Population dynamics p systems on CUDA

  • Authors:

  • Miguel A. Martínez-Del-Amor;Ignacio Pérez-Hurtado;Adolfo Gastalver-Rubio;Anne C. Elster;Mario J. Pérez-Jiménez

  • Affiliations:

  • Research Group on Natural Computing, Department of Computer Science and Artificial Intelligence, University of Seville, Sevilla, Spain;Research Group on Natural Computing, Department of Computer Science and Artificial Intelligence, University of Seville, Sevilla, Spain;Research Group on Natural Computing, Department of Computer Science and Artificial Intelligence, University of Seville, Sevilla, Spain;HPC-Lab, Department of Computer and Information Science, Norwegian University of Science and Technology, Trondheim, Norway;Research Group on Natural Computing, Department of Computer Science and Artificial Intelligence, University of Seville, Sevilla, Spain

  • Venue:
  • CMSB'12 Proceedings of the 10th international conference on Computational Methods in Systems Biology
  • Year:
  • 2012

Quantified Score

Hi-index 0.00

Visualization

Abstract

Population Dynamics P systems (PDP systems, in short) provide a new formal bio-inspired modeling framework, which has been successfully used by ecologists. These models are validated using software tools against actual measurements. The goal is to use P systems simulations to adopt a priori management strategies for real ecosystems. Software for PDP systems is still in an early stage. The simulation of PDP systems is both computationally and data intensive for large models. Therefore, the development of efficient simulators is needed for this field. In this paper, we introduce a novel simulator for PDP systems accelerated by the use of the computational power of GPUs. We discuss the implementation of each part of the simulator, and show how to achieve up to a 7x speedup on a NVIDA Tesla C1060 compared to an optimized multicore version on a Intel 4-core i5 Xeon for large systems. Other results and testing methodologies are also included.