Parallel Molecular Dynamics on the Connection Machines

Abstract Abstract:We have demonstrated using vectorized parallel Lennard-Jones fluid program that vectorizing general-purpose parallel molecular package for simulating biomolecules which currently runs on the Connection Machine CM-5 using CMMD message passing would offer a significant improvement over 4 non-vectorized version. Our results indicate that the Lennard-Jones fluid program written in C*/CMNID is five times faster than the same program written in C/CMMD.

Dynamic Parallel Method for Eulerian Method of Elastoplastic Hydrodynamics in Three Dimension

Eulerian method is a main numerical simulation method in elastoplastic hydrodynamics, which is suitable for the problems with multi-component and large deformation. As the feature of the problems to be simulated, such as detonation and penetration, the dynamic parallel method （DPM） is designed to adjust the computational domain dynamically to get better load balance. Dynamic parallel method can be separated into two parts： one is division of initial computational domain and location of the data, the other is expansion of the computational domain and adjustment of the data location. DPM program can greatly shorten computational time and be preferable in simulating actual problems. The speedup of the DPM program is linear in parallel test. DPM can be popularized to parallel program of other multi-component high dimension Eulerian methods naturally.

Parallelism and Optimization of Numerical Ocean Forecasting Model

According to the characteristics of Chinese marginal seas, the Marginal Sea Model of China(MSMC) has been developed independently in China. Because the model requires long simulation time, as a routine forecasting model, the parallelism of MSMC becomes necessary to be introduced to improve the performance of it. However, some methods used in MSMC, such as Successive Over Relaxation(SOR) algorithm, are not suitable for parallelism. In this paper, methods are developedto solve the parallel problem of the SOR algorithm following the steps as below. First, based on a 3D computing grid system, an automatic data partition method is implemented to dynamically divide the computing grid according to computing resources. Next, based on the characteristics of the numerical forecasting model, a parallel method is designed to solve the parallel problem of the SOR algorithm. Lastly, a communication optimization method is provided to avoid the cost of communication. In the communication optimization method, the non-blocking communication of Message Passing Interface(MPI) is used to implement the parallelism of MSMC with complex physical equations, and the process of communication is overlapped with the computations for improving the performance of parallel MSMC. The experiments show that the parallel MSMC runs 97.2 times faster than the serial MSMC, and root mean square error between the parallel MSMC and the serial MSMC is less than 0.01 for a 30-day simulation(172800 time steps), which meets the requirements of timeliness and accuracy for numerical ocean forecasting products.

Parallel Dispatch:A New Paradigm of Electrical Power System Dispatch

Modern power systems are evolving into sociotechnical systems with massive complexity, whose real-time operation and dispatch go beyond human capability. Thus,the need for developing and applying new intelligent power system dispatch tools are of great practical significance. In this paper, we introduce the overall business model of power system dispatch, the top level design approach of an intelligent dispatch system, and the parallel intelligent technology with its dispatch applications. We expect that a new dispatch paradigm,namely the parallel dispatch, can be established by incorporating various intelligent technologies, especially the parallel intelligent technology, to enable secure operation of complex power grids,extend system operators' capabilities, suggest optimal dispatch strategies, and to provide decision-making recommendations according to power system operational goals.

Large-scale high performance computation on 3D explosion and shockproblems

Explosion and shock often involve large deformation, interface treatment between multi-material, and strong discontinuity. The Eulerian method has advantages for solving these problems. In parallel computation of the Eulerian method, the physical quantities of the computaional cells do not change before the disturbance reaches to these cells. Computational efficiency is low when using fixed partition because of load imbalance. To solve this problem, a dynamic parallel method in which the computation domain expands with disturbance is used. The dynamic parallel program is designed based on the generally used message passing interface model. The numerical test of dynamic parallel program agrees well with that of the original parallel program, also agrees with the actual situation.

A STUDY ON THE STRUCTURAL TRANSITION OF A SINGLE POLYMER CHAIN BY PARALLEL TEMPERING MOLECULAR DYNAMICS SIMULATION

The structural transition of a single polymer chain with chain length of 100,200 and 300 beads was investigated by parallel tempering MD simulation.Our simulation results can capture the structural change from random coil to orientationally ordered structure with decreasing temperature.The clear transition was observed on the curves of radius of gyration and global orientational order parameter P as the function of temperature,which demonstrated structural formation of a single polymer chain.The linear relationships between three components of square radius of gyration R_（gx）~2,R_（gx）~2,R_（gz）~2 and global orientational order P can be obtained under the structurally transformational process.The slope of the linear relationship between x（or y-axis） component R_（gx）~2（or R_（gy）~2） and P is negative,while that of RL as the function of P is positive.The absolute value of slope is proportional to the chain length.Once the single polymer chain takes the random coil or ordered configuration,the linear relationship is invalid.The conformational change was also analyzed on microscopic scale.The polymer chain can be treated as the construction of rigid stems connecting by flexible loops.The deviation from exponentially decreased behavior of stem length distribution becomes prominent,indicating a stiffening of the chain arises leading to more and more segments ending up in the trans state with decreasing temperature.The stem length N_（tr） is about 21 bonds indicating the polymer chain is ordered with the specific fold length.So,the simulation results,which show the prototype of a liquid-crystalline polymer chain,are helpful to understand the crystallization process of crystalline polymers.

Investigation into improving the efficiency and accuracy of CFD/DEM simulations

The Euler-Lagrange approach combined with a discrete element method has frequently been applied to elucidate the hydrodynamic behavior of dense fluid-solid flows in fluidized beds. In this work, the efficiency and accuracy of this model are investigated. Parameter studies are performed; in these studies, the stiffness coefficient, the fluid time step and the processor number are varied under conditions with different numbers of particles and different particle diameters. The obtained results are compared with measurements to derive the optimum parameters for CFD/DEM simulations. The results suggest that the application of higher stiffness coefficients slightly improves the simulation accuracy. However, the average computing time increases exponentially. At larger fluid time steps, the results show that the average computation time is independent of the applied fluid time step whereas the simulation accuracy decreases greatly with increasing the fluid time step. The use of smaller time steps leads to negligible improvements in the simulation accuracy but results in an exponential rise in the average computing time. The parallelization accelerates the DEM simulations if the critical number for the domain decomposition is not reached. Above this number, the performance is no longer proportional to the number of processors. The critical number for the domain decomposition depends on the number of particles. An increase in solid contents results in a shift of the critical decomposition number to higher numbers of CPUs.