P systems simulations on massively parallel architectures

TitleP systems simulations on massively parallel architectures
Publication TypeConference Contributions
Year of Publication2010
AuthorsCecilia, J. M., García J. M., Guerrero G. D., Martínez-del-Amor M. A., Pérez-Jiménez M. J., & Ujaldón M.
Conference NameThird International Workshop on Parallel Architectures and Bioinspired Algorithms
ISBN Number978-84-693-6141-2
Place PublishedVienna, Austria
Date PublishedSeptember 2010

Membrane Computing is an emergent research area studying the behaviour of living cells to define bio-inspired computing devices, also called P systems. Such devices provide polynomial time solutions to NP-complete problems by trading time for space. The efficient simulation of P systems poses challenges in three different aspects: an intrinsic massively parallelism of P systems, an exponential computational workspace, and a non-intensive floating point nature. In this paper, we analyze the simulation of a family of recognizer P systems with active membranes that solves the Satisfiability (SAT) problem in linear time on three different architectures: a shared memory system, a distributed memory system, and a set of Graphics Processing Units (GPUs). For an efficient handling of the exponential workspace created by the P systems computation, we enable different data policies on those architectures to increase memory bandwidth and exploit data locality through tiling. Parallelism inherent to the target P system is also managed on each architecture to demonstrate that GPUs offer a valid alternative for high-performance computing at a considerably lower cost: Considering the largest problem size we were able to run on the three parallel platforms involving four processors, execution times were 20049.70 ms. using OpenMP on the shared memory multiprocessor, 4954.03 ms. using MPI on the distributed memory multiprocessor and 565.56 ms. using CUDA in our four GPUs, which results in speed factors of 35.44x and 8.75x, respectively.


Third International Workshop on Parallel Architectures and Bioinspired Algorithms (WPABA' 10) in conjuntion with the Nineteenth International Conference on Parallel Architectures and Compulations Techniques (PACT' 10)