TY - JOUR
T1 - Performance of hybrid programming models for multiscale cardiac simulations
T2 - Preparing for petascale computation
AU - Pope, Bernard J.
AU - Fitch, Blake G.
AU - Pitman, Michael C.
AU - Rice, John J.
AU - Reumann, Matthias
N1 - Funding Information:
Manuscript received March 23, 2011; revised June 4, 2011; accepted June 8, 2011. Date of publication July 14, 2011; date of current version September 21, 2011. This research was supported by a Victorian Life Sciences Computation Initiative (VLSCI), Carlton, Australia, under Grant VR0088 on its Peak Computing Facility at the University of Melbourne, Carlton, Australia, an initiative of the Victorian Government. Asterisk indicates corresponding author.
PY - 2011/10
Y1 - 2011/10
N2 - 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.
AB - 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.
KW - High-performance computing (HPC)
KW - hybrid programming models
KW - multiphysics cardiac model
KW - multiscale
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U2 - 10.1109/TBME.2011.2161580
DO - 10.1109/TBME.2011.2161580
M3 - Article
C2 - 21768044
AN - SCOPUS:80053140672
SN - 0018-9294
VL - 58
SP - 2965
EP - 2969
JO - IEEE Transactions on Biomedical Engineering
JF - IEEE Transactions on Biomedical Engineering
IS - 10 PART 2
M1 - 5951744
ER -