On the scalability of multi-criteria protein structure comparison in the grid

Authors:
Gianluigi Folino;Azhar Ali Shah;Natalio Krasnogor
Affiliations:
Institute of High Performance Computing and Networking, Italian National Research Council, Cosenza, Italy;School of Computer Science, University of Nottingham, UK;School of Computer Science, University of Nottingham, UK
Venue:
Euro-Par 2010 Proceedings of the 2010 conference on Parallel processing
Year:
2010

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Abstract

Multi-Criteria Protein Structure Comparison (MC-PSC) is one of the Grand Challenge Applications (GCAs) in the field of structural proteomics. The solution of the MC-PSC grand challenge requires the use of distributed algorithms, architectures and environments. This paper is aimed at the analysis of the scalability of our newly developed distributed algorithm for MC-PSC in the grid environment. The scalability in the grid environment indicates the capacity of the distributed algorithm to effectively utilize an increasing number of processors across multiple sites. The results of the experiments conducted on the UK's National Grid Service (NGS) infrastructure are reported in terms of speedup, efficiency and cross-site communication overhead.