Paper Info
Title
Implementation and characterization of protein folding on a desktop computational grid. Is CHARMM a suitable candidate for the United Devices MetaProcessor?
Abstract
CHARMMis a popular molecular dynamics code for computational biology. For many CHARMMapplications such as protein folding, desktop grids could become viable alternatives to clusters of PCs. In this paper, we present a prototype and discuss the viability of a protein folding application with CHARMM on the United Devices MetaProcessor, a platform for widely distributed computing. We identify the algorithmic approach of protein folding as a hybrid search algorithm with best-first, depth-first and breadth-first components and address the issues of task scheduling and fault tolerance. The performance evaluation of our system indicates that the calculation is robust against the heterogeneity of compute nodes and limitedcommunication capabilities typically found in desktop grids. We show that there is an interesting tradeoff between accuracy and task parallelism resulting in optimal work-pool size for a given platform and a given simulation. Surprisingly the platform heterogeneity of a desktop grid positively affects the quality of protein folding simulations. Protein folding calculations with CHARMM turn out to be well suitable for desktop grids like e.g. the United Devices MetaProcessor. Our software system can make a large amount of nearly free compute cycles available to computational biologists.
Year
DOI
Venue
2003
10.1109/IPDPS.2003.1213141
International Parallel and Distributed Processing Symposium/International Parallel Processing Symposium
Keywords
Field
DocType
biology computing,grid computing,molecular dynamics method,proteins,tree searching,wide area networks,CHARMM,United Devices MetaProcessor,algorithmic approach,best-first components,breadth-first components,computational biology,depth-first components,desktop grids,fault tolerance,hybrid search algorithm,molecular dynamics code,nearly free compute cycles,optimal work-pool size,performance evaluation,protein folding application,task parallelism,task scheduling,widely distributed computing
Grid computing,Search algorithm,Scheduling (computing),Task parallelism,Computer science,Parallel computing,Software system,Fault tolerance,Cluster analysis,Grid,Distributed computing
Conference
ISSN
ISBN
Citations 
1530-2075
0-7695-1926-1
4
PageRank 
References 
Authors
0.54
6
4
Name
Order
Citations
PageRank
Uk, B.140.54
Taufer, M.21317.81
Stricker, T.340.54
Giovanni Settanni4283.96