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

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