%0 Journal Article %1 puetz98a %A Pütz, M. %A Kolb, A. %D 1998 %J Comp. Phys. Comm. %K Domain Link Many-body Massively Molecular Partial Short algorithm. cell computers. data decomposition. dynamics. forces. interactions. parallel range replication. %P 145--167 %T Optimization techniques for parallel molecular dynamics using domain decomposition %V 113 %X In this paper we describe the implementation of a new parallelized Molecular Dynamics code for many-particle problems with short-ranged interactions. While the basic algorithms have their foundation in the fairly standard methods of domain decomposition, linked-cell pair search and Verlet pair list, we have developed some refined techniques for optimizing them. The rewards of these optimizations are a up to 45 percent overall improvement in the scalar performance and very good scaling behavior in the number of processors even down to a few hundred particles per processor on a GRAY T3E. The best speedup can be obtained for systems with pair forces only since then the data structures can be organized in a very simple manner. To deal with more complex situations as well, we have developed a partial replicated data scheme which is suitable to simulate many molecules consisting of many simple particles (e.g. polymer chains) for many types of short-range interactions.

@article{puetz98a, abstract = {In this paper we describe the implementation of a new parallelized Molecular Dynamics code for many-particle problems with short-ranged interactions. While the basic algorithms have their foundation in the fairly standard methods of domain decomposition, linked-cell pair search and Verlet pair list, we have developed some refined techniques for optimizing them. The rewards of these optimizations are a up to 45 percent overall improvement in the scalar performance and very good scaling behavior in the number of processors even down to a few hundred particles per processor on a GRAY T3E. The best speedup can be obtained for systems with pair forces only since then the data structures can be organized in a very simple manner. To deal with more complex situations as well, we have developed a partial replicated data scheme which is suitable to simulate many molecules consisting of many simple particles (e.g. polymer chains) for many types of short-range interactions.}, added-at = {2007-06-15T17:33:15.000+0200}, author = {P{\"u}tz, M. and Kolb, A.}, biburl = {https://www.bibsonomy.org/bibtex/233435ac393d64de0f166a53386f9d4f7/kaigrass}, interhash = {e401b64f6f7ca26d92a1846ee598c86a}, intrahash = {33435ac393d64de0f166a53386f9d4f7}, journal = {Comp. Phys. Comm.}, keywords = {Domain Link Many-body Massively Molecular Partial Short algorithm. cell computers. data decomposition. dynamics. forces. interactions. parallel range replication.}, pages = {145--167}, timestamp = {2007-06-15T17:33:23.000+0200}, title = {Optimization techniques for parallel molecular dynamics using domain decomposition}, volume = 113, year = 1998 }