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Petascale computation performance of lightweight multiscale cardiac models using hybrid programming models.

Bernard J Pope1, Blake G Fitch, Michael C Pitman

  • 1Victorian Life Science Computation Initiative, 187 Grattan Street, Carlton, VIC 3010, Australia. bjpope@unimelb.edu.au

Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference
|January 19, 2012
PubMed
Summary

Hybrid programming models for lightweight cardiac simulations show no performance advantage over Message Passing Interface (MPI) alone. However, future complex models on larger high-performance computing (HPC) systems may benefit from hybrid approaches.

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Area of Science:

  • Computational biology
  • Multiscale modeling
  • High-performance computing (HPC)

Background:

  • Multiscale and multiphysics models are crucial for advancing human disease research and translational medical science.
  • Computationally efficient multiscale models necessitate sophisticated hybrid programming models, combining distributed message passing (MPI) with multithreading (OpenMP, POSIX pthreads).

Purpose of the Study:

  • To compare the performance of hybrid programming models against traditional Message Passing Interface (MPI)-only implementations for a lightweight multiscale cardiac model.
  • To evaluate the applicability of hybrid programming for future, more complex multiscale cardiac simulations on large HPC systems.

Main Methods:

  • Simulation of a lightweight multiscale cardiac model.
  • Performance comparison between a hybrid programming approach (MPI + multithreading) and an MPI-only implementation.
  • Analysis of computational efficiency across different high-performance computing (HPC) configurations.

Main Results:

  • Hybrid programming models did not yield performance benefits for the lightweight cardiac model compared to an MPI-only implementation.
  • This finding contrasts with previous results obtained using more complex physiological models.
  • The study suggests that for simpler models, the added complexity of hybrid programming may not be necessary.

Conclusions:

  • For lightweight multiscale cardiac models, a hybrid programming approach does not currently offer performance advantages over MPI alone.
  • Increased model complexity and larger HPC systems in the future may necessitate and benefit from hybrid programming strategies.
  • Faster-than-real-time multiscale cardiac simulations are foreseeable with hybrid models on future HPC architectures.