Improving the performance of molecular dynamics simulations on parallel clusters

Urban Borstnik; Milan Hodoscek; Dusanka Janezic

doi:10.1021/ci034261e

Improving the performance of molecular dynamics simulations on parallel clusters

J Chem Inf Comput Sci. 2004 Mar-Apr;44(2):359-64. doi: 10.1021/ci034261e.

Authors

Urban Borstnik¹, Milan Hodoscek, Dusanka Janezic

Affiliation

¹ National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia.

PMID: 15032512
DOI: 10.1021/ci034261e

Abstract

In this article a procedure is derived to obtain a performance gain for molecular dynamics (MD) simulations on existing parallel clusters. Parallel clusters use a wide array of interconnection technologies to connect multiple processors together, often at different speeds, such as multiple processor computers and networking. It is demonstrated how to configure existing programs for MD simulations to efficiently handle collective communication on parallel clusters with processor interconnections of different speeds.