Висока продуктивність java-сокетів для оперування накопиченими даними в медицині

Computer clouds are using in health science for its data collections, manipulations and providing security needs in communications to exchange. The clouds distribution data character is using in science applications created to evaluate the data of the health-care. The science programs like medical visualization, genetic and protein conclusions, map-drag therapy and clinical decisions systems of support (CDSS) require high performance messaging libraries with minimum computer and communication spends and the effective utilization of the resources. The highperformance Java sockets (HPJS) encapsulate the needs of message high communications between cloud platforms science applications. HPJS effectively uses the Java socket realization for high-performance inner-process communications. With single-copy protocol, re-usability of the thread and communication overhead reduction, HPJS can use the message exchange in two times quickly to conventional buffered communication libraries.Компьютерные накопления данных используются в здравохранении для сохранения данных отдельных личностей, их манипуляции и обеспечения необходимости безопасного обмена. Характер распределения таких накоплений данных может быть разработан для использования в научных приложениях, которые разработаны для формирования оценки данных здравохранения. Такие научные программы як медицинская визуализация, генетические и протеиновые заключения, лечебно-профилактическая терапия та клинические системы поддержки принятия решений (CDSS) требуют библиотек скоростного обмена сообщениями с минимальными компьютерными и коммуникационными рас ходами, а также эффективным разграничением ресурсов. Высокопродуктивные Java-сокеты (HPJS) инкапсулируют необходимость высокопродуктивного обмена сообщениями между научными приложениями для cloud-платформ та эффективно используют Java-сокетную реализацию для образования высокоэффективной связи между процессами. С единой копией протокола и повторном использовании ниток та уменьшении накладных расходов связи высокопродуктивные Java-сокеты могут исполнять обмен сообщениями в два раза быстрее с обыкновенными буферизированными библиотекамисвязи.Комп’ютерні нагромадження даних використовуються в області охорони здоров’я для зберігання даних осіб, їх маніпуляції і забезпечення потреб безпечного обміну. Характер розподілу подібних нагромаджень даних може бути розроблений для застосування в наукових додатках, які розроблені для формування оцінки даних охорони здоров’я. Такі наукові програми як медична візуалізація, генетичні і протеїнові заключення, лікувально-профілактична терапія та клінічні системи підтримки прийняття рішень (CDSS) вимагають бібліотек швидкого обміну повідомленнями з мінімальними комп’ютерними і комунікаційними затратами та ефективним розшаруванням ресурсів. Високопродуктивні Java-сокети (HPJS) інкапсулюють потреби високопродуктивного обміну повідомленнями між науковими додатками для cloud-платформ та ефективно використовують Java-сокетну реалізацію для утворення високоефективного зв’язку між процесами. З єдиною копією протоколу при повторному використанні ниток та зменшенні накладних витрат зв’язку високопродуктивні Java-сокети можуть виконувати обмін повідомленнями в два рази швидше із звичайними буферизованими бібліотеками зв’язку

Low‐latency Java communication devices on RDMA‐enabled networks

This is the peer reviewed version of the following article: Expósito, R. R., Taboada, G. L., Ramos, S., Touriño, J., & Doallo, R. (2015). Low‐latency Java communication devices on RDMA‐enabled networks. Concurrency and Computation: Practice and Experience, 27(17), 4852-4879., which has been published in final form at https://doi.org/10.1002/cpe.3473. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions.[Abstract] Providing high‐performance inter‐node communication is a key capability for running high performance computing applications efficiently on parallel architectures. In fact, current systems deployments are aggregating a significant number of cores interconnected via advanced networking hardware with Remote Direct Memory Access (RDMA) mechanisms, that enable zero‐copy and kernel‐bypass features. The use of Java for parallel programming is becoming more promising thanks to some useful characteristics of this language, particularly its built‐in multithreading support, portability, easy‐to‐learn properties, and high productivity, along with the continuous increase in the performance of the Java virtual machine. However, current parallel Java applications generally suffer from inefficient communication middleware, mainly based on protocols with high communication overhead that do not take full advantage of RDMA‐enabled networks. This paper presents efficient low‐level Java communication devices that overcome these constraints by fully exploiting the underlying RDMA hardware, providing low‐latency and high‐bandwidth communications for parallel Java applications. The performance evaluation conducted on representative RDMA networks and parallel systems has shown significant point‐to‐point performance increases compared with previous Java communication middleware, allowing to obtain up to 40% improvement in application‐level performance on 4096 cores of a Cray XE6 supercomputer.Ministerio de Economía y Competitividad; TIN2013-42148-PXunta de Galicia; GRC2013/055Ministerio de Educación y Ciencia; AP2010-434

Device level communication libraries for high‐performance computing in Java

This is the peer reviewed version of the following article: Taboada, G. L., Touriño, J. , Doallo, R. , Shafi, A. , Baker, M. and Carpenter, B. (2011), Device level communication libraries for high‐performance computing in Java. Concurrency Computat.: Pract. Exper., 23: 2382-2403. doi:10.1002/cpe.1777, which has been published in final form at https://doi.org/10.1002/cpe.1777. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions.[Abstract] Since its release, the Java programming language has attracted considerable attention from the high‐performance computing (HPC) community because of its portability, high programming productivity, and built‐in multithreading and networking support. As a consequence, several initiatives have been taken to develop a high‐performance Java message‐passing library to program distributed memory architectures, such as clusters. The performance of Java message‐passing applications relies heavily on the communications performance. Thus, the design and implementation of low‐level communication devices that support message‐passing libraries is an important research issue in Java for HPC. MPJ Express is our Java message‐passing implementation for developing high‐performance parallel Java applications. Its public release currently contains three communication devices: the first one is built using the Java New Input/Output (NIO) package for the TCP/IP; the second one is specifically designed for the Myrinet Express library on Myrinet; and the third one supports thread‐based shared memory communications. Although these devices have been successfully deployed in many production environments, previous performance evaluations of MPJ Express suggest that the buffering layer, tightly coupled with these devices, incurs a certain degree of copying overhead, which represents one of the main performance penalties. This paper presents a more efficient Java message‐passing communications device, based on Java Input/Output sockets, that avoids this buffering overhead. Moreover, this device implements several strategies, both in the communication protocol and in the HPC hardware support, which optimizes Java message‐passing communications. In order to evaluate its benefits, this paper analyzes the performance of this device comparatively with other Java and native message‐passing libraries on various high‐speed networks, such as Gigabit Ethernet, Scalable Coherent Interface, Myrinet, and InfiniBand, as well as on a shared memory multicore scenario. The reported communication overhead reduction encourages the upcoming incorporation of this device in MPJ ExpressMinisterio de Ciencia e Innovación; TIN2010-16735

FastMPJ: a scalable and efficient Java message-passing library

This is a post-peer-review, pre-copyedit version of an article published in Cluster Computing. The final authenticated version is available online at: http://dx.doi.org/https://doi.org/10.1007/s10586-014-0345-4[Abstract] The performance and scalability of communications are key for high performance computing (HPC) applications in the current multi-core era. Despite the significant benefits (e.g., productivity, portability, multithreading) of Java for parallel programming, its poor communications support has hindered its adoption in the HPC community. This paper presents FastMPJ, an efficient message-passing in Java (MPJ) library, boosting Java for HPC by: (1) providing high-performance shared memory communications using Java threads; (2) taking full advantage of high-speed cluster networks (e.g., InfiniBand) to provide low-latency and high bandwidth communications; (3) including a scalable collective library with topology aware primitives, automatically selected at runtime; (4) avoiding Java data buffering overheads through zero-copy protocols; and (5) implementing the most widely extended MPI-like Java bindings for a highly productive development. The comprehensive performance evaluation on representative testbeds (InfiniBand, 10 Gigabit Ethernet, Myrinet, and shared memory systems) has shown that FastMPJ communication primitives rival native MPI implementations, significantly improving the efficiency and scalability of Java HPC parallel applications.Ministerio de Educación y Ciencia; AP2010-4348Ministerio de Economía y Competitividad; TIN2010-16735Xunta de Galicia; CN2012/211Xunta de Galicia; GRC2013/05

Nonblocking collectives for scalable Java communications

This is the peer reviewed version of the following article: Ramos, S., Taboada, G. L., Expósito, R. R., & Touriño, J. (2015). Nonblocking collectives for scalable Java communications. Concurrency and Computation: Practice and Experience, 27(5), 1169-1187, which has been published in final form at https://doi.org/10.1002/cpe.3279. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions.[Abstract] This paper presents a Java implementation of the recently published MPI 3.0 nonblocking message passing collectives in order to analyze and assess the feasibility of taking advantage of these operations in shared memory systems using Java. Nonblocking collectives aim to exploit the overlapping between computation and communication for collective operations to increase scalability of message passing codes, as it has been carried out for nonblocking point‐to‐point primitives. This scalability has become crucial not only for clusters but also for shared memory systems because of the current trend of increasing the number of cores per chip, which is leading to the generalization of multi‐core and many‐core processors. Message passing libraries based on remote direct memory access, thread‐based progression, or implementing pure multi‐threading shared memory support could potentially benefit from the lack of imposed synchronization by nonblocking collectives. But, although the distributed memory scenario has been well studied, the shared memory one has not been tackled yet. Hence, nonblocking collectives support has been included in FastMPJ, a Message Passing in Java (MPJ) implementation, and evaluated on a representative shared memory system, obtaining significant improvements because of overlapping and lack of implicit synchronization, and with barely any overhead imposed over common blocking operations.Ministerio de Ciencia e Innovación; TIN2010-16735Xunta de Galicia; CN2012/211Xunta de Galicia; GRC2013/05

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