title: A performance/cost evaluation for a GPU-based drug discovery application on volunteer computing.
abstract: Bioinformatics is an interdisciplinary research field that develops tools for the analysis of large biological databases, and, thus, the use of high performance computing (HPC) platforms is mandatory for the generation of useful biological knowledge. The latest generation of graphics processing units (GPUs) has democratized the use of HPC as they push desktop computers to cluster-level performance. Many applications within this field have been developed to leverage these powerful and low-cost architectures. However, these applications still need to scale to larger GPU-based systems to enable remarkable advances in the fields of healthcare, drug discovery, genome research, etc. The inclusion of GPUs in HPC systems exacerbates power and temperature issues, increasing the total cost of ownership (TCO). This paper explores the benefits of volunteer computing to scale bioinformatics applications as an alternative to own large GPU-based local infrastructures. We use as a benchmark a GPU-based drug discovery application called BINDSURF that their computational requirements go beyond a single desktop machine. Volunteer computing is presented as a cheap and valid HPC system for those bioinformatics applications that need to process huge amounts of data and where the response time is not a critical factor.
authors.affiliation: National Laboratory for High Performance Computing, Center of Mathematical Modeling, University of Chile, 8370456 Santiago, Chile.
authors.forename: Ginés D
authors.initials: GD
authors.lastname: Guerrero
authors.affiliation: Universidad Católica San Antonio de Murcia (UCAM), 30107 Guadalupe, Spain.
authors.forename: Baldomero
authors.initials: B
authors.lastname: Imbernón
authors.affiliation: Universidad Católica San Antonio de Murcia (UCAM), 30107 Guadalupe, Spain.
authors.forename: Horacio
authors.identifier: 0000-0001-6045-0343
authors.initials: H
authors.lastname: Pérez-Sánchez
authors.affiliation: Institute for Biocomputation and Physics of Complex Systems, 50018 Zaragoza, Spain.
authors.forename: Francisco
authors.identifier: 0000-0002-3953-9471
authors.initials: F
authors.lastname: Sanz
authors.affiliation: Computer Engineering Department, University of Murcia, 30100 Murcia, Spain.
authors.forename: José M
authors.initials: JM
authors.lastname: García
authors.affiliation: Universidad Católica San Antonio de Murcia (UCAM), 30107 Guadalupe, Spain.
authors.forename: José M
authors.identifier: 0000-0001-5648-214X
authors.initials: JM
authors.lastname: Cecilia
mesh_terms: D019295:Computational Biology / Q000379:methods*; D003196:Computer Graphics; D003205:Computing Methodologies; D016208:Databases, Factual; D055808:Drug Discovery / Q000379:methods*; D006801:Humans; D012984:Software