A Performance/Cost Evaluation for a GPU-Based Drug Discovery Application on Volunteer Computing

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 unit...

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Bibliographic Details
Published in:BioMed research international 2014-01, Vol.2014 (2014), p.1-8
Main Authors: Guerrero, Ginés D., Imbernón, Baldomero, Pérez-Sánchez, Horacio, Sanz, Francisco, García, José M., Cecilia, José M.
Format: Article
Language:English
Subjects:
Binding sites
Bioinformatics
Computational Biology - methods
Computer Graphics
Computing Methodologies
Cost control
Databases, Factual
Distributed processing
Drug discovery
Drug Discovery - methods
Energy consumption
Graphics coprocessors
High performance computing
Humans
Infrastructure
Ligands
Proteins
Simulation
Software
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Summary: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.
ISSN:2314-6133
2314-6141
DOI:10.1155/2014/474219