Performance of Hybrid Programming Models for Multiscale Cardiac Simulations: Preparing for Petascale Computation

Future multiscale and multiphysics models that support research into human disease, translational medical science, and treatment can utilize the power of high-performance computing (HPC) systems. We anticipate that computationally efficient multiscale models will require the use of sophisticated hyb...

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Veröffentlicht in:IEEE transactions on biomedical engineering Jg. 58; H. 10; S. 2965 - 2969
Hauptverfasser: Pope, Bernard J., Fitch, Blake G., Pitman, Michael C., Rice, John J., Reumann, Matthias
Format: Journal Article
Sprache:Englisch
Veröffentlicht: United States IEEE 01.10.2011
The Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Schlagworte:
Biological system modeling
Computation
Computational efficiency
Computational modeling
Computer Simulation
Computing Methodologies
Cores
Data models
Female
High-performance computing (HPC)
Human
Humans
hybrid programming models
Instruction sets
Load modeling
Mathematical models
Microprocessors
Models, Cardiovascular
multiphysics cardiac model
multiscale
Myocytes, Cardiac - cytology
Phases
Programming
Software
Studies
Synchronization
Visible Human Projects
ISSN:0018-9294, 1558-2531, 1558-2531
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Zusammenfassung:Future multiscale and multiphysics models that support research into human disease, translational medical science, and treatment can utilize the power of high-performance computing (HPC) systems. We anticipate that computationally efficient multiscale models will require the use of sophisticated hybrid programming models, mixing distributed message-passing processes [e.g., the message-passing interface (MPI)] with multithreading (e.g., OpenMP, Pthreads). The objective of this study is to compare the performance of such hybrid programming models when applied to the simulation of a realistic physiological multiscale model of the heart. Our results show that the hybrid models perform favorably when compared to an implementation using only the MPI and, furthermore, that OpenMP in combination with the MPI provides a satisfactory compromise between performance and code complexity. Having the ability to use threads within MPI processes enables the sophisticated use of all processor cores for both computation and communication phases. Considering that HPC systems in 2012 will have two orders of magnitude more cores than what was used in this study, we believe that faster than real-time multiscale cardiac simulations can be achieved on these systems.
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ISSN:0018-9294
1558-2531
1558-2531
DOI:10.1109/TBME.2011.2161580