Title :
Task-parallel global optimization with application to protein folding
Author :
Voglis, C. ; Hadjidoukas, P.E. ; Dimakopoulos, V.V. ; Lagaris, I.E. ; Papageorgiou, D.G.
Author_Institution :
Dept. of Comput. Sci., Univ. of Ioannina, Ioannina, Greece
Abstract :
This paper presents a software framework for high performance numerical global optimization. At the core, a run time library implements a programming environment for irregular and adaptive task-based parallelism. Building on this, we extract and exploit the multilevel parallelism of a global optimization application that is based on numerical differentiation and Newton-based local optimizations. Our framework is used in the efficient parallelization of a real application case that concerns the protein folding problem. The experimental evaluation presents performance results of our software system on a multicore cluster.
Keywords :
biology computing; differentiation; multiprocessing systems; optimisation; parallel programming; programming environments; proteins; Newton-based local optimizations; adaptive task-based parallelism; experimental evaluation; global optimization application; high performance numerical global optimization; irregular task-based parallelism; multicore cluster; multilevel parallelism; numerical differentiation; parallelization; programming environment; protein folding problem; run time library; software framework; software system; task-parallel global optimization; Approximation algorithms; Approximation methods; Multicore processing; Newton method; Optimization; Parallel processing; Proteins; cluster programming; global optimization; numerical differentiation; protein folding; task parallelism;
Conference_Titel :
High Performance Computing and Simulation (HPCS), 2011 International Conference on
Conference_Location :
Istanbul
Print_ISBN :
978-1-61284-380-3
DOI :
10.1109/HPCSim.2011.5999823
