Model-driven development of data intensive applications over cloud resources

The proliferation of sensors over the last years has generated large amounts of raw data, forming data streams that need to be processed. In many cases, cloud resources are used for such processing, exploiting their flexibility, but these sensor streaming applications often need to support operational and control actions that have real-time and low-latency requirements that go beyond the cost effective and flexible solutions supported by existing cloud frameworks, such as Apache Kafka, Apache Spark Streaming, or Map-Reduce Streams. In this paper, we describe a model-driven and stepwise refinement methodological approach for streaming applications executed over clouds. The central role is assigned to a set of Petri Net models for specifying functional and non-functional requirements. They support model reuse, and a way to combine formal analysis, simulation, and approximate computation of minimal and maximal boundaries of non-functional requirements when the problem is either mathematically or computationally intractable. We show how our proposal can assist developers in their design and implementation decisions from a performance perspective. Our methodology allows to conduct performance analysis: The methodology is intended for all the engineering process stages, and we can (i) analyse how it can be mapped onto cloud resources, and (ii) obtain key performance indicators, including throughput or economic cost, so that developers are assisted in their development tasks and in their decision taking. In order to illustrate our approach, we make use of the pipelined wavefront array

Autotuning wavefront patterns for heterogeneous architectures

Manual tuning of applications for heterogeneous parallel systems is tedious and complex. Optimizations are often not portable, and the whole process must be repeated when moving to a new system, or sometimes even to a different problem size. Pattern based parallel programming models were originally designed to provide programmers with an abstract layer, hiding tedious parallel boilerplate code, and allowing a focus on only application specific issues. However, the constrained algorithmic model associated with each pattern also enables the creation of pattern-specific optimization strategies. These can capture more complex variations than would be accessible by analysis of equivalent unstructured source code. These variations create complex optimization spaces. Machine learning offers well established techniques for exploring such spaces. In this thesis we use machine learning to create autotuning strategies for heterogeneous parallel implementations of applications which follow the wavefront pattern. In a wavefront, computation starts from one corner of the problem grid and proceeds diagonally like a wave to the opposite corner in either two or three dimensions. Our framework partitions and optimizes the work created by these applications across systems comprising multicore CPUs and multiple GPU accelerators. The tuning opportunities for a wavefront include controlling the amount of computation to be offloaded onto GPU accelerators, choosing the number of CPU and GPU threads to process tasks, tiling for both CPU and GPU memory structures, and trading redundant halo computation against communication for multiple GPUs. Our exhaustive search of the problem space shows that these parameters are very sensitive to the combination of architecture, wavefront instance and problem size. We design and investigate a family of autotuning strategies, targeting single and multiple CPU + GPU systems, and both two and three dimensional wavefront instances. These yield an average of 87% of the performance found by offline exhaustive search, with up to 99% in some cases

MC64-Cluster: Many-Core CPU Cluster Architecture and Performance Analysis in B-Tree Searches

The MC64-Cluster computer platform was designed, based on many-core CPU microprocessors: Tile64. MC64-Cluster architecture was outlined in terms of both hardware and software, including commands available to manage jobs and provided application programming interfaces to communicate and synchronize tiles, making this system easy to use. Massively, concurrent-searches of keys in B-trees, which are used in many applications, including bioinformatics, were used. Remarkable performance improvements were obtained when the cluster resources were combined with those available in host machine (hybrid or heterogeneous environments). These results were even more outstanding when analyzed in terms of performance-per-watt, highlighting their green-computing advantages. Together with the cluster architecture, they represent the main contributions of this work. To our knowledge, this is the first cluster implementation of this kind being developed

Automated cache optimisations of stencil computations for partial differential equations

This thesis focuses on numerical methods that solve partial differential equations. Our focal point is the finite difference method, which solves partial differential equations by approximating derivatives with explicit finite differences. These partial differential equation solvers consist of stencil computations on structured grids. Stencils for computing real-world practical applications are patterns often characterised by many memory accesses and non-trivial arithmetic expressions that lead to high computational costs compared to simple stencils used in much prior proof-of-concept work. In addition, the loop nests to express stencils on structured grids may often be complicated. This work is highly motivated by a specific domain of stencil computations where one of the challenges is non-aligned to the structured grid ("off-the-grid") operations. These operations update neighbouring grid points through scatter and gather operations via non-affine memory accesses, such as {A[B[i]]}. In addition to this challenge, these practical stencils often include many computation fields (need to store multiple grid copies), complex data dependencies and imperfect loop nests. In this work, we aim to increase the performance of stencil kernel execution. We study automated cache-memory-dependent optimisations for stencil computations. This work consists of two core parts with their respective contributions.The first part of our work tries to reduce the data movement in stencil computations of practical interest. Data movement is a dominant factor affecting the performance of high-performance computing applications. It has long been a target of optimisations due to its impact on execution time and energy consumption. This thesis tries to relieve this cost by applying temporal blocking optimisations, also known as time-tiling, to stencil computations. Temporal blocking is a well-known technique to enhance data reuse in stencil computations. However, it is rarely used in practical applications but rather in theoretical examples to prove its efficacy. Applying temporal blocking to scientific simulations is more complex. More specifically, in this work, we focus on the application context of seismic and medical imaging. In this area, we often encounter scatter and gather operations due to signal sources and receivers at arbitrary locations in the computational domain. These operations make the application of temporal blocking challenging. We present an approach to overcome this challenge and successfully apply temporal blocking.In the second part of our work, we extend the first part as an automated approach targeting a wide range of simulations modelled with partial differential equations. Since temporal blocking is error-prone, tedious to apply by hand and highly complex to assimilate theoretically and practically, we are motivated to automate its application and automatically generate code that benefits from it. We discuss algorithmic approaches and present a generalised compiler pipeline to automate the application of temporal blocking. These passes are written in the Devito compiler. They are used to accelerate the computation of stencil kernels in areas such as seismic and medical imaging, computational fluid dynamics and machine learning. \href{www.devitoproject.org}{Devito} is a Python package to implement optimised stencil computation (e.g., finite differences, image processing, machine learning) from high-level symbolic problem definitions. Devito builds on \href{www.sympy.org}{SymPy} and employs automated code generation and just-in-time compilation to execute optimised computational kernels on several computer platforms, including CPUs, GPUs, and clusters thereof. We show how we automate temporal blocking code generation without user intervention and often achieve better time-to-solution. We enable domain-specific optimisation through compiler passes and offer temporal blocking gains from a high-level symbolic abstraction. These automated optimisations benefit various computational kernels for solving real-world application problems.Open Acces

Doctor of Philosophy

dissertationStochastic methods, dense free-form mapping, atlas construction, and total variation are examples of advanced image processing techniques which are robust but computationally demanding. These algorithms often require a large amount of computational power as well as massive memory bandwidth. These requirements used to be ful lled only by supercomputers. The development of heterogeneous parallel subsystems and computation-specialized devices such as Graphic Processing Units (GPUs) has brought the requisite power to commodity hardware, opening up opportunities for scientists to experiment and evaluate the in uence of these techniques on their research and practical applications. However, harnessing the processing power from modern hardware is challenging. The di fferences between multicore parallel processing systems and conventional models are signi ficant, often requiring algorithms and data structures to be redesigned signi ficantly for efficiency. It also demands in-depth knowledge about modern hardware architectures to optimize these implementations, sometimes on a per-architecture basis. The goal of this dissertation is to introduce a solution for this problem based on a 3D image processing framework, using high performance APIs at the core level to utilize parallel processing power of the GPUs. The design of the framework facilitates an efficient application development process, which does not require scientists to have extensive knowledge about GPU systems, and encourages them to harness this power to solve their computationally challenging problems. To present the development of this framework, four main problems are described, and the solutions are discussed and evaluated: (1) essential components of a general 3D image processing library: data structures and algorithms, as well as how to implement these building blocks on the GPU architecture for optimal performance; (2) an implementation of unbiased atlas construction algorithms|an illustration of how to solve a highly complex and computationally expensive algorithm using this framework; (3) an extension of the framework to account for geometry descriptors to solve registration challenges with large scale shape changes and high intensity-contrast di fferences; and (4) an out-of-core streaming model, which enables developers to implement multi-image processing techniques on commodity hardware

Optimización del rendimiento y la eficiencia energética en sistemas masivamente paralelos

RESUMEN Los sistemas heterogéneos son cada vez más relevantes, debido a sus capacidades de rendimiento y eficiencia energética, estando presentes en todo tipo de plataformas de cómputo, desde dispositivos embebidos y servidores, hasta nodos HPC de grandes centros de datos. Su complejidad hace que sean habitualmente usados bajo el paradigma de tareas y el modelo de programación host-device. Esto penaliza fuertemente el aprovechamiento de los aceleradores y el consumo energético del sistema, además de dificultar la adaptación de las aplicaciones. La co-ejecución permite que todos los dispositivos cooperen para computar el mismo problema, consumiendo menos tiempo y energía. No obstante, los programadores deben encargarse de toda la gestión de los dispositivos, la distribución de la carga y la portabilidad del código entre sistemas, complicando notablemente su programación. Esta tesis ofrece contribuciones para mejorar el rendimiento y la eficiencia energética en estos sistemas masivamente paralelos. Se realizan propuestas que abordan objetivos generalmente contrapuestos: se mejora la usabilidad y la programabilidad, a la vez que se garantiza una mayor abstracción y extensibilidad del sistema, y al mismo tiempo se aumenta el rendimiento, la escalabilidad y la eficiencia energética. Para ello, se proponen dos motores de ejecución con enfoques completamente distintos. EngineCL, centrado en OpenCL y con una API de alto nivel, favorece la máxima compatibilidad entre todo tipo de dispositivos y proporciona un sistema modular extensible. Su versatilidad permite adaptarlo a entornos para los que no fue concebido, como aplicaciones con ejecuciones restringidas por tiempo o simuladores HPC de dinámica molecular, como el utilizado en un centro de investigación internacional. Considerando las tendencias industriales y enfatizando la aplicabilidad profesional, CoexecutorRuntime proporciona un sistema flexible centrado en C++/SYCL que dota de soporte a la co-ejecución a la tecnología oneAPI. Este runtime acerca a los programadores al dominio del problema, posibilitando la explotación de estrategias dinámicas adaptativas que mejoran la eficiencia en todo tipo de aplicaciones.ABSTRACT Heterogeneous systems are becoming increasingly relevant, due to their performance and energy efficiency capabilities, being present in all types of computing platforms, from embedded devices and servers to HPC nodes in large data centers. Their complexity implies that they are usually used under the task paradigm and the host-device programming model. This strongly penalizes accelerator utilization and system energy consumption, as well as making it difficult to adapt applications. Co-execution allows all devices to simultaneously compute the same problem, cooperating to consume less time and energy. However, programmers must handle all device management, workload distribution and code portability between systems, significantly complicating their programming. This thesis offers contributions to improve performance and energy efficiency in these massively parallel systems. The proposals address the following generally conflicting objectives: usability and programmability are improved, while ensuring enhanced system abstraction and extensibility, and at the same time performance, scalability and energy efficiency are increased. To achieve this, two runtime systems with completely different approaches are proposed. EngineCL, focused on OpenCL and with a high-level API, provides an extensible modular system and favors maximum compatibility between all types of devices. Its versatility allows it to be adapted to environments for which it was not originally designed, including applications with time-constrained executions or molecular dynamics HPC simulators, such as the one used in an international research center. Considering industrial trends and emphasizing professional applicability, CoexecutorRuntime provides a flexible C++/SYCL-based system that provides co-execution support for oneAPI technology. This runtime brings programmers closer to the problem domain, enabling the exploitation of dynamic adaptive strategies that improve efficiency in all types of applications.Funding: This PhD has been supported by the Spanish Ministry of Education (FPU16/03299 grant), the Spanish Science and Technology Commission under contracts TIN2016-76635-C2-2-R and PID2019-105660RB-C22. This work has also been partially supported by the Mont-Blanc 3: European Scalable and Power Efficient HPC Platform based on Low-Power Embedded Technology project (G.A. No. 671697) from the European Union’s Horizon 2020 Research and Innovation Programme (H2020 Programme). Some activities have also been funded by the Spanish Science and Technology Commission under contract TIN2016-81840-REDT (CAPAP-H6 network). The Integration II: Hybrid programming models of Chapter 4 has been partially performed under the Project HPC-EUROPA3 (INFRAIA-2016-1-730897), with the support of the EC Research Innovation Action under the H2020 Programme. In particular, the author gratefully acknowledges the support of the SPMT Department of the High Performance Computing Center Stuttgart (HLRS)

Efficient Evaluation of Data-intensive Batch-queries in Open Simulation Laboratories

Better instruments, faster and bigger supercomputers and easier collaboration and sharing of data in the sciences have introduced the need to manage increasingly large datasets. Advances in high-performance computing (HPC) have empowered many science disciplines' computational branches. However, many scientists lack access to HPC facilities or the necessary sophistication to develop and run HPC codes. The benefits of testing new theories and experimenting with large numerical simulations have thus been restricted to a few top users. In this dissertation, I describe the ``remote immersive analysis" approach to computational science and present new techniques and methods for the efficient evaluation of scientific analysis tasks in analysis cluster environments. I will discuss several techniques developed for the efficient evaluation of data-intensive batch-queries in large numerical simulation databases. An I/O streaming method for the evaluation of decomposable kernel computations utilizes partial-sums to evaluate a batch query by performing a single sequential pass over the data. Spatial filtering computations, which use a box filter, share not only data, but also computation and can be evaluated over an intermediate summed volumes dataset derived from the original data. This is more efficient for certain workloads even when the intermediate dataset is computed dynamically. Threshold queries have immense data requirements and potentially operate over entire time-steps of the simulation. An efficient and scalable data-parallel approach evaluates threshold queries of fields derived from the raw simulation data and stores their results in an application-aware semantic cache for fast subsequent retrieval. Finally, synchronization at a mediator, task parallel and data-parallel approaches for the evaluation of particle tracking queries are compared and examined. These techniques are developed, deployed and evaluated in the Johns Hopkins Turbulence Databases (JHTDB), an open simulation laboratory for turbulence research. The JHTDB stores the output of world-class numerical simulations of turbulence and provides public access to and means to explore their complete space-time history. The techniques discussed implement core scientific analysis routines and significantly increase the utility of the service. Additionally, they improve the performance of these routines by up-to an order of magnitude or more when compared with direct implementations or implementations adapted from the simulation code

Design and performance optimization of asynchronous networks-on-chip

As digital systems continue to grow in complexity, the design of conventional synchronous systems is facing unprecedented challenges. The number of transistors on individual chips is already in the multi-billion range, and a greatly increasing number of components are being integrated onto a single chip. As a consequence, modern digital designs are under strong time-to-market pressure, and there is a critical need for composable design approaches for large complex systems. In the past two decades, networks-on-chip (NoC’s) have been a highly active research area. In a NoC-based system, functional blocks are first designed individually and may run at different clock rates. These modules are then connected through a structured network for on-chip global communication. However, due to the rigidity of centrally-clocked NoC’s, there have been bottlenecks of system scalability, energy and performance, which cannot be easily solved with synchronous approaches. As a result, there has been significant recent interest in combing the notion of asynchrony with NoC designs. Since the NoC approach inherently separates the communication infrastructure, and its timing, from computational elements, it is a natural match for an asynchronous paradigm. Asynchronous NoC’s, therefore, enable a modular and extensible system composition for an ‘object-orient’ design style. The thesis aims to significantly advance the state-of-art and viability of asynchronous and globally-asynchronous locally-synchronous (GALS) networks-on-chip, to enable high-performance and low-energy systems. The proposed asynchronous NoC’s are nearly entirely based on standard cells, which eases their integration into industrial design flows. The contributions are instantiated in three different directions. First, practical acceleration techniques are proposed for optimizing the system latency, in order to break through the latency bottleneck in the memory interfaces of many on-chip parallel processors. Novel asynchronous network protocols are proposed, along with concrete NoC designs. A new concept, called ‘monitoring network’, is introduced. Monitoring networks are lightweight shadow networks used for fast-forwarding anticipated traffic information, ahead of the actual packet traffic. The routers are therefore allowed to initiate and perform arbitration and channel allocation in advance. The technique is successfully applied to two topologies which belong to two different categories – a variant mesh-of-trees (MoT) structure and a 2D-mesh topology. Considerable and stable latency improvements are observed across a wide range of traffic patterns, along with moderate throughput gains. Second, for the first time, a high-performance and low-power asynchronous NoC router is compared directly to a leading commercial synchronous counterpart in an advanced industrial technology. The asynchronous router design shows significant performance improvements, as well as area and power savings. The proposed asynchronous router integrates several advanced techniques, including a low-latency circular FIFO for buffer design, and a novel end-to-end credit-based virtual channel (VC) flow control. In addition, a semi-automated design flow is created, which uses portions of a standard synchronous tool flow. Finally, a high-performance multi-resource asynchronous arbiter design is developed. This small but important component can be directly used in existing asynchronous NoC’s for performance optimization. In addition, this standalone design promises use in opening up new NoC directions, as well as for general use in parallel systems. In the proposed arbiter design, the allocation of a resource to a client is divided into several steps. Multiple successive client-resource pairs can be selected rapidly in pipelined sequence, and the completion of the assignments can overlap in parallel. In sum, the thesis provides a set of advanced design solutions for performance optimization of asynchronous and GALS networks-on-chip. These solutions are at different levels, from network protocols, down to router- and component-level optimizations, which can be directly applied to existing basic asynchronous NoC designs to provide a leap in performance improvement

Application Driven MOdels for Resource Management in Cloud Environments

El despliegue y la ejecución de aplicaciones de gran escala en sistemas distribuidos con unos parametros de Calidad de Servicio adecuados necesita gestionar de manera eficiente los recursos computacionales. Para desacoplar los requirimientos funcionales y los no funcionales (u operacionales) de dichas aplicaciones, se puede distinguir dos niveles de abstracción: i) el nivel funcional, que contempla aquellos requerimientos relacionados con funcionalidades de la aplicación; y ii) el nivel operacional, que depende del sistema distribuido donde se despliegue y garantizará aquellos parámetros relacionados con la Calidad del Servicio, disponibilidad, tolerancia a fallos y coste económico, entre otros. De entre las diferentes alternativas del nivel operacional, en la presente tesis se contempla un entorno cloud basado en la virtualización de contenedores, como puede ofrecer Kubernetes.El uso de modelos para el diseño de aplicaciones en ambos niveles permite garantizar que dichos requerimientos sean satisfechos. Según la complejidad del modelo que describa la aplicación, o el conocimiento que el nivel operacional tenga de ella, se diferencian tres tipos de aplicaciones: i) aplicaciones dirigidas por el modelo, como es el caso de la simulación de eventos discretos, donde el propio modelo, por ejemplo Redes de Petri de Alto Nivel, describen la aplicación; ii) aplicaciones dirigidas por los datos, como es el caso de la ejecución de analíticas sobre Data Stream; y iii) aplicaciones dirigidas por el sistema, donde el nivel operacional rige el despliegue al considerarlas como una caja negra.En la presente tesis doctoral, se propone el uso de un scheduler específico para cada tipo de aplicación y modelo, con ejemplos concretos, de manera que el cliente de la infraestructura pueda utilizar información del modelo descriptivo y del modelo operacional. Esta solución permite rellenar el hueco conceptual entre ambos niveles. De esta manera, se proponen diferentes métodos y técnicas para desplegar diferentes aplicaciones: una simulación de un sistema de Vehículos Eléctricos descrita a través de Redes de Petri; procesado de algoritmos sobre un grafo que llega siguiendo el paradigma Data Stream; y el propio sistema operacional como sujeto de estudio.En este último caso de estudio, se ha analizado cómo determinados parámetros del nivel operacional (por ejemplo, la agrupación de contenedores, o la compartición de recursos entre contenedores alojados en una misma máquina) tienen un impacto en las prestaciones. Para analizar dicho impacto, se propone un modelo formal de una infrastructura operacional concreta (Kubernetes). Por último, se propone una metodología para construir índices de interferencia para caracterizar aplicaciones y estimar la degradación de prestaciones incurrida cuando dos contenedores son desplegados y ejecutados juntos. Estos índices modelan cómo los recursos del nivel operacional son usados por las applicaciones. Esto supone que el nivel operacional maneja información cercana a la aplicación y le permite tomar mejores decisiones de despliegue y distribución.<br /