Implementation on CUDA of the Smoothing Problem with Tissue-Like P Systems

2011 ◽  
Vol 2 (3) ◽  
pp. 25-34 ◽  
Author(s):  
Francisco Peña-Cantillana ◽  
Daniel Díaz-Pernil ◽  
Hepzibah A. Christinal ◽  
Miguel A. Gutiérrez-Naranjo
Keyword(s):  
Membrane Computing ◽  
Parallel Implementation ◽  
P Systems ◽  
Compute Unified Device Architecture ◽  
Digital Imagery ◽  
Graphics Processors ◽  
Novel Device ◽  
Device Architecture ◽  
Formal Framework

Smoothing is often used in Digital Imagery for improving the quality of an image by reducing its level of noise. This paper presents a parallel implementation of an algorithm for smoothing 2D images in the framework of Membrane Computing. The chosen formal framework has been tissue-like P systems. The algorithm has been implemented by using a novel device architecture called CUDA (Compute Unified Device Architecture) which allows the parallel NVIDIA Graphics Processors Units (GPUs) to solve many complex computational problems. Some examples are presented and compared; research lines for the future are also discussed.

Implementation on CUDA of the Smoothing Problem with Tissue-Like P Systems

2014 ◽  
pp. 184-193 ◽  
Author(s):  
Francisco Peña-Cantillana ◽  
Daniel Díaz-Pernil ◽  
Hepzibah A. Christinal ◽  
Miguel A. Gutiérrez-Naranjo
Keyword(s):  
Parallel Implementation ◽  
P Systems ◽  
Compute Unified Device Architecture ◽  
Digital Imagery ◽  
Graphics Processors ◽  
Novel Device ◽  
Device Architecture ◽  
Formal Framework ◽  
2D Images

Smoothing is often used in Digital Imagery for improving the quality of an image by reducing its level of noise. This paper presents a parallel implementation of an algorithm for smoothing 2D images in the framework of Membrane Computing. The chosen formal framework has been tissue-like P systems. The algorithm has been implemented by using a novel device architecture called CUDA (Compute Unified Device Architecture) which allows the parallel NVIDIA Graphics Processors Units (GPUs) to solve many complex computational problems. Some examples are presented and compared; research lines for the future are also discussed.

scholarly journals Dictionary Search and Update by P Systems with String-Objects and Active Membranes

2009 ◽  
Vol 4 (3) ◽  
pp. 206
Author(s):  
Artiom Alhazov ◽  
Svetlana Cojocaru ◽  
Ludmila Malahova ◽  
Yurii Rogozhin
Keyword(s):  
Membrane Computing ◽  
P Systems ◽  
Membrane Systems ◽  
Prefix Tree ◽  
Active Membranes ◽  
Formal Framework

Membrane computing is a formal framework of distributed parallel com- puting. In this paper we implement the work with the prefix tree by P systems with strings and active membranes. We present the algorithms of searching in a dictionary and updating it implemented as membrane systems. The systems are constructed as reusable modules, so they are suitable for using as sub-algorithms for solving more complicated problems.

HARNESSING THE POWER OF IDLE GPUS FOR ACCELERATION OF BIOLOGICAL SEQUENCE ALIGNMENT

2009 ◽  
Vol 19 (04) ◽  
pp. 513-533 ◽  
Author(s):  
FUMIHIKO INO ◽  
YUKI KOTANI ◽  
YUMA MUNEKAWA ◽  
KENICHI HAGIHARA
Keyword(s):  
Sequence Alignment ◽  
Graphics Processing Unit ◽  
Parallel Implementation ◽  
Processing Unit ◽  
Compute Unified Device Architecture ◽  
Grid System ◽  
Biological Sequence ◽  
Device Architecture ◽  
Linear Speedup ◽  
Graphics Processing

This paper presents a parallel system capable of accelerating biological sequence alignment on the graphics processing unit (GPU) grid. The GPU grid in this paper is a desktop grid system that utilizes idle GPUs and CPUs in the office and home. Our parallel implementation employs a master-worker paradigm to accelerate an OpenGL-based algorithm that runs on a single GPU. We integrate this implementation into a screensaver-based grid system that detects idle resources on which the alignment code can run. We also show some experimental results comparing our implementation with three different implementations running on a single GPU, a single CPU, or multiple CPUs. As a result, we find that a single non-dedicated GPU can provide us almost the same throughput as two dedicated CPUs in our laboratory environment, where GPU-equipped machines are ordinarily used to develop GPU applications. In a dedicated environment, the GPU-accelerated code achieves five times higher throughput than the CPU-based code. Furthermore, a linear speedup of 30.7X is observed on a 32-node cluster of dedicated GPUs. We also implement a compute unified device architecture (CUDA) based algorithm to demonstrate further acceleration.

EXPLOITING THE MEMORY HIERARCHY OF MULTICORE SYSTEMS FOR PARALLEL TRIANGULATION REFINEMENT

2012 ◽  
Vol 22 (03) ◽  
pp. 1250007 ◽  
Author(s):  
PEDRO RODRÍGUEZ ◽  
MARÍA CECILIA RIVARA ◽  
ISAAC D. SCHERSON
Keyword(s):  
Parallel Implementation ◽  
Memory Hierarchy ◽  
Random Selection ◽  
Multicore Systems ◽  
Algorithm Performance ◽  
Bisection Algorithm ◽  
Improve Algorithm ◽  
Triangulation Refinement ◽  
Selection Of

A novel parallelization of the Lepp-bisection algorithm for triangulation refinement on multicore systems is presented. Randomization and wise use of the memory hierarchy are shown to highly improve algorithm performance. Given a list of selected triangles to be refined, random selection of candidates together with pre-fetching of Lepp-submeshes lead to a scalable and efficient multi-core parallel implementation. The quality of the refinement is shown to be preserved.

scholarly journals Impact of Membrane Computing and P Systems in ISI WoS. Celebrating the 65th Birthday of Gheorghe Păun

2015 ◽  
Vol 10 (5) ◽  
Author(s):  
Ioan DZITAC
Keyword(s):  
Computer Science ◽  
Membrane Computing ◽  
Research Area ◽  
P Systems ◽  
65Th Birthday ◽  
Membrane Systems ◽  
Journal Paper ◽  
Technical Report ◽  
The Impact

Membrane Computing is a branch of Computer Science initiated by<br />Gheorghe Păun in 1998, in a technical report of Turku Centre for Computer Science<br />published as a journal paper ("Computing with Membranes" in Journal of Computer<br />and System Sciences) in 2000. Membrane systems, as Gheorghe Păun called the<br />models he has introduced, are known nowadays as "P Systems" (with the letter P<br />coming from the initial of the name of this research area "father").<br />This note is an overview of the impact in ISI WoS of Gheorghe Păun’s works, focused<br />on Membrane Computing and P Systems field, on the occasion of his 65th birthday<br />anniversary.

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