title: Petascale computation performance of lightweight multiscale cardiac models using hybrid programming models.
abstract: Future multiscale and multiphysics models must use the power of high performance computing (HPC) systems to enable research into human disease, translational medical science, and treatment. Previously we showed 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, POSIX pthreads). The objective of this work is to compare the performance of such hybrid programming models when applied to the simulation of a lightweight multiscale cardiac model. Our results show that the hybrid models do not perform favourably when compared to an implementation using only MPI which is in contrast to our results using complex physiological models. Thus, with regards to lightweight multiscale cardiac models, the user may not need to increase programming complexity by using a hybrid programming approach. However, considering that model complexity will increase as well as the HPC system size in both node count and number of cores per node, it is still foreseeable that we will achieve faster than real time multiscale cardiac simulations on these systems using hybrid programming models.
authors.affiliation: Victorian Life Science Computation Initiative, 187 Grattan Street, Carlton, VIC 3010, Australia. bjpope@unimelb.edu.au
authors.forename: Bernard J
authors.initials: BJ
authors.lastname: Pope
authors.forename: Blake G
authors.initials: BG
authors.lastname: Fitch
authors.forename: Michael C
authors.initials: MC
authors.lastname: Pitman
authors.forename: John J
authors.initials: JJ
authors.lastname: Rice
authors.forename: Matthias
authors.initials: M
authors.lastname: Reumann
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D006321:Heart / Q000502:physiology*; D006801:Humans; D008955:Models, Cardiovascular; D011381:Programming Languages