Cargando…

Parallel Processing Transport Model MT3DMS by Using OpenMP

Solute transport modeling resolves advection, dispersion, and chemical reactions in groundwater systems with its accuracy depending on the resolution of domain at all scales, thus the computational efficiency of a simulator becomes a bottleneck for the wide application of numerical simulations. Howe...

Descripción completa

Detalles Bibliográficos
Autores principales: Huang, Linxian, Wang, Lichun, Shao, Jingli, Liu, Xingwei, Hao, Qichen, Xing, Liting, Zheng, Lizhi, Xiao, Yong
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6025348/
https://www.ncbi.nlm.nih.gov/pubmed/29794989
http://dx.doi.org/10.3390/ijerph15061063
_version_ 1783336259940253696
author Huang, Linxian
Wang, Lichun
Shao, Jingli
Liu, Xingwei
Hao, Qichen
Xing, Liting
Zheng, Lizhi
Xiao, Yong
author_facet Huang, Linxian
Wang, Lichun
Shao, Jingli
Liu, Xingwei
Hao, Qichen
Xing, Liting
Zheng, Lizhi
Xiao, Yong
author_sort Huang, Linxian
collection PubMed
description Solute transport modeling resolves advection, dispersion, and chemical reactions in groundwater systems with its accuracy depending on the resolution of domain at all scales, thus the computational efficiency of a simulator becomes a bottleneck for the wide application of numerical simulations. However, the traditional serial numerical simulators have reached their limits for the prohibitive computational time and memory requirement in solving large-scale problems. These limitations have greatly hindered the wide application of groundwater solute transport modeling. Thus, the development of an efficient method for handling large-scale groundwater solute transport simulation is urgently required. In this study, we developed and assessed a parallelized MT3DMS (Modular Three-Dimensional Multispecies Transport Model) by using OpenMP (Open specifications for Multi-Processing) to accelerate the solute transport simulation process. The parallelization was achieved by adding OpenMP compile directives (i.e., defining various types of parallel regions) into the most time-consuming packages, including the Advection package (ADV), Dispersion package (DSP), and Generalized Conjugate Gradient Solver package (GCG). This allows parallel processing on shared-memory multiprocessors, i.e., both the memory requirement and computing efforts are automatically distributed among all processors. Moreover, we discussed two different parallelization strategies for handling numerical models with either many layers or few layers. The performance of parallelized MT3DMS was assessed by two benchmark numerical models with different model domain sizes via a workstation with two quad-core processors. Results showed that the running time of parallelized MT3DMS can be 4.15 times faster than that using sequential MT3DMS. The effects of using different preconditioners (procedures that transform a given problem into a form that is more suitable for numerical solving methods) in the GCG package were additionally evaluated. The modified strategy for handling numerical models with few layers also achieved satisfactory results with running time two times faster than that via sequential simulation. Thus, the proposed parallelization allows high-resolution groundwater transport simulation with higher efficiency for large-scale or multimillion-cell simulation problems.
format Online
Article
Text
id pubmed-6025348
institution National Center for Biotechnology Information
language English
publishDate 2018
publisher MDPI
record_format MEDLINE/PubMed
spelling pubmed-60253482018-07-16 Parallel Processing Transport Model MT3DMS by Using OpenMP Huang, Linxian Wang, Lichun Shao, Jingli Liu, Xingwei Hao, Qichen Xing, Liting Zheng, Lizhi Xiao, Yong Int J Environ Res Public Health Article Solute transport modeling resolves advection, dispersion, and chemical reactions in groundwater systems with its accuracy depending on the resolution of domain at all scales, thus the computational efficiency of a simulator becomes a bottleneck for the wide application of numerical simulations. However, the traditional serial numerical simulators have reached their limits for the prohibitive computational time and memory requirement in solving large-scale problems. These limitations have greatly hindered the wide application of groundwater solute transport modeling. Thus, the development of an efficient method for handling large-scale groundwater solute transport simulation is urgently required. In this study, we developed and assessed a parallelized MT3DMS (Modular Three-Dimensional Multispecies Transport Model) by using OpenMP (Open specifications for Multi-Processing) to accelerate the solute transport simulation process. The parallelization was achieved by adding OpenMP compile directives (i.e., defining various types of parallel regions) into the most time-consuming packages, including the Advection package (ADV), Dispersion package (DSP), and Generalized Conjugate Gradient Solver package (GCG). This allows parallel processing on shared-memory multiprocessors, i.e., both the memory requirement and computing efforts are automatically distributed among all processors. Moreover, we discussed two different parallelization strategies for handling numerical models with either many layers or few layers. The performance of parallelized MT3DMS was assessed by two benchmark numerical models with different model domain sizes via a workstation with two quad-core processors. Results showed that the running time of parallelized MT3DMS can be 4.15 times faster than that using sequential MT3DMS. The effects of using different preconditioners (procedures that transform a given problem into a form that is more suitable for numerical solving methods) in the GCG package were additionally evaluated. The modified strategy for handling numerical models with few layers also achieved satisfactory results with running time two times faster than that via sequential simulation. Thus, the proposed parallelization allows high-resolution groundwater transport simulation with higher efficiency for large-scale or multimillion-cell simulation problems. MDPI 2018-05-24 2018-06 /pmc/articles/PMC6025348/ /pubmed/29794989 http://dx.doi.org/10.3390/ijerph15061063 Text en © 2018 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Huang, Linxian
Wang, Lichun
Shao, Jingli
Liu, Xingwei
Hao, Qichen
Xing, Liting
Zheng, Lizhi
Xiao, Yong
Parallel Processing Transport Model MT3DMS by Using OpenMP
title Parallel Processing Transport Model MT3DMS by Using OpenMP
title_full Parallel Processing Transport Model MT3DMS by Using OpenMP
title_fullStr Parallel Processing Transport Model MT3DMS by Using OpenMP
title_full_unstemmed Parallel Processing Transport Model MT3DMS by Using OpenMP
title_short Parallel Processing Transport Model MT3DMS by Using OpenMP
title_sort parallel processing transport model mt3dms by using openmp
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6025348/
https://www.ncbi.nlm.nih.gov/pubmed/29794989
http://dx.doi.org/10.3390/ijerph15061063
work_keys_str_mv AT huanglinxian parallelprocessingtransportmodelmt3dmsbyusingopenmp
AT wanglichun parallelprocessingtransportmodelmt3dmsbyusingopenmp
AT shaojingli parallelprocessingtransportmodelmt3dmsbyusingopenmp
AT liuxingwei parallelprocessingtransportmodelmt3dmsbyusingopenmp
AT haoqichen parallelprocessingtransportmodelmt3dmsbyusingopenmp
AT xingliting parallelprocessingtransportmodelmt3dmsbyusingopenmp
AT zhenglizhi parallelprocessingtransportmodelmt3dmsbyusingopenmp
AT xiaoyong parallelprocessingtransportmodelmt3dmsbyusingopenmp