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Course: CS 596, Fall 2008
School: USC
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Assignment CSCI596 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 number of processors) is assigned a subsystem in the range [pLx, (p+1)Lx] of the total system length PLx. Each subsystem of length Lx is discretized into Nx mesh points...

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Assignment CSCI596 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 number of processors) is assigned a subsystem in the range [pLx, (p+1)Lx] of the total system length PLx. Each subsystem of length Lx is discretized into Nx mesh points of interval x = Lx/Nx. In addition to properly setting up an MPI program (e.g., MPI initializationMPI_Init() and finalizationMPI_Finalize(), and finding out the rankMPI_Comm_rank() and the total number of processesMPI_Comm_size(), etc.), the following changes are required in qd1.c for the parallelization: 1. In functions init_prop() and init_wavefn(), the global position must be used to calculate the potential energy function and initialize the wave function, respectively. For process p, the global position of the i-th mesh point is x = ix + pLx. 2. In init_wavefn(), the squared wave function values must be first summed over all the local mesh points for each process, and then MPI_Allreduce() must be used to calculate the global sum. Also use MPI_Allreduce()to calculate the global kinetic and potential energies, ekin and epot, in calc_energy(). 3. Rewrite periodic_bc() such that the wave function values at the subsystem boundaries, psi[0][] and psi[NX+1][], of process are p, copied from the lower and upper neighbor processors, plw = (p1+P) mod P and pup = (p+1) mod P, respectively. Use the 3-stage message-passing procedure(i) message buffering to compose a message in array dbuf[], (ii) message send (of dbuf[])/receive (of dbufr[]), and (iii) message storing by copying from dbufr[] to the destination arrayas in the function atom_copy() in the parallel molecular dynamics program pmd.c. (Assignment) 1. Submit the source code of your MPI program. 2. Run the resulting parallel program on 4 processors with Nx = 128, and submit the plot of the kinetic, potential and total energies as a function of simulated (not wall-clock) time. For the run, use the following input parameters: LX = 12.5, DT = 1.0e-3, NSTEP = 8000, NECAL = 10; X0 = 12.5, S0 = 3.0, E0 = 5.0, BH = 5.0, BW = 1.0, EH = 50.0. The...

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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
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Minimal Complex Analysis Complex function: A mapping from a complex variable z = x + iy (i = f(z) C.&quot;1) to a complex numberDifferentiation: A complex function f(z) at z is differentiable if the quantity ! f (z + &quot;z) # f (z)&quot;zconverges to a
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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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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
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OpenMP ProgrammingAiichiro NakanoCollaboratory for Advanced Computing &amp; Simulations Department of Computer Science Department of Physics &amp; Astronomy Department of Chemical Engineering &amp; Materials Science University of Southern California Email: ana
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Hybrid MPI+OpenMP Parallel MDAiichiro NakanoCollaboratory for Advanced Computing &amp; Simulations Department of Computer Science Department of Physics &amp; Astronomy Department of Chemical Engineering &amp; Materials Science University of Southern California
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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
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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
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Computer Physics CommunicationsELSEVIER Computer Physics Communications 83 (1994) 181196Massively parallel algorithms for computational nanoelectronics based on quantum molecular dynamicsAiichiro Nakano, Priya Vashishta, Rajiv K. KaliaConcurrent
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Comput. Methods Appl. Mech. Engrg. 196 (2007) 908922 www.elsevier.com/locate/cmaGeneralized mathematical homogenization of atomistic media at nite temperatures in three dimensionsJacob Fish *, Wen Chen, Renge LiRensselaer Polytechnic Institute, T