Scientific workflow orchestration interoperating HTC and HPC resources

8 páginas, 7 figuras.-- El Pdf del artículo es la versión pre-print.In this work we describe our developments towards the provision of a unified access method to different types of computing infrastructures at the interop- eration level. For that, we have developed a middleware suite which bridges not interoperable middleware stacks used for building distributed computing infrastructues, UNICORE and gLite. Our solution allows to transparently access and operate on HPC and HTC resources from a single interface. Using Kepler as workflow manager, we provide users with the needed integration of codes to create scientific workflows accessing both types of infrastructures.Peer reviewe

Scientific workflow orchestration interoperating HTC and HPC resources

8 páginas, 7 figuras.-- El Pdf del artículo es la versión pre-print.In this work we describe our developments towards the provision of a unified access method to different types of computing infrastructures at the interop- eration level. For that, we have developed a middleware suite which bridges not interoperable middleware stacks used for building distributed computing infrastructues, UNICORE and gLite. Our solution allows to transparently access and operate on HPC and HTC resources from a single interface. Using Kepler as workflow manager, we provide users with the needed integration of codes to create scientific workflows accessing both types of infrastructures.Peer reviewe

Join query enhancement processing (jqpro) with big rdf data on a distributed system using hashing-merge join technique

Semantic web technologies have emerged in the last few years across different fields of study and their data are still growing rapidly. Specifically, the increased data storage and publishing capabilities in standard open web formats have made the technology much more successful. So, the data have become readable by humans, and they can be processed on a computer. The demand for complex multiple RDF queries is becoming significant with the increasing number of RDF triples. Such complex queries occasionally produce many common subexpressions. It is therefore extremely challenging to reduce the amount of RDF queries and transmission time for a vast number of related RDF data. Moreover, Recent literature shows that join query processing of Big RDF data has introduced many problems with respect to execution time and throughput. The hash-based encoding induces low execution time, which takes a long time to load and hence does not load all graphs. This is because the Resource Description Framework (RDF) collects and analyses large data in swarms, thereby having to deal with the inherent challenge of efficient swarm storage. The effective storage and data retrieval, which could be applied to high amounts of possible schema-less data, has also proven exceedingly difficult for RDF data storage. For instance, it is particularly difficult to view semantic and SPARQL query languages, as well as huge and complex graph patterns. To address this problem, a Join Query Processing Model (JQPro) is introduced for Big RDF data. The objectives of this research are: (i) formulate plan generator algorithms for join query processing on the basis of the previous research. (ii) develop an enhancement model of Join Query Processing (JQPro) based on SPARQL and Hadoop MapReduce using hashing-merge join technique to process Big RDF Data. (iii) evaluate and compare the performance based on the execution time, throughput, and CPU utilization of the JQPro model with existing models. On the other hand, the throughput was employed to measure the units of information that a system can process in each time frame. In addition, the CPU utilization was used in the big join query processing as an important resource element particularly during the map, to reduce phases. Furthermore, the hash-join and Sort-Merge algorithms were used to generate the join query processing, and this was employed due to their capacity to allow for more data sets to be joined. Both processes were sorted by algorithms on join attributes and the sorted relations was merged. Therefore, the join column sorted the groups of datasets with the same value. The sort–merge–join algorithm sorts the datasets on the joining attribute and then searches for tuples by merging the two datasets. Then, a processing framework for RDF queries was introduced and the benchmark was used for performance evaluation. Finally, the validation was conducted by standard statistical analysis to validate and compare the performance of the JQPro model with current models. In addition, the synthetic benchmarks Lehigh University Benchmark (LUBM) and Waterloo SPARQL Diversity Test Suite (WatDiv) v06 were used for measurement. The experiment was carried out on three datasets ranging from 10 million to 1 billion RDF triples produced by the generator of WatDiv data with a scale factor of 10, 100 and 1000, respectively. A selective dataset for each experimental query was also used for the processing of RDFs with a LUBM benchmark in sizes 500, 1000 and 2000 million triples. The result revealed that there is a strong correlation between execution time and throughput with a strength of 99.9% percent as confirmed by the Pearson correlation coefficient. Furthermore, the findings show that the JQPro solution was comparable to gStore RDF-3X, RDFox and PARJ and the percentage of improved performance was 87.77% in terms of execution time. The CPU utilization was significantly increased by extensive mapping and reduced code computing. It is therefore inferred that the JQPro solution is timely and innovative, as it provides an efficient execution time and CPU utilization where users could perform better queries for Big RDF data processing in a seamless manne

Elastic, Interoperable and Container-based Cloud Infrastructures for High Performance Computing

Tesis por compendio[ES] Las aplicaciones científicas implican generalmente una carga computacional variable y no predecible a la que las instituciones deben hacer frente variando dinámicamente la asignación de recursos en función de las distintas necesidades computacionales. Las aplicaciones científicas pueden necesitar grandes requisitos. Por ejemplo, una gran cantidad de recursos computacionales para el procesado de numerosos trabajos independientes (High Throughput Computing o HTC) o recursos de alto rendimiento para la resolución de un problema individual (High Performance Computing o HPC). Los recursos computacionales necesarios en este tipo de aplicaciones suelen acarrear un coste muy alto que puede exceder la disponibilidad de los recursos de la institución o estos pueden no adaptarse correctamente a las necesidades de las aplicaciones científicas, especialmente en el caso de infraestructuras preparadas para la ejecución de aplicaciones de HPC. De hecho, es posible que las diferentes partes de una aplicación necesiten distintos tipos de recursos computacionales. Actualmente las plataformas de servicios en la nube se han convertido en una solución eficiente para satisfacer la demanda de las aplicaciones HTC, ya que proporcionan un abanico de recursos computacionales accesibles bajo demanda. Por esta razón, se ha producido un incremento en la cantidad de clouds híbridos, los cuales son una combinación de infraestructuras alojadas en servicios en la nube y en las propias instituciones (on-premise). Dado que las aplicaciones pueden ser procesadas en distintas infraestructuras, actualmente la portabilidad de las aplicaciones se ha convertido en un aspecto clave. Probablemente, las tecnologías de contenedores son la tecnología más popular para la entrega de aplicaciones gracias a que permiten reproducibilidad, trazabilidad, versionado, aislamiento y portabilidad. El objetivo de la tesis es proporcionar una arquitectura y una serie de servicios para proveer infraestructuras elásticas híbridas de procesamiento que puedan dar respuesta a las diferentes cargas de trabajo. Para ello, se ha considerado la utilización de elasticidad vertical y horizontal desarrollando una prueba de concepto para proporcionar elasticidad vertical y se ha diseñado una arquitectura cloud elástica de procesamiento de Análisis de Datos. Después, se ha trabajo en una arquitectura cloud de recursos heterogéneos de procesamiento de imágenes médicas que proporciona distintas colas de procesamiento para trabajos con diferentes requisitos. Esta arquitectura ha estado enmarcada en una colaboración con la empresa QUIBIM. En la última parte de la tesis, se ha evolucionado esta arquitectura para diseñar e implementar un cloud elástico, multi-site y multi-tenant para el procesamiento de imágenes médicas en el marco del proyecto europeo PRIMAGE. Esta arquitectura utiliza un almacenamiento distribuido integrando servicios externos para la autenticación y la autorización basados en OpenID Connect (OIDC). Para ello, se ha desarrollado la herramienta kube-authorizer que, de manera automatizada y a partir de la información obtenida en el proceso de autenticación, proporciona el control de acceso a los recursos de la infraestructura de procesamiento mediante la creación de las políticas y roles. Finalmente, se ha desarrollado otra herramienta, hpc-connector, que permite la integración de infraestructuras de procesamiento HPC en infraestructuras cloud sin necesitar realizar cambios en la infraestructura HPC ni en la arquitectura cloud. Cabe destacar que, durante la realización de esta tesis, se han utilizado distintas tecnologías de gestión de trabajos y de contenedores de código abierto, se han desarrollado herramientas y componentes de código abierto y se han implementado recetas para la configuración automatizada de las distintas arquitecturas diseñadas desde la perspectiva DevOps.[CA] Les aplicacions científiques impliquen generalment una càrrega computacional variable i no predictible a què les institucions han de fer front variant dinàmicament l'assignació de recursos en funció de les diferents necessitats computacionals. Les aplicacions científiques poden necessitar grans requisits. Per exemple, una gran quantitat de recursos computacionals per al processament de nombrosos treballs independents (High Throughput Computing o HTC) o recursos d'alt rendiment per a la resolució d'un problema individual (High Performance Computing o HPC). Els recursos computacionals necessaris en aquest tipus d'aplicacions solen comportar un cost molt elevat que pot excedir la disponibilitat dels recursos de la institució o aquests poden no adaptar-se correctament a les necessitats de les aplicacions científiques, especialment en el cas d'infraestructures preparades per a l'avaluació d'aplicacions d'HPC. De fet, és possible que les diferents parts d'una aplicació necessiten diferents tipus de recursos computacionals. Actualment les plataformes de servicis al núvol han esdevingut una solució eficient per satisfer la demanda de les aplicacions HTC, ja que proporcionen un ventall de recursos computacionals accessibles a demanda. Per aquest motiu, s'ha produït un increment de la quantitat de clouds híbrids, els quals són una combinació d'infraestructures allotjades a servicis en el núvol i a les mateixes institucions (on-premise). Donat que les aplicacions poden ser processades en diferents infraestructures, actualment la portabilitat de les aplicacions s'ha convertit en un aspecte clau. Probablement, les tecnologies de contenidors són la tecnologia més popular per a l'entrega d'aplicacions gràcies al fet que permeten reproductibilitat, traçabilitat, versionat, aïllament i portabilitat. L'objectiu de la tesi és proporcionar una arquitectura i una sèrie de servicis per proveir infraestructures elàstiques híbrides de processament que puguen donar resposta a les diferents càrregues de treball. Per a això, s'ha considerat la utilització d'elasticitat vertical i horitzontal desenvolupant una prova de concepte per proporcionar elasticitat vertical i s'ha dissenyat una arquitectura cloud elàstica de processament d'Anàlisi de Dades. Després, s'ha treballat en una arquitectura cloud de recursos heterogenis de processament d'imatges mèdiques que proporciona distintes cues de processament per a treballs amb diferents requisits. Aquesta arquitectura ha estat emmarcada en una col·laboració amb l'empresa QUIBIM. En l'última part de la tesi, s'ha evolucionat aquesta arquitectura per dissenyar i implementar un cloud elàstic, multi-site i multi-tenant per al processament d'imatges mèdiques en el marc del projecte europeu PRIMAGE. Aquesta arquitectura utilitza un emmagatzemament integrant servicis externs per a l'autenticació i autorització basats en OpenID Connect (OIDC). Per a això, s'ha desenvolupat la ferramenta kube-authorizer que, de manera automatitzada i a partir de la informació obtinguda en el procés d'autenticació, proporciona el control d'accés als recursos de la infraestructura de processament mitjançant la creació de les polítiques i rols. Finalment, s'ha desenvolupat una altra ferramenta, hpc-connector, que permet la integració d'infraestructures de processament HPC en infraestructures cloud sense necessitat de realitzar canvis en la infraestructura HPC ni en l'arquitectura cloud. Es pot destacar que, durant la realització d'aquesta tesi, s'han utilitzat diferents tecnologies de gestió de treballs i de contenidors de codi obert, s'han desenvolupat ferramentes i components de codi obert, i s'han implementat receptes per a la configuració automatitzada de les distintes arquitectures dissenyades des de la perspectiva DevOps.[EN] Scientific applications generally imply a variable and an unpredictable computational workload that institutions must address by dynamically adjusting the allocation of resources to their different computational needs. Scientific applications could require a high capacity, e.g. the concurrent usage of computational resources for processing several independent jobs (High Throughput Computing or HTC) or a high capability by means of using high-performance resources for solving complex problems (High Performance Computing or HPC). The computational resources required in this type of applications usually have a very high cost that may exceed the availability of the institution's resources or they are may not be successfully adapted to the scientific applications, especially in the case of infrastructures prepared for the execution of HPC applications. Indeed, it is possible that the different parts that compose an application require different type of computational resources. Nowadays, cloud service platforms have become an efficient solution to meet the need of HTC applications as they provide a wide range of computing resources accessible on demand. For this reason, the number of hybrid computational infrastructures has increased during the last years. The hybrid computation infrastructures are the combination of infrastructures hosted in cloud platforms and the computation resources hosted in the institutions, which are named on-premise infrastructures. As scientific applications can be processed on different infrastructures, the application delivery has become a key issue. Nowadays, containers are probably the most popular technology for application delivery as they ease reproducibility, traceability, versioning, isolation, and portability. The main objective of this thesis is to provide an architecture and a set of services to build up hybrid processing infrastructures that fit the need of different workloads. Hence, the thesis considered aspects such as elasticity and federation. The use of vertical and horizontal elasticity by developing a proof of concept to provide vertical elasticity on top of an elastic cloud architecture for data analytics. Afterwards, an elastic cloud architecture comprising heterogeneous computational resources has been implemented for medical imaging processing using multiple processing queues for jobs with different requirements. The development of this architecture has been framed in a collaboration with a company called QUIBIM. In the last part of the thesis, the previous work has been evolved to design and implement an elastic, multi-site and multi-tenant cloud architecture for medical image processing has been designed in the framework of a European project PRIMAGE. This architecture uses a storage integrating external services for the authentication and authorization based on OpenID Connect (OIDC). The tool kube-authorizer has been developed to provide access control to the resources of the processing infrastructure in an automatic way from the information obtained in the authentication process, by creating policies and roles. Finally, another tool, hpc-connector, has been developed to enable the integration of HPC processing infrastructures into cloud infrastructures without requiring modifications in both infrastructures, cloud and HPC. It should be noted that, during the realization of this thesis, different contributions to open source container and job management technologies have been performed by developing open source tools and components and configuration recipes for the automated configuration of the different architectures designed from the DevOps perspective. The results obtained support the feasibility of the vertical elasticity combined with the horizontal elasticity to implement QoS policies based on a deadline, as well as the feasibility of the federated authentication model to combine public and on-premise clouds.López Huguet, S. (2021). Elastic, Interoperable and Container-based Cloud Infrastructures for High Performance Computing [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/172327TESISCompendi

Seamlessly Managing HPC Workloads Through Kubernetes

[EN] This paper describes an approach to integrate the jobs management of High Performance Computing (HPC) infrastructures in cloud architectures by managing HPC workloads seamlessly from the cloud job scheduler. The paper presents hpc-connector, an open source tool that is designed for managing the full life cycle of jobs in the HPC infrastructure from the cloud job scheduler interacting with the workload manager of the HPC system. The key point is that, thanks to running hpc-connector in the cloud infrastructure, it is possible to reflect in the cloud infrastructure, the execution of a job running in the HPC infrastructure managed by hpc-connector. If the user cancels the cloud-job, as hpc-connector catches Operating System (OS) signals (for example, SIGINT), it will cancel the job in the HPC infrastructure too. Furthermore, it can retrieve logs if requested. Therefore, by using hpc-connector, the cloud job scheduler can manage the jobs in the HPC infrastructure without requiring any special privilege, as it does not need changes on the Job scheduler. Finally, we perform an experiment training a neural network for automated segmentation of Neuroblastoma tumours in the Prometheus supercomputer using hpc-connector as a batch job from a Kubernetes infrastructure.The work presented in this article has been partially funded by the regional government of the Comunitat Valenciana (Spain), co-funded by the European Union ERDF funds (European Regional Development Fund) of the Comunitat Valenciana 2014¿2020, with reference IDIFEDER/2018/032 (High-Performance Algorithms for the Modeling, Simulation and early Detection of diseases in Personalized Medicine). The work is also co-funded by PRIMAGE (PRedictive In-silico Multiscale Analytics to support cancer personalised diaGnosis and prognosis, empowered by imaging biomarkers) a Horizon 2020 RIA project funded under the topic SC1-DTH-07-2018 by the European Commission, with grant agreement no: 826494.López-Huguet, S.; Segrelles Quilis, JD.; Kasztelnik, M.; Bubak, M.; Blanquer Espert, I. (2020). Seamlessly Managing HPC Workloads Through Kubernetes. Springer. 310-320. https://doi.org/10.1007/978-3-030-59851-8_20S310320Azure for health. https://azure.microsoft.com/en-us/industries/healthcare/#security. Accessed 07 May 2020Cloud access to mammograms enables earlier breast cancer detection. https://www.itnonline.com/content/cloud-access-mammograms-enables-earlier-breast-cancer-detection. Accessed 07 May 2020Getting to the heart of the HPC and AI the edge in healthcare. https://www.nextplatform.com/2018/03/28/getting-to-the-heart-of-hpc-and-ai-at-the-edge-in-healthcare/. 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