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Parallel STEPS: Large Scale Stochastic Spatial Reaction-Diffusion Simulation with High Performance Computers
https://oist.repo.nii.ac.jp/records/211
https://oist.repo.nii.ac.jp/records/211dd5acf06-8cbf-4c38-a9fa-118794a6e7cd
名前 / ファイル | ライセンス | アクション |
---|---|---|
fninf-11-00013 (4.5 MB)
|
Creative Commons Attribution 4.0 International
(http://creativecommons.org/licenses/by/4.0/) |
Item type | 学術雑誌論文 / Journal Article(1) | |||||
---|---|---|---|---|---|---|
公開日 | 2018-01-11 | |||||
タイトル | ||||||
タイトル | Parallel STEPS: Large Scale Stochastic Spatial Reaction-Diffusion Simulation with High Performance Computers | |||||
タイトル | ||||||
言語 | en | |||||
タイトル | Parallel STEPS: Large Scale Stochastic Spatial Reaction-Diffusion Simulation with High Performance Computers | |||||
言語 | ||||||
言語 | eng | |||||
資源タイプ | ||||||
資源タイプ識別子 | http://purl.org/coar/resource_type/c_6501 | |||||
資源タイプ | journal article | |||||
著者(英) |
Chen, Weiliang
× Chen, Weiliang× De Schutter, Erik |
|||||
書誌情報 |
en : Frontiers in Neuroinformatics 巻 11, p. 13, 発行日 2017-02-10 |
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抄録 | ||||||
内容記述タイプ | Other | |||||
内容記述 | Stochastic, spatial reaction-diffusion simulations have been widely used in systems biology and computational neuroscience. However, the increasing scale and complexity of models and morphologies have exceeded the capacity of any serial implementation. This led to the development of parallel solutions that benefit from the boost in performance of modern supercomputers. In this paper, we describe an MPI-based, parallel operator-splitting implementation for stochastic spatial reaction-diffusion simulations with irregular tetrahedral meshes. The performance of our implementation is first examined and analyzed with simulations of a simple model. We then demonstrate its application to real-world research by simulating the reaction-diffusion components of a published calcium burst model in both Purkinje neuron sub-branch and full dendrite morphologies. Simulation results indicate that our implementation is capable of achieving super-linear speedup for balanced loading simulations with reasonable molecule density and mesh quality. In the best scenario, a parallel simulation with 2,000 processes runs more than 3,600 times faster than its serial SSA counterpart, and achieves more than 20-fold speedup relative to parallel simulation with 100 processes. In a more realistic scenario with dynamic calcium influx and data recording, the parallel simulation with 1,000 processes and no load balancing is still 500 times faster than the conventional serial SSA simulation. | |||||
出版者 | ||||||
出版者 | Frontiers Media S.A. | |||||
ISSN | ||||||
収録物識別子タイプ | ISSN | |||||
収録物識別子 | 1662-5196 | |||||
PubMed番号 | ||||||
関連タイプ | isIdenticalTo | |||||
識別子タイプ | PMID | |||||
関連識別子 | info:pmid/28239346 | |||||
DOI | ||||||
関連タイプ | isIdenticalTo | |||||
識別子タイプ | DOI | |||||
関連識別子 | info:doi/10.3389/fninf.2017.00013 | |||||
権利 | ||||||
権利情報 | © 2017 Chen and De Schutter. | |||||
関連サイト | ||||||
識別子タイプ | URI | |||||
関連識別子 | https://www.frontiersin.org/articles/10.3389/fninf.2017.00013/full#h1 | |||||
著者版フラグ | ||||||
出版タイプ | VoR | |||||
出版タイプResource | http://purl.org/coar/version/c_970fb48d4fbd8a85 |