A fast algorithm for particle simulations
Journal of Computational Physics
Solving problems on concurrent processors
Solving problems on concurrent processors
Multilevel matrix multiplication and fast solution of integral equations
Journal of Computational Physics
NAMD2: greater scalability for parallel molecular dynamics
Journal of Computational Physics - Special issue on computational molecular biophysics
Brook for GPUs: stream computing on graphics hardware
ACM SIGGRAPH 2004 Papers
ACM SIGGRAPH 2004 Papers
ClawHMMER: A Streaming HMMer-Search Implementatio
SC '05 Proceedings of the 2005 ACM/IEEE conference on Supercomputing
General purpose molecular dynamics simulations fully implemented on graphics processing units
Journal of Computational Physics
Scalable Parallel Programming with CUDA
Queue - GPU Computing
GPU acceleration of cutoff pair potentials for molecular modeling applications
Proceedings of the 5th conference on Computing frontiers
Initial experiences porting a bioinformatics application to a graphics processor
PCI'05 Proceedings of the 10th Panhellenic conference on Advances in Informatics
Proceedings of 2nd Workshop on General Purpose Processing on Graphics Processing Units
Probing biomolecular machines with graphics processors
Communications of the ACM - A View of Parallel Computing
Probing Biomolecular Machines with Graphics Processors
Queue - Bioscience
Molecular Dynamics Simulations on High-Performance Reconfigurable Computing Systems
ACM Transactions on Reconfigurable Technology and Systems (TRETS)
Optimal Utilization of Heterogeneous Resources for Biomolecular Simulations
Proceedings of the 2010 ACM/IEEE International Conference for High Performance Computing, Networking, Storage and Analysis
Optimizing fine-grained communication in a biomolecular simulation application on Cray XK6
SC '12 Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis
Computational physics on graphics processing units
PARA'12 Proceedings of the 11th international conference on Applied Parallel and Scientific Computing
Recent progress and challenges in exploiting graphics processors in computational fluid dynamics
The Journal of Supercomputing
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Physical and engineering practicalities involved in microprocessor design have resulted in flat performance growth for traditional single-core microprocessors. The urgent need for continuing increases in the performance of scientific applications requires the use of many-core processors and accelerators such as graphics processing units (GPUs). This paper discusses GPU acceleration of the multilevel summation method for computing electrostatic potentials and forces for a system of charged atoms, which is a problem of paramount importance in biomolecular modeling applications. We present and test a new GPU algorithm for the long-range part of the potentials that computes a cutoff pair potential between lattice points, essentially convolving a fixed 3D lattice of ''weights'' over all sub-cubes of a much larger lattice. The implementation exploits the different memory subsystems provided on the GPU to stream optimally sized data sets through the multiprocessors. We demonstrate for the full multilevel summation calculation speedups of up to 26 using a single GPU and 46 using multiple GPUs, enabling the computation of a high-resolution map of the electrostatic potential for a system of 1.5 million atoms in under 12s.