Efficient Interaction between High-Speed Networks and Distributed Storage in Clusters

Parallel applications running on clusters require both high-performance communications between nodes and efficient access to the storage system. We propose to improve the performance of distributed storage systems in clusters by efficiently using the underlying high-performance network to access distant storage systems. We show that storage requirements are very different from those of parallel computation and that a modification of the network programming interface is required. We detail several propositions for these interfaces which make their utilization easier in the context of distributed storage. Performance evaluations show that their integration makes it easy to use and very efficient in the context of storage

Interaction efficace entre les réseaux rapides et le stockage distribué dans les grappes de calcul

National audienceLes applications parallèles s'exécutant sur les grappes nécessitent à la fois des communications performantes entre les différents noeuds et des accès efficaces au système de stockage. Nous proposons dans ce travail d'améliorer les performances du stockage distribué dans les grappes en utilisant au mieux le réseau haute performance sous-jacent. Nous montrons que les besoins du stockage sont très différents de ceux du calcul parallèle et proposons différentes solutions pour résoudre, les problèmes liés au contrôle du réseau mais montrons qu'il est nécessaire de modifier l'interface de programmation réseau et le système d'explotation pour venir à bout des difficultés liées au transfert de données. Des expérimentations montrent qu'elles permettent une utilisation aisée et efficace des réseaux rapides dans le cadre du stockage distribué

Master of Science

thesisEfficient movement of massive amounts of data over high-speed networks at high throughput is essential for a modern-day in-memory storage system. In response to the growing needs of throughput and latency demands at scale, a new class of database systems was developed in recent years. The development of these systems was guided by increased access to high throughput, low latency network fabrics, and declining cost of Dynamic Random Access Memory (DRAM). These systems were designed with On-Line Transactional Processing (OLTP) workloads in mind, and, as a result, are optimized for fast dispatch and perform well under small request-response scenarios. However, massive server responses such as those for range queries and data migration for load balancing poses challenges for this design. This thesis analyzes the effects of large transfers on scale-out systems through the lens of a modern Network Interface Card (NIC). The present-day NIC offers new and exciting opportunities and challenges for large transfers, but using them efficiently requires smart data layout and concurrency control. We evaluated the impact of modern NICs in designing data layout by measuring transmit performance and full system impact by observing the effects of Direct Memory Access (DMA), Remote Direct Memory Access (RDMA), and caching improvements such as Intel® Data Direct I/O (DDIO). We discovered that use of techniques such as Zero Copy yield around 25% savings in CPU cycles and a 50% reduction in the memory bandwidth utilization on a server by using a client-assisted design with records that are not updated in place. We also set up experiments that underlined the bottlenecks in the current approach to data migration in RAMCloud and propose guidelines for a fast and efficient migration protocol for RAMCloud

A shared-disk parallel cluster file system

Dissertação apresentada para obtenção do Grau de Doutor em Informática Pela Universidade Nova de Lisboa, Faculdade de Ciências e TecnologiaToday, clusters are the de facto cost effective platform both for high performance computing (HPC) as well as IT environments. HPC and IT are quite different environments and differences include, among others, their choices on file systems and storage: HPC favours parallel file systems geared towards maximum I/O bandwidth, but which are not fully POSIX-compliant and were devised to run on top of (fault prone) partitioned storage; conversely, IT data centres favour both external disk arrays (to provide highly available storage) and POSIX compliant file systems, (either general purpose or shared-disk cluster file systems, CFSs). These specialised file systems do perform very well in their target environments provided that applications do not require some lateral features, e.g., no file locking on parallel file systems, and no high performance writes over cluster-wide shared files on CFSs. In brief, we can say that none of the above approaches solves the problem of providing high levels of reliability and performance to both worlds. Our pCFS proposal makes a contribution to change this situation: the rationale is to take advantage on the best of both – the reliability of cluster file systems and the high performance of parallel file systems. We don’t claim to provide the absolute best of each, but we aim at full POSIX compliance, a rich feature set, and levels of reliability and performance good enough for broad usage – e.g., traditional as well as HPC applications, support of clustered DBMS engines that may run over regular files, and video streaming. pCFS’ main ideas include: · Cooperative caching, a technique that has been used in file systems for distributed disks but, as far as we know, was never used either in SAN based cluster file systems or in parallel file systems. As a result, pCFS may use all infrastructures (LAN and SAN) to move data. · Fine-grain locking, whereby processes running across distinct nodes may define nonoverlapping byte-range regions in a file (instead of the whole file) and access them in parallel, reading and writing over those regions at the infrastructure’s full speed (provided that no major metadata changes are required). A prototype was built on top of GFS (a Red Hat shared disk CFS): GFS’ kernel code was slightly modified, and two kernel modules and a user-level daemon were added. In the prototype, fine grain locking is fully implemented and a cluster-wide coherent cache is maintained through data (page fragments) movement over the LAN. Our benchmarks for non-overlapping writers over a single file shared among processes running on different nodes show that pCFS’ bandwidth is 2 times greater than NFS’ while being comparable to that of the Parallel Virtual File System (PVFS), both requiring about 10 times more CPU. And pCFS’ bandwidth also surpasses GFS’ (600 times for small record sizes, e.g., 4 KB, decreasing down to 2 times for large record sizes, e.g., 4 MB), at about the same CPU usage.Lusitania, Companhia de Seguros S.A, Programa IBM Shared University Research (SUR

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

Optimisation des caches de fichiers dans les environnements virtualisés

Les besoins en ressources de calcul sont en forte augmentation depuis plusieurs décennies, que ce soit pour des applications du domaine des réseaux sociaux, du calcul haute performance, ou du big data. Les entreprises se tournent alors vers des solutions d'externalisation de leurs services informatiques comme le Cloud Computing. Le Cloud Computing permet une mutalisation des ressources informatiques dans un datacenter et repose généralement sur la virtualisation. Cette dernière permet de décomposer une machine physique, appelée hôte, en plusieurs machines virtuelles (VM) invitées. La virtualisation engendre de nouveaux défis dans la conception des systèmes d'exploitation, en particulier pour la gestion de la mémoire. La mémoire est souvent utilisée pour accélérer les coûteux accès aux disques, en conservant ou préchargeant les données du disque dans le cache fichiers. Seulement la mémoire est une ressource limitée et limitante pour les environnements virtualisés, affectant ainsi les performances des applications utilisateurs. Il est alors nécessaire d'optimiser l'utilisation du cache de fichiers dans ces environnements. Dans cette thèse, nous proposons deux approches orthogonales pour améliorer les performances des applications à l'aide d'une meilleure utilisation du cache fichiers. Dans les environnements virtualisés, hôte et invités exécutent chacun leur propre système d'exploitation (OS) et ont donc chacun un cache de fichiers. Lors de la lecture d'un fichier, les données se retrouvent présentes dans les deux caches. Seulement, les deux OS exploitent la même mémoire physique. On parle de duplication des pages du cache. La première contribution vise à pallier ce problème avec Cacol, une politique d'éviction de cache s'exécutant dans l'hôte et non intrusive vis-à-vis de la VM. Cacol évite ces doublons de pages réduisant ainsi l'utilisation de la mémoire d'une machine physique. La seconde approche est d'étendre le cache fichiers des VM en exploitant de la mémoire disponible sur d'autres machines du datacenter. Cette seconde contribution, appelée Infinicache, s'appuie sur Infiniband, un réseau RDMA à haute vitesse, et exploite sa capacité à lire et à écrire sur de la mémoire à distance. Directement implémenté dans le cache invité, Infinicache stocke les pages évincées de son cache sur de la mémoire à distance. Les futurs accès à ces pages sont alors plus rapides que des accès aux disques de stockage, améliorant par conséquent les performances des applications. De plus, le taux d'utilisation de la mémoire à l'échelle du datacenter est augmenté, réduisant le gaspillage de manière globale

Mitigating Load Imbalance in Distributed Data Serving with Rack-Scale Memory Pooling

To provide low-latency and high-throughput guarantees, most large key-value stores keep the data in the memory of many servers. Despite the natural parallelism across lookups, the load imbalance, introduced by heavy skew in the popularity distribution of keys, limits performance. To avoid violating tail latency service-level objectives, systems tend to keep server utilization low and organize the data in micro-shards, which provides units of migration and replication for the purpose of load balancing. These techniques reduce the skew but incur additional monitoring, data replication, and consistency maintenance overheads. In this work, we introduce RackOut, a memory pooling technique that leverages the one-sided remote read primitive of emerging rack-scale systems to mitigate load imbalance while respecting service-level objectives. In RackOut, the data are aggregated at rack-scale granularity, with all of the participating servers in the rack jointly servicing all of the rack’s micro-shards. We develop a queuing model to evaluate the impact of RackOut at the datacenter scale. In addition, we implement a RackOut proof-of-concept key value store, evaluate it on two experimental platforms based on RDMA and Scale-Out NUMA, and use these results to validate the model. We devise two distinct approaches to load balancing within a RackOut unit, one based on random selection of nodes—RackOut_static—and another one based on an adaptive load balancing mechanism— RackOut_adaptive. Our results show that RackOut_static increases throughput by up to 6× for RDMA and 8.6× for Scale-Out NUMA compared to a scale-out deployment, while respecting tight tail latency service-level objectives. RackOut_adaptive improves the throughput by 30% for workloads with 20% of writes over RackOut_static