ARVO-CL: The OpenCL version of the ARVO package — An efficient tool for computing the accessible surface area and the excluded volume of proteins via analytical equations

Abstract

Introduction of Graphical Processing Units (GPUs) and computing using GPUs in recent years opened possibilities for simple parallelization of programs. In this update, we present the modernized version of program ARVO [J. Busa, J. Dzurina, E. Hayryan, S. Hayryan, C.-K. Hu, J. Plavka, I. Pokorný, J. Skivanek, M.-C. Wu, Comput. Phys. Comm. 165 (2005) 59]. The whole package has been rewritten in the C language andparallelized usingOpenCL. Somenew tricks have been added to the algorithm in order to savememory much needed for efficient usage of graphical cards. A new tool called ‘input_structure’ was added for conversion of pdb files into files suitable for work with the C and OpenCL version of ARVO. New version program summary Program title: ARVO-CL Catalog identifier: ADUL_v2_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/ADUL_v2_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 11834 No. of bytes in distributed program, including test data, etc.: 182528 Distribution format: tar.gz Programming language: C, OpenCL. Computer: PC Pentium; SPP’2000. Operating system: All OpenCL capable systems. Has the code been vectorized or parallelized?: Parallelized using GPUs. A serial version (non GPU) is also included in the package.