Analytic Performance Modeling and Analysis of Detailed Neuron Simulations

Big science initiatives are trying to reconstruct and model the brain by attempting to simulate brain tissue at larger scales and with increasingly more biological detail than previously thought possible. The exponential growth of parallel computer performance has been supporting these developments, and at the same time maintainers of neuroscientific simulation code have strived to optimally and efficiently exploit new hardware features. Current state of the art software for the simulation of biological networks has so far been developed using performance engineering practices, but a thorough analysis and modeling of the computational and performance characteristics, especially in the case of morphologically detailed neuron simulations, is lacking. Other computational sciences have successfully used analytic performance engineering and modeling methods to gain insight on the computational properties of simulation kernels, aid developers in performance optimizations and eventually drive co-design efforts, but to our knowledge a model-based performance analysis of neuron simulations has not yet been conducted. We present a detailed study of the shared-memory performance of morphologically detailed neuron simulations based on the Execution-Cache-Memory (ECM) performance model. We demonstrate that this model can deliver accurate predictions of the runtime of almost all the kernels that constitute the neuron models under investigation. The gained insight is used to identify the main governing mechanisms underlying performance bottlenecks in the simulation. The implications of this analysis on the optimization of neural simulation software and eventually co-design of future hardware architectures are discussed. In this sense, our work represents a valuable conceptual and quantitative contribution to understanding the performance properties of biological networks simulations.Comment: 18 pages, 6 figures, 15 table

Numerical Representation of Directed Acyclic Graphs for Efficient Dataflow Embedded Resource Allocation

International audienceStream processing applications running on Heterogeneous Multi-Processor Systems on Chips (HMPSoCs) require efficient resource allocation and management, both at compile-time and at runtime. To cope with modern adaptive applications whose behavior can not be exhaustively predicted at compile-time, runtime managers must be able to take resource allocation decisions on-the-fly, with a minimum overhead on application performance. Resource allocation algorithms often rely on an internal modeling of an application. Directed Acyclic Graph (DAGs) are the most commonly used models for capturing control and data dependencies between tasks. DAGs are notably often used as an intermediate representation for deploying applications modeled with a dataflow Model of Computation (MoC) on HMPSoCs. Building such intermediate representation at runtime for massively parallel applications is costly both in terms of computation and memory overhead. In this paper, an intermediate representation of DAGs for resource allocation is presented. This new representation shows improved performance for run-time analysis of dataflow graphs with less overhead in both computation time and memory footprint. The performances of the proposed representation are evaluated on a set of computer vision and machine learning applications

Modeling and Software Synthesis for Multiprocessor Implementation of Wireless Communication Systems

In recent years, the complexity of designing embedded signal processing systems for wireless communications has increased significantly based on the need to support increasing levels of operational flexibility and adaptivity, while also supporting increasing data rates and bandwidths. These trends pose important design and implementation challenges to meet the required demands on communication system performance, real-time operation, energy efficiency, and reconfigurability. Dataflow models of computation provide a useful framework that can be built upon to address these challenges. Dataflow models provide high-level abstractions for specifying, analyzing and implementing a wide range of embedded signal processing applications. They allow designers to specify an application using high-level, platform-independent representations, and synthesize optimized embedded software that is targeted to specific types of hardware resources and design constraints. The growing complexity of wireless communication systems, as motivated above, along with the complexity of system-on-chip platforms for embedded signal processing result in new problems that must be addressed in developing effective dataflow-based design methodologies. First, significant improvements to dataflow-based models and methods are needed to effectively utilize heterogeneous computing platforms and multiple forms of parallelism under stringent constraints on real-time performance and energy consumption. Second, effective modeling and analysis methods for handling dynamic parameters within dataflow graph components are needed for reliable and efficient management of system-level adaptivity and reconfiguration. In this thesis, we address these problems by developing an integrated framework that exploits pipeline, data and task-level parallelism in dataflow models under memory constraints, and proposing novel dataflow modeling concepts and performance optimization techniques for design and implementation of dynamically parameterized communication systems. The main contributions of the thesis are summarized as follows: (1) Software synthesis framework for heterogeneous signal processing platforms. We have developed an integrated dataflow-based design framework called DIF-GPU, which provides a toolset for specification, optimization and software synthesis of embedded software targeted to heterogeneous CPU-GPU platforms. DIF-GPU incorporates novel models and methods in the dataflow interchange format (DIF) that are geared toward design optimization of signal processing systems on heterogeneous architectures composed of multicore CPUs and GPUs. DIF-GPU helps to free developers from low-level, platform-specific fine-tuning, and allows them to focus on higher-level aspects of communication system design. (2) Vectorization in DIF-GPU. In the context of dataflow models for embedded signal processing, vectorization is an important transformation for exploiting data parallelism. We have developed new techniques for integrated dataflow graph vectorization and scheduling on heterogeneous platforms. These techniques are developed in the DIF-GPU framework to provide optimized vectorization and scheduling capabilities for hybrid CPU-GPU platforms under memory constraints. For the targeted class of platforms, these techniques are shown to provide significantly better processing throughput compared to previous methods for a given memory constraint. We demonstrate our integrated vectorization and scheduling techniques by applying them to an Orthogonal Frequency Division Multiplexing (OFDM) receiver system. (3) Modeling parameterized, dynamic dataflow behavior. We introduce a novel modeling method, called parameterized sets of modes (PSMs), that enables efficient representation and analysis of adaptive and dynamically reconfigurable signal processing functionality. PSMs can be viewed as high-level abstractions that model parameterized functionality involving groups of related regimes of operation ("modes") for dynamic dataflow models. We develop formal foundations for PSM-based modeling, and demonstrate the utility of this form of modeling by using it to develop efficient methods for scheduling dynamically parameterized dataflow graphs on different types of relevant platforms

Assessment of Two Task Frameworks with Dependencies for Matrix Factorizations on a Multicore Architecture

In this study, we evaluate two task frameworks with dependencies for important application kernels coming from the numerical linear algebra. In this approach, the algorithms of the matrix factorization are considered, namely the tiled LU and the WZ factorizations both without pivoting. In tiled algorithms, the operations are represented as a sequence of small tasks which operate on square blocks (tiles) of the data. The dependencies among tasks are expressed as a direct acyclic graph and the runtime system runs the graph on a multicore architecture. The performance of applications based on the task dependencies is related to efficient compilers and the runtime systems. We report the performance and the scalability of two task frameworks with dependencies on the multicore architecture for the matrix factorizations. Namely, we compare OpenMP and Intel Thread Building Blocks. Our results show that the number of tiles in both factorizations always have an impact on the performance and the speedup. Both the frameworks show their suitability for efficient parallelization of such applications, although both have their own merits and flaws

On the co-design of scientific applications and long vector architectures

The landscape of High Performance Computing (HPC) system architectures keeps expanding with new technologies and increased complexity. To improve the efficiency of next-generation compute devices, architects are looking for solutions beyond the commodity CPU approach. In 2021, the five most powerful supercomputers in the world use either GP-GPU (General-purpose computing on graphics processing units) accelerators or a customized CPU specially designed to target HPC applications. This trend is only expected to grow in the next years motivated by the compute demands of science and industry. As architectures evolve, the ecosystem of tools and applications must follow. The choices in the number of cores in a socket, the floating point-units per core and the bandwidth through the memory hierarchy among others, have a large impact in the power consumption and compute capabilities of the devices. To balance CPU and accelerators, designers require accurate tools for analyzing and predicting the impact of new architectural features on the performance of complex scientific applications at scale. In such a large design space, capturing and modeling with simulators the complex interactions between the system software and hardware components is a defying challenge. Moreover, applications must be able to exploit those designs with aggressive compute capabilities and memory bandwidth configurations. Algorithms and data structures will need to be redesigned accordingly to expose a high degree of data-level parallelism allowing them to scale in large systems. Therefore, next-generation computing devices will be the result of a co-design effort in hardware and applications supported by advanced simulation tools. In this thesis, we focus our work on the co-design of scientific applications and long vector architectures. We significantly extend a multi-scale simulation toolchain enabling accurate performance and power estimations of large-scale HPC systems. Through simulation, we explore the large design space in current HPC trends over a wide range of applications. We extract speedup and energy consumption figures analyzing the trade-offs and optimal configurations for each of the applications. We describe in detail the optimization process of two challenging applications on real vector accelerators, achieving outstanding operation performance and full memory bandwidth utilization. Overall, we provide evidence-based architectural and programming recommendations that will serve as hardware and software co-design guidelines for the next generation of specialized compute devices.El panorama de las arquitecturas de los sistemas para la Computación de Alto Rendimiento (HPC, de sus siglas en inglés) sigue expandiéndose con nuevas tecnologías y complejidad adicional. Para mejorar la eficiencia de la próxima generación de dispositivos de computación, los arquitectos están buscando soluciones más allá de las CPUs. En 2021, los cinco supercomputadores más potentes del mundo utilizan aceleradores gráficos aplicados a propósito general (GP-GPU, de sus siglas en inglés) o CPUs diseñadas especialmente para aplicaciones HPC. En los próximos años, se espera que esta tendencia siga creciendo motivada por las demandas de más potencia de computación de la ciencia y la industria. A medida que las arquitecturas evolucionan, el ecosistema de herramientas y aplicaciones les debe seguir. Las decisiones eligiendo el número de núcleos por zócalo, las unidades de coma flotante por núcleo y el ancho de banda a través de la jerarquía de memoría entre otros, tienen un gran impacto en el consumo de energía y las capacidades de cómputo de los dispositivos. Para equilibrar las CPUs y los aceleradores, los diseñadores deben utilizar herramientas precisas para analizar y predecir el impacto de nuevas características de la arquitectura en el rendimiento de complejas aplicaciones científicas a gran escala. Dado semejante espacio de diseño, capturar y modelar con simuladores las complejas interacciones entre el software de sistema y los componentes de hardware es un reto desafiante. Además, las aplicaciones deben ser capaces de explotar tales diseños con agresivas capacidades de cómputo y ancho de banda de memoria. Los algoritmos y estructuras de datos deberán ser rediseñadas para exponer un alto grado de paralelismo de datos permitiendo así escalarlos en grandes sistemas. Por lo tanto, la siguiente generación de dispósitivos de cálculo será el resultado de un esfuerzo de codiseño tanto en hardware como en aplicaciones y soportado por avanzadas herramientas de simulación. En esta tesis, centramos nuestro trabajo en el codiseño de aplicaciones científicas y arquitecturas vectoriales largas. Extendemos significativamente una serie de herramientas para la simulación multiescala permitiendo así obtener estimaciones de rendimiento y potencia de sistemas HPC de gran escala. A través de simulaciones, exploramos el gran espacio de diseño de las tendencias actuales en HPC sobre un amplio rango de aplicaciones. Extraemos datos sobre la mejora y el consumo energético analizando las contrapartidas y las configuraciones óptimas para cada una de las aplicaciones. Describimos en detalle el proceso de optimización de dos aplicaciones en aceleradores vectoriales, obteniendo un rendimiento extraordinario a nivel de operaciones y completa utilización del ancho de memoria disponible. Con todo, ofrecemos recomendaciones empíricas a nivel de arquitectura y programación que servirán como instrucciones para diseñar mejor hardware y software para la siguiente generación de dispositivos de cálculo especializados.Postprint (published version