Parametrizing multicore architectures for multiple sequence alignment

Sebastian Isaza, Friman Sanchez, Felipe Cabarcas, Alex Ramirez, Georgi Gaydadjiev

Producción científica: Capítulo en Libro/InformeContribución a la conferencia

1 Cita (Scopus)

Resumen

Sequence alignment is one of the fundamental tasks in bioinformatics. Due to the exponential growth of biological data and the computational complexity of the algorithms used, high performance computing systems are required. Although multicore architectures have the potential of exploiting the task-level parallelism found in these workloads, efficiently harnessing systems with hundreds of cores requires deep understanding of the applications and the architecture. When incorporating large numbers of cores, performance scalability will likely saturate shared hardware resources like buses and memories. In this paper we evaluate the performance impact of various configurations of an accelerator-based multicore architecture with the aim of revealing and quantifying the bottlenecks. Then, we compare against a multicore using general-purpose processors and discuss the performance gap. Our target application is ClustalW, one of the most popular programs for Multiple Sequence Alignment. Different input data sets are characterized and we show how they influence performance. Simulation results show that due to the high computation-to-communication ratio and the transfer of data in large chunks, memory latency is well tolerated. However, bandwidth is critical to achieving maximum performance. Using a 32KB cache configuration with 4 banks can capture most of the memory traffic and therefore avoid expensive off-chip transactions. On the other hand, using a hardware queue for the tasks synchronization allows us to handle a large number of cores. Finally, we show that using a simple load balancing strategy, we can increase performance of general-purpose cores by 28%.

Idioma originalInglés estadounidense
Título de la publicación alojadaProceedings of the 8th ACM International Conference on Computing Frontiers, CF'11
DOI
EstadoPublicada - 2011
Publicado de forma externa
Evento8th ACM International Conference on Computing Frontiers, CF'11 - Ischia, Italia
Duración: may. 3 2011may. 5 2011

Serie de la publicación

NombreProceedings of the 8th ACM International Conference on Computing Frontiers, CF'11

Conferencia

Conferencia8th ACM International Conference on Computing Frontiers, CF'11
País/TerritorioItalia
CiudadIschia
Período5/3/115/5/11

Áreas temáticas de ASJC Scopus

  • Teoría computacional y matemáticas
  • Matemáticas aplicadas

Huella

Profundice en los temas de investigación de 'Parametrizing multicore architectures for multiple sequence alignment'. En conjunto forman una huella única.

Citar esto