Computer Science Department
School of Computer Science, Carnegie Mellon University


From Physical Modeling to Scientific Understanding
- An End-to-End Approach to Parallel Supercomputing

Tiankai Tu, Hongfeng Yu, Leonardo Ramirez-Guzman
Jacobo Bielak, Omar Ghattas, Kwan-Liu Ma, David R. O'Hallaron

January 2006

Keywords: Physical simulations, end-to-end approach, parallel computing, finite element method, octrees, mesh generation, visualization

Conventional parallel scientific computing uses files as interface between simulation components such as meshing, partitioning, solving and visualizing. This approach results in time-consuming file transfers, disk I/O and data format conversions that consume large amounts of network, storage, and computing resources while contributing nothing to applications. We propose an end-to-end approach to parallel supercomputing. The key idea is to replace the cumbersome file interface with a scalable, parallel, runtime data structure, on top of which all simulation components are constructed in a tightly coupled way. We have implemented this new methodology within an octree-based finite element simulation system named Hercules. The only input to Hercules is material property descriptions of a problem domain; the only outputs are lightweight jpegformated images generated as they are simulated at every visualization time step. There is absolutely no other intermediary file I/O. Performance evaluation of Hercules on up to 2048 processors on the AlphaServer system at Pittsburgh Supercomputing Center has shown good isogranular scalability and fixed-size scalability.

27 pages

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