DMCA
Scalable Data-Privatization Threading for Hybrid MPI/OpenMP Parallelization of Molecular Dynamics
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BibTeX
@MISC{Kunaseth_scalabledata-privatization,
author = {Manaschai Kunaseth and David F. Richards and James N. Glosli and Rajiv K. Kalia and Aiichiro Nakano and Priya Vashishta},
title = {Scalable Data-Privatization Threading for Hybrid MPI/OpenMP Parallelization of Molecular Dynamics},
year = {}
}
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Abstract
Abstract — Calculation of the Coulomb potential in the molecular dynamics code ddcMD has been parallelized based on a hybrid MPI/OpenMP scheme. The explicit pair kernel of the particleparticle/particle-mesh algorithm is multi-threaded using OpenMP, while communication between multicore nodes is handled by MPI. We have designed a load balancing spanning forest (LBSF) partitioning algorithm, which combines: 1) finegrain dynamic load balancing; and 2) minimal memory-footprint data privatization via nucleation-growth allocation. This algorithm reduces the memory requirement for thread-private data from O(np) to O(n + p 1/3 n 2/3)—amounting to 75 % memory saving for p = 16 threads working on n = 8,192 particles, while maintaining the average thread-level load-imbalance less than 5%. Strong-scaling speedup for the kernel is 14.4 with 16-way threading on a four quad-core AMD Opteron node. In addition, our MPI/OpenMP code shows 2.58! and 2.16! speedups over the MPI-only implementation, respectively, for 0.84 and 1.68 million particles systems on 32,768 cores of BlueGene/P.
Keyphrases
molecular dynamic scalable data-privatization threading hybrid mpi openmp parallelization mpi openmp code abstract calculation finegrain dynamic load balancing strong-scaling speedup molecular dynamic code ddcmd minimal memory-footprint data privatization multicore node quad-core amd opteron node nucleation-growth allocation thread-private data hybrid mpi openmp scheme average thread-level load-imbalance particleparticle particle-mesh algorithm memory requirement mpi-only implementation coulomb potential explicit pair kernel particle system
