Parallel network simulations with NEURON (Migliore et al 2006)

 Download zip file   Auto-launch 
Help downloading and running models
Accession:64229
The NEURON simulation environment has been extended to support parallel network simulations. The performance of three published network models with very different spike patterns exhibits superlinear speedup on Beowulf clusters.
Reference:
1 . Migliore M, Cannia C, Lytton WW, Markram H, Hines ML (2006) Parallel Network Simulations with NEURON. J Comp Neurosci 21:110-119 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network;
Brain Region(s)/Organism:
Cell Type(s):
Channel(s):
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s): Methods;
Implementer(s): Hines, Michael [Michael.Hines at Yale.edu];
/
netmod
parbulbNet
parbush
pardentategyrus
parscalebush
perf1
README
mkdll.sh
mosinit.hoc
                            
parbush, parbulbNet, and pardentategyrus contain the original and parallelized
versions of the ModelDB models used in fig 4 of
Migliore, Cannia, Lytton, Markram, and Hines (2006)
Parallel Network Simulations with NEURON
J. Comput. Neurosci. 21:110-119
i.e.
http://senselab.med.yale.edu/senselab/modeldb/ShowModel.asp?model=52034
http://senselab.med.yale.edu/senselab/modeldb/ShowModel.asp?model=2730
http://senselab.med.yale.edu/senselab/modeldb/ShowModel.asp?model=51781

The parscalebush directory contains the extended Bush model used to
develop fig 5.

The perf1 directory contains the artificial spikeing net model used to
develop fig 6.

Note: for autolaunch from ModelDB, after the choice of which of the three
figure 4 models to run, an attempt is made to do the appropriate
nrnivmodl or mknrndll and dynamically load the shared library or dll.
In those three directories, see the test1.sh files for an example of how
these simulations were run in parallel. When executed, an out.dat file
containing the spike pattern is created as well as some performance information
written to the perf.dat file.

20120125 update solve methods in parbush/kca.mod parscalebush/kca.mod
from euler to cnexp as per
http://www.neuron.yale.edu/phpbb/viewtopic.php?f=28&t=592
20120323 Replace VERBATIM block use of local dt with dtt since dt is
now a macro.  Update a function prototype used in a VERBATIM block.
20150219 With Michael Hines suggestion, parbush/kca.mod and
parscalebush/kca.mod updated to a derivative block compatible with
cnexp (restores original model epileptiform activity).

Migliore M, Cannia C, Lytton WW, Markram H, Hines ML (2006) Parallel Network Simulations with NEURON. J Comp Neurosci 21:110-119[PubMed]

References and models cited by this paper

References and models that cite this paper

Almasi G, Heidelberger P, Archer CJ, Martorell X, Erway CC, Moreira JE, Steinmacher-burow B, (2005) Optimization of MPI collective communication on BlueGene-L systems Proc. 19th annual international conference on Supercomputing :253-262

Bush PC, Prince DA, Miller KD (1999) Increased pyramidal excitability and NMDA conductance can explain posttraumatic epileptogenesis without disinhibition: a model. J Neurophysiol 82:1748-58 [Journal] [PubMed]

   Cortical network model of posttraumatic epileptogenesis (Bush et al 1999) [Model]

Carriero N, Gelernter D (1989) Linda in context Communications of the ACM, April 1989

Davison AP, Feng J, Brown D (2003) Dendrodendritic inhibition and simulated odor responses in a detailed olfactory bulb network model. J Neurophysiol 90:1921-1935 [Journal] [PubMed]

   Olfactory Bulb Network (Davison et al 2003) [Model]

Delorme A, Thorpe SJ (2003) SpikeNET: an event-driven simulation package for modelling large networks of spiking neurons. Network 14:613-27

Goddard N, Hood G, Howell F, Hines M, De_Schutter E (2001) NEOSIM: Portable largescaleplug and play modelling Neurocomputing 38-40:1657-1661

Goddard NH, Hood G () Large scale simulation with PGENESIS. The Book Of Genesis: Exploring Realistic Neural Models With The General Neural Simulation System

Hammarlund P, Wilhelmsson T, Lansner A (1996) Large neural network simulations on multiple hardware platforms The Neurobiology of Computation, Bower J, ed.

Hindmarsh A, Serban R (2002) User documentation for Cvodes, an ode solver with sensitivity analysis capabilities Tech Rep

Hines ML, Carnevale NT (1997) The NEURON simulation environment. Neural Comput 9:1179-209 [PubMed]

Hines ML, Carnevale NT (2004) Discrete event simulation in the NEURON environment. Neurocomputing 58-60:1117-1122 [Journal]

   Discrete event simulation in the NEURON environment (Hines and Carnevale 2004) [Model]

Howell FW, Dyrhfjeld-johnsen J, Maex R, Goddard N, De_schutter E (2000) A large scale model of the cerebellar cortex using P GENESIS Neurocomuting 32-33:1041-1046

Karypis G, Kumar V (1998) Multilevel k-way partitioning scheme for irregular graphs Journal Of Parallel And Distributed Computing 48:96-129

Lytton WW, Hines ML (2005) Independent variable time-step integration of individual neurons for network simulations. Neural Comput 17:903-21 [Journal] [PubMed]

   Local variable time step method (Lytton, Hines 2005) [Model]

Markram H (2006) The blue brain project. Nat Rev Neurosci 7:153-60 [Journal] [PubMed]

   [241 reconstructed morphologies on NeuroMorpho.Org]

Mattia M, Del Giudice P (2000) Efficient event-driven simulation of large networks of spiking neurons and dynamical synapses. Neural Comput 12:2305-29 [PubMed]

Migliore M, Hoffman DA, Magee JC, Johnston D (1999) Role of an A-type K+ conductance in the back-propagation of action potentials in the dendrites of hippocampal pyramidal neurons. J Comput Neurosci 7:5-15 [Journal] [PubMed]

   CA1 pyramidal neuron (Migliore et al 1999) [Model]

Morrison A, Mehring C, Geisel T, Aertsen AD, Diesmann M (2005) Advancing the boundaries of high-connectivity network simulation with distributed computing. Neural Comput 17:1776-801 [PubMed]

Myers R (2000) http:--www.mtsu.edu-~csjudy-STL-HashMap.h

Santhakumar V, Aradi I, Soltesz I (2005) Role of mossy fiber sprouting and mossy cell loss in hyperexcitability: a network model of the dentate gyrus incorporating cell types and axonal topography. J Neurophysiol 93:437-53 [Journal] [PubMed]

   Dentate gyrus network model (Santhakumar et al 2005) [Model]
   Dentate gyrus (Morgan et al. 2007, 2008, Santhakumar et al. 2005, Dyhrfjeld-Johnsen et al. 2007) [Model]

Wilson EC, Goodman PH, Harris FC (2001) Implementation of a Biologically Realistic Parallel Neocortical-Neural Network Simulator Proceedings of the Tenth SIAM Conference on Parallel Process. for Science Computation

Aisa B, Mingus B, O`Reilly R (2008) The Emergent neural modeling system. Neural Netw [Journal] [PubMed]

Garci­a-Grajales JA, Rucabado G, Garci­a-Dopico A, Pena JM, Jerusalem A (2015) Neurite, a Finite Difference Large Scale Parallel Program for the Simulation of Electrical Signal Propagation in Neurites under Mechanical Loading. PLoS One 10(2):e0116532 [Journal] [PubMed]

   Neurite: electrophysiological-mechanical coupling simulation framework (Garcia-Grajales et al 2015) [Model]

Giugliano M, Gambazzi L, Ballerini L, Prato M, Campidelli S (2012) Carbon nanotubes as electrical interfaces to neurons Nanotechnology for Biology and Medicine, Parpura V, Silva GA, ed. pp.187 [Journal]

   Carbon nanotubes as electrical interfaces to neurons (Giugliano et al. 2008) [Model]

Gleeson P, Steuber V, Silver RA (2007) neuroConstruct: a tool for modeling networks of neurons in 3D space. Neuron 54:219-35 [Journal] [PubMed]

Hines M, Eichner H, Schuermann F (2008) Neuron splitting in compute-bound parallel network simulations enables runtime scaling with twice as many processors J Comput Neurosci 25(1):203-210 [Journal] [PubMed]

   Cell splitting in neural networks extends strong scaling (Hines et al. 2008) [Model]

Hines M, Kumar S, Schuermann F (2011) Comparison of neuronal spike exchange methods on a Blue Gene/P supercomputer. Frontiers in Computational Neuroscience 5:49 [Journal]

   Spike exchange methods for a Blue Gene/P supercomputer (Hines et al., 2011) [Model]

Hines ML, Davison AP, Muller E (2009) NEURON and Python Frontiers in Neuroinformatics 3:1 [Journal] [PubMed]

   NEURON + Python (Hines et al. 2009) [Model]

Hines ML, Markram H, Schuermann F (2008) Fully Implicit Parallel Simulation of Single Neurons J Comp Neurosci 25:439-448 [Journal] [PubMed]

   Fully Implicit Parallel Simulation of Single Neurons (Hines et al. 2008) [Model]

Kozloski J, Wagner J (2011) An Ultrascalable Solution to Large-scale Neural Tissue Simulation. Front Neuroinform 5:15 [Journal] [PubMed]

Linaro D, Storace M, Giugliano M (2011) Accurate and fast simulation of channel noise in conductance-based model neurons by diffusion approximation PLOS 7:e1001102 [Journal] [PubMed]

   Accurate and fast simulation of channel noise in conductance-based model neurons (Linaro et al 2011) [Model]

Lytton WW, Neymotin SA, Hines ML (2008) The virtual slice setup. J Neurosci Methods 171:309-15 [Journal] [PubMed]

   The virtual slice setup (Lytton et al. 2008) [Model]

Lytton WW, Omurtag A (2007) Tonic-clonic transitions in computer simulation. J Clin Neurophysiol 24:175-81 [PubMed]

   Tonic-clonic transitions in a seizure simulation (Lytton and Omurtag 2007) [Model]

Lytton WW, Seidenstein AH, Dura-Bernal S, McDougal RA, Schurmann F, Hines ML (2016) Simulation Neurotechnologies for Advancing Brain Research: Parallelizing Large Networks in NEURON. Neural Comput :1-28 [Journal] [PubMed]

   Parallelizing large networks in NEURON (Lytton et al. 2016) [Model]

Markram H, Muller E, Ramaswamy S, Reimann MW, Abdellah M, Sanchez CA, Ailamaki A, Alonso-Nanclares L, Antille N, Arsever S, Kahou GA, Berger TK, Bilgili A, Buncic N, Chalimourda A, Chindemi G, Courcol JD, Delalondre F, Delattre V, Druckmann S, Dumusc R, Dynes J, Eilemann S, Gal E, Gevaert ME, Ghobril JP, Gidon A, Graham JW, Gupta A, Haenel V, Hay E, Heinis T, Hernando JB, Hines M, Kanari L, Keller D, Kenyon J, Khazen G, Kim Y, King JG, Kisvarday Z, Kumbhar P, Lasserre S, Le Be JV, Magalhães BR, Merchan-Perez A, Meystre J, Morrice BR, Muller J, Muñoz-Cespedes A, et al. (2015) Reconstruction and Simulation of Neocortical Microcircuitry. Cell 163:456-92 [Journal] [PubMed]

McDougal RA, Bulanova AS, Lytton WW (2016) Reproducibility in computational neuroscience models and simulations Transactions on Biomedical Engineering, online before print [Journal]

Schneider CJ, Cuntz H, Soltesz I (2014) Linking Macroscopic with Microscopic Neuroanatomy Using Synthetic Neuronal Populations. PLoS Comput Biol 10:e1003921 [Journal] [PubMed]

   Generation of granule cell dendritic morphology (Schneider et al. 2014) [Model]

Soudry D, Meir R (2014) The neuronal response at extended timescales: a linearized spiking input-output relation. Front Comput Neurosci 8:29 [Journal] [PubMed]

   Method for deriving general HH neuron model`s spiking input-output relation (Soudry & Meir 2014) [Model]

van Drongelen W, Lee HC, Stevens RL, Hereld M (2007) propagation of seizure-like activity in a model of neocortex. J Clin Neurophysiol 24:182-8 [PubMed]

(39 refs)