MESH REFINEMENT AND PARALLELIZATION OF VCELL PDE SOLVERS

VCELL PDE 求解器的网格细化和并行化

• 批准号: 8362498
• 负责人: BORIS SLEPCHENKO
• 金额: $ 3.16万
• 依托单位: UNIVERSITY OF CONNECTICUT SCH OF MED/DNT
• 依托单位国家: 美国
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-05-01 至 2012-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8362498
• 关键词: Cells; Communities; Computer software; Development; Evaluation; Funding; Grant; Libraries; Methods; Modeling; National Center for Research Resources; Performance; Phase; Principal Investigator; Research; Research Infrastructure; Resources; Source; Speed; Structure; Technology; United States National Institutes of Health; base; cost; evaluation/testing; improved; parallel computing; simulation; three-dimensional modeling

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. The project focuses on improving computational efficiency of VCell. This will be achieved by applying adaptive meshes, which allow for more precise modeling of geometry, and by using parallel solvers. Departure from uniform grids and incorporation of parallel solvers in VCell will speed up very large, computationally intensive simulations, particularly of three-dimensional models with multiple spatial scales. The research plan is based on synergistic development of mesh adaptivity and parallel implementation of the solvers, which will take advantage, wherever possible, of available technologies, software, and robust approaches that have been validated by the scientific community. Getting good performance out of available libraries, however, will require extensive testing and evaluation depending on the particular type of problems that need to be solved. The initial phase of the project will include evaluation of PETSc' (Portable, Extensible Toolkit for Scientific computation) parallel solvers and research on current methods for structured mesh refinement.

该副本是利用资源的众多研究子项目之一 由NIH/NCRR资助的中心赠款提供。对该子弹的主要支持 而且，副投影的主要研究员可能是其他来源提供的 包括其他NIH来源。 列出的总费用可能 代表subproject使用的中心基础架构的估计量， NCRR赠款不直接向子弹或副本人员提供的直接资金。 该项目着重于提高VCELL的计算效率。这将通过应用自适应网格来实现，从而可以对几何形状进行更精确的建模，并使用并行求解器进行更精确的建模。偏离统一的网格和在VCELL中的平行求解器的结合将加快非常大的计算密集型模拟，尤其是具有多个空间尺度的三维模型。该研究计划基于网格适应性的协同开发和求解器的平行实现，该计划将尽可能利用科学界验证的可用技术，软件和强大方法的优势。但是，从可用库中获得良好的性能将需要大量的测试和评估，具体取决于需要解决的特定类型的问题。该项目的初始阶段将包括评估PETSC（用于科学计算的便携式，可扩展的工具包）以及对当前结构网格细化方法的研究。