Biomolecular electrostatics simulation with a parallel FMM-based BEM, using up to 512 GPUs

Rio Yokota, Jaydeep P. Bardhan, Matthew G. Knepley, L. A. Barba, Tsuyoshi Hamada
Department of Mechanical Engineering, Boston University, Boston MA 02215
arXiv:1007.4591v2 [cs.CE] (17 Oct 2010)


   title={Determination of the Decay Exponent in Mechanically Stirred Isotropic Turbulence},

   author={Perot, J.B. and Bonnet, L. and Ambrosio, L.A. and Zamboni-Rached, M. and Hern{‘a}ndez-Figueroa, H.E. and Shvedov, V. and Fadeyeva, T. and Shostka, N. and Alexeyev, C. and Volyar, A. and others},

   journal={Arxiv preprint arXiv:1007.5043},



We present teraflop-scale simulations of biomolecular electrostatics enabled by the combination of algorithmic and hardware acceleration. The algorithmic acceleration is achieved with the fast multipole method (FMM) in conjunction with a boundary element method (BEM) formulation of the continuum electrostatic model, as well as the BIBEE approximation to BEM. The hardware acceleration is achieved through graphics processors, GPUs. We demonstrate the power of our algorithms and software for the calculation of the electrostatic interactions between biological molecules in solution. The applications demonstrated include the electrostatics of protein-drug binding and several multi-million atom systems consisting of hundreds to thousands of copies of lysozyme molecules. The parallel scalability of the software was studied in a cluster at the Nagasaki Advanced Computing Center, using 128 nodes, each with 4 GPUs. Delicate tuning has resulted in a strong scaling with parallel efficiency of 0.5 for 512 GPUs. For the largest application run, with over 20 million atoms and one billion unknowns required only one minute on 512 GPUs. We are currently adapting our BEM software to solve the linearized Poisson-Boltzmann equation for dilute ionic solutions, and it is also designed to be flexible enough to be extended for a variety of integral equation problems, ranging from Poisson problems to Helmholtz problems in electromagnetics and acoustics to high Reynolds number flow. The software is open-source and available through the PetFMM library of fast multipole method applications.
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