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Hybrid message-passing and shared-memory programming in a molecular dynamics application on multicore clusters

Chorley, Martin, Walker, David and Guest, Martyn Frederick 2009. Hybrid message-passing and shared-memory programming in a molecular dynamics application on multicore clusters. International Journal of High Performance Computing Applications 23 (3) , pp. 196-211. 10.1177/1094342009106188

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Abstract

Hybrid programming, whereby shared-memory and message-passing programming techniques are combined within a single parallel application, has often been discussed as a method for increasing code performance on clusters of symmetric multiprocessors (SMPs). This paper examines whether the hybrid model brings any performance benefits for clusters based on multicore processors. A molecular dynamics application has been parallelized using both MPI and hybrid MPI/OpenMP programming models. The performance of this application has been examined on two high-end multicore clusters using both Infiniband and Gigabit Ethernet interconnects. The hybrid model has been found to perform well on the higher-latency Gigabit Ethernet connection, but offers no performance benefit on low-latency Infiniband interconnects. The changes in performance are attributed to the differing communication profiles of the hybrid and MPI codes.

Item Type: Article
Status: Published
Schools: Advanced Research Computing @ Cardiff (ARCCA)
Computer Science & Informatics
Information Services
Subjects: Q Science > QA Mathematics > QA75 Electronic computers. Computer science
Uncontrolled Keywords: message passing; shared memory; multicore; clusters; hybrid programming
Publisher: Sage
ISSN: 1094-3420
Last Modified: 04 Jun 2017 02:00
URI: http://orca.cf.ac.uk/id/eprint/7376

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