Rodica Ceterchi, Miguel Angel Martinez-del-Amor, Mario J. Perez-Jimenez
We introduce P systems with dynamic communication graphs which simulate the functioning of the CUDA architecture when solving the parallel reduction problem.
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Ali Maroosi, Ravie Chandren Muniyandi, Elankovan A. Sundararajan, Abdullah Mohd Zin
Membrane computing is a theoretical model of computation that inspired from the structure and functioning of cells. Membrane computing models naturally have parallel structure. Most of the simulations of membrane computing have been done in a serial way on a machine with a central processing unit (CPU). This has neglected the advantage of parallelism in […]
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Miguel A. Martinez-del-Amor, Ignacio Perez-Hurtado, Mario J. Perez-Jimenez, Jose M. Cecilia, Gines D. Guerrero, Jose M. Garcia
Software development for cellular computing is growing up yielding new applications. In this paper, we describe a simulator for the class of recognizer P systems with active membranes, which exploits the massively parallel nature of P systems computations by using GPUs (Graphics Processing Units). The newest generation of GPUs provide a massively parallel framework to […]
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Miguel A. Martinez-del-Amor, Jesus Perez-Carrasco, Mario J. Perez-Jimenez
In order to provide efficient software tools to deal with large membrane systems, high-throughput simulators are required. Parallel computing platforms are good candidates, since they are capable of partially implementing the inherently parallel nature of the model. In this concern, today GPUs (Graphics Processing Unit) are considered as highly parallel processors, and they are being […]
Salah Zaher, Amr Badr, Ibrahim Farag, Tarek AbdElmaged
Simulators are limited by the available resources on the GPU as well as the CPU. Simulation of P systems with active membrane using GPUs is a new concept in the development of applications for membrane computing. P systems are an alternative approach to extract all performance available on GPUs due to its parallel nature. In […]
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Francis George C. Cabarle, Henry N. Adorna, Miguel A. Martinez-Del-Amor, Mario J. Perez-Jimenez
In this work we present further extensions and improvements of a Spiking Neural P system (for short, SNP systems) simulator on graphics processing units (for short, GPUs). Using previous results on representing SNP system computations using linear algebra, we analyze and implement a computation simulation algorithm on the GPU. A two-level parallelism is introduced for […]
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Richelle Ann B. Juayong, Francis George C. Cabarle, Henry N. Adorna, Miguel A. Martinez-del-Amor
In this report, we present our initial proposal on simulating computations on a restricted variant of Evolution-Communication P system with energy (ECPe system) which will then be implemented in Graphics Processing Units (GPUs). This ECPe systems variant prohibits the use of antiport rules for communication. Several possible levels of parallelizations for simulating ECPe systems computations […]
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Francis Cabarle, Henry Adorna, Miguel A. Martinez-del-Amor
In this paper we present a Spiking Neural P system (SNP system) simulator based on graphics processing units (GPUs). In particular we implement the simulator using NVIDIA CUDA enabled GPUs. The massively parallel architecture of current GPUs is very suitable for the maximally parallel computations of SNP systems. We simulate a wider variety of SNP […]
Jose Cecilia, Jose Garcia, Gines Guerrero, Miguel Martinez-del-Amor, Mario Perez-Jimenez, Manuel Ujaldon
Membrane Computing is a discipline aiming to abstract formal computing models, called membrane systems or P systems, from the structure and functioning of the living cells as well as from the cooperation of cells in tissues, organs, and other higher order structures. This framework provides polynomial time solutions to NP-complete problems by trading space for […]
Francis Cabarle, Henry Adorna, Miguel A. Martinez-del-Amor
We present in this paper our work regarding simulating a type of P system known as a spiking neural P system (SNP system) using graphics processing units (GPUs). GPUs, because of their architectural optimization for parallel computations, are well-suited for highly parallelizable problems. Due to the advent of general purpose GPU computing in recent years, […]
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Narayan Ganesan, Michela Taufer, Sandeep Patel
In this short paper we present a GPU code for MD simulations of large membrane regions in the NVT and NVE ensembles with explicit solvent. We give an overview of the code and present preliminary performance results.
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Jose M. Cecilia, Jose M. Garcia, Gines D. Guerrero, Miguel A. Martinez-del-Amor, Ignacio Perez-Hurtado, Mario J. Perez-Jimenez
P systems are inherently parallel and non-deterministic theoretical computing devices defined inside the field of Membrane Computing. Many P system simulators have been presented in this area, but they are inefficient since they can not handle the parallelism of these devices. Nowadays, we are witnessing the consolidation of the GPUs as a parallel framework to […]
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