Performance Measurements of Supercomputing and Cloud Storage Solutions

Increasing amounts of data from varied sources, particularly in the fields of machine learning and graph analytics, are causing storage requirements to grow rapidly. A variety of technologies exist for storing and sharing these data, ranging from parallel file systems used by supercomputers to distributed block storage systems found in clouds. Relatively few comparative measurements exist to inform decisions about which storage systems are best suited for particular tasks. This work provides these measurements for two of the most popular storage technologies: Lustre and Amazon S3. Lustre is an open-source, high performance, parallel file system used by many of the largest supercomputers in the world. Amazon's Simple Storage Service, or S3, is part of the Amazon Web Services offering, and offers a scalable, distributed option to store and retrieve data from anywhere on the Internet. Parallel processing is essential for achieving high performance on modern storage systems. The performance tests used span the gamut of parallel I/O scenarios, ranging from single-client, single-node Amazon S3 and Lustre performance to a large-scale, multi-client test designed to demonstrate the capabilities of a modern storage appliance under heavy load. These results show that, when parallel I/O is used correctly (i.e., many simultaneous read or write processes), full network bandwidth performance is achievable and ranged from 10 gigabits/s over a 10 GigE S3 connection to 0.35 terabits/s using Lustre on a 1200 port 10 GigE switch. These results demonstrate that S3 is well-suited to sharing vast quantities of data over the Internet, while Lustre is well-suited to processing large quantities of data locally.Comment: 5 pages, 4 figures, to appear in IEEE HPEC 201

Software Reuse Methods to Improve Technological Infrastructure for e-Science

Social computing has the potential to contribute to scientific research. Ongoing developments in information and communications technology improve capabilities for enabling scientific research, including research fostered by social computing capabilities. The recent emergence of e-Science practices has demonstrated the benefits from improvements in the technological infrastructure, or cyber-infrastructure, that has been developed to support science. Cloud computing is one example of this e-Science trend. Our own work in the area of software reuse offers methods that can be used to improve new technological development, including cloud computing capabilities, to support scientific research practices. In this paper, we focus on software reuse and its potential to contribute to the development and evaluation of information systems and related services designed to support new capabilities for conducting scientific research

Comparing FutureGrid, Amazon EC2, and Open Science Grid for Scientific Workflows

Scientists have a number of computing infrastructures available to conduct their research, including grids and public or private clouds. This paper explores the use of these cyberinfrastructures to execute scientific workflows, an important class of scientific applications. It examines the benefits and drawbacks of cloud and grid systems using the case study of an astronomy application. The application analyzes data from the NASA Kepler mission in order to compute periodograms, which help astronomers detect the periodic dips in the intensity of starlight caused by exoplanets as they transit their host star. In this paper we describe our experiences modeling the periodogram application as a scientific workflow using Pegasus, and deploying it on the FutureGrid scientific cloud testbed, the Amazon EC2 commercial cloud, and the Open Science Grid. We compare and contrast the infrastructures in terms of setup, usability, cost, resource availability and performance

Executing Large Scale Scientific Workflows in Public Clouds

Scientists in different fields, such as high-energy physics, earth science, and astronomy are developing large-scale workflow applications. In many use cases, scientists need to run a set of interrelated but independent workflows (i.e., workflow ensembles) for the entire scientific analysis. As a workflow ensemble usually contains many sub-workflows in each of which hundreds or thousands of jobs exist with precedence constraints, the execution of such a workflow ensemble makes a great concern with cost even using elastic and pay-as-you-go cloud resources. In this thesis, we develop a set of methods to optimize the execution of large-scale scientific workflows in public clouds with both cost and deadline constraints with a two-step approach. Firstly, we present a set of methods to optimize the execution of scientific workflow in public clouds, with the Montage astronomical mosaic engine running on Amazon EC2 as an example. Secondly, we address three main challenges in realizing benefits of using public clouds when executing large-scale workflow ensembles: (1) execution coordination, (2) resource provisioning, and (3) data staging. To this end, we develop a new pulling-based workflow execution system with a profiling-based resource provisioning strategy. Our results show that our solution system can achieve 80% speed-up, by removing scheduling overhead, compared to the well-known Pegasus workflow management system when running scientific workflow ensembles. Besides, our evaluation using Montage workflow ensembles on around 1000-core Amazon EC2 clusters has demonstrated the efficacy of our resource provisioning strategy in terms of cost effectiveness within deadline

Optimización de la ejecución de flujos de trabajos empresariales en infraestructuras cloud

En la actualidad, el uso del Cloud Computing se está incrementando y existen muchos proveedores que ofrecen servicios que hacen uso de esta tecnología. Uno de ellos es Amazon Web Services, que a través de su servicio Amazon EC2, nos ofrece diferentes tipos de instancias que podemos utilizar según nuestras necesidades. El modelo de negocio de AWS se basa en el pago por uso, es decir, solo realizamos el pago por el tiempo que se utilicen las instancias. En este trabajo se implementa en Amazon EC2, una aplicación cuyo objetivo es extraer de diferentes fuentes de información, los datos de las ventas realizadas por las editoriales y librerías de España. Estos datos son procesados, cargados en una base de datos y con ellos se generan reportes estadísticos, que ayudarán a los clientes a tomar mejores decisiones. Debido a que la aplicación procesa una gran cantidad de datos, se propone el desarrollo y validación de un modelo, que nos permita obtener una ejecución óptima en Amazon EC2. En este modelo se tienen en cuenta el tiempo de ejecución, el coste por uso y una métrica de coste/rendimiento. Adicionalmente, se utilizará la tecnología de contenedores Docker para llevar a cabo un caso específico del despliegue de la aplicación

Simulation of the performance of complex data-intensive workflows

PhD ThesisRecently, cloud computing has been used for analytical and data-intensive processes as it offers many attractive features, including resource pooling, on-demand capability and rapid elasticity. Scientific workflows use these features to tackle the problems of complex data-intensive applications. Data-intensive workflows are composed of many tasks that may involve large input data sets and produce large amounts of data as output, which typically runs in highly dynamic environments. However, the resources should be allocated dynamically depending on the demand changes of the work flow, as over-provisioning increases the cost and under-provisioning causes Service Level Agreement (SLA) violation and poor Quality of Service (QoS). Performance prediction of complex workflows is a necessary step prior to the deployment of the workflow. Performance analysis of complex data-intensive workflows is a challenging task due to the complexity of their structure, diversity of big data, and data dependencies, in addition to the required examination to the performance and challenges associated with running their workflows in the real cloud. In this thesis, a solution is explored to address these challenges, using a Next Generation Sequencing (NGS) workflow pipeline as a case study, which may require hundreds/ thousands of CPU hours to process a terabyte of data. We propose a methodology to model, simulate and predict runtime and the number of resources used by the complex data-intensive workflows. One contribution of our simulation methodology is that it provides an ability to extract the simulation parameters (e.g., MIPs and BW values) that are required for constructing a training set and a fairly accurate prediction of the run time for input for cluster sizes much larger than ones used in training of the prediction model. The proposed methodology permits the derivation of run time prediction based on historical data from the provenance fi les. We present the run time prediction of the complex workflow by considering different cases of its running in the cloud such as execution failure and library deployment time. In case of failure, the framework can apply the prediction only partially considering the successful parts of the pipeline, in the other case the framework can predict with or without considering the time to deploy libraries. To further improve the accuracy of prediction, we propose a simulation model that handles I/O contention

Provendo robustez a escalonadores de workflows sensíveis às incertezas da largura de banda disponível

Orientadores: Edmundo Roberto Mauro Madeira, Luiz Fernando BittencourtTese (doutorado) - Universidade Estadual de Campinas, Instituto de ComputaçãoResumo: Para que escalonadores de aplicações científicas modeladas como workflows derivem escalonamentos eficientes em nuvens híbridas, é necessário que se forneçam, além da descrição da demanda computacional desses aplicativos, as informações sobre o poder de computação dos recursos disponíveis, especialmente aqueles dados relacionados com a largura de banda disponível. Entretanto, a imprecisão das ferramentas de medição fazem com que as informações da largura de banda disponível fornecida aos escalonadores difiram dos valores reais que deveriam ser considerados para se obter escalonamentos quase ótimos. Escalonadores especialmente projetados para nuvens híbridas simplesmente ignoram a existência de tais imprecisões e terminam produzindo escalonamentos enganosos e de baixo desempenho, o que os tornam sensíveis às informações incertas. A presente Tese introduz um procedimento pró-ativo para fornecer um certo nível de robustez a escalonamentos derivados de escalonadores não projetados para serem robustos frente às incertezas decorrentes do uso de informações imprecisas dadas por ferramentas de medições de rede. Para tornar os escalonamentos sensíveis às incertezas em escalonamentos robustos às essas imprecisões, o procedimento propõe um refinamento (uma deflação) das estimativas da largura de banda antes de serem utilizadas pelo escalonador não robusto. Ao propor o uso de estimativas refinadas da largura de banda disponível, escalonadores inicialmente sensíveis às incertezas passaram a produzir escalonamentos com um certo nível de robustez às essas imprecisões. A eficácia e a eficiência do procedimento proposto são avaliadas através de simulação. Comparam-se, portanto, os escalonamentos gerados por escalonadores que passaram a usar o procedimento proposto com aqueles produzidos pelos mesmos escalonadores mas sem aplicar esse procedimento. Os resultados das simulações mostram que o procedimento proposto é capaz de prover robustez às incertezas da informação da largura de banda a escalonamentos derivados de escalonardes não robustos às tais incertezas. Adicionalmente, esta Tese também propõe um escalonador de aplicações científicas especialmente compostas por um conjunto de workflows. A novidade desse escalonador é que ele é flexível, ou seja, permite o uso de diferentes categorias de funções objetivos. Embora a flexibilidade proposta seja uma novidade no estado da arte, esse escalonador também é sensível às imprecisões da largura de banda. Entretanto, o procedimento mostrou-se capaz de provê-lo de robustez frente às tais incertezas. É mostrado nesta Tese que o procedimento proposto aumentou a eficácia e a eficiência de escalonadores de workflows não robustos projetados para nuvens híbridas, já que eles passaram a produzir escalonamentos com um certo nível de robustez na presença de estimativas incertas da largura de banda disponível. Dessa forma, o procedimento proposto nesta Tese é uma importante ferramenta para aprimorar os escalonadores sensíveis às estimativas incertas da banda disponível especialmente projetados para um ambiente computacional onde esses valores são imprecisos por natureza. Portanto, esta Tese propõe um procedimento que promove melhorias nas execuções de aplicações científicas em nuvens híbridasAbstract: To derive efficient schedules for the tasks of scientific applications modelled as workflows, schedulers need information on the application demands as well as on the resource availability, especially those regarding the available bandwidth. However, the lack of precision of bandwidth estimates provided by monitoring/measurement tools should be considered by the scheduler to achieve near-optimal schedules. Uncertainties of available bandwidth can be a result of imprecise measurement and monitoring network tools and/or their incapacity of estimating in advance the real value of the available bandwidth expected for the application during the scheduling step of the application. Schedulers specially designed for hybrid clouds simply ignore the inaccuracies of the given estimates and end up producing non-robust, low-performance schedules, which makes them sensitive to the uncertainties stemming from using these networking tools. This thesis introduces a proactive procedure to provide a certain level of robustness for schedules derived from schedulers that were not designed to be robust in the face of uncertainties of bandwidth estimates stemming from using unreliable networking tools. To make non-robust schedulers into robust schedulers, the procedure applies a deflation on imprecise bandwidth estimates before being used as input to non-robust schedulers. By proposing the use of refined (deflated) estimates of the available bandwidth, non-robust schedulers initially sensitive to these uncertainties started to produce robust schedules that are insensitive to these inaccuracies. The effectiveness and efficiency of the procedure in providing robustness to non-robust schedulers are evaluated through simulation. Schedules generated by induced-robustness schedulers through the use of the procedure is compared to that of produced by sensitive schedulers. In addition, this thesis also introduces a flexible scheduler for a special case of scientific applications modelled as a set of workflows grouped into ensembles. Although the novelty of this scheduler is the replacement of objective functions according to the user's needs, it is still a non-robust scheduler. However, the procedure was able to provide the necessary robustness for this flexible scheduler be able to produce robust schedules under uncertain bandwidth estimates. It is shown in this thesis that the proposed procedure enhanced the robustness of workflow schedulers designed especially for hybrid clouds as they started to produce robust schedules in the presence of uncertainties stemming from using networking tools. The proposed procedure is an important tool to furnish robustness to non-robust schedulers that are originally designed to work in a computational environment where bandwidth estimates are very likely to vary and cannot be estimated precisely in advance, bringing, therefore, improvements to the executions of scientific applications in hybrid cloudsDoutoradoCiência da ComputaçãoDoutor em Ciência da Computação2012/02778-6FAPES

Design and Evaluation of Low-Latency Communication Middleware on High Performance Computing Systems

[Resumen]El interés en Java para computación paralela está motivado por sus interesantes características, tales como su soporte multithread, portabilidad, facilidad de aprendizaje,alta productividad y el aumento significativo en su rendimiento omputacional. No obstante, las aplicaciones paralelas en Java carecen generalmente de mecanismos de comunicación eficientes, los cuales utilizan a menudo protocolos basados en sockets incapaces de obtener el máximo provecho de las redes de baja latencia, obstaculizando la adopción de Java en computación de altas prestaciones (High Per- formance Computing, HPC). Esta Tesis Doctoral presenta el diseño, implementación y evaluación de soluciones de comunicación en Java que superan esta limitación. En consecuencia, se desarrollaron múltiples dispositivos de comunicación a bajo nivel para paso de mensajes en Java (Message-Passing in Java, MPJ) que aprovechan al máximo el hardware de red subyacente mediante operaciones de acceso directo a memoria remota que proporcionan comunicaciones de baja latencia. También se incluye una biblioteca de paso de mensajes en Java totalmente funcional, FastMPJ, en la cual se integraron los dispositivos de comunicación. La evaluación experimental ha mostrado que las primitivas de comunicación de FastMPJ son competitivas en comparación con bibliotecas nativas, aumentando significativamente la escalabilidad de aplicaciones MPJ. Por otro lado, esta Tesis analiza el potencial de la computación en la nube (cloud computing) para HPC, donde el modelo de distribución de infraestructura como servicio (Infrastructure as a Service, IaaS) emerge como una alternativa viable a los sistemas HPC tradicionales. La evaluación del rendimiento de recursos cloud específicos para HPC del proveedor líder, Amazon EC2, ha puesto de manifiesto el impacto significativo que la virtualización impone en la red, impidiendo mover las aplicaciones intensivas en comunicaciones a la nube. La clave reside en un soporte de virtualización apropiado, como el acceso directo al hardware de red, junto con las directrices para la optimización del rendimiento sugeridas en esta Tesis.[Resumo]O interese en Java para computación paralela está motivado polas súas interesantes características, tales como o seu apoio multithread, portabilidade, facilidade de aprendizaxe, alta produtividade e o aumento signi cativo no seu rendemento computacional. No entanto, as aplicacións paralelas en Java carecen xeralmente de mecanismos de comunicación e cientes, os cales adoitan usar protocolos baseados en sockets que son incapaces de obter o máximo proveito das redes de baixa latencia, obstaculizando a adopción de Java na computación de altas prestacións (High Performance Computing, HPC). Esta Tese de Doutoramento presenta o deseño, implementaci ón e avaliación de solucións de comunicación en Java que superan esta limitación. En consecuencia, desenvolvéronse múltiples dispositivos de comunicación a baixo nivel para paso de mensaxes en Java (Message-Passing in Java, MPJ) que aproveitan ao máaximo o hardware de rede subxacente mediante operacións de acceso directo a memoria remota que proporcionan comunicacións de baixa latencia. Tamén se inclúe unha biblioteca de paso de mensaxes en Java totalmente funcional, FastMPJ, na cal foron integrados os dispositivos de comunicación. A avaliación experimental amosou que as primitivas de comunicación de FastMPJ son competitivas en comparación con bibliotecas nativas, aumentando signi cativamente a escalabilidade de aplicacións MPJ. Por outra banda, esta Tese analiza o potencial da computación na nube (cloud computing) para HPC, onde o modelo de distribución de infraestrutura como servizo (Infrastructure as a Service, IaaS) xorde como unha alternativa viable aos sistemas HPC tradicionais. A ampla avaliación do rendemento de recursos cloud específi cos para HPC do proveedor líder, Amazon EC2, puxo de manifesto o impacto signi ficativo que a virtualización impón na rede, impedindo mover as aplicacións intensivas en comunicacións á nube. A clave atópase no soporte de virtualización apropiado, como o acceso directo ao hardware de rede, xunto coas directrices para a optimización do rendemento suxeridas nesta Tese.[Abstract]The use of Java for parallel computing is becoming more promising owing to its appealing features, particularly its multithreading support, portability, easy-tolearn properties, high programming productivity and the noticeable improvement in its computational performance. However, parallel Java applications generally su er from inefficient communication middleware, most of which use socket-based protocols that are unable to take full advantage of high-speed networks, hindering the adoption of Java in the High Performance Computing (HPC) area. This PhD Thesis presents the design, development and evaluation of scalable Java communication solutions that overcome these constraints. Hence, we have implemented several lowlevel message-passing devices that fully exploit the underlying network hardware while taking advantage of Remote Direct Memory Access (RDMA) operations to provide low-latency communications. Moreover, we have developed a productionquality Java message-passing middleware, FastMPJ, in which the devices have been integrated seamlessly, thus allowing the productive development of Message-Passing in Java (MPJ) applications. The performance evaluation has shown that FastMPJ communication primitives are competitive with native message-passing libraries, improving signi cantly the scalability of MPJ applications. Furthermore, this Thesis has analyzed the potential of cloud computing towards spreading the outreach of HPC, where Infrastructure as a Service (IaaS) o erings have emerged as a feasible alternative to traditional HPC systems. Several cloud resources from the leading IaaS provider, Amazon EC2, which speci cally target HPC workloads, have been thoroughly assessed. The experimental results have shown the signi cant impact that virtualized environments still have on network performance, which hampers porting communication-intensive codes to the cloud. The key is the availability of the proper virtualization support, such as the direct access to the network hardware, along with the guidelines for performance optimization suggested in this Thesis