency. Further experimental results indicate that application processing time depends on input data storage in conjunction with locality levels and executor run time is largely dominated by the disk I/O time especially, the read time cost. With respect to horizontal node scaling, Spark scales with increasing homogeneous computing nodes but the speed-up degrades with heterogeneous nodes. Finally, this study shows that the effectiveness of speculative tasks execution in mitigating the impact of slow nodes varies for the applications

Distributed Shared Memory based Live VM Migration

Cloud computing is the new trend in computing services and IT industry, this computing paradigm has numerous benefits to utilize IT infrastructure resources and reduce services cost. The key feature of cloud computing depends on mobility and scalability of the computing resources, by managing virtual machines. The virtualization decouples the software from the hardware and manages the software and hardware resources in an easy way without interruption of services. Live virtual machine migration is an essential tool for dynamic resource management in current data centers. Live virtual machine is defined as the process of moving a running virtual machine or application between different physical machines without disconnecting the client or application. Many techniques have been developed to achieve this goal based on several metrics (total migration time, downtime, size of data sent and application performance) that are used to measure the performance of live migration. These metrics measure the quality of the VM services that clients care about, because the main goal of clients is keeping the applications performance with minimum service interruption. The pre-copy live VM migration is done in four phases: preparation, iterative migration, stop and copy, and resume and commitment. During the preparation phase, the source and destination physical servers are selected, the resources in destination physical server are reserved, and the critical VM is selected to be migrated. The cloud manager responsibility is to make all of these decisions. VM state migration takes place and memory state is transferred to the target node during iterative migration phase. Meanwhile, the migrated VM continues to execute and dirties its memory. In the stop and copy phase, VM virtual CPU is stopped and then the processor and network states are transferred to the destination host. Service downtime results from stopping VM execution and moving the VM CPU and network states. Finally in the resume and commitment phase, the migrated VM is resumed running in the destination physical host, the remaining memory pages are pulled by destination machine from the source machine. The source machine resources are released and eliminated. In this thesis, pre-copy live VM migration using Distributed Shared Memory (DSM) computing model is proposed. The setup is built using two identical computation nodes to construct all the proposed environment services architecture namely the virtualization infrastructure (Xenserver6.2 hypervisor), the shared storage server (the network file system), and the DSM and High Performance Computing (HPC) cluster. The custom DSM framework is based on a low latency memory update named Grappa. Moreover, HPC cluster is used to parallelize the work load by using CPUs computation nodes. HPC cluster employs OPENMPI and MPI libraries to support parallelization and auto-parallelization. The DSM allows the cluster CPUs to access the same memory space pages resulting in less memory data updates, which reduces the amount of data transferred through the network. The thesis proposed model achieves a good enhancement of the live VM migration metrics. Downtime is reduced by 50 % in the idle workload of Windows VM and 66.6% in case of Ubuntu Linux idle workload. In general, the proposed model not only reduces the downtime and the total amount of data sent, but also does not degrade other metrics like the total migration time and the applications performance

Prefetching techniques for client server object-oriented database systems

The performance of many object-oriented database applications suffers from the page fetch latency which is determined by the expense of disk access. In this work we suggest several prefetching techniques to avoid, or at least to reduce, page fetch latency. In practice no prediction technique is perfect and no prefetching technique can entirely eliminate delay due to page fetch latency. Therefore we are interested in the trade-off between the level of accuracy required for obtaining good results in terms of elapsed time reduction and the processing overhead needed to achieve this level of accuracy. If prefetching accuracy is high then the total elapsed time of an application can be reduced significantly otherwise if the prefetching accuracy is low, many incorrect pages are prefetched and the extra load on the client, network, server and disks decreases the whole system performance. Access pattern of object-oriented databases are often complex and usually hard to predict accurately. The ..

Practical database replication

Tese de doutoramento em InformáticaSoftware-based replication is a cost-effective approach for fault-tolerance when combined with commodity hardware. In particular, shared-nothing database clusters built upon commodity machines and synchronized through eager software-based replication protocols have been driven by the distributed systems community in the last decade. The efforts on eager database replication, however, stem from the late 1970s with initial proposals designed by the database community. From that time, we have the distributed locking and atomic commitment protocols. Briefly speaking, before updating a data item, all copies are locked through a distributed lock, and upon commit, an atomic commitment protocol is responsible for guaranteeing that the transaction’s changes are written to a non-volatile storage at all replicas before committing it. Both these processes contributed to a poor performance. The distributed systems community improved these processes by reducing the number of interactions among replicas through the use of group communication and by relaxing the durability requirements imposed by the atomic commitment protocol. The approach requires at most two interactions among replicas and disseminates updates without necessarily applying them before committing a transaction. This relies on a high number of machines to reduce the likelihood of failures and ensure data resilience. Clearly, the availability of commodity machines and their increasing processing power makes this feasible. Proving the feasibility of this approach requires us to build several prototypes and evaluate them with different workloads and scenarios. Although simulation environments are a good starting point, mainly those that allow us to combine real (e.g., replication protocols, group communication) and simulated-code (e.g., database, network), full-fledged implementations should be developed and tested. Unfortunately, database vendors usually do not provide native support for the development of third-party replication protocols, thus forcing protocol developers to either change the database engines, when the source code is available, or construct in the middleware server wrappers that intercept client requests otherwise. The former solution is hard to maintain as new database releases are constantly being produced, whereas the latter represents a strenuous development effort as it requires us to rebuild several database features at the middleware. Unfortunately, the group-based replication protocols, optimistic or conservative, that had been proposed so far have drawbacks that present a major hurdle to their practicability. The optimistic protocols make it difficult to commit transactions in the presence of hot-spots, whereas the conservative protocols have a poor performance due to concurrency issues. In this thesis, we propose using a generic architecture and programming interface, titled GAPI, to facilitate the development of different replication strategies. The idea consists of providing key extensions to multiple DBMSs (Database Management Systems), thus enabling a replication strategy to be developed once and tested on several databases that have such extensions, i.e., those that are replication-friendly. To tackle the aforementioned problems in groupbased replication protocols, we propose using a novel protocol, titled AKARA. AKARA guarantees fairness, and thus all transactions have a chance to commit, and ensures great performance while exploiting parallelism as provided by local database engines. Finally, we outline a simple but comprehensive set of components to build group-based replication protocols and discuss key points in its design and implementation.A replicação baseada em software é uma abordagem que fornece um bom custo benefício para tolerância a falhas quando combinada com hardware commodity. Em particular, os clusters de base de dados “shared-nothing” construídos com hardware commodity e sincronizados através de protocolos “eager” têm sido impulsionados pela comunidade de sistemas distribuídos na última década. Os primeiros esforços na utilização dos protocolos “eager”, decorrem da década de 70 do século XX com as propostas da comunidade de base de dados. Dessa época, temos os protocolos de bloqueio distribuído e de terminação atómica (i.e. “two-phase commit”). De forma sucinta, antes de actualizar um item de dados, todas as cópias são bloqueadas através de um protocolo de bloqueio distribuído e, no momento de efetivar uma transacção, um protocolo de terminação atómica é responsável por garantir que as alterações da transacção são gravadas em todas as réplicas num sistema de armazenamento não-volátil. No entanto, ambos os processos contribuem para um mau desempenho do sistema. A comunidade de sistemas distribuídos melhorou esses processos, reduzindo o número de interacções entre réplicas, através do uso da comunicação em grupo e minimizando a rigidez os requisitos de durabilidade impostos pelo protocolo de terminação atómica. Essa abordagem requer no máximo duas interacções entre as réplicas e dissemina actualizações sem necessariamente aplicá-las antes de efectivar uma transacção. Para funcionar, a solução depende de um elevado número de máquinas para reduzirem a probabilidade de falhas e garantir a resiliência de dados. Claramente, a disponibilidade de hardware commodity e o seu poder de processamento crescente tornam essa abordagem possível. Comprovar a viabilidade desta abordagem obriga-nos a construir vários protótipos e a avaliálos com diferentes cargas de trabalho e cenários. Embora os ambientes de simulação sejam um bom ponto de partida, principalmente aqueles que nos permitem combinar o código real (por exemplo, protocolos de replicação, a comunicação em grupo) e o simulado (por exemplo, base de dados, rede), implementações reais devem ser desenvolvidas e testadas. Infelizmente, os fornecedores de base de dados, geralmente, não possuem suporte nativo para o desenvolvimento de protocolos de replicação de terceiros, forçando os desenvolvedores de protocolo a mudar o motor de base de dados, quando o código fonte está disponível, ou a construir no middleware abordagens que interceptam as solicitações do cliente. A primeira solução é difícil de manter já que novas “releases” das bases de dados estão constantemente a serem produzidas, enquanto a segunda representa um desenvolvimento árduo, pois obriga-nos a reconstruir vários recursos de uma base de dados no middleware. Infelizmente, os protocolos de replicação baseados em comunicação em grupo, optimistas ou conservadores, que foram propostos até agora apresentam inconvenientes que são um grande obstáculo à sua utilização. Com os protocolos optimistas é difícil efectivar transacções na presença de “hot-spots”, enquanto que os protocolos conservadores têm um fraco desempenho devido a problemas de concorrência. Nesta tese, propomos utilizar uma arquitetura genérica e uma interface de programação, intitulada GAPI, para facilitar o desenvolvimento de diferentes estratégias de replicação. A ideia consiste em fornecer extensões chaves para múltiplos SGBDs (Database Management Systems), permitindo assim que uma estratégia de replicação possa ser desenvolvida uma única vez e testada em várias bases de dados que possuam tais extensões, ou seja, aquelas que são “replicationfriendly”. Para resolver os problemas acima referidos nos protocolos de replicação baseados em comunicação em grupo, propomos utilizar um novo protocolo, intitulado AKARA. AKARA garante a equidade, portanto, todas as operações têm uma oportunidade de serem efectivadas, e garante um excelente desempenho ao tirar partido do paralelismo fornecido pelos motores de base de dados. Finalmente, propomos um conjunto simples, mas abrangente de componentes para construir protocolos de replicação baseados em comunicação em grupo e discutimos pontoschave na sua concepção e implementação

A Study of Client-based Caching for Parallel I/O

The trend in parallel computing toward large-scale cluster computers running thousands of cooperating processes per application has led to an I/O bottleneck that has only gotten more severe as the the number of processing cores per CPU has increased. Current parallel file systems are able to provide high bandwidth file access for large contiguous file region accesses; however, applications repeatedly accessing small file regions on unaligned file region boundaries continue to experience poor I/O throughput due to the high overhead associated with accessing parallel file system data. In this dissertation we demonstrate how client-side file data caching can improve parallel file system throughput for applications performing frequent small and unaligned file I/O. We explore the impacts of cache page size and cache capacity using the popular FLASH I/O benchmark and explore a novel cache sharing approach that leverages the trend toward multi-core processors. We also explore a technique we call progressive page caching that represents cache data using dynamic data structures rather than fixed-size pages of file data. Finally, we explore a cache aggregation scheme that leverages the high-level file I/O interfaces provided by the PVFS file system to provide further performance enhancements. In summary, our results indicate that a correctly configured middleware-based file data cache can dramatically improve the performance of I/O workloads dominated by small unaligned file accesses. Further, we demonstrate that a well designed cache can offer stable performance even when the selected cache page granularity is not well matched to the provided workload. Finally, we have shown that high-level file system interfaces can significantly accelerate application performance, and interfaces beyond those currently envisioned by the MPI-IO standard could provide further performance benefits

Energy-Aware Data Management on NUMA Architectures

The ever-increasing need for more computing and data processing power demands for a continuous and rapid growth of power-hungry data center capacities all over the world. As a first study in 2008 revealed, energy consumption of such data centers is becoming a critical problem, since their power consumption is about to double every 5 years. However, a recently (2016) released follow-up study points out that this threatening trend was dramatically throttled within the past years, due to the increased energy efficiency actions taken by data center operators. Furthermore, the authors of the study emphasize that making and keeping data centers energy-efficient is a continuous task, because more and more computing power is demanded from the same or an even lower energy budget, and that this threatening energy consumption trend will resume as soon as energy efficiency research efforts and its market adoption are reduced. An important class of applications running in data centers are data management systems, which are a fundamental component of nearly every application stack. While those systems were traditionally designed as disk-based databases that are optimized for keeping disk accesses as low a possible, modern state-of-the-art database systems are main memory-centric and store the entire data pool in the main memory, which replaces the disk as main bottleneck. To scale up such in-memory database systems, non-uniform memory access (NUMA) hardware architectures are employed that face a decreased bandwidth and an increased latency when accessing remote memory compared to the local memory. In this thesis, we investigate energy awareness aspects of large scale-up NUMA systems in the context of in-memory data management systems. To do so, we pick up the idea of a fine-grained data-oriented architecture and improve the concept in a way that it keeps pace with increased absolute performance numbers of a pure in-memory DBMS and scales up on NUMA systems in the large scale. To achieve this goal, we design and build ERIS, the first scale-up in-memory data management system that is designed from scratch to implement a data-oriented architecture. With the help of the ERIS platform, we explore our novel core concept for energy awareness, which is Energy Awareness by Adaptivity. The concept describes that software and especially database systems have to quickly respond to environmental changes (i.e., workload changes) by adapting themselves to enter a state of low energy consumption. We present the hierarchically organized Energy-Control Loop (ECL), which is a reactive control loop and provides two concrete implementations of our Energy Awareness by Adaptivity concept, namely the hardware-centric Resource Adaptivity and the software-centric Storage Adaptivity. Finally, we will give an exhaustive evaluation regarding the scalability of ERIS as well as our adaptivity facilities