TCB Publications - Abstract

John E. Stone, Jan Saam, David J. Hardy, Kirby L. Vandivort, Wen-mei W. Hwu, and Klaus Schulten. High performance computation and interactive display of molecular orbitals on GPUs and multi-core CPUs. In Proceedings of the 2nd Workshop on General-Purpose Processing on Graphics Processing Units, ACM International Conference Proceeding Series, volume 383, pp. 9-18, New York, NY, USA, 2009. ACM.

STON2009 The visualization of molecular orbitals (MOs) is important for analyzing the results of quantum chemistry simulations. The functions describing the MOs are computed on a three-dimensional lattice, and the resulting data can then be used for plotting isocontours or isosurfaces for visualization as well as for other types of analyses. Existing software packages that render MOs perform calculations on the CPU and require runtimes of tens to hundreds of seconds depending on the complexity of the molecular system.

We present novel data-parallel algorithms for computing lattices of MOs on modern graphics processing units (GPUs) and multi-core CPUs. The fastest GPU algorithm achieves up to a 125-fold speedup over an optimized CPU implementation running on one CPU core. We also demonstrate possible benefits of dynamic GPU kernel generation and just-in-time compilation for MO calculation. We have implemented these algorithms within the popular molecular visualization program VMD, which can now produce high quality MO renderings for large systems in less than a second, and achieves the first-ever interactive animations of quantum chemistry simulation trajectories using only on-the-fly calculation.

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