106 Int. J. Computational Science and Engineering, Vol. 9, Nos. 1/2, 2014 Population-based harmony search using GPU applied to protein structure prediction Marlon H. Scalabrin* Electrical Engineering and Industrial Informatics Post-Graduate Programme, Federal University of Technology – Paran´ a (UTFPR), Av. 7 de setembro, 3165 – 80230-901 Curitiba, Brazil Fax: +55-41-3310-4683 E-mail: marlonscalabrin@yahoo.com.br *Corresponding author Rafael S. Parpinelli Department of Computer Science, Santa Catarina State University (UDESC), Campus Universit´ ario Prof. Avelino Marcante s/n, 89223-100 Joinville (SC), Brazil Fax: +55-47-4009-7940 E-mail: parpinelli@joinville.udesc.br Cesar M.V. Ben ´ ıtez and Heitor S. Lopes Electrical Engineering and Industrial Informatics Post-Graduate Programme, Federal University of Technology – Paran´ a (UTFPR), Av. 7 de setembro, 3165 – 80230-901 Curitiba, Brazil Fax: +55-41-3310-4683 E-mail: cesarvargasb@gmail.com E-mail: hslopes@utfpr.edu.br Abstract: This work presents a new evolutionary algorithm based on the standard harmony search strategy, called population-based harmony search (PBHS). Also, this work provides a parallelisation method for the proposed PBHS by using graphical processing units (GPU), allowing multiple function evaluations at the same time. Experiments were done using a benchmark of a hard scientific problem: protein structure prediction with the AB-2D off-lattice model. The performance and the solution quality were evaluated and compared using four implementations: two concerning the standard HS, one running in CPU and another running in GPU, and two implementations concerning the PBHS, also running in CPU and in GPU. Results show that the quality of solutions and speed-ups achieved by the PBHS is significantly better than the HS. Keywords: population-based metaheuristics; harmony search; protein structure prediction; PSP; graphics processing units; GPU; compute unified device architecture; CUDA; evolutionary algorithms. Reference to this paper should be made as follows: Scalabrin, M.H., Parpinelli, R.S., Ben ´ ıtez, C.M.V. and Lopes, H.S. (2014) ‘Population-based harmony search using GPU applied to protein structure prediction’, Int. J. Computational Science and Engineering, Vol. 9, Nos. 1/2, pp.106–118. Biographical notes: Marlon H. Scalabrin graduated in Computer Engineering at Ponta Grossa State University in 2007 and received his MSc from the Federal University of Technology Paran´ a in 2012. His research interests are evolutionary computation and parallel computing. Rafael S. Parpinelli graduated in Computer Science by the Maring´ a State University (1999) and received his MSc from the Federal University of Technology Paran´ a in 2001. Since 2004, he has been an Assistant Professor at the Santa Catarina State University in Joinville, Brazil. His research interests are evolutionary computation and bioinformatics. Cesar M.V. Ben ´ ıtez graduated in Electronic Engineering and received his MSc from the Federal University of Technology Paran´ a in 2007 and 2010, respectively. His research interests are evolutionary computation, bioinformatics and reconfigurable computing. Copyright © 2014 Inderscience Enterprises Ltd.