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USC - CS - 596
Parallel Quantum Dynamics Aiichiro NakanoCollaboratory for Advanced Computing & Simulations Department of Computer Science Department of Physics & Astronomy Department of Chemical Engineering & Materials Science University of Southern California Em
USC - CS - 596
Hybrid MPI+OpenMP Parallel MD Aiichiro NakanoCollaboratory for Advanced Computing & Simulations Department of Computer Science Department of Physics & Astronomy Department of Chemical Engineering & Materials Science University of Southern Californi
USC - CS - 596
Optimizing Molecular Dynamics Aiichiro NakanoCollaboratory for Advanced Computing & Simulations Department of Computer Science Department of Physics & Astronomy Department of Chemical Engineering & Materials Science University of Southern Californi
USC - CS - 596
Advanced Topics in Parallel Molecular Dynamics Aiichiro NakanoCollaboratory for Advanced Computing & Simulations Department of Computer Science Department of Physics & Astronomy Department of Chemical Engineering & Materials Science University of S
USC - CS - 596
Divide-&-Conquer Parallelism Aiichiro NakanoCollaboratory for Advanced Computing & Simulations Department of Computer Science Department of Physics & Astronomy Department of Chemical Engineering & Materials Science University of Southern California
USC - CS - 596
CSCI596: Scientic Computing & VisualizationSummaryAiichiro NakanoCollaboratory for Advanced Computing & Simulations Department of Computer Science Department of Physics & Astronomy Department of Chemical Engineering & Materials Science University o
USC - CS - 596
Least Square Fit of a LineProblem: Given a set of N pairs of numbers, {(xi, yi) | i = 1, ., N}, what is the best linear fit, y = ax + b,Nin the sense that it minimizes the square error, S = # ( axi + b " yi ) .i=12Answer: S is a quadratic fu
USC - CS - 596
How to Install OpenGLWINDOWSInstall your favorite integrated development environment (IDE). This tutorial assumes that you have Microsoft Visual Studio installed on your machine. 1. Install OpenGL OpenGL software runtime is included as part of oper
USC - CS - 596
Scientific Virtual-Reality ApplicationsThis lecture note describes interactive three-dimensional visualization of scientific datasets, using the earliest immersive and interactive visualization platforms, CAVE and ImmersaDesk, and the associated CAV
USC - CS - 596
Massive Dataset VisualizationAiichiro Nakano Collaboratory for Advanced Computing & Simulations Dept. of Computer Science, Dept. of Physics & Astronomy, Dept. of Chemical Engineering & Materials Science University of Southern California Email:
USC - CS - 596
Ashish Sharma sharmaa@usc.edu Collaboratory for Advanced Computing and Simulations Dept. of Computer Science Aiichiro Nakano anakano@usc.edu Dept. of Computer Science Rajiv K. Kalia rkalia@usc.edu Dept. of Physics & Astronomy Priya Vashishta priyav@u
USC - CS - 596
A Spatially Decomposed Parallel Visualization AlgorithmInternational Journal of Computational Science 1992-6669 (Print) 1992-6677 (Online) Global Information Publisher 2007, Vol. 1, No. 4, 407-421ParaViz: A Spatially Decomposed Parallel Visualiza
USC - CS - 653
International Journal of Parallel Programming, Vol. 29, No. 3, 2001Improving Memory Hierarchy Performance for Irregular Applications Using Data and Computation Reorderings 1John Mellor-Crummey, 2, 4 David Whalley, 3 and Ken Kennedy 2Received Octo
USC - CS - 653
124IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING,VOL. 13,NO. 1, JANUARY/FEBRUARY 2001Analysis of the Clustering Properties of the Hilbert Space-Filling CurveBongki Moon, H.V. Jagadish, Christos Faloutsos, Member, IEEE, and Joel H. Salt
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Cache-Oblivious AlgorithmsEXTENDED ABSTRACT SUBMITTED FOR PUBLICATION.Matteo Frigo Charles E. Leiserson Harald Prokop Sridhar Ramachandran MIT Laboratory for Computer Science, 545 Technology Square, Cambridge, MA 021393 0 8 ( B8 & 8 3 & 2
USC - CS - 596
CSCI596 (Scientific Computing and Visualization) Assignment 1Molecular Dynamics Due: September 15 (Mon), 2008, at the class The purpose of this assignment is to familiarize yourself with the simple molecular dynamics (MD) program, md.c (and its linke
USC - CS - 596
CSCI596 Assignment 2Message Passing Interface Due: September 24 (Wed), 2008, at the class In this assignment, you will write your own global summation program (equivalent to using MPI_Send and MPI_Recv. Your program should run on P = 2l processors (l
USC - CS - 596
CSCI596 Assignment 3Parallel Computation of Due: October 1 (Wed), 2008 Part I: Programming Write a message passing interface (MPI) program, global_pi.c, to compute the value of based on the lecture note on Parallel Computation of Pi and using the g
USC - CS - 596
CSCI596 Assignment 4Parallel Molecular Dynamics Due: October 8 (Wed), 2008 The purpose of this assignment is to get familiar with the message-passing scheme used in the parallel molecular dynamics (MD) program, pmd.c, and asynchronous messages in the
USC - CS - 596
CSCI596 Assignment 5: Molecular Dynamics Animation Due: October 22 (Wed), 2008 Combine md.c and atomv.c to write a C/OpenGL program that animates molecular dynamics (MD) simulation in real time. (Follow the lecture note on Visualizing Molecular Dynam
USC - CS - 596
CSCI596 Assignment 6: Parallel Quantum Dynamics Due: November 3 (Mon), 2008 (at the class) Parallelize the one-dimensional quantum dynamics (QD) simulation program qd1.c, using MPI. Use spatial decomposition, so that processor p [0, P-1] (P is the n
USC - CS - 596
CSCI596 (Scientific Computing and Visualization) Assignment 7 Hybrid MPI+OpenMP Parallel Molecular Dynamics Due: November 12 (Wed), 2008 (at the class) 1. Write a hybrid MPI+OpenMP parallel molecular dynamics (MD) program (name it hmd.c), starting fr
USC - CS - 596
CSCI596 (Scientific Computing and Visualization) Final Project Anything Related to What You Have Learned in the Class Due: December 17 (Wed), 2008 Submit the following project by Wednesday, December 17. In addition, at 3:30-4:50pm on Wednesday, Decem
USC - CS - 596
Guidelines for the Final Project I. II. Programming Critical review (>2-3 pages) Dont repeat what the paper says. 1. 2. 3. 4. * III. Problem: Whats the problem? Method: How to solve it? Results: Bottom line? So what? Critique: Flaw? Improvement (how
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84Computer Physics Communications 63 (1991) 8494 North-HollandVisualizing quantum scattering on the CM-2 supercomputerJohn L. Richardson1Received 2 February 1990 Thinking Machines Corporation, 245 First Street, Cambridge, MA 02142-1214, USAWe
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CSCI653: High Performance Computing & SimulationsAiichiro NakanoCollaboratory for Advanced Computing & Simulations Department of Computer Science Department of Physics & Astronomy Department of Chemical Engineering & Materials Science University of
USC - CS - 653
Molecular Dynamics I: PrinciplesBasics of the molecular-dynamics (MD) method1-3 are described, along with corresponding data structures in program, md.c.Newtons Second Law of MotionTRAJECTORY, COORDINATE, AND ACCELERATION Physical system = a set
USC - CS - 653
Minimal Complex Analysis Complex function: A mapping from a complex variable z = x + iy (i = f(z) C."1) to a complex numberDifferentiation: A complex function f(z) at z is differentiable if the quantity ! f (z + "z) # f (z)"zconverges to a
USC - CS - 653
JOURNALOF COMPUTATIONALPHYSICS73, 315-348 (1987)A Fast Algorithmfor ParticleANDSimulations*L. GREENCARDV. ROKHLINDepartment of Computer Science, Yale Lnipersiry, New Haven, Connecticut 06520 Received June 10. 1986; revised February
USC - CS - 653
ELSEYIER2s -/.-I@Computer Physics Communications Computer Physics Communications ( 1997)59-69 104Parallel multilevel preconditioned conjugate-gradient approach to variable-charge molecular dynamicsAiichiro Nakano Depurtment of Computer Scienc
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Computer Physics Communications 153 (2003) 445461 www.elsevier.com/locate/cpcScalable and portable implementation of the fast multipole method on parallel computers Shuji Ogata a , Timothy J. Campbell b , Rajiv K. Kalia c,d , Aiichiro Nakano c,d,
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Reversiblemultipletime scale moleculardynamicsM. Tuckermar?) G. J. Martynaand B. J. BerneDepartment of Chemistry, Columbia University, New York, New York 10027 Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvani
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Computer Physics CommunicationsELSEVIERComputer Physics Communications 83 (1994) 197214Multiresolution molecular dynamics algorithm for realistic materials modeling on parallel computersAiichiro Nakano, Rajiv K. Kalia, Priya VashishtaConcurrent
USC - CS - 653
Message Passing Interface (MPI) ProgrammingMPI (Message Passing Interface) is a standard message passing system that enables us to write and run applications on parallel computers. In 1992, MPI Forum was formed to develop a portable message passing
USC - CS - 653
OpenMP ProgrammingAiichiro NakanoCollaboratory for Advanced Computing & Simulations Department of Computer Science Department of Physics & Astronomy Department of Chemical Engineering & Materials Science University of Southern California Email: ana
USC - CS - 653
Hybrid MPI+OpenMP Parallel MDAiichiro NakanoCollaboratory for Advanced Computing & Simulations Department of Computer Science Department of Physics & Astronomy Department of Chemical Engineering & Materials Science University of Southern California
USC - CS - 653
Parallel Molecular DynamicsThis chapter explains the example parallel MD program, pmd.c, in detail.Spatial Decomposition Spatial decomposition: The physical system to be simulated is partitioned into subsystems of equal volume. Processors in a pa
USC - CS - 653
Parallel Molecular DynamicsAiichiro NakanoCollaboratory for Advanced Computing & Simulations Department of Computer Science Department of Physics & Astronomy Department of Chemical Engineering & Materials Science University of Southern California E
USC - CS - 653
Scalability Metrics for Parallel Molecular DynamicsParallel EfficiencyWe define the efficiency of a parallel program running on P processors to solve a problem of size W. Let T(W, P) be the execution time of this parallel program. Speed of the prog
USC - CS - 653
Anton, a Special-Purpose Machine for Molecular Dynamics SimulationDavid E. Shaw, Martin M. Deneroff, Ron O. Dror, Jeffrey S. Kuskin, Richard H. Larson, John K. Salmon, Cliff Young, Brannon Batson, Kevin J. Bowers, Jack C. Chao, Michael P. Eastwood,
USC - CS - 653
A Fast, Scalable Method for the Parallel Evaluation of Distance-Limited Pairwise Particle InteractionsDAVID E. SHAWD. E. Shaw Research and Development, LLC and Center for Computational Biology and Bioinformatics, Columbia University, 120 W. 45th S
USC - CS - 653
Divide-and-Conquer Parallelization ParadigmDivide-and-Conquer Simulation Algorithms Divide-and-conquer (DC) algorithms: Recursively partition a problem into subprogram of roughly equal size. If subprogram can be solved independently, there is a pos
USC - CS - 653
Divide-&-Conquer ParallelismAiichiro NakanoCollaboratory for Advanced Computing & Simulations Department of Computer Science Department of Physics & Astronomy Department of Chemical Engineering & Materials Science University of Southern California
USC - CS - 653
Computational Materials Science 38 (2007) 642652 www.elsevier.com/locate/commatsciA divide-and-conquer/cellular-decomposition framework for million-to-billion atom simulations of chemical reactionsAiichiro Nakano a,*, Rajiv K. Kalia a, Ken-ichi No
USC - CS - 653
DE NOVO ULTRASCALE ATOMISTIC SIMULATIONS ON HIGH-END PARALLEL SUPERCOMPUTERSAiichiro Nakano Rajiv K. Kalia1 Ken-ichi Nomura1 Ashish Sharma1, 2 Priya Vashishta1 Fuyuki Shimojo1,3 4 Adri C. T. van Duin 4 William A. Goddard, III 5 Rupak Biswas Deepak S
USC - CS - 653
Load BalancingAiichiro NakanoCollaboratory for Advanced Computing & Simulations Department of Computer Science Department of Physics & Astronomy Department of Chemical Engineering & Materials Science University of Southern California Email: anakano
USC - CS - 653
Lanczos Method for EigensystemsAiichiro NakanoCollaboratory for Advanced Computing & Simulations Department of Computer Science Department of Physics & Astronomy Department of Chemical Engineering & Materials Science University of Southern Californ
USC - CS - 653
Supplementary Derivations for the Lanczos-Algorithm LectureSpectral representation The eigenvalues and eigenvectors satisfyn n$ Aij q (" ) = #" qi(" ) = $ qi(" ) #%&%" , jj=1%=1()(1)where "#$ = 1 ($ = #); 0 ($ % #). Define an orthogona
USC - CS - 653
C3P 913June 1990Performance of Dynamic Load Balancing Algorithms for Unstructured Mesh CalculationsRoy D. WilliamsConcurrent Supercomputing Facility California Institute of Technology Pasadena, CaliforniaAbstract If a nite element mesh has a
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SIAM J. SCI. COMPUT. Vol. 20, No. 1, pp. 359392c 1998 Society for Industrial and Applied MathematicsA FAST AND HIGH QUALITY MULTILEVEL SCHEME FOR PARTITIONING IRREGULAR GRAPHSGEORGE KARYPIS AND VIPIN KUMAR Abstract. Recently, a number of researc
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Applied Numerical Mathematics 52 (2005) 133152www.elsevier.com/locate/apnumNew challenges in dynamic load balancingKaren D. Devine a, , Erik G. Boman a , Robert T. Heaphy a , Bruce A. Hendrickson a , James D. Teresco b,1 , Jamal Faik c , Joseph E
USC - CS - 653
Hypergraph-based Dynamic Load Balancing for Adaptive Scientic ComputationsUmit V. Catalyurek, Erik G. Boman, Karen D. Devine, Doruk Bozda , Robert Heaphy, g and Lee Ann Riesen Ohio State University Sandia National Laboratories Dept. of Biomedical
USC - CS - 653
Optimizing Molecular DynamicsAiichiro NakanoCollaboratory for Advanced Computing & Simulations Department of Computer Science Department of Physics & Astronomy Department of Chemical Engineering & Materials Science University of Southern California
USC - CS - 653
Improving Memory Hierarchy Performance for Irregular Applications*John Mellor-Crummeyt, T Department of Computer Science, MS 132 Rice University 6100 Main Houston, TX 77005 David Whalleyz, Ken Kennedy?Cjohnmc,ken}@cs.rice.edu AbstractThe gap betw
USC - CS - 653
Metrics and Models for Reordering TransformationsMichelle Mills StroutMathematics and Computer Science Division Argonne National Laboratory Argonne, IL 60439 USAPaul D. HovlandMathematics and Computer Science Division Argonne National Laboratory
USC - CS - 653
SIAM REVIEW Vol. 46, No. 1, pp. 345c 2004 Society for Industrial and Applied MathematicsRecursive Blocked Algorithms and Hybrid Data Structures for Dense Matrix Library SoftwareErik Elmroth Fred Gustavson Isak Jonsson Bo K gstrom aAbstract. Ma
USC - CS - 653
Lattice-Boltzmann (LB) Fluid Simulation on a Playstation3 (PS3) ClusterKen-ichi Nomura, Liu Peng & Richard SeymourCollaboratory for Advanced Computing & Simulations Dept. of Computer Science, Dept. of Physics & Astronomy, Dept. of Chemical Engineer
USC - CS - 653
SCOP3A Rough Guide to Scientic Computing On the PlayStation 3Technical Report UT-CS-07-595 Version 0.1by Alfredo Buttari Piotr Luszczek Jakub Kurzak Jack Dongarra George Bosilca Innovative Computing Laboratory University of Tennessee Knoxville Ap
USC - CS - 653
Parallel Lattice Boltzmann Flow Simulation on a Low-cost PlayStation3 ClusterInternational Journal of Computational Science 1992-6669 (Print) 1992-6677 (Online) www.gip.hk/ijcs 2008 Global Information Publisher (H.K) Co., Ltd. All rights reserved.