Cluster Molecular Dynamics on Massively Parallel Computers

1992 ◽  
Vol 278 ◽  
Author(s):  
K. M. Nelson ◽  
S. T. Smith ◽  
L. T. Wille
Keyword(s):  
Molecular Dynamics ◽  
Noble Gas ◽  
Equations Of Motion ◽  
Pair Potential ◽  
Parallel Computer ◽  
Massively Parallel ◽  
Massively Parallel Computers ◽  
Gas Clusters ◽  
Element Array ◽  
Small Clusters

AbstractWe report the results of computer simulations of phase transitions in noble-gas clusters. The calculations were performed on a MasPar MP-l massively parallel computer with 8,192 processing elements (PE's). We discuss the efficient implementation of molecular dynamics algorithms for small clusters on this type of architecture. The simulations are based on a classical Lennard-Jones pair potential and follow the temporal evolution of the system by numerically integrating Newton's equations of motion using the Gear algorithm. Because the number of particles is much smaller than the number of PE's, optimal partitioning of the processing element array is an essential and non-trivial task.

IMD: A Software Package for Molecular Dynamics Studies on Parallel Computers

1997 ◽  
Vol 08 (05) ◽  
pp. 1131-1140 ◽  
Author(s):  
J. Stadler ◽  
R. Mikulla ◽  
H.-R. Trebin
Keyword(s):  
Molecular Dynamics ◽  
Software Package ◽  
Large Scale ◽  
Md Simulation ◽  
Parallel Computers ◽  
Massively Parallel ◽  
Massively Parallel Computers ◽  
Communication Scheme ◽  
And Performance ◽  
Dynamics Simulations

We report on implementation and performance of the program IMD, designed for short range molecular dynamics simulations on massively parallel computers. After a short explanation of the cell-based algorithm, its extension to parallel computers as well as two variants of the communication scheme are discussed. We provide performance numbers for simulations of different sizes and compare them with values found in the literature. Finally we describe two applications, namely a very large scale simulation with more than 1.23×109 atoms, to our knowledge the largest published MD simulation up to this day and a simulation of a crack propagating in a two-dimensional quasicrystal.

Molecular dynamics for very large systems on massively parallel computers: The MPSim program

1997 ◽  
Vol 18 (4) ◽  
pp. 501-521 ◽  
Author(s):  
Kian-Tat Lim ◽  
Sharon Brunett ◽  
Mihail Iotov ◽  
Richard B. McClurg ◽  
Nagarajan Vaidehi ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Parallel Computers ◽  
Massively Parallel ◽  
Massively Parallel Computers ◽  
Large Systems

PERFORMANCE EVALUATION OF PRACTICAL PARALLEL COMPUTER MODEL LogPQ

2001 ◽  
Vol 12 (03) ◽  
pp. 325-340
Author(s):  
TAKAYOSHI TOUYAMA ◽  
SUSUMU HORIGUCHI
Keyword(s):  
Matrix Multiplication ◽  
Parallel Computer ◽  
Massively Parallel ◽  
Computation Model ◽  
Computing Power ◽  
Matrix Multiplication Algorithm ◽  
Processing Elements ◽  
Message Size ◽  
Massively Parallel Computers ◽  
Super Computer

The present super computer will be replaced by a massively parallel computer consisting of a large number of processing elements which satisfy the continuous increasing depend for computing power. Practical parallel computing model has been expected to develop efficient parallel algorithms on massively parallel computers. Thus, we have presented a practical parallel computation model LogPQ by taking account of communication queues into the LogP model. This paper addresses the performance of a parallel matrix multiplication algorithm using LogPQ and LogP models. The parallel algorithm is implemented on Cray T3E and the parallel performances are compared with on the old machine CM-5. This shows that the communication network of T3E has superior buffering behavior than CM-5, in which we don't need to prepare extra buffering on T3E. Although, a little effect remains for both of the send and receive bufferings. On the other hand, the effect of message size remains, which shows the necessity of the overhead and gap proportional to the message size.

Ab-Initio Molecular Dynamics of Organic Compounds on a Massively Parallel Computer

1995 ◽  
Vol 408 ◽  
Author(s):  
François Gygi
Keyword(s):  
Experimental Data ◽  
Molecular Dynamics ◽  
Ab Initio ◽  
Molecular Dynamics Simulations ◽  
Organic Compounds ◽  
Organic Molecules ◽  
Curvilinear Coordinates ◽  
Parallel Computer ◽  
Massively Parallel ◽  
Dynamics Simulations

AbstractWe present results of ab-initio electronic structure calculations and molecular dynamics simulations of organic molecules carried out using adaptive curvilinear coordinates, within the local density approximation of density functional theory. This approach allows for an accurate treatment of first-row elements, which makes it particularly suitable for investigations of organic compounds. A recent formulation of this method relies on a real-space approach which combines the advantages of finite-difference methods with the accuracy of adaptive coordinates, and is well suited for implementation on massively parallel computers. We used molecular dynamics simulations to obtain the fully relaxed structures of nitrosyl fluoride (FNO), and of the aromatic heterocycles furan and pyrrole. The equilibrium geometries obtained show excellent agreement with experimental data. The harmonic vibrational frequencies of furan and pyrrole were calculated by diagonalization of their dynamical matrix and are found to agree with experimental data within an rms error of 25 cm-1 and 28 cm-1 for furan and pyrrole respectively. This accuracy is comparable to that attained for smaller organic molecules using elaborate quantum chemistry methods.

scholarly journals The DL_POLY molecular dynamics package

2005 ◽  
Vol 220 (5/6) ◽  
Author(s):  
William Smith ◽  
Ilian T. Todorov ◽  
Maurice Leslie
Keyword(s):  
Molecular Dynamics ◽  
Parallel Computers ◽  
Massively Parallel ◽  
Small Systems ◽  
Molecular Systems ◽  
Classical Molecular Dynamics ◽  
Massively Parallel Computers ◽  
Wide Range ◽  
Single Processor

AbstractThe DL_POLY package provides a set of classical molecular dynamics programs that have application over a wide range of atomic and molecular systems. Written for parallel computers they offer capabilities stretching from small systems consisting of a few hundred atoms running on a single processor, up to systems of several million atoms running on massively parallel computers with thousands of processors. In this article we describe the structure of the programs and some applications.

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