Recent DNA pre-alignment filter designs employ DRAM for storing the reference genome and its associated meta-data. However, DRAM incurs increasingly high energy consumption background and refresh energy as devices scale. To overcome this problem, this paper explores a design with racetrack memory (RTM)--an emerging non-volatile memory that promises higher storage density, faster access latency, and lower energy consumption. Multi-bit storage cells in RTM are inherently sequential and thus require data placement strategies to mitigate the performance and energy impacts of shifting during data accesses. We propose a near-memory pre-alignment filter with a novel data mapping and several shift reduction strategies designed explicitly for RTM. On a set of four input genomes from the 1000 Genome Project, our approach improves performance and energy efficiency by 68% and 52%, respectively, compared to the state of the art proposed DRAM-based architecture.
翻译:DNA前连接过滤器的设计最近采用DRAM来储存参考基因组及其相关元数据。 但是, DRAM的能量消耗背景和作为设备规模的更新能源含量越来越高。 为了解决这一问题,本文件探讨了一种带有种族内存(RTM)的新兴非挥发性内存的设计,这种内存可以保证更高的储存密度、更快的存取时间和较低的能源消耗。RTM中的多位位存储细胞本质上是相继的,因此需要数据放置战略来减轻数据存取期间移动的性能和能源影响。 我们提议了一种近模化的预接过滤器,配有新的数据映射和为RTM专门设计的几种转移削减战略。关于1000个基因组项目的一组四个输入基因组,我们的方法与提议的DRAM结构相比,分别提高了68%和52%的性能和能源效率。