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)

Generating and auto-tuning parallel stencil codes

In this thesis, we present a software framework, Patus, which generates high performance stencil codes for different types of hardware platforms, including current multicore CPU and graphics processing unit architectures. The ultimate goals of the framework are productivity, portability (of both the code and performance), and achieving a high performance on the target platform. A stencil computation updates every grid point in a structured grid based on the values of its neighboring points. This class of computations occurs frequently in scientific and general purpose computing (e.g., in partial differential equation solvers or in image processing), justifying the focus on this kind of computation. The proposed key ingredients to achieve the goals of productivity, portability, and performance are domain specific languages (DSLs) and the auto-tuning methodology. The Patus stencil specification DSL allows the programmer to express a stencil computation in a concise way independently of hardware architecture-specific details. Thus, it increases the programmer productivity by disburdening her or him of low level programming model issues and of manually applying hardware platform-specific code optimization techniques. The use of domain specific languages also implies code reusability: once implemented, the same stencil specification can be reused on different hardware platforms, i.e., the specification code is portable across hardware architectures. Constructing the language to be geared towards a special purpose makes it amenable to more aggressive optimizations and therefore to potentially higher performance. Auto-tuning provides performance and performance portability by automated adaptation of implementation-specific parameters to the characteristics of the hardware on which the code will run. By automating the process of parameter tuning — which essentially amounts to solving an integer programming problem in which the objective function is the number representing the code's performance as a function of the parameter configuration, — the system can also be used more productively than if the programmer had to fine-tune the code manually. We show performance results for a variety of stencils, for which Patus was used to generate the corresponding implementations. The selection includes stencils taken from two real-world applications: a simulation of the temperature within the human body during hyperthermia cancer treatment and a seismic application. These examples demonstrate the framework's flexibility and ability to produce high performance code

IXIAM: ISA EXtension for Integrated Accelerator Management

During the last few years, hardware accelerators have been gaining popularity thanks to their ability to achieve higher performance and efficiency than classic general-purpose solutions. They are fundamentally shaping the current generations of Systems-on-Chip (SoCs), which are becoming increasingly heterogeneous. However, despite their widespread use, a standard, general solution to manage them while providing speed and consistency has not yet been found. Common methodologies rely on OS mediation and a mix of user-space and kernel-space drivers, which can be inefficient, especially for fine-grained tasks. This paper addresses these sources of inefficiencies by proposing an ISA eXtension for Integrated Accelerator Management (IXIAM), a cost-effective HW-SW framework to control a wide variety of accelerators in a standard way, and directly from the cores. The proposed instructions include reservation, work offloading, data transfer, and synchronization. They can be wrapped in a high-level software API or even integrated into a compiler. IXIAM features also a user-space interrupt mechanism to signal events directly to the user process. We implement it as a RISC-V extension in the gem5 simulator and demonstrate detailed support for complex accelerators, as well as the ability to specify sequences of memory transfers and computations directly from the ISA and with significantly lower overhead than driver-based schemes. IXIAM provides a performance advantage that is more evident for small and medium workloads, reaching around 90x in the best case. This way, we enlarge the set of workloads that would benefit from hardware acceleration

Improving efficiency for GPUs with decoupled delegate

GPUs are increasingly used for general-purpose computation. For many applications, GPUs achieve significant performance advantages over CPUs, largely due to GPUs’ ability to exploit massive parallelism. However, massive parallelism can cause inefficiency for many operations, such as concurrent data structures. Symptoms include synchronization bottleneck and redundant overheads. To make such operations efficient, our key strategy is to decouple them from the rest of GPU program. Then, we use a few threads acting as a delegate to perform the decoupled operations on behalf of all other threads. This reduces the synchronization for decoupled operations because fewer threads are used. In addition, the delegate amortizes overheads for other threads, similar to the way in which vector execution amortizes instruction overheads. The cost of our approach is the need for communication between the delegate and other threads. We develop innovative ways to reduce the communication so that the benefit strongly outweighs the cost. Based on the strategy, we propose three solutions for both regular and irregular workloads. For regular GPU workloads, our solution reduces repetitive ALU OPs and instruction execution, while reducing memory latency with non-speculative prefetching. This approach enabled our solution to achieve 40.7% speedup and 20.2% energy reduction on average for 29 benchmarks. For lock-based workloads, our solution avoids destructive lock contention in global memory and thus achieves an average speedup of 3.6x, implemented entirely in software. Finally, we introduce a new GPU single source shortest path (SSSP) algorithm with a complex worklist; it offers many benefits compared to a simpler worklist but incurs significant overheads. However, our decoupled delegate approach reduces the overheads and makes the complex worklist design efficient for GPUs. Hence, our solution, implemented in software, achieved an average speedup of 2.8x over 226 graphs compared with state-of-the-art approaches.Computational Science, Engineering, and Mathematic

Alternative Route Techniques and their Applications to the Stochastics on-time Arrival Problem

This thesis takes a close look at a wide range of different techniques for the computation of alternative routes on the two most popular speed-up techniques currently in use. From the standpoint of an algorithm engineer, we explore how to exploit the different techniques for their full potential

Evolutionary genomics : statistical and computational methods

This open access book addresses the challenge of analyzing and understanding the evolutionary dynamics of complex biological systems at the genomic level, and elaborates on some promising strategies that would bring us closer to uncovering of the vital relationships between genotype and phenotype. After a few educational primers, the book continues with sections on sequence homology and alignment, phylogenetic methods to study genome evolution, methodologies for evaluating selective pressures on genomic sequences as well as genomic evolution in light of protein domain architecture and transposable elements, population genomics and other omics, and discussions of current bottlenecks in handling and analyzing genomic data. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of detail and expert implementation advice that lead to the best results. Authoritative and comprehensive, Evolutionary Genomics: Statistical and Computational Methods, Second Edition aims to serve both novices in biology with strong statistics and computational skills, and molecular biologists with a good grasp of standard mathematical concepts, in moving this important field of study forward

Evolutionary Genomics

This open access book addresses the challenge of analyzing and understanding the evolutionary dynamics of complex biological systems at the genomic level, and elaborates on some promising strategies that would bring us closer to uncovering of the vital relationships between genotype and phenotype. After a few educational primers, the book continues with sections on sequence homology and alignment, phylogenetic methods to study genome evolution, methodologies for evaluating selective pressures on genomic sequences as well as genomic evolution in light of protein domain architecture and transposable elements, population genomics and other omics, and discussions of current bottlenecks in handling and analyzing genomic data. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of detail and expert implementation advice that lead to the best results. Authoritative and comprehensive, Evolutionary Genomics: Statistical and Computational Methods, Second Edition aims to serve both novices in biology with strong statistics and computational skills, and molecular biologists with a good grasp of standard mathematical concepts, in moving this important field of study forward

Engineering Algorithms for Route Planning in Multimodal Transportation Networks

Practical algorithms for route planning in transportation networks are a showpiece of successful Algorithm Engineering. This has produced many speedup techniques, varying in preprocessing time, space, query performance, simplicity, and ease of implementation. This thesis explores solutions to more realistic scenarios, taking into account, e.g., traffic, user preferences, public transit schedules, and the options offered by the many modalities of modern transportation networks