2026-05-28T13:21:38Zhttps://riuma.uma.es/rest/oai/request

oai:riuma.uma.es:10630/294102026-02-03T11:03:47Zcom_10630_2254col_10630_37953

00925njm 22002777a 4500 dc Herruzo-Ruiz, José Manuel author González-Navarro, Sonia author Ibáñez, Pablo author Viñals, Victor author Alastruey-Benedé, Jesús author Óscar, Plata author 2020-07-01 FM-index is a compact data structure suitable for fast matches of short reads to large reference genomes. The matching algorithm using this index exhibits irregular memory access patterns that cause frequent cache misses, resulting in a memory bound problem. This paper analyzes different FM-index versions presented in the literature, focusing on those computing aspects related to the data access. As a result of the analysis, we propose a new organization of FM-index that minimizes the demand for memory bandwidth, allowing a great improvement of performance on processors with high-bandwidth memory, such as the second-generation Intel Xeon Phi (Knights Landing, or KNL), integrating ultra high-bandwidth stacked memory technology. As the roofline model shows, our implementation reaches 95 percent of the peak random access bandwidth limit when executed on the KNL and almost all of the available bandwidth when executed on other Intel Xeon architectures with conventional DDR memory. In addition, the obtained throughput in KNL is much higher than the results reported for GPUs in the literature. https://hdl.handle.net/10630/29410 https://doi.org/10.1109/TCBB.2018.2884701 Bioinformática Accelerating Sequence Alignments Based on FM-Index Using the Intel KNL Processor