Communication Dans Un Congrès Année : 2025

Protein database search using Processing-in-Memory architecture

Résumé

This paper describes the implementation of alignment search within a protein sequence database using the Processing-in-Memory concept. The PiM memory component used is a specialized DRAM developed by UPMEM. The study examines two main aspects: the acceleration achieved compared to a traditional multi-core server and the energy savings enabled by this architecture. These evaluations highlight the potential of PiM technology for enhancing the performance and efficiency of computationally intensive bioinformatics applications.

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Dates et versions

hal-05375748 , version 1 (21-11-2025)

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Charly Airault, Charles Deltel, Florestan de Moor, Erwan Drezen, Meven Mognol, et al.. Protein database search using Processing-in-Memory architecture. IPDPS 2025 - IEEE International Parallel and Distributed Processing Symposium, IPDPS, Jun 2025, Milano, Italy. pp.939-948, ⟨10.1109/IPDPSW66978.2025.00146⟩. ⟨hal-05375748⟩
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