CAVE-CL: An OpenCL version of the package for detection and quantitative analysis of internal cavities in a system of overlapping balls: Application to proteins

Here we present the revised and newly rewritten version of our earlier published CAVE package (Buša et al., 2010) which was originally written in FORTRAN. The package has been rewritten in C language, the algorithm has been parallelized and implemented using OpenCL. This makes the program convenient to run on platforms with Graphical Processing Units (GPUs). Improvements include also some modifications/optimizations of the original algorithm. A considerable improvement in the performance of the code has been achieved. A new tool called input_structure has been added which helps the user to make the data input and conversion more easier and universal. New version program summary Program Title: CAVE-CL, CAVE C Catalogue identifier: AEHC_v2_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/aehc_v2_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: Standard CPC license, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 32646 No. of bytes in distributed program, including test data, etc.: 444248 Distribution format: tar.gz Programming language: C, C++, OpenCL. Computer: PC with GPU. Operating system: OpenCL compatible systems. Has the code been vectorized or parallelized?: Parallelized using GPUs. A revised serial version (non GPU) is included in the package as well.