10854

Accelerating Dissipative Particle Dynamics Simulations on GPUs: Algorithms, Numerics and Applications

Yu-Hang Tang, George Em Karniadakis
Division of Applied Mathematics, Brown University, Providence, Rhode Island, USA
arXiv:1311.0402 [cs.DC], (2 Nov 2013)
@article{2013arXiv1311.0402A,

   author={Tang, Yu-Hang and Karniadakis, George Em},

   title={Accelerating Dissipative Particle Dynamics Simulations on GPUs: Algorithms, Numerics and Applications},

   journal={ArXiv e-prints},

   archivePrefix={"arXiv"},

   eprint={1311.0402},

   primaryClass={"cs.DC"},

   keywords={Computer Science – Distributed, Parallel, and Cluster Computing, Physics – Computational Physics},

   year={2013},

   month={nov}

}

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We present a scalable dissipative particle dynamics simulation code, fully implemented on the Graphics Processing Units (GPUs) using a hybrid CUDA/MPI programming model, which achieves 10-30 times speedup on a single GPU over 16 CPU cores and almost linear weak scaling across a thousand nodes. A unified framework is developed within which the efficient generation of the neighbor list and maintaining particle data locality are addressed. Our algorithm generates strictly ordered neighbor lists in parallel, while the construction is deterministic and makes no use of atomic operations or sorting. Such neighbor list leads to optimal data loading efficiency when combined with a two-level particle reordering scheme. A faster in situ generation scheme for Gaussian random numbers is proposed using precomputed binary signatures. We designed custom transcendental functions that are fast and accurate for evaluating the pairwise interaction. The correctness and accuracy of the code is verified through a set of test cases simulating Poiseuille flow and spontaneous vesicle formation. Computer benchmarks demonstrate the speedup of our implementation over the CPU implementation as well as strong and weak scalability. A large-scale simulation of spontaneous vesicle formation consisting of 128 million particles was conducted to further illustrate the practicality of our code in real-world applications.
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