GPU-Accelerated Stochastic Simulation of Biochemical Networks

Pilsung KANG  

IEICE TRANSACTIONS on Information and Systems   Vol.E101-D   No.3   pp.786-790
Publication Date: 2018/03/01
Online ISSN: 1745-1361
Type of Manuscript: LETTER
Category: Fundamentals of Information Systems
GPU computing,  parallel programming,  stochastic simulation,  

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We present a GPU (graphics processing unit) accelerated stochastic algorithm implementation for simulating biochemical reaction networks using the latest NVidia architecture. To effectively utilize the massive parallelism offered by the NVidia Pascal hardware, we apply a set of performance tuning methods and guidelines such as exploiting the architecture's memory hierarchy in our algorithm implementation. Based on our experimentation results as well as comparative analysis using CPU-based implementations, we report our initial experiences on the performance of modern GPUs in the context of scientific computing.