Implementation of scalable bidomain-based 3D cardiac simulations on a graphics processing unit cluster
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Desai AS, Stevenson LW (2012) Rehospitalization for heart failure: predict or prevent? Circulation 126(4):501–506
Cheng A, Dalal D, Butcher B, Norgard S, Zhang Y, Dickfeld T, Eldadah ZA, Ellenbogen KA, Guallar E, Tomaselli GF (2013) Prospective observational study of implantable cardioverter-defibrillators in primary prevention of sudden cardiac death: study design and cohort description. J Am Heart Assoc 2(1):e000083
Nimmagadda VK, Akoglu A, Hariri S, Moukabary T (2012) Cardiac simulation on multi-GPU platform. J Supercomput 59(3):1360–1378
Biffard R, Leon LJ (2003) Cardiac tissue simulation using graphics hardware. In: Proceedings of the 25th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, 2003. IEEE, vol 3, pp 2838–2840
Rocha BM, Campos FO, Amorim RM, Plank G, dos Santos RW, Liebmann M, Haase G (2011) Accelerating cardiac excitation spread simulations using graphics processing units. Concurr Comput Pract Exp 23(7):708–720
Vigmond EJ, Boyle PM, Leon LJ, Plank G (2009) Near-real-time simulations of biolelectric activity in small mammalian hearts using graphical processing units. In: Annual International Conference of the IEEE Engineering in Medicine and Biology Society, 2009. EMBC 2009. IEEE, pp 3290–3293
Amorim R, Haase G, Liebmann M, Dos Santos RW (2009) Comparing CUDA and OpenGL implementations for a Jacobi iteration. In: HPCS’09. International Conference on High Performance Computing & Simulation, 2009. IEEE, pp 22–32
Amorim RM, Rocha BM, Campos FO, dos Santos RW (2010) Automatic code generation for solvers of cardiac cellular membrane dynamics in GPUs. In: 2010 Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC). IEEE, pp 2666–2669
Bartocci E, Cherry EM, Glimm J, Grosu R, Smolka SA, Fenton FH (2011) Toward real-time simulation of cardiac dynamics. In: Proceedings of the 9th International Conference on Computational Methods in Systems Biology. ACM, pp 103–112
Garcia VM, Liberos A, Climent AM, Vidal A, Millet J, Gonzalez A (2011) An adaptive step size GPU ODE solver for simulating the electric cardiac activity. In: Computing in Cardiology, 2011. IEEE, pp 233–236
García-Molla VM, Liberos A, Vidal A, Guillem M, Millet J, Gonzalez A, Martínez-Zaldívar FJ, Climent AM (2014) Adaptive step ODE algorithms for the 3D simulation of electric heart activity with graphics processing units. Comput Biol Med 44:15–26
Jararweh Y, Jarrah M, Hariri S (2012) Exploiting GPUs for compute-intensive medical applications. In: 2012 International Conference on Multimedia Computing and Systems (ICMCS). IEEE, pp 29–34
Esmaili E, Akoglu A, Ditzler G, Hariri S, Moukabary T, Szep J (2017) Autonomic management of 3D cardiac simulations. In: 2017 International Conference on Cloud and Autonomic Computing (ICCAC). IEEE, pp 1–9
Yu D, Du D, Yang H, Tu Y (2014) Parallel computing simulation of electrical excitation and conduction in the 3D human heart. In: 2014 36th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC). IEEE, pp 4315–4319
Chai J, Wen M, Wu N, Huang D, Yang J, Cai X, Zhang C, Yang Q (2013) Simulating cardiac electrophysiology in the era of GPU-cluster computing. IEICE Trans Inf Syst 96(12):2587–2595
Neic A, Liebmann M, Hoetzl E, Mitchell L, Vigmond EJ, Haase G, Plank G (2012) Accelerating cardiac bidomain simulations using graphics processing units. IEEE Trans Biomed Eng 59(8):2281–2290
Higham J, Aslanidi O, Zhang H (2011) Large speed increase using novel GPU based algorithms to simulate cardiac excitation waves in 3D rabbit ventricles. In: Computing in Cardiology, 2011. IEEE, pp 9–12
Zhang L, Wang K, Zuo W, Gai C (2014) G-Heart: a GPU-based system for electrophysiological simulation and multi-modality cardiac visualization. J Comput 9(2):360–368
Xia Y, Wang K, Zhang H (2015) Parallel optimization of 3D cardiac electrophysiological model using GPU. Comput Math Methods Med 2015:1–10
Mirams GR, Arthurs CJ, Bernabeu MO, Bordas R, Cooper J, Corrias A, Davit Y, Dunn SJ, Fletcher AG, Harvey DG et al (2013) Chaste: an open source C++ library for computational physiology and biology. PLoS Comput Biol 9(3):e1002970
Yang J, Chai J, Wen M, Wu N, Zhang C (2013) Solving the cardiac model using multi-core CPU and many integrated cores (MIC). In: 2013 IEEE 10th International Conference on High Performance Computing and Communications & 2013 IEEE International Conference on Embedded and Ubiquitous Computing (HPCC\_EUC). IEEE, pp 1009–1015
Langguth J, Lan Q, Gaur N, Cai X, Wen M, Zhang CY (2016) Enabling tissue-scale cardiac simulations using heterogeneous computing on Tianhe-2. In: 2016 IEEE 22nd International Conference on Parallel and Distributed Systems (ICPADS). IEEE, pp 843–852
Arevalo HJ, Vadakkumpadan F, Guallar E, Jebb A, Malamas P, Wu KC, Trayanova NA (2016) Arrhythmia risk stratification of patients after myocardial infarction using personalized heart models. Nat Commun 7:11437
Karma A (1994) Electrical alternans and spiral wave breakup in cardiac tissue. Chaos: an Interdisciplinary. J Nonlinear Sci 4(3):461–472
Iyer V, Mazhari R, Winslow RL (2004) A computational model of the human left-ventricular epicardial myocyte. Biophys J 87(3):1507–1525
Ten Tusscher K, Noble D, Noble PJ, Panfilov AV (2004) A model for human ventricular tissue. Am J Physiol-Heart Circ Physiol 286(4):H1573–H1589
Ten Tusscher KH, Panfilov AV (2006) Alternans and spiral breakup in a human ventricular tissue model. Am J Physiol-Heart Circ Physiol 291(3):H1088–H1100
Luo Ch, Rudy Y (1991) A model of the ventricular cardiac action potential. Depolarization, repolarization, and their interaction. Circ Res 68(6):1501–1526
Mahajan A, Shiferaw Y, Sato D, Baher A, Olcese R, Xie LH, Yang MJ, Chen PS, Restrepo JG, Karma A et al (2008) A rabbit ventricular action potential model replicating cardiac dynamics at rapid heart rates. Biophys J 94(2):392–410
Bondarenko VE, Szigeti GP, Bett GC, Kim SJ, Rasmusson RL (2004) Computer model of action potential of mouse ventricular myocytes. Am J Physiol-Heart Circ Physiol 287(3):H1378–H1403
Shannon TR, Wang F, Puglisi J, Weber C, Bers DM (2004) A mathematical treatment of integrated Ca dynamics within the ventricular myocyte. Biophys J 87(5):3351–3371
Nickerson DP, Hunter PJ (2010) Cardiac cellular electrophysiological modeling. Cardiac electrophysiology methods and models. Springer, Boston, pp 135–158
Majumder R, Nayak AR, Pandit R (2011) Scroll-wave dynamics in human cardiac tissue: lessons from a mathematical model with inhomogeneities and fiber architecture. PLOS ONE 6(4):e18052
Majumder R, Nayak AR, Pandit R (2012) Nonequilibrium arrhythmic states and transitions in a mathematical model for diffuse fibrosis in human cardiac tissue. PLoS ONE 7(10):e45040
Nayak AR, Shajahan T, Panfilov A, Pandit R (2013) Spiral-wave dynamics in a mathematical model of human ventricular tissue with myocytes and fibroblasts. PloS ONE 8(9):e72950
Smaill BH, Hunter PJ (2010) Computer modeling of electrical activation: from cellular dynamics to the whole heart. Cardiac electrophysiology methods and models. Springer, Boston, pp 159–185
Morton KW, Mayers DF (2005) Numerical solution of partial differential equations: an introduction. Cambridge University Press, Cambridge
Cuellar AA, Lloyd CM, Nielsen PF, Bullivant DP, Nickerson DP, Hunter PJ (2003) An overview of CellML 1.1, a biological model description language. Simulation 79(12):740–747
Nvidia Corporation (2017) Nvidia CUDA C programming guide, version 8.0. https://docs.nvidia.com/cuda/cuda-c-programming-guide/ . Accessed June 2017
Eager DL, Zahorjan J, Lazowska ED (1989) Speedup versus efficiency in parallel systems. IEEE Trans Comput 38(3):408–423
Arioli M (2004) A stopping criterion for the conjugate gradient algorithm in a finite element method framework. Numer Math 97(1):1–24
Zhang C, Lan H, Ye Y, Estrade BD (2005) Parallel SOR iterative algorithms and performance evaluation on a Linux cluster. Technical report, Naval Research Laboratory Stennis Space Center MS Oceanography Division
Hadjidimos A (2000) Successive overrelaxation (SOR) and related methods. J Comput Appl Math 123(1–2):177–199
Hackbusch W (1994) Iterative solution of large sparse systems of equations, vol 95. Springer, New York
Marsh M (2012) An assessment of numerical methods for cardiac simulation. Ph.D. thesis, University of Saskatchewan