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Molecular dynamics for proteins: Performance evaluation on massively parallel computers based on mesh networks using a space decomposition approach
Author(s) -
Ballestrero P.,
Baglietto P.,
Ruggiero C.
Publication year - 1996
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/(sici)1096-987x(199603)17:4<469::aid-jcc7>3.0.co;2-s
Subject(s) - granularity , massively parallel , computer science , decomposition , parallel computing , computation , space (punctuation) , computational science , algorithm , chemistry , organic chemistry , operating system
Parallel computing seems to be the solution for molecular dynamics of large atomic systems, such as proteins in water environments, but the simulation time critically depends on the processor allocation strategy. A study of the optimal processor allocation based on a space decomposition algorithm for single instruction multiple data flow mesh computers is presented. A particular effort has been made to identify the best criterion according to which the atoms can be allocated to the processors using a spatial decomposition approach. The computing time depends on the granularity of the space decomposition among processing elements and on the ratio between the computation power of processing elements and the communication speed of the interprocessor network. © 1996 by John Wiley & Sons, Inc.