Towards high performance computing for molecular structure prediction using IBM Cell Broadband Engine - an implementation perspe

Background: RNA structure prediction problem is a computationally complex task, especially with pseudo-knots. The problem is well-studied in existing literature and predominantly uses highly coupled Dynamic Programming (DP) solutions. The problem scale and complexity become embarrassingly humungous to handle as sequence size increases. This makes the case for parallelization. Parallelization can be achieved by way of networked platforms (clusters, grids, etc) as well as using modern day multi-core chips. Methods: In this paper, we exploit the parallelism capabilities of the IBM Cell Broadband Engine to parallelize an existing Dynamic Programming (DP) algorithm for RNA secondary structure prediction. We design three different implementation strategies that exploit the inherent data, code and/or hybrid parallelism, referred to as C-Par, D-Par and H-Par, and analyze their performances. Our approach attempts to introduce parallelism in critical sections of the algorithm. We ran our experi...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: S. P. T. Krishnan, Sim Sze Liang, Bharadwaj Veeravalli
• Keywords: BMCBI 2010, Cell Broadband Engine, IBM Cell, IBM Cell Broadband