Parallel network simulations with NEURON
The NEURON simulation environment has been extended to support parallel network simulations. Each processor integrates the equations for its subnet over an interval equal to the minimum (interprocessor) presynaptic spike generation to postsynaptic spike delivery connection delay. The performance of three published network models with very different spike patterns exhibits superlinear speedup on Beowulf clusters and demonstrates that spike communication overhead is often less than the benefit of an increased fraction of the entire problem fitting into high speed cache. On the EPFL IBM Blue Gene, almost linear speedup was obtained up to 100 processors. Increasing one model from 500 to 40,000 realistic cells exhibited almost linear speedup on 2000 processors, with an integration time of 9.8 seconds and communication time of 1.3 seconds. The potential for speed-ups of several orders of magnitude makes practical the running of large network simulations that could otherwise not be explored.
KeywordsComputer simulation Realistic modeling Parallel computation Spiking networks
- Almási G, Heidelberger P, Archer CJ, Martorell X, Erway CC, Moreira JE, Steinmacher-Burow B, Zheng Y (2005) Optimization of MPI collective communication on BlueGene/L systems, Proc. 19th annual international conference on Supercomputing, Cambridge MA, pp. 253–262.Google Scholar
- Carriero N, Gelernter D (1989) Linda in context. Communications of the ACM, April 1989.Google Scholar
- Goddard NH, Hood G (1998) Large-scale simulation using parallel GENESIS. In: JM Bower, D Beeman eds. The Book of GENESIS, 2nd edn. Springer-Verlag.Google Scholar
- Hammarlund P, Ekeberg Ö, Wilhelmsson T, Lansner A (1996): Large neural network simulations on multiple hardware platforms. In: JM Bower (ed), The Neurobiology of Computation, Boston.Google Scholar
- Hindmarsh A, Serban R (2002) User documentation for CVODES, an ODE solver with sensitivity analysis capabilities.Tech. rep., Lawrence Livermore National Laboratory. http://www.llnl.gov/ CASC/sundials/.
- Markram H (2006) The Blue Brain project, Nature Rev. Neurosci 7: 153–160.Google Scholar
- Myers R (2000) http://www.mtsu.edu/~csjudy/STL/HashMap.h
- Wilson EC, Goodman PH, Harris FC (2001) Implementation of a Biologically Realistic Parallel Neocortical-Neural Network Simulator. Proceedings of the Tenth SIAM Conf. on Parallel Process. for Sci. Comp. March 12–14, 2001 Portsmouth, Virginia.Google Scholar