Exploiting hierarchy parallelism for molecular dynamics on a petascale heterogeneous system

[1]  Tao Tang,et al.  Fast parallel cutoff pair interactions for molecular dynamics on heterogeneous systems , 2012 .

[2]  Canqun Yang,et al.  A Fast Parallel Implementation of Molecular Dynamics with the Morse Potential on a Heterogeneous Petascale Supercomputer , 2012, 2012 IEEE 26th International Parallel and Distributed Processing Symposium Workshops & PhD Forum.

[3]  Steven J. Plimpton,et al.  Implementing molecular dynamics on hybrid high performance computers - Particle-particle particle-mesh , 2012, Comput. Phys. Commun..

[4]  Igor V. Morozov,et al.  Molecular dynamics simulations of the relaxation processes in the condensed matter on GPUs , 2011, Comput. Phys. Commun..

[5]  Canqun Yang,et al.  Optimizing Linpack Benchmark on GPU-Accelerated Petascale Supercomputer , 2011, Journal of Computer Science and Technology.

[6]  Kai Lu,et al.  The TianHe-1A Supercomputer: Its Hardware and Software , 2011, Journal of Computer Science and Technology.

[7]  Michela Taufer,et al.  Molecular dynamics simulations of aqueous ions at the liquid–vapor interface accelerated using graphics processors , 2011, J. Comput. Chem..

[8]  Kai Lu,et al.  Adaptive Optimization for Petascale Heterogeneous CPU/GPU Computing , 2010, 2010 IEEE International Conference on Cluster Computing.

[9]  Pradeep Dubey,et al.  Debunking the 100X GPU vs. CPU myth: an evaluation of throughput computing on CPU and GPU , 2010, ISCA.

[10]  John E. Stone,et al.  GPU clusters for high-performance computing , 2009, 2009 IEEE International Conference on Cluster Computing and Workshops.

[11]  Aaftab Munshi,et al.  The OpenCL specification , 2009, 2009 IEEE Hot Chips 21 Symposium (HCS).

[12]  Weiqiang Wang,et al.  A metascalable computing framework for large spatiotemporal-scale atomistic simulations , 2009, 2009 IEEE International Symposium on Parallel & Distributed Processing.

[13]  Vijay S. Pande,et al.  Accelerating molecular dynamic simulation on graphics processing units , 2009, J. Comput. Chem..

[14]  Michela Taufer,et al.  Towards Large-Scale Molecular Dynamics Simulations on Graphics Processors , 2009, BICoB.

[15]  S. Glotzer,et al.  Stability of the double gyroid phase to nanoparticle polydispersity in polymer-tethered nanosphere systems , 2009 .

[16]  Robert Strzodka,et al.  Using GPUs to improve multigrid solver performance on a cluster , 2008, Int. J. Comput. Sci. Eng..

[17]  Alejandro Duran,et al.  Evaluation of OpenMP Task Scheduling Strategies , 2008, IWOMP.

[18]  Klaus Schulten,et al.  GPU acceleration of cutoff pair potentials for molecular modeling applications , 2008, CF '08.

[19]  Joshua A. Anderson,et al.  General purpose molecular dynamics simulations fully implemented on graphics processing units , 2008, J. Comput. Phys..

[20]  Weiguo Liu,et al.  Molecular Dynamics Simulations on Commodity GPUs with CUDA , 2007, HiPC.

[21]  Guangcai Zhang,et al.  Material-point simulation of cavity collapse under shock , 2007, 0706.2521.

[22]  Federico D. Sacerdoti,et al.  Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters , 2006, ACM/IEEE SC 2006 Conference (SC'06).

[23]  Holger Gohlke,et al.  The Amber biomolecular simulation programs , 2005, J. Comput. Chem..

[24]  B. Holian.  Molecular dynamics comes of age for shockwave research , 2004 .

[25]  Herbert H. J. Hum,et al.  Compilation, architectural support, and evaluation of SIMD graphics pipeline programs on a general-purpose CPU , 2003, 2003 12th International Conference on Parallel Architectures and Compilation Techniques.

[26]  Rajiv K. Kalia,et al.  Multimillion atom simulation of materials on parallel computers - Nanopixel, interfacial fracture, nanoindentation, and oxidation , 2001 .

[27]  Arthur F. Voter,et al.  Structural stability and lattice defects in copper: Ab initio , tight-binding, and embedded-atom calculations , 2001 .

[28]  Rohit Chandra,et al.  Parallel programming in openMP , 2000 .

[29]  Bruce Hendrickson,et al.  Dynamic load balancing in computational mechanics , 2000 .

[30]  D. Wolff,et al.  Tabulated potentials in molecular dynamics simulations , 1999 .

[31]  D. Rapaport.  The Art of Molecular Dynamics Simulation , 1997 .

[32]  K. Schulten,et al.  NAMD: a Parallel, Object-Oriented Molecular Dynamics Program , 1996, Int. J. High Perform. Comput. Appl..

[33]  H J Berendsen,et al.  Bio-Molecular Dynamics Comes of Age , 1996, Science.

[34]  K Schulten,et al.  VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.

[35]  Bruce Hendrickson,et al.  A Multi-Level Algorithm For Partitioning Graphs , 1995, Proceedings of the IEEE/ACM SC95 Conference.

[36]  B. Berne,et al.  A new molecular dynamics method combining the reference system propagator algorithm with a fast multipole method for simulating proteins and other complex systems , 1995 .

[37]  Steve Plimpton,et al.  Fast parallel algorithms for short-range molecular dynamics , 1993 .

[38]  J. W. Causey,et al.  Accelerated molecular dynamics simulation with the parallel fast multipole algorithm , 1992 .

[39]  Roscoe Giles,et al.  A parallel scalable approach to short-range molecular dynamics on the CM-5 , 1992, Proceedings Scalable High Performance Computing Conference SHPCC-92..

[40]  M. Karplus,et al.  Molecular dynamics simulations in biology , 1990, Nature.

[41]  M. Karplus,et al.  CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .

[42]  Xuejun Yang,et al.  Tianhe-1A Interconnect and Message-Passing Services , 2012, IEEE Micro.

[43]  David Kofke,et al.  Accelerating Molecular Dynamics Simulations with GPUs , 2008, PDCCS.

[44]  Michael Griebel,et al.  Numerical Simulation in Molecular Dynamics: Numerics, Algorithms, Parallelization, Applications , 2007 .

[45]  Peter S. Lomdahl,et al.  LARGE-SCALE MOLECULAR-DYNAMICS SIMULATION OF 19 BILLION PARTICLES , 2004 .

[46]  Christos Faloutsos,et al.  Analysis of the Clustering Properties of the Hilbert Space-Filling Curve , 2001, IEEE Trans. Knowl. Data Eng..

[47]  William Gropp,et al.  Skjellum using mpi: portable parallel programming with the message-passing interface , 1994 .

[48]  Anthony Skjellum,et al.  Using MPI - portable parallel programming with the message-parsing interface , 1994 .

[49]  Steven J. Plimpton,et al.  Parallel Molecular Dynamics With the Embedded Atom Method , 1992 .