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Hybrid MPI-OpenMP parallelism in the ONETEP linear-scaling electronic structure code: application to the delamination of cellulose nanofibrils

Hybrid MPI-OpenMP parallelism in the ONETEP linear-scaling electronic structure code: application to the delamination of cellulose nanofibrils
Hybrid MPI-OpenMP parallelism in the ONETEP linear-scaling electronic structure code: application to the delamination of cellulose nanofibrils
We present a hybrid MPI-OpenMP implementation of Linear-Scaling Density Functional Theory within the ONETEP code. We illustrate its performance on a range of high performance computing (HPC) platforms comprising shared-memory nodes with fast interconnect. Our work has focused on applying OpenMP parallelism to the routines which dominate the computational load, attempting where possible to parallelize different loops from those already parallelized within MPI. This includes 3D FFT box operations, sparse matrix algebra operations, calculation of integrals, and Ewald summation. While the underlying numerical methods are unchanged, these developments represent significant changes to the algorithms used within ONETEP to distribute the workload across CPU cores. The new hybrid code exhibits much-improved strong scaling relative to the MPI-only code and permits calculations with a much higher ratio of cores to atoms. These developments result in a significantly shorter time to solution than was possible using MPI alone and facilitate the application of the ONETEP code to systems larger than previously feasible. We illustrate this with benchmark calculations from an amyloid fibril trimer containing 41,907 atoms. We use the code to study the mechanism of delamination of cellulose nanofibrils when undergoing sonification, a process which is controlled by a large number of interactions that collectively determine the structural properties of the fibrils. Many energy evaluations were needed for these simulations, and as these systems comprise up to 21,276 atoms this would not have been feasible without the developments described here.
1549-9618
4782-4794
Wilkinson, Karl
8e2e967a-138c-4833-8526-908a1db8abee
Hine, Nicholas D.M.
6acbd836-08cc-45fe-96aa-5274a388e05d
Skylaris, Chris
8f593d13-3ace-4558-ba08-04e48211af61
Wilkinson, Karl
8e2e967a-138c-4833-8526-908a1db8abee
Hine, Nicholas D.M.
6acbd836-08cc-45fe-96aa-5274a388e05d
Skylaris, Chris
8f593d13-3ace-4558-ba08-04e48211af61

Wilkinson, Karl, Hine, Nicholas D.M. and Skylaris, Chris (2014) Hybrid MPI-OpenMP parallelism in the ONETEP linear-scaling electronic structure code: application to the delamination of cellulose nanofibrils. Journal of Chemical Theory and Computation, 10 (11), 4782-4794. (doi:10.1021/ct500686r). (PMID:26584365)

Record type: Article

Abstract

We present a hybrid MPI-OpenMP implementation of Linear-Scaling Density Functional Theory within the ONETEP code. We illustrate its performance on a range of high performance computing (HPC) platforms comprising shared-memory nodes with fast interconnect. Our work has focused on applying OpenMP parallelism to the routines which dominate the computational load, attempting where possible to parallelize different loops from those already parallelized within MPI. This includes 3D FFT box operations, sparse matrix algebra operations, calculation of integrals, and Ewald summation. While the underlying numerical methods are unchanged, these developments represent significant changes to the algorithms used within ONETEP to distribute the workload across CPU cores. The new hybrid code exhibits much-improved strong scaling relative to the MPI-only code and permits calculations with a much higher ratio of cores to atoms. These developments result in a significantly shorter time to solution than was possible using MPI alone and facilitate the application of the ONETEP code to systems larger than previously feasible. We illustrate this with benchmark calculations from an amyloid fibril trimer containing 41,907 atoms. We use the code to study the mechanism of delamination of cellulose nanofibrils when undergoing sonification, a process which is controlled by a large number of interactions that collectively determine the structural properties of the fibrils. Many energy evaluations were needed for these simulations, and as these systems comprise up to 21,276 atoms this would not have been feasible without the developments described here.

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e-pub ahead of print date: 10 October 2014
Published date: 11 November 2014
Organisations: Computational Systems Chemistry

Identifiers

Local EPrints ID: 395999
URI: http://eprints.soton.ac.uk/id/eprint/395999
ISSN: 1549-9618
PURE UUID: 83664bf1-2686-4c88-9778-5614407cfa21
ORCID for Chris Skylaris: ORCID iD orcid.org/0000-0003-0258-3433

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Date deposited: 02 Jun 2016 08:58
Last modified: 03 Dec 2019 01:46

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