Performance analysis and optimization of a parallel carbon molecular dynamic code on a Cray T3E

Mihai Horoi, Richard J. Enbody

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

1 Scopus citations

Abstract

An analysis of the primary factors influencing the performance of a parallel implementation on a Cray T3E of a Carbon Molecular Dynamics code developed at Department of Physics and Astronomy at Michigan State University is presented. We show that classical load-sharing techniques combined with careful analysis of Amdahl's law can be successfully used to significantly increase the performance of the code. This report describes the quantitative analysis of these factors and the solutions used to diminish or eliminate their effects. By slightly modifying the code we reduced its sequential portion to less than 0.1%. We also demonstrate that the MPI collective communications implementation on the Cray T3E dramatically reduces the communication overhead for our code. In the end, a speedup of 170 was obtained using 256 Cray T3E processing elements. These results create the prospect of simulating the dynamics of 1,000-atom nanotubes in the microsecond regime (≈1,000,000 time steps).

Original languageEnglish
Title of host publicationProceedings - 1998 International Conference on Parallel Processing, ICPP 1998
EditorsTen H. Lai
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages62-69
Number of pages8
ISBN (Electronic)0818686502
DOIs
StatePublished - 1998
Event1998 International Conference on Parallel Processing, ICPP 1998 - Minneapolis, United States
Duration: Aug 10 1998Aug 14 1998

Publication series

NameProceedings of the International Conference on Parallel Processing
ISSN (Print)0190-3918

Conference

Conference1998 International Conference on Parallel Processing, ICPP 1998
Country/TerritoryUnited States
CityMinneapolis
Period08/10/9808/14/98

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