Parametrizing multicore architectures for multiple sequence alignment

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

Research output: Chapter in Book/ReportConference contribution

1 Scopus citations


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%.

Original languageEnglish (US)
Title of host publicationProceedings of the 8th ACM International Conference on Computing Frontiers, CF'11
StatePublished - 2011
Externally publishedYes
Event8th ACM International Conference on Computing Frontiers, CF'11 - Ischia, Italy
Duration: May 3 2011May 5 2011

Publication series

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


Conference8th ACM International Conference on Computing Frontiers, CF'11

All Science Journal Classification (ASJC) codes

  • Computational Theory and Mathematics
  • Applied Mathematics


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