Programming and parallelising applications for distributed infrastructures

The last decade has witnessed unprecedented changes in parallel and distributed infrastructures. Due to the diminished gains in processor performance from increasing clock frequency, manufacturers have moved from uniprocessor architectures to multicores; as a result, clusters of computers have incorporated such new CPU designs. Furthermore, the ever-growing need of scienti c applications for computing and storage capabilities has motivated the appearance of grids: geographically-distributed, multi-domain infrastructures based on sharing of resources to accomplish large and complex tasks. More recently, clouds have emerged by combining virtualisation technologies, service-orientation and business models to deliver IT resources on demand over the Internet. The size and complexity of these new infrastructures poses a challenge for programmers to exploit them. On the one hand, some of the di culties are inherent to concurrent and distributed programming themselves, e.g. dealing with thread creation and synchronisation, messaging, data partitioning and transfer, etc. On the other hand, other issues are related to the singularities of each scenario, like the heterogeneity of Grid middleware and resources or the risk of vendor lock-in when writing an application for a particular Cloud provider. In the face of such a challenge, programming productivity - understood as a tradeo between programmability and performance - has become crucial for software developers. There is a strong need for high-productivity programming models and languages, which should provide simple means for writing parallel and distributed applications that can run on current infrastructures without sacri cing performance. In that sense, this thesis contributes with Java StarSs, a programming model and runtime system for developing and parallelising Java applications on distributed infrastructures. The model has two key features: first, the user programs in a fully-sequential standard-Java fashion - no parallel construct, API call or pragma must be included in the application code; second, it is completely infrastructure-unaware, i.e. programs do not contain any details about deployment or resource management, so that the same application can run in di erent infrastructures with no changes. The only requirement for the user is to select the application tasks, which are the model's unit of parallelism. Tasks can be either regular Java methods or web service operations, and they can handle any data type supported by the Java language, namely les, objects, arrays and primitives. For the sake of simplicity of the model, Java StarSs shifts the burden of parallelisation from the programmer to the runtime system. The runtime is responsible from modifying the original application to make it create asynchronous tasks and synchronise data accesses from the main program. Moreover, the implicit inter-task concurrency is automatically found as the application executes, thanks to a data dependency detection mechanism that integrates all the Java data types. This thesis provides a fairly comprehensive evaluation of Java StarSs on three di erent distributed scenarios: Grid, Cluster and Cloud. For each of them, a runtime system was designed and implemented to exploit their particular characteristics as well as to address their issues, while keeping the infrastructure unawareness of the programming model. The evaluation compares Java StarSs against state-of-the-art solutions, both in terms of programmability and performance, and demonstrates how the model can bring remarkable productivity to programmers of parallel distributed applications

Scalable system software for high performance large-scale applications

In the last decades, high-performance large-scale systems have been a fundamental tool for scientific discovery and engineering advances. The sustained growth of supercomputing performance and the concurrent reduction in cost have made this technology available for a large number of scientists and engineers working on many different problems. The design of next-generation supercomputers will include traditional HPC requirements as well as the new requirements to handle data-intensive computations. Data intensive applications will hence play an important role in a variety of fields, and are the current focus of several research trends in HPC. Due to the challenges of scalability and power efficiency, next-generation of supercomputers needs a redesign of the whole software stack. Being at the bottom of the software stack, system software is expected to change drastically to support the upcoming hardware and to meet new application requirements. This PhD thesis addresses the scalability of system software. The thesis start at the Operating System level: first studying general-purpose OS (ex. Linux) and then studying lightweight kernels (ex. CNK). Then, we focus on the runtime system: we implement a runtime system for distributed memory systems that includes many of the system services required by next-generation applications. Finally we focus on hardware features that can be exploited at user-level to improve applications performance, and potentially included into our advanced runtime system. The thesis contributions are the following: Operating System Scalability: We provide an accurate study of the scalability problems of modern Operating Systems for HPC. We design and implement a methodology whereby detailed quantitative information may be obtained for each OS noise event. We validate our approach by comparing it to other well-known standard techniques to analyze OS noise, such FTQ (Fixed Time Quantum). Evaluation of the address translation management for a lightweight kernel: we provide a performance evaluation of different TLB management approaches ¿ dynamic memory mapping, static memory mapping with replaceable TLB entries, and static memory mapping with fixed TLB entries (no TLB misses) on a IBM BlueGene/P system. Runtime System Scalability: We show that a runtime system can efficiently incorporate system services and improve scalability for a specific class of applications. We design and implement a full-featured runtime system and programming model to execute irregular appli- cations on a commodity cluster. The runtime library is called Global Memory and Threading library (GMT) and integrates a locality-aware Partitioned Global Address Space communication model with a fork/join program structure. It supports massive lightweight multi-threading, overlapping of communication and computation and small messages aggregation to tolerate network latencies. We compare GMT to other PGAS models, hand-optimized MPI code and custom architectures (Cray XMT) on a set of large scale irregular applications: breadth first search, random walk and concurrent hash map access. Our runtime system shows performance orders of magnitude higher than other solutions on commodity clusters and competitive with custom architectures. User-level Scalability Exploiting Hardware Features: We show the high complexity of low-level hardware optimizations for single applications, as a motivation to incorporate this logic into an adaptive runtime system. We evaluate the effects of controllable hardware-thread priority mechanism that controls the rate at which each hardware-thread decodes instruction on IBM POWER5 and POWER6 processors. Finally, we show how to effectively exploits cache locality and network-on-chip on the Tilera many-core architecture to improve intra-core scalability

Programming models for parallel computing

Mit dem Auftauchen von Multicore Prozessoren beginnt parallele Programmierung den Massenmarkt zu erobern. Derzeit ist der Parallelismus noch relativ eingeschränkt, da aktuelle Prozessoren nur über eine geringe Anzahl an Kernen verfügen, doch schon bald wird der Schritt zu Prozessoren mit Hunderten an Kernen vollzogen sein. Während sich die Hardware unaufhaltsam in Richtung Parallelismus weiterentwickelt, ist es für Softwareentwickler schwierig, mit diesen Entwicklungen Schritt zu halten. Parallele Programmierung erfordert neue Ansätze gegenüber den bisher verwendeten sequentiellen Programmiermodellen. In der Vergangenheit war es ausreichend, die nächste Prozessorgeneration abzuwarten, um Computerprogramme zu beschleunigen. Heute jedoch kann ein sequentielles Programm mit einem neuen Prozessor sogar langsamer werden, da die Geschwindigkeit eines einzelnen Prozessorkerns nun oft zugunsten einer größeren Gesamtzahl an Kernen in einem Prozessor reduziert wird. Angesichts dieser Tatsache wird es in der Softwareentwicklung in Zukunft notwendig sein, Parallelismus explizit auszunutzen, um weiterhin performante Programme zu entwickeln, die auch auf zukünftigen Prozessorgenerationen skalieren. Die Problematik liegt dabei darin, dass aktuelle Programmiermodelle weiterhin auf dem sogenannten "Assembler der parallelen Programmierung", d.h. auf Multithreading für Shared-Memory- sowie auf Message Passing für Distributed-Memory Architekturen basieren, was zu einer geringen Produktivität und einer hohen Fehleranfälligkeit führt. Um dies zu ändern, wird an neuen Programmiermodellen, -sprachen und -werkzeugen, die Parallelismus auf einer höheren Abstraktionsebene als bisherige Programmiermodelle zu behandeln versprechen, geforscht. Auch wenn bereits einige Teilerfolge erzielt wurden und es gute, performante Lösungen für bestimmte Bereiche gibt, konnte bis jetzt noch kein allgemeingültiges paralleles Programmiermodell entwickelt werden - viele bezweifeln, dass das überhaupt möglich ist. Das Ziel dieser Arbeit ist es, einen Überblick über aktuelle Entwicklungen bei parallelen Programmiermodellen zu geben. Da homogenen Multi- und Manycore Prozessoren in nächster Zukunft die meiste Bedeutung zukommen wird, wird das Hauptaugenmerk darauf gelegt, inwieweit die behandelten Programmiermodelle für diese Plattformen nützlich sind. Durch den Vergleich unterschiedlicher, auch experimenteller Ansätze soll erkennbar werden, wohin die Entwicklung geht und welche Werkzeuge aktuell verwendet werden können.With the emergence of multi-core processors in the consumer market, parallel computing is moving to the mainstream. Currently parallelism is still very restricted as modern consumer computers only contain a small number of cores. Nonetheless, the number is constantly increasing, and the time will come when we move to hundreds of cores. For software developers it is becoming more difficult to keep up with these new developments. Parallel programming requires a new way of thinking. No longer will a new processor generation accelerate every existing program. On the contrary, some programs might even get slower because good single-thread performance of a processor is traded in for a higher level of parallelism. For that reason, it becomes necessary to exploit parallelism explicitly and to make sure that the program scales well. Unfortunately, parallelism in current programming models is mostly based on the "assembler of parallel programming", namely low level threading for shared multiprocessors and message passing for distributed multiprocessors. This leads to low programmer productivity and erroneous programs. Because of this, a lot of effort is put into developing new high level programming models, languages and tools that should help parallel programming to keep up with hardware development. Although there have been successes in different areas, no good all-round solution has emerged until now, and there are doubts that there ever will be one. The aim of this work is to give an overview of current developments in the area of parallel programming models. The focus is put onto programming models for multi- and many-core architectures as this is the area most relevant for the near future. Through the comparison of different approaches, including experimental ones, the reader will be able to see which existing programming models can be used for which tasks and to anticipate future developments

Advanced semantics for accelerated graph processing

Large-scale graph applications are of great national, commercial, and societal importance, with direct use in fields such as counter-intelligence, proteomics, and data mining. Unfortunately, graph-based problems exhibit certain basic characteristics that make them a poor match for conventional computing systems in terms of structure, scale, and semantics. Graph processing kernels emphasize sparse data structures and computations with irregular memory access patterns that destroy the temporal and spatial locality upon which modern processors rely for performance. Furthermore, applications in this area utilize large data sets, and have been shown to be more data intensive than typical floating-point applications, two properties that lead to inefficient utilization of the hierarchical memory system. Current approaches to processing large graph data sets leverage traditional HPC systems and programming models, for shared memory and message-passing computation, and are thus limited in efficiency, scalability, and programmability. The research presented in this thesis investigates the potential of a new model of execution that is hypothesized as a promising alternative for graph-based applications to conventional practices. A new approach to graph processing is developed and presented in this thesis. The application of the experimental ParalleX execution model to graph processing balances continuation-migration style fine-grain concurrency with constraint-based synchronization through embedded futures. A collection of parallel graph application kernels provide experiment control drivers for analysis and evaluation of this innovative strategy. Finally, an experimental software library for scalable graph processing, the ParalleX Graph Library, is defined using the HPX runtime system, providing an implementation of the key concepts and a framework for development of ParalleX-based graph applications

Massivel y parallel declarative computational models

Current computer archictectures are parallel, with an increasing number of processors. Parallel programming is an error-prone task and declarative models such as those based on constraints relieve the programmer from some of its difficult aspects, because they abstract control away. In this work we study and develop techniques for declarative computational models based on constraints using GPI, aiming at large scale parallel execution. The main contributions of this work are: A GPI implementation of a scalable dynamic load balancing scheme based on work stealing, suitable for tree shaped computations and effective for systems with thousands of threads. A parallel constraint solver, MaCS, implemented to take advantage of the GPI programming model. Experimental evaluation shows very good scalability results on systems with hundreds of cores. A GPI parallel version of the Adaptive Search algorithm, including different variants. The study on different problems advances the understanding of scalability issues known to exist with large numbers of cores; ### SUMÁRIO: Actualmente as arquitecturas de computadores são paralelas, com um crescente número de processadores. A programação paralela é uma tarefa propensa a erros e modelos declarativos baseados em restrições aliviam o programador de aspectos difíceis dado que abstraem o controlo. Neste trabalho estudamos e desenvolvemos técnicas para modelos de computação declarativos baseados em restrições usando o GPI, uma ferramenta e modelo de programação recente. O Objectivo é a execução paralela em larga escala. As contribuições deste trabalho são as seguintes: a implementação de um esquema dinâmico para balanceamento da computação baseado no GPI. O esquema é adequado para computações em árvores e efectiva em sistemas compostos por milhares de unidades de computação. Uma abordagem à resolução paralela de restrições denominadas de MaCS, que tira partido do modelo de programação do GPI. A Avaliação experimental revelou boa escalabilidade num sistema com centenas de processadores. Uma versão paralela do algoritmo Adaptive Search baseada no GPI, que inclui diferentes variantes. O estudo de diversos problemas aumenta a compreensão de aspectos relacionados com a escalabilidade e presentes na execução deste tipo de algoritmos num grande número de processadores

Methodology for malleable applications on distributed memory systems

A la portada logo BSC(English) The dominant programming approach for scientific and industrial computing on clusters is MPI+X. While there are a variety of approaches within the node, denoted by the ``X'', Message Passing interface (MPI) is the standard for programming multiple nodes with distributed memory. This thesis argues that the OmpSs-2 tasking model can be extended beyond the node to naturally support distributed memory, with three benefits: First, at small to medium scale the tasking model is a simpler and more productive alternative to MPI. It eliminates the need to distribute the data explicitly and convert all dependencies into explicit message passing. It also avoids the complexity of hybrid programming using MPI+X. Second, the ability to offload parts of the computation among the nodes enables the runtime to automatically balance the loads in a full-scale MPI+X program. This approach does not require a cost model, and it is able to transparently balance the computational loads across the whole program, on all its nodes. Third, because the runtime handles all low-level aspects of data distribution and communication, it can change the resource allocation dynamically, in a way that is transparent to the application. This thesis describes the design, development and evaluation of OmpSs-2@Cluster, a programming model and runtime system that extends the OmpSs-2 model to allow a virtually unmodified OmpSs-2 program to run across multiple distributed memory nodes. For well-balanced applications it provides similar performance to MPI+OpenMP on up to 16 nodes, and it improves performance by up to 2x for irregular and unbalanced applications like Cholesky factorization. This work also extended OmpSs-2@Cluster for interoperability with MPI and Barcelona Supercomputing Center (BSC)'s state-of-the-art Dynamic Load Balance (DLB) library in order to dynamically balance MPI+OmpSs-2 applications by transparently offloading tasks among nodes. This approach reduces the execution time of a microscale solid mechanics application by 46% on 64 nodes and on a synthetic benchmark, it is within 10% of perfect load balancing on up to 8 nodes. Finally, the runtime was extended to transparently support malleability for pure OmpSs-2@Cluster programs and interoperate with the Resources Management System (RMS). The only change to the application is to explicitly call an API function to control the addition or removal of nodes. In this regard we additionally provide the runtime with the ability to semi-transparently save and recover part of the application status to perform checkpoint and restart. Such a feature hides the complexity of data redistribution and parallel IO from the user while allowing the program to recover and continue previous executions. Our work is a starting point for future research on fault tolerance. In summary, OmpSs-2@Cluster expands the OmpSs-2 programming model to encompass distributed memory clusters. It allows an existing OmpSs-2 program, with few if any changes, to run across multiple nodes. OmpSs-2@Cluster supports transparent multi-node dynamic load balancing for MPI+OmpSs-2 programs, and enables semi-transparent malleability for OmpSs-2@Cluster programs. The runtime system has a high level of stability and performance, and it opens several avenues for future work.(Español) El modelo de programación dominante para clusters tanto en ciencia como industria es actualmente MPI+X. A pesar de que hay alguna variedad de alternativas para programar dentro de un nodo (indicado por la "X"), el estandar para programar múltiples nodos con memoria distribuida sigue siendo Message Passing Interface (MPI). Esta tesis propone la extensión del modelo de programación basado en tareas OmpSs-2 para su funcionamiento en sistemas de memoria distribuida, destacando 3 beneficios principales: En primer lugar; a pequeña y mediana escala, un modelo basado en tareas es más simple y productivo que MPI y elimina la necesidad de distribuir los datos explícitamente y convertir todas las dependencias en mensajes. Además, evita la complejidad de la programacion híbrida MPI+X. En segundo lugar; la capacidad de enviar partes del cálculo entre los nodos permite a la librería balancear la carga de trabajo en programas MPI+X a gran escala. Este enfoque no necesita un modelo de coste y permite equilibrar cargas transversalmente en todo el programa y todos los nodos. En tercer lugar; teniendo en cuenta que es la librería quien maneja todos los aspectos relacionados con distribución y transferencia de datos, es posible la modificación dinámica y transparente de los recursos que utiliza la aplicación. Esta tesis describe el diseño, desarrollo y evaluación de OmpSs-2@Cluster; un modelo de programación y librería que extiende OmpSs-2 permitiendo la ejecución de programas OmpSs-2 existentes en múltiples nodos sin prácticamente necesidad de modificarlos. Para aplicaciones balanceadas, este modelo proporciona un rendimiento similar a MPI+OpenMP hasta 16 nodos y duplica el rendimiento en aplicaciones irregulares o desbalanceadas como la factorización de Cholesky. Este trabajo incluye la extensión de OmpSs-2@Cluster para interactuar con MPI y la librería de balanceo de carga Dynamic Load Balancing (DLB) desarrollada en el Barcelona Supercomputing Center (BSC). De este modo es posible equilibrar aplicaciones MPI+OmpSs-2 mediante la transferencia transparente de tareas entre nodos. Este enfoque reduce el tiempo de ejecución de una aplicación de mecánica de sólidos a micro-escala en un 46% en 64 nodos; en algunos experimentos hasta 8 nodos se pudo equilibrar perfectamente la carga con una diferencia inferior al 10% del equilibrio perfecto. Finalmente, se implementó otra extensión de la librería para realizar operaciones de maleabilidad en programas OmpSs-2@Cluster e interactuar con el Sistema de Manejo de Recursos (RMS). El único cambio requerido en la aplicación es la llamada explicita a una función de la interfaz que controla la adición o eliminación de nodos. Además, se agregó la funcionalidad de guardar y recuperar parte del estado de la aplicación de forma semitransparente con el objetivo de realizar operaciones de salva-reinicio. Dicha funcionalidad oculta al usuario la complejidad de la redistribución de datos y las operaciones de lectura-escritura en paralelo, mientras permite al programa recuperar y continuar ejecuciones previas. Este es un punto de partida para futuras investigaciones en tolerancia a fallos. En resumen, OmpSs-2@Cluster amplía el modelo de programación de OmpSs-2 para abarcar sistemas de memoria distribuida. El modelo permite la ejecución de programas OmpSs-2 en múltiples nodos prácticamente sin necesidad de modificarlos. OmpSs-2@Cluster permite además el balanceo dinámico de carga en aplicaciones híbridas MPI+OmpSs-2 ejecutadas en varios nodos y es capaz de realizar maleabilidad semi-transparente en programas OmpSs-2@Cluster puros. La librería tiene un niveles de rendimiento y estabilidad altos y abre varios caminos para trabajos futuro.Arquitectura de computador

3rd Many-core Applications Research Community (MARC) Symposium. (KIT Scientific Reports ; 7598)

This manuscript includes recent scientific work regarding the Intel Single Chip Cloud computer and describes approaches for novel approaches for programming and run-time organization

Rack-Scale Memory Pooling for Datacenters

The rise of web-scale services has led to a staggering growth in user data on the Internet. To transform such a vast raw data into valuable information for the user and provide quality assurances, it is important to minimize access latency and enable in-memory processing. For more than a decade, the only practical way to accommodate for ever-growing data in memory has been to scale out server resources, which has led to the emergence of large-scale datacenters and distributed non-relational databases (NoSQL). Such horizontal scaling of resources translates to an increasing number of servers that participate in processing individual user requests. Typically, each user request results in hundreds of independent queries targeting different NoSQL nodes - servers, and the larger the number of servers involved, the higher the fan-out. To complete a single user request, all of the queries associated with that request have to complete first, and thus, the slowest query determines the completion time. Because of skewed popularity distributions and resource contention, the more servers we have, the harder it is to achieve high throughput and facilitate server utilization, without violating service level objectives. This thesis proposes rack-scale memory pooling (RSMP), a new scaling technique for future datacenters that reduces networking overheads and improves the performance of core datacenter software. RSMP is an approach to building larger, rack-scale capacity units for datacenters through specialized fabric interconnects with support for one-sided operations, and using them, in lieu of conventional servers (e.g. 1U), to scale out. We define an RSMP unit to be a server rack connecting 10s to 100s of servers to a secondary network enabling direct, low-latency access to the global memory of the rack. We, then, propose a new RSMP design - Scale-Out NUMA that leverages integration and a NUMA fabric to bridge the gap between local and remote memory to only 5× difference in access latency. Finally, we show how RSMP impacts NoSQL data serving, a key datacenter service used by most web-scale applications today. We show that using fewer larger data shards leads to less load imbalance and higher effective throughput, without violating applications¿ service level objectives. For example, by using Scale-Out NUMA, RSMP improves the throughput of a key-value store up to 8.2× over a traditional scale-out deployment