Accelerator Memory Reuse in the Dark Silicon Era

Accelerators integrated on-die with General-Purpose CPUs (GP-CPUs) can yield significant performance and power improvements. Their extensive use, however, is ultimately limited by their area overhead; due to their high degree of specialization, the opportunity cost of investing die real estate on accelerators can become prohibitive, especially for general-purpose architectures. In this paper we present a novel technique aimed at mitigating this opportunity cost by allowing GP-CPU cores to reuse accelerator memory as a non-uniform cache architecture (NUCA) substrate. On a system with a last level-2 cache of 128kB, our technique achieves on average a 25% performance improvement when reusing four 512 kB accelerator memory blocks to form a level-3 cache. Making these blocks reusable as NUCA slices incurs on average in a 1.89% area overhead with respect to equally-sized ad hoc cache slice

Automated Genome-Wide Protein Domain Exploration

Exploiting the exponentially growing genomics and proteomics data requires high quality, automated analysis. Protein domain modeling is a key area of molecular biology as it unravels the mysteries of evolution, protein structures, and protein functions. A plethora of sequences exist in protein databases with incomplete domain knowledge. Hence this research explores automated bioinformatics tools for faster protein domain analysis. Automated tool chains described in this dissertation generate new protein domain models thus enabling more effective genome-wide protein domain analysis. To validate the new tool chains, the Shewanella oneidensis and Escherichia coli genomes were processed, resulting in a new peptide domain database, detection of poor domain models, and identification of likely new domains. The automated tool chains will require months or years to model a small genome when executing on a single workstation. Therefore the dissertation investigates approaches with grid computing and parallel processing to significantly accelerate these bioinformatics tool chains

Planificación consciente de la contención y gestión de recursos en arquitecturas multicore emergentes

Tesis inédita de la Universidad Complutense de Madrid, Facultad de Informática, Departamento de Arquitectura de Computadores y Automática, leída el 14-12-2021Chip multicore processors (CMPs) currently constitute the architecture of choice for mosto general-pùrpose computing systems, and they will likely continue to be dominant in the near future. Advances in technology have enabled to pack an increasing number of cores and bigger caches on the same chip. Nevertheless, contention on shared resources on CMPs -present since the advent of these architectures- still poses a big challenge. Cores in a CMP typically share a last-level cache (LLC) and other memory-related resources with the remaining cores, such as a DRAM controller and an interconnection network. This causes that co-running applications may intensively compete with each other for these shared resources, leading to substantial and uneven performance degradation...Los procesadores multinúcleo o CMPs (Chip Multicore Processors) son actualmente la arquitectura más usada por la mayoría de sistemas de computación de propósito general, y muy probablemente se mantendrían en esa posición dominante en el futuro cercano. Los avances tecnológicos han permitido integrar progresivamente en el mismo chip más cores y aumentar los tamaños de los distintos niveles de cache. No obstante, la contención de recursos compartidos en CMPs {presente desde la aparición de estas arquitecturas{ todavía representa un reto importante que afrontar. Los cores en un CMP comparten en la mayor parte de los diseños una cache de último nivel o LLC (Last-Level Cache) y otros recursos, como el controlador de DRAM o una red de interconexión. La existencia de dichos recursos compartidos provoca en ocasiones que cuando se ejecutan dos o más aplicaciones simultáneamente en el sistema, se produzca una degradación sustancial y potencialmente desigual del rendimiento entre aplicaciones...Fac. de InformáticaTRUEunpu