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

Chorley, Martin ORCID: https://orcid.org/0000-0001-8744-260X, Walker, David ORCID: https://orcid.org/0000-0002-1360-6330 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 University IT
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:	07 Nov 2023 07:24
URI:	https://orca.cardiff.ac.uk/id/eprint/7376

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