{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/gpu-scheduler-for-de-novo-genome-assembly","title":"GPU Scheduler for De Novo Genome Assembly with Multiple MPI Processes","arxiv_id":"2309.07270","date":"2023-09-13","proceeding":null,"authors":["Minhao Li","Siyu Wang","Guanghao Wei"],"abstract":"$\\textit{De Novo}$ 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.","url_abs":"https://arxiv.org/abs/2309.07270v2","url_pdf":"https://arxiv.org/pdf/2309.07270v2.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"links_only","authors_date_abstract":"arXiv metadata, CC0 1.0 (https://info.arxiv.org/help/license), from the Kaggle arXiv metadata snapshot of 2026-09-12"},"code_links":[{"paper_slug":"gpu-scheduler-for-de-novo-genome-assembly","repo_url":"https://github.com/garywei944/ELBA","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"none","reach":null}],"tasks":[],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"syntology_url":null,"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}