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Parallel and distributed computing models on a graphics processing unit to accelerate simulation of membrane systems
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DOI：10.1016/j.simpat.2014.05.005.png)
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Abstract
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Membrane systems are parallel distributed computing models that are used in a wide variety of areas. Use of a sequential machine to simulate membrane systems loses the advantage of parallelism in Membrane Computing. In this paper, an innovative classification algorithm based on a weighted network is introduced. Two new algorithms have been proposed for simulating membrane systems models on a Graphics Processing Unit (GPU). Communication and synchronization between threads and thread blocks in a CPU are time-consuming processes. In previous studies, dependent objects were assigned to different threads. This increases the need for communication between threads, and as a result, performance decreases. In previous studies, dependent membranes have also been assigned to different thread blocks, requiring inter-block communications and decreasing performance. The speedup of the proposed algorithm on a CPU that classifies dependent objects using a sequential approach, for example with 512 objects per membrane, was 82x, while for the previous approach (Algorithm 1), it was 8.2x. For a membrane system with high dependency among membranes, the speedup of the second proposed algorithm (Algorithm 3) was 12 x, while for the previous approach (Algorithm 1) and the first proposed algorithm (Algorithm 2) that assign each membrane to one thread block, it was 1.8x. (C) 2014 Elsevier B.V. All rights reserved.
Keywords:
Membrane Computing
Graphics processing unit
Membrane systems
Distributed computing
Parallel processing
Weighted network
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