Parallel Languages and Compilers: Perspective From the Titanium Experience
International Journal of High Performance Computing Applications
Petascale Direct Numerical Simulation of Blood Flow on 200K Cores and Heterogeneous Architectures
Proceedings of the 2010 ACM/IEEE International Conference for High Performance Computing, Networking, Storage and Analysis
An architecture for a data-intensive computer
Proceedings of the first international workshop on Network-aware data management
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The immersed boundary method is a general numerical method for modeling elastic boundaries immersed within a viscous, incompressible fluid. It has been applied to several biological and engineering systems, including large-scale models of the heart and cochlea. These simulations have the potential to improve our basic understanding of the biological systems they model and aid in the development of surgical treatments and prosthetic devices. Despite the popularity of the immersed boundary method and the desire to scale the problems to accurately capture the details of the physical systems, parallelization for large-scale distributed memory machines has proved challenging. The primary difficulty is in achieving a load-balanced computation, while maintaining low communication costs when modeling the interactions between the fluid and the moving immersed boundary. In this paper we describe a parallelized algorithm for the immersed boundary method that is designed for scalability on distributed memory multiprocessors and clusters of SMPs. It is implemented using the Titanium language, a Java-based language designed for high performance scientific computing. Our software package, called IB, takes advantage of the object-oriented features of Titanium to provide a framework for simulating immersed boundaries that separates the generic immersed boundary method code from the specific application features that define the immersed boundary structure and the forces that arise from those structures. Our results demonstrate the scalability of our design and the feasibility of large-scale immersed boundary computations with the IB package.