MESH REFINEMENT AND PARALLELIZATION OF VCELL PDE SOLVERS

这个子项目是利用资源的许多研究子项目之一。 由NIH/NCRR资助的中心拨款提供。对子项目的主要支持 子项目的首席调查员可能是由其他来源提供的， 包括美国国立卫生研究院的其他来源。为子项目列出的总成本可能 表示该子项目使用的中心基础设施的估计数量， 不是由NCRR赠款提供给次级项目或次级项目工作人员的直接资金。 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和使用并行解算器来实现，自适应网格允许对几何体进行更精确的建模。离开统一网格并在Vcell中并入并行解算器将加快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的模拟。研究计划的基础是网格适应性的协同开发和解算器的并行实施，这将尽可能利用已得到科学界验证的现有技术、软件和可靠的方法。然而，要从可用库中获得良好的性能，将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对PETSc(可移植、可扩展的科学计算工具包)并行求解器的评估，以及对当前结构化网格细化方法的研究。

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.