title: Large-scale modeling of epileptic seizures: scaling properties of two parallel neuronal network simulation algorithms.
abstract: Our limited understanding of the relationship between the behavior of individual neurons and large neuronal networks is an important limitation in current epilepsy research and may be one of the main causes of our inadequate ability to treat it. Addressing this problem directly via experiments is impossibly complex; thus, we have been developing and studying medium-large-scale simulations of detailed neuronal networks to guide us. Flexibility in the connection schemas and a complete description of the cortical tissue seem necessary for this purpose. In this paper we examine some of the basic issues encountered in these multiscale simulations. We have determined the detailed behavior of two such simulators on parallel computer systems. The observed memory and computation-time scaling behavior for a distributed memory implementation were very good over the range studied, both in terms of network sizes (2,000 to 400,000 neurons) and processor pool sizes (1 to 256 processors). Our simulations required between a few megabytes and about 150 gigabytes of RAM and lasted between a few minutes and about a week, well within the capability of most multinode clusters. Therefore, simulations of epileptic seizures on networks with millions of cells should be feasible on current supercomputers.
authors.affiliation: Department of Pediatrics, The University of Chicago, Chicago, IL 60637, USA ; Computation Institute, The University of Chicago and Argonne National Laboratories, Argonne, IL 60439, USA.
authors.forename: Lorenzo L
authors.initials: LL
authors.lastname: Pesce
authors.affiliation: Department of Pediatrics, The University of Chicago, Chicago, IL 60637, USA.
authors.forename: Hyong C
authors.initials: HC
authors.lastname: Lee
authors.affiliation: Computation Institute, The University of Chicago and Argonne National Laboratories, Argonne, IL 60439, USA ; Mathematics and Computer Science Division, Argonne National Laboratories, IL 60439, USA.
authors.forename: Mark
authors.initials: M
authors.lastname: Hereld
authors.affiliation: Department of Pediatrics, The University of Chicago, Chicago, IL 60637, USA.
authors.forename: Sid
authors.initials: S
authors.lastname: Visser
authors.affiliation: Computation Institute, The University of Chicago and Argonne National Laboratories, Argonne, IL 60439, USA ; Mathematics and Computer Science Division, Argonne National Laboratories, IL 60439, USA.
authors.forename: Rick L
authors.initials: RL
authors.lastname: Stevens
authors.affiliation: Department of Pediatrics, The University of Chicago, Chicago, IL 60637, USA.
authors.forename: Albert
authors.initials: A
authors.lastname: Wildeman
authors.affiliation: Department of Pediatrics, The University of Chicago, Chicago, IL 60637, USA ; Department of Neurology, The University of Chicago, Chicago, IL 60637, USA ; Committee on Computational Neuroscience, The University of Chicago, Chicago, IL 60637, USA.
authors.forename: Wim
authors.initials: W
authors.lastname: van Drongelen
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D004569:Electroencephalography; D004827:Epilepsy / Q000503:physiopathology*; D006801:Humans; D008954:Models, Biological; D016571:Neural Networks, Computer; D009474:Neurons / Q000502:physiology; D011381:Programming Languages; D012815:Signal Processing, Computer-Assisted; D012984:Software