Population Dynamics P Systems on CUDA

TitlePopulation Dynamics P Systems on CUDA
Publication TypeJournal Papers
Year of Publication2012
AuthorsMartínez-del-Amor, M. A., Pérez-Hurtado I., Gastalver-Rubio A., Elster A. C., & Pérez-Jiménez M. J.
EditorsGilbert, D., & Heiner M.
Journal TitleLecture Notes in Bioinformatics
ISBN Number978-3-642-33635-5
PublisherSpringer Berlin / Heidelberg
EditionComputational Methods in Systems Biology

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.

KeywordsCUDA, Ecological Modeling, GPU Computing, Membrane computing, Parallel Simulation, Population Dynamics