A framework for high-throughput sequence alignment using real processing-in-memory systems

Safaa Diab, Amir Nassereldine, Mohammed Alser, Juan Gómez-Luna, Onur Mutlu, Izzat El Hajj

Abstract: Sequence alignment is a memory bound computation whose performance in modern systems is limited by the memory bandwidth bottleneck. Processing-in-memory (PIM) architectures alleviate this bottleneck by providing the memory with computing competencies. We propose Alignment-in-Memory (AIM), a framework for high-throughput sequence alignment using PIM, and evaluate it on UPMEM, the first publicly available general-purpose programmable PIM system.