Doctor of Philosophy

dissertationHigh-performance supercomputers on the Top500 list are commonly designed around commodity CPUs. Most of the codes executed on these machines are message-passing codes using the message-passing toolkit (MPI). Thus it makes sense to look at these machines from a holistic systems architecture perspective and consider optimizations to commodity processors that make them more efficient in message-passing architectures. Described herein is a new User-Level Notification (ULN) architecture that significantly improves message-passing performance. The architecture integrates a simultaneous multithreaded (SMT) processor with a user-level network interface (NI) that can directly control the execution scheduling of threads on the processor. By allowing the network interface to control the execution of message handling code at the user level, the operating system (OS) related overhead for handling interrupts and user code dispatch related to notifications is eliminated. By using an SMT processor, message handling can be performed in one thread concurrent to user computation in other threads, thus most of the overhead of executing message handlers can be hidden. This dissertation presents measurements showing the OS overheads related to message-passing are significant in modern architectures and describes a new architecture that significantly reduces these overheads. On a communication-intensive real-world application, the ULN architecture provides a 50.9% performance improvement over a more traditional OS-based NIC and a 5.29-31.9% improvement over a best-of-class user-level NIC due to the user-level notifications

Design of efficient Java communications for high performance computing

[Abstract] There is an increasing interest to adopt Java as the parallel programming language for the multi-core era. Although Java offers important advantages, such as built-in multithreading and networking support, productivity and portability, the lack of efficient communication middleware is an important drawback for its uptake in High Performance Computing (HPC). This PhD Thesis presents the design, implementation and evaluation of several solutions to improve this situation: (1) a high performance Java sockets implementation (JFS, Java Fast Sockets) on high-speed networks (e.g., Myrinet, InfiniBand) and shared memory (e.g., multi-core) machines; (2) a low-level messaging device, iodev, which efficiently overlaps communication and computation; and (3) a more scalable Java message-passing library, Fast MPJ (F-MPJ). Furthermore, new Java parallel benchmarks have been implemented and used for the performance evaluation of the developed middleware. The final and main conclusion is that the use of Java for HPC is feasible and even advisable when looking for productive development, provided that efficient communication middleware is made available, such as the projects presented in this Thesis.[Resumen] La tesis doctoral "Design of Efficient Java Communications for High Performance Computing" parte de la hipótesis inicial de que es posible desarrollar aplicaciones Java en computación de altas prestaciones, un ámbito en el que el rendimiento es crucial, siempre que esté disponible un middleware de comunicación eficiente. Así, se han diseñado, desarrollado y evaluado diferentes bibliotecas de comunicación en Java, desde el nivel de sockets al de paso de mensajes, obteniendo notables incrementos de eficiencia, confirmando que la hipótesis inicial es factible

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

Multithreading opportunities for program optimizations

The introduction of Multiprocessor On Chip (CMP) led to a substantial reformulation of the Moore law stating that the number of cores in a single chip doubles every one year and a half. The tech boom related to CMP gave a strong impulse to parallel program design diminishing its ``gap'' with parallel architectures. Nowadays a leading trend related to high performance products is represented by CMP with multithreading CPU nodes. Basically the CPU multithreading feature tries to overcome the underutilization of superscalar processors, due to the lack of exploitable instruction level parallelism (ILP), allowing the simultaneous processing of different programs during the same time slot. In multithreading architectures a thread is a concurrent computational entity supported directly at firmware level (these threads are usually called hardware threads). Multithreading technology opens a broad range of possible optimizations that can be applied to improve the performance of sequential and parallel applications. This thesis treat four possible optimization targeted for multithreading architectures: Speculative Precomputation, Threaded Multipath Execution, Speculative Multithreading and Communication threads. L'introduzione dei Multiprocessor On Chip (CMP) ha portato ad una sostanziale riformulazione della legge di Moore la quale afferma che il numero di cores in un singolo chip raddoppia ogni anno e mezzo. Il boom tecnologico relativo ai CMP ha dato un grande impulso al design relativo alla programmazione parallela diminuendo il gap con le architetture parallele. Allo stato attuale delle cose, un trend prominente relativo ai prodotti di high performance computing è rappresentato da CMP con nodi caratterizzati da hardware multithreading. Questa tecnologia prova a risolvere il sottoutilizzo di processori superscalari, dovuto alla mancanza di ILP (instruction level parallelism), permettendo la computazione simultanea di diversi programmi durante lo stesso time slot La tecnologia multithreading ha aperto un ampio spettro di possibili ottimizzazioni che possono essere utilizzate al fine di migliorare le performance di applicazioni sequenziali e parallele. Questa tesi tratta quattro possibili ottimizzazioni indirizzate per architetture multithreading: Speculative Precomputation (Helper Thread), Threaded Multipath Execution, Speculative Multithreading and Communication Threads

Enabling the use of embedded and mobile technologies for high-performance computing

In the late 1990s, powerful economic forces led to the adoption of commodity desktop processors in High-Performance Computing(HPC). This transformation has been so effective that the November 2016 TOP500 list is still dominated by x86 architecture. In 2016, the largest commodity market in computing is not PCs or servers, but mobile computing, comprising smartphones andtablets, most of which are built with ARM-based Systems on Chips (SoC). This suggests that once mobile SoCs deliver sufficient performance, mobile SoCs can help reduce the cost of HPC. This thesis addresses this question in detail.We analyze the trend in mobile SoC performance, comparing it with the similar trend in the 1990s. Through development of real system prototypes and their performance analysis we assess the feasibility of building an HPCsystem based on mobile SoCs. Through simulation of the future mobile SoC, we identify the missing features and suggest improvements that would enable theuse of future mobile SoCs in HPC environment. Thus, we present design guidelines for future generations mobile SoCs, and HPC systems built around them, enabling the newclass of cheap supercomputers.A finales de la década de los 90, razones económicas llevaron a la adopción de procesadores de uso general en sistemas de Computación de Altas Prestaciones (HPC). Esta transformación ha sido tan efectiva que la lista TOP500 de noviembre de 2016 sigue aun dominada por la arquitectura x86. En 2016, el mayor mercado de productos básicos en computación no son los ordenadores de sobremesa o los servidores, sino la computación móvil, que incluye teléfonos inteligentes y tabletas, la mayoría de los cuales están construidos con sistemas en chip(SoC) de arquitectura ARM. Esto sugiere que una vez que los SoC móviles ofrezcan un rendimiento suficiente, podrán utilizarse para reducir el costo desistemas HPC. Esta tesis aborda esta cuestión en detalle. Analizamos la tendencia del rendimiento de los SoC para móvil, comparándola con la tendencia similar ocurrida en los añosnoventa. A través del desarrollo de prototipos de sistemas reales y su análisis de rendimiento, evaluamos la factibilidad de construir unsistema HPC basado en SoCs móviles. A través de la simulación de SoCs móviles futuros, identificamos las características que faltan y sugerimos mejoras quepermitirían su uso en entornos HPC. Por lo tanto, presentamos directrices de diseño para futuras generaciones de SoCs móviles y sistemas HPC construidos a sualrededor, para permitir la construcción de una nueva clase de supercomputadores de coste reducido

The readying of applications for heterogeneous computing

High performance computing is approaching a potentially significant change in architectural design. With pressures on the cost and sheer amount of power, additional architectural features are emerging which require a re-think to the programming models deployed over the last two decades. Today's emerging high performance computing (HPC) systems are maximising performance per unit of power consumed resulting in the constituent parts of the system to be made up of a range of different specialised building blocks, each with their own purpose. This heterogeneity is not just limited to the hardware components but also in the mechanisms that exploit the hardware components. These multiple levels of parallelism, instruction sets and memory hierarchies, result in truly heterogeneous computing in all aspects of the global system. These emerging architectural solutions will require the software to exploit tremendous amounts of on-node parallelism and indeed programming models to address this are emerging. In theory, the application developer can design new software using these models to exploit emerging low power architectures. However, in practice, real industrial scale applications last the lifetimes of many architectural generations and therefore require a migration path to these next generation supercomputing platforms. Identifying that migration path is non-trivial: With applications spanning many decades, consisting of many millions of lines of code and multiple scientific algorithms, any changes to the programming model will be extensive and invasive and may turn out to be the incorrect model for the application in question. This makes exploration of these emerging architectures and programming models using the applications themselves problematic. Additionally, the source code of many industrial applications is not available either due to commercial or security sensitivity constraints. This thesis highlights this problem by assessing current and emerging hard- ware with an industrial strength code, and demonstrating those issues described. In turn it looks at the methodology of using proxy applications in place of real industry applications, to assess their suitability on the next generation of low power HPC offerings. It shows there are significant benefits to be realised in using proxy applications, in that fundamental issues inhibiting exploration of a particular architecture are easier to identify and hence address. Evaluations of the maturity and performance portability are explored for a number of alternative programming methodologies, on a number of architectures and highlighting the broader adoption of these proxy applications, both within the authors own organisation, and across the industry as a whole

Parallel and Distributed Computing

The 14 chapters presented in this book cover a wide variety of representative works ranging from hardware design to application development. Particularly, the topics that are addressed are programmable and reconfigurable devices and systems, dependability of GPUs (General Purpose Units), network topologies, cache coherence protocols, resource allocation, scheduling algorithms, peertopeer networks, largescale network simulation, and parallel routines and algorithms. In this way, the articles included in this book constitute an excellent reference for engineers and researchers who have particular interests in each of these topics in parallel and distributed computing

Effective data parallel computing on multicore processors

The rise of chip multiprocessing or the integration of multiple general purpose processing cores on a single chip (multicores), has impacted all computing platforms including high performance, servers, desktops, mobile, and embedded processors. Programmers can no longer expect continued increases in software performance without developing parallel, memory hierarchy friendly software that can effectively exploit the chip level multiprocessing paradigm of multicores. The goal of this dissertation is to demonstrate a design process for data parallel problems that starts with a sequential algorithm and ends with a high performance implementation on a multicore platform. Our design process combines theoretical algorithm analysis with practical optimization techniques. Our target multicores are quad-core processors from Intel and the eight-SPE IBM Cell B.E. Target applications include Matrix Multiplications (MM), Finite Difference Time Domain (FDTD), LU Decomposition (LUD), and Power Flow Solver based on Gauss-Seidel (PFS-GS) algorithms. These applications are popular computation methods in science and engineering problems and are characterized by unit-stride (MM, LUD, and PFS-GS) or 2-point stencil (FDTD) memory access pattern. The main contributions of this dissertation include a cache- and space-efficient algorithm model, integrated data pre-fetching and caching strategies, and in-core optimization techniques. Our multicore efficient implementations of the above described applications outperform nai¨ve parallel implementations by at least 2x and scales well with problem size and with the number of processing cores

On the simulation and design of manycore CMPs

The progression of Moore’s Law has resulted in both embedded and performance computing systems which use an ever increasing number of processing cores integrated in a single chip. Commercial systems are now available which provide hundreds of cores, and academics have proposed architectures for up to 1024 cores. Embedded multicores are increasingly popular as it is easier to guarantee hard-realtime constraints using individual cores dedicated for tasks, than to use traditional time-multiplexed processing. However, finding the optimal hardware configuration to meet these requirements at minimum cost requires extensive trial and error approaches to investigate the design space. This thesis tackles the problems encountered in the design of these large scale multicore systems by first addressing the problem of fast, detailed micro-architectural simulation. Initially addressing embedded systems, this work exploits the lack of hardware cache-coherence support in many deeply embedded systems to increase the available parallelism in the simulation. Then, through partitioning the NoC and using packet counting and cycle skipping reduces the amount of computation required to accurately model the NoC interconnect. In combination, this enables simulation speeds significantly higher than the state of the art, while maintaining less error, when compared to real hardware, than any similar simulator. Simulation speeds reach up to 370MIPS (Million (target) Instructions Per Second), or 110MHz, which is better than typical FPGA prototypes, and approaching final ASIC production speeds. This is achieved while maintaining an error of only 2.1%, significantly lower than other similar simulators. The thesis continues by scaling the simulator past large embedded systems up to 64-1024 core processors, adding support for coherent architectures using the same packet counting techniques along with low overhead context switching to enable the simulation of such large systems with stricter synchronisation requirements. The new interconnect model was partitioned to enable parallel simulation to further improve simulation speeds in a manner which did not sacrifice any accuracy. These innovations were leveraged to investigate significant novel energy saving optimisations to the coherency protocol, processor ISA, and processor micro-architecture. By introducing a new instruction, with the name wait-on-address, the energy spent during spin-wait style synchronisation events can be significantly reduced. This functions by putting the core into a low-power idle state while the cache line of the indicated address is monitored for coherency action. Upon an update or invalidation (or traditional timer or external interrupts) the core will resume execution, but the active energy of running the core pipeline and repeatedly accessing the data and instruction caches is effectively reduced to static idle power. The thesis also shows that existing combined software-hardware schemes to track data regions which do not require coherency can adequately address the directory-associativity problem, and introduces a new coherency sharer encoding which reduces the energy consumed by sharer invalidations when sharers are grouped closely together, such as would be the case with a system running many tasks with a small degree of parallelism in each. The research concludes by using the extremely fast simulation speeds developed to produce a large set of training data, collecting various runtime and energy statistics for a wide range of embedded applications on a huge diverse range of potential MPSoC designs. This data was used to train a series of machine learning based models which were then evaluated on their capacity to predict performance characteristics of unseen workload combinations across the explored MPSoC design space, using only two sample simulations, with promising results from some of the machine learning techniques. The models were then used to produce a ranking of predicted performance across the design space, and on average Random Forest was able to predict the best design within 89% of the runtime performance of the actual best tested design, and better than 93% of the alternative design space. When predicting for a weighted metric of energy, delay and area, Random Forest on average produced results within 93% of the optimum result. In summary this thesis improves upon the state of the art for cycle accurate multicore simulation, introduces novel energy saving changes the the ISA and microarchitecture of future multicore processors, and demonstrates the viability of machine learning techniques to significantly accelerate the design space exploration required to bring a new manycore design to market

Castell: a heterogeneous cmp architecture scalable to hundreds of processors

Technology improvements and power constrains have taken multicore architectures to dominate microprocessor designs over uniprocessors. At the same time, accelerator based architectures have shown that heterogeneous multicores are very efficient and can provide high throughput for parallel applications, but with a high-programming effort. We propose Castell a scalable chip multiprocessor architecture that can be programmed as uniprocessors, and provides the high throughput of accelerator-based architectures. Castell relies on task-based programming models that simplify software development. These models use a runtime system that dynamically finds, schedules, and adds hardware-specific features to parallel tasks. One of these features is DMA transfers to overlap computation and data movement, which is known as double buffering. This feature allows applications on Castell to tolerate large memory latencies and lets us design the memory system focusing on memory bandwidth. In addition to provide programmability and the design of the memory system, we have used a hierarchical NoC and added a synchronization module. The NoC design distributes memory traffic efficiently to allow the architecture to scale. The synchronization module is a consequence of the large performance degradation of application for large synchronization latencies. Castell is mainly an architecture framework that enables the definition of domain-specific implementations, fine-tuned to a particular problem or application. So far, Castell has been successfully used to propose heterogeneous multicore architectures for scientific kernels, video decoding (using H.264), and protein sequence alignment (using Smith-Waterman and clustalW). It has also been used to explore a number of architecture optimizations such as enhanced DMA controllers, and architecture support for task-based programming models. ii