GPU Scheduler for De Novo Genome Assembly with Multiple MPI Processes

• Published in: arXiv.org 2023-10
• Main Authors: Li, Minhao, Wang, Siyu, Guanghao Wei
• Format: Article
• Language: English
• Subjects: Algorithms; Assembly; Distributed memory; Performance enhancement
• ISSN: 2331-8422

\(\textit{De Novo}\) Genome assembly is one of the most important tasks in computational biology. ELBA is the state-of-the-art distributed-memory parallel algorithm for overlap detection and layout simplification steps of \(\textit{De Novo}\) genome assembly but exists a performance bottleneck in pairwise alignment. In this work, we proposed 3 GPU schedulers for ELBA to accommodate multiple MPI processes and multiple GPUs. The GPU schedulers enable multiple MPI processes to perform computation on GPUs in a round-robin fashion. Both strong and weak scaling experiments show that 3 schedulers are able to significantly improve the performance of baseline while there is a trade-off between parallelism and GPU scheduler overhead. For the best performance implementation, the one-to-one scheduler achieves \(\sim\)7-8\(\times\) speed-up using 25 MPI processes compared with the baseline vanilla ELBA GPU scheduler.