PMCGPU Wiki
Parallel simulators for Membrane Computing on the GPU
Status: Beta
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TABLE OF CONTENTS
NOTE: This project is planned to migrate to github soon
I. Description
Membrane Computing is a research area (within Natural Computing) that aims to provide computing devices abstracted from the functioning and structure of living cells. These devices are called P systems.
PMCGPU (Parallel simulators for Membrane Computing on the GPU) is a project aimed to bring together all the researchers working on the development of parallel simulators for P systems, specially those using GPGPU (e.g. CUDA, OpenCL, etc). Other parallel platforms are also welcome (multicore and manycore, FPGAs, etc). These bio-inspired computing devices are massively parallel and non-deterministic. For this reason, the creation of efficient simulators is a challenge for the scientific community of Membrane Computing.
This project has been initiated by the Research Group on Natural Computing (Department of Computer Science and Artificial Intelligence, University of Seville). PMCGPU was born inside the P-Lingua project, of the same research group.
PMCGPU is a GNU project, so all the applications developed within it are released under the GPLv3 license.
If you want to participate in this project, just send a message to the administrator (mdelamor). You will need a sourceforge user.
II. Available simulators
The following simulators are available under the PMCGPU project:
- Parallel simulation of P systems with active membranes (PCUDA)
- Parallel simulation of a family of P systems with active membranes solving SAT in linear time (PCUDASAT)
- Parallel simulation of a family of tissue-like P systems with cell division solving SAT in linear time (TSPCUDASAT)
- Parallel simulation of Population Dynamics P systems (ABCD-GPU)
- Parallel simulation of Enzymatic Numerical P systems (ENPS-GPU)
III. Related simulators
The following simulators are related with the PMCGPU project, but still out of its scope:
IV. Related theses and publications
This software project is purely academic, so the developers are mainly graduate and undergraduate students. This section lists some of the Ph.D. and master theses that have contributed to the PMCGPU project. For research publications, please visit each simulator wiki webpage to see the related papers.
A survey publication
The following reference is a publication which surveys the work developed in the PMCGPU project, and related research lines:
- M.A. Martínez-del-Amor, M. García-Quismondo, L.F. Macías-Ramos, L. Valencia-Cabrera, A. Riscos-Núñez, M.J. Pérez-Jiménez. Simulating P systems on GPU devices: a survey. Fundamenta Informaticae, 136, 3 (2015), 269-284.
Ph.D. Theses
- Modelling and Simulation of Real-Life Phenomena in Membrane Computing. Manuel García-Quismondo. 2014, University of Seville. Advised by Mario J. Pérez-Jiménez and Miguel Á. Martínez-del-Amor.
- Accelerating Membrane Systems Simulators using High Performance Computing with GPU. Miguel Á. Martínez-del-Amor. 2013, University of Seville. Advised by Mario J. Pérez-Jiménez and Ignacio Pérez-Hurtado.
- The GPU as a Processor for Novel Computation: Analysis and Contributions. José M. Cecilia. 2011, University of Murcia. Advised by J.M. García and M. Ujaldón.
- Desarrollo y aplicaciones de un entorno de programación para Computación Celular: P-Lingua. Ignacio Pérez-Hurtado. 2010, University of Seville. Advised by Mario J. Pérez-Jiménez and Agustín Riscos-Núñez.
Master Theses
- Simulation of probabilistic P systems on GPUs. Adolfo Gastalver-Rubio. 2012, University of Seville. Advised by Miguel Á. Martínez-del-Amor and Ignacio Pérez-Hurtado.
- Acceleration of membrane system simulations on solutions to SAT using GPUs. Jesús Pérez-Carrasco. 2012, University of Seville, Advised by Miguel Á. Martínez-del-Amor.
- Análisis y diseño de un simulador de sistems P con membranas activas en CUDA. Ginés D. Guerrero. 2009. University of Murcia. Advised by José M. García and José M. Cecilia.
