Publication

Parallelization of the molecular dynamics code GROMOS87 for distributed memory parallel architectures

Green, DG., Meacham, KE. & vanHoesel, F., 1995, HIGH-PERFORMANCE COMPUTING AND NETWORKING. Hertzberger, B. & Serazzi, G. (eds.). BERLIN 33: Springer, p. 875-879 5 p. (LECTURE NOTES IN COMPUTER SCIENCE; vol. 919).

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

This paper describes the techniques and methodologies employed during parallelization of the Molecular Dynamics (MD) code GROMOS87, with the specific requirement that the program run efficiently on a range of distributed-memory parallel platforms. We discuss the preliminary results of our parallel port and indicate to what extent we are able to satisfy the basic requirements of industrial users with regard to code performance and scalability. We introduce a scheme which is used to dynamically allocate charge groups to processors reducing the time imbalance during the non-bonded force calculation phase from 30 - 40% to <1%. We propose a new method for parallelizing the constraint dynamics algorithm (SHAKE) where the emphasis is placed on reducing the number and size of communicated packets during the iterative SHAKEing process.

Original languageEnglish
Title of host publicationHIGH-PERFORMANCE COMPUTING AND NETWORKING
EditorsB Hertzberger, G Serazzi
Place of PublicationBERLIN 33
PublisherSpringer
Pages875-879
Number of pages5
ISBN (Print)3-540-59393-4
Publication statusPublished - 1995
EventInternational Conference and Exhibition on High-Performance Computing and Networking - , Italy
Duration: 3-May-19955-May-1995

Publication series

NameLECTURE NOTES IN COMPUTER SCIENCE
PublisherSPRINGER-VERLAG BERLIN
Volume919
ISSN (Print)0302-9743

Other

OtherInternational Conference and Exhibition on High-Performance Computing and Networking
CountryItaly
Period03/05/199505/05/1995

Event

International Conference and Exhibition on High-Performance Computing and Networking

03/05/199505/05/1995

Italy

Event: Other

ID: 6409751