{"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/an-asynchronous-distributed-memory-parallel","title":"An Asynchronous Distributed-Memory Parallel Algorithm for k-mer Counting","arxiv_id":"2505.04431","date":"2025-05-07","proceeding":null,"authors":["Souvadra Hati","Akihiro Hayashi","Richard Vuduc"],"abstract":"This paper describes a new asynchronous algorithm and implementation for the problem of k-mer counting (KC), which concerns quantifying the frequency of length k substrings in a DNA sequence. This operation is common to many computational biology workloads and can take up to 77% of the total runtime of de novo genome assembly. The performance and scalability of the current state-of-the-art distributed-memory KC algorithm are hampered by multiple rounds of Many-To-Many collectives. Therefore, we develop an asynchronous algorithm (DAKC) that uses fine-grained, asynchronous messages to obviate most of this global communication while utilizing network bandwidth efficiently via custom message aggregation protocols. DAKC can perform strong scaling up to 256 nodes (512 sockets / 6K cores) and can count k-mers up to 9x faster than the state-of-the-art distributed-memory algorithm, and up to 100x faster than the shared-memory alternative. We also provide an analytical model to understand the hardware resource utilization of our asynchronous KC algorithm and provide insights on the performance.","url_abs":"https://arxiv.org/abs/2505.04431v1","url_pdf":"https://arxiv.org/pdf/2505.04431v1.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":"an-asynchronous-distributed-memory-parallel","repo_url":"https://github.com/souvadra/dakc","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}