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Related Experiment Video

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Patient-specific Modeling of the Heart: Estimation of Ventricular Fiber Orientations
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Orthogonal recursive bisection data decomposition for high performance computing in cardiac model simulations:

Matthias Reumann1, Blake G Fitch, Aleksandr Rayshubskiy

  • 1Computational Biology Center, IBM TJ Watson Research Center, Yorktown Heights, 1101 Kitchawan Road, Route 134, NY 10598, USA. mreumann@ieee.org

Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference
|December 8, 2009
PubMed
Summary

Optimizing cardiac model simulations requires careful data decomposition. Rotating anatomical data significantly impacts load balancing and simulation runtime, especially on smaller supercomputer partitions.

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Area of Science:

  • Computational science
  • Biomedical engineering
  • High-performance computing

Background:

  • Orthogonal recursive bisection (ORB) is a data decomposition strategy for supercomputing.
  • ORB's efficiency depends on computational load distribution.
  • Previous studies showed good scaling with ORB.

Purpose of the Study:

  • Investigate how anatomical data orientation affects ORB load balancing.
  • Optimize data decomposition for improved computational efficiency in cardiac models.

Main Methods:

  • Rotated Visible Female cardiac dataset (0.2 mm resolution) around x, y, and z axes.
  • Created 14 datasets with varying orientations and positions.
  • Simulated cardiac electrophysiology using the ten Tusscher model on an IBM Blue Gene/L.

Main Results:

  • Data decomposition efficiency is dependent on anatomical orientation and position.
  • Run time differences of 10s for 1ms simulations translate to significant differences for longer runs.
  • The impact of orientation diminishes with larger processor partitions.

Conclusions:

  • Anatomical data orientation is a critical factor for load balancing in ORB.
  • Consideration of data orientation is necessary for optimizing long cardiac simulations.
  • Future work should focus on orientation-dependent optimizations for large-scale simulations.