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Enhancing the simulation of P systems for the SAT problem on GPUs

J.M. Cecilia, J.M. Garcia, G.D. Guerrero, M.A. Martinez-Amor, M.J. Perez-Jimenez, M. Ujaldon
Computer Engineering and Technology Department, University of Murcia, Spain
Symposium on Application Accelerators in High Performance Computing, 2010

@article{cecilia2010enhancing,

   title={Enhancing the simulation of P systems for the SAT problem on GPUs},

   author={Cecilia, JM and Garc{i}a, JM and Guerrero, GD and Mart{i}nez-Amor, MA and P{‘e}rez-Jim{‘e}nez, MJ and Ujald{‘o}n, M.},

   booktitle={Application Accelerators in High Performance Computing, 2010 Symposium, Papers},

   year={2010}

}

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GPUs constitute nowadays a solid alternative for high performance computing, and the advent of CUDA/OpenCL allow programmers a friendly model to accelerate a broad range of applications. The way GPUs exploit parallelism differ from multi-core CPUs, which raises new challenges to take advantage of its tremendous computing power. In this respect, P systems or Membrane Systems provide a high-level computational modeling framework that combines the structure and dynamic aspects of biological systems while being inherently parallel and nondeterministic. In this work, we implement on GPUs the simulation for a solution provided by Membrane Computing to solve the Satisfiability (SAT) problem. The overall speed up reaches 100x versus a sequential CPU, with an additional 16x due to CUDA optimizations. A promising scalability is also proven on more sophisticated GPU clusters and/or demanding problem sizes.
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