Computer simulation of liquids
Computer simulation of liquids
LogP: towards a realistic model of parallel computation
PPOPP '93 Proceedings of the fourth ACM SIGPLAN symposium on Principles and practice of parallel programming
Journal of Computational Physics
Fast parallel algorithms for short-range molecular dynamics
Journal of Computational Physics
Performance modeling and evaluation of MPI
Journal of Parallel and Distributed Computing
Balancing load versus decreasing communication: parameterizing the tradeoff
Journal of Parallel and Distributed Computing
Measurement and prediction of communication delays in myrinet networks
Journal of Parallel and Distributed Computing - Special issue on cluster and network-based computing
The Art of Molecular Dynamics Simulation
The Art of Molecular Dynamics Simulation
Fast Measurement of LogP Parameters for Message Passing Platforms
IPDPS '00 Proceedings of the 15 IPDPS 2000 Workshops on Parallel and Distributed Processing
An Evaluation of Current High-Performance Networks
IPDPS '03 Proceedings of the 17th International Symposium on Parallel and Distributed Processing
Modelling and analysis of communication overhead for parallel matrix algorithms
Mathematical and Computer Modelling: An International Journal
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This paper describes the performance of a portable molecular dynamics code running on an eight-node PC cluster. The molecular dynamics code is based on the atom decomposition method for distributing the computation load among the processors and the MPI protocol for managing communications among processors. We discuss the changes made to the serial code with an effort to maintain its readability. We examined the program performance for system sizes of order 10^2 to 10^4 atoms and number of processors varying from 1 to 8, by measuring the total execution time and the corresponding speedup, as well as the communication time for data exchange and the time for the calculation of interatomic forces. Using simple communication and computation load considerations, we propose models in order to explain the observed behaviour and predict the optimal usage of the cluster. It turns out that using few parameters that can be easily measured one can predict quite accurately the optimal usage of small clusters running short range molecular dynamics programs.