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: 8169571
• 负责人: BORIS SLEPCHENKO
• 金额: $ 4.89万
• 依托单位: UNIVERSITY OF CONNECTICUT SCH OF MED/DNT
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-05-01 至 2011-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8169571
• 关键词: Communities; Computer Retrieval of Information on Scientific Projects Database; Computer software; Development; Evaluation; Funding; Grant; Institution; Libraries; Methods; Modeling; Performance; Phase; Research; Research Personnel; Resources; Source; Speed; Structure; Technology; United States National Institutes of Health; base; 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. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. 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.

这个子项目是许多研究子项目中的一个 由NIH/NCRR资助的中心赠款提供的资源。子项目和 研究者（PI）可能从另一个NIH来源获得了主要资金， 因此可在其他CRISP条目中表示。所列机构为 研究中心，而研究中心不一定是研究者所在的机构。 该项目的重点是提高VCell的计算效率。这将通过应用自适应网格（允许更精确的几何建模）和使用并行求解器来实现。脱离均匀网格并在VCell中引入并行求解器将加速非常大的计算密集型模拟，特别是具有多个空间尺度的三维模型。该研究计划基于网格自适应性的协同发展和求解器的并行实现，这将尽可能利用科学界已经验证的现有技术，软件和强大的方法。然而，要从可用的库中获得良好的性能，需要根据需要解决的特定类型的问题进行广泛的测试和评估。该项目的初始阶段将包括评估PETSc（便携式可扩展科学计算工具包）并行求解器和研究结构化网格细化的当前方法。