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Molecular Dynamics Simulations of Clathrate Hydrates on Specialised Hardware Platforms
Irish Centre for High-End Computing, Trinity Enterprise Tower, Pearse St., Dublin 2, Ireland
The SEC Strategic Research Cluster and the Centre for Synthesis and Chemical Biology, School of Chemical and Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, Ireland
Scalable Algorithms, Sandia National Laboratories, Albuquerque, NM 87185-1322, USA
Present Address: Research and Development, Curtin University, GPO Box U 1987, Perth, WA 6845, Australia and iVEC, 26 Dick Perry Ave, Kensington WA 6151, Australia
* Author to whom correspondence should be addressed.
Received: 29 June 2012; in revised form: 28 August 2012 / Accepted: 29 August 2012 / Published: 12 September 2012
Abstract: Classical equilibrium molecular dynamics (MD) simulations have been performed to investigate the computational performance of the Simple Point Charge (SPC) and TIP4P water models applied to simulation of methane hydrates, and also of liquid water, on a variety of specialised hardware platforms, in addition to estimation of various equilibrium properties of clathrate hydrates. The FPGA-based accelerator MD-GRAPE 3 was used to accelerate substantially the computation of non-bonded forces, while GPU-based platforms were also used in conjunction with CUDA-enabled versions of the LAMMPS MD software packages to reduce computational time dramatically. The dependence of molecular system size and scaling with number of processors was also investigated. Considering performance relative to power consumption, it is seen that GPU-based computing is quite attractive.
Keywords: hydrate; GPU; FPGA; molecular dynamics
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Varini, N.; English, N.J.; Trott, C.R. Molecular Dynamics Simulations of Clathrate Hydrates on Specialised Hardware Platforms. Energies 2012, 5, 3526-3533.
Varini N, English NJ, Trott CR. Molecular Dynamics Simulations of Clathrate Hydrates on Specialised Hardware Platforms. Energies. 2012; 5(9):3526-3533.
Varini, Nicola; English, Niall J.; Trott, Christian R. 2012. "Molecular Dynamics Simulations of Clathrate Hydrates on Specialised Hardware Platforms." Energies 5, no. 9: 3526-3533.