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

 Download zip file   Auto-launch 
Help downloading and running models
Tests several spike exchange methods on a Blue Gene/P supercomputer on up to 64K cores.
1 . 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
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network;
Brain Region(s)/Organism:
Cell Type(s):
Gap Junctions:
Simulation Environment: NEURON;
Model Concept(s): Methods;
Implementer(s): Hines, Michael [Michael.Hines at Yale.edu];
Generates figures 3-9 of 
Hines M, Kumar S, Schuermann F (2011).
Comparison of neuronal spike exchange methods on a Blue Gene/P supercomputer.
Frontiers in Computational Neuroscience.

See http://www.neuron.yale.edu/hg/z/neuron/nrnbgp/ for the NEURON version
actually used to carry out the simulation on the Blue Gene/P.
Figures 3 and 9 require this version as the hoc code uses several features
not yet available in the standard versions. The relevant statements are:
init.hoc: {pc.timeout(1)}
net.hoc: pc.gid_clear(4)
param.hoc and perfrun.hoc: any use of pc.send_time(x) with x > 4

The DCMF_Multicast methods used in the paper are specific to the Blue Gene/P.
However the MPI multisend implementation can be used on any MPI installed
system. In particular the two-phase exchange method may be useful.
The exchange methods are implemented mostly in src/nrniv/bgpdma.cpp .

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

References and models cited by this paper

References and models that cite this paper

Ananthanarayanan R, Esser SK, Simon HD, Modha DS (2009) The cat is out of the bag:cortical simulations with 10^9 neurons and 10^13 synapses Supercomputing `09: Proceedings of the ACM/IEEE SC2009 Conference on High Performance Networking and Computing, Portland, OR

Ananthanarayanan R, Modha DS (2007) Anatomy of a cortical simulator Supercomputing `07: Proceedings of the ACM/IEEE SC2007 Conference on High Performance Netowrking and Computing, Reno, NV

Djurfeldt M, Hjorth J, Eppler JM, Dudani N, Helias M, Potjans TC, Bhalla US, Diesmann M, Kota (2010) Run-time interoperability between neuronal network simulators based on the MUSIC framework. Neuroinformatics 8:43-60 [PubMed]

Djurfeldt M, Johansson C, Ekeberg O, Rehn M, Lundqvist M, Lansner A (2005) Massively parallel simulationof brain-scale neuronal network models Technical Report TRITA-NA-P0513, School of Computer Science and Communication, Stockholm

Eppler JM, Plesser HE, Morrison A, Diesmann M, Gewaltig MO (2007) Multithreaded and distributed simulation of large biological neuronal networks Proceedings of European PVM-MPI 2007 4757:391-392

Gewaltig M-O, Diesmann M (2007) NEST (Neural Simulation Tool) Scholarpedia 2:1430

Hereld M, Stevens RL, Teller J, Drongelen W (2005) Large neural simulations on large parallel computers Int J Bioelectromagn 7:44-46

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

Kumar S, Et AL (2008) The deep computing messaging framework: generalized scalable message passing on the Blue Gene/P Supercomputer The 22nd ACM International Conference on Supercomputing (ICS), Island of Kos, Greece

Kumar S, Heidelberger P, Chen D, Hines M (2010) Optimization of applications with non-blocking neighborhood collectives via multisends on the blue gene/p supercomputer Proceedings IEEE International Parallel & Distributed Processing (IPDPS) Symposium, Atlanta, GA :1-11

Kunkel S, Potjans TC, Morrison A, Diesmann M (2009) Simulating macroscale brain circuits with microscale resolution Frontiers in Neuroinformatics. Conference Abstract: 2nd INCF Congress of Neuroinformatics

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

   [241 reconstructed morphologies on NeuroMorpho.Org]

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

   Parallel network simulations with NEURON (Migliore et al 2006) [Model]

Tam A, Wang C (2000) Efficient scheduling of complete exchange on clusters The 13th International Conference on Parallel and Distributed Computing Systems (PDCS), Las Vegas

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

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]

   [5 reconstructed morphologies on NeuroMorpho.Org]

Migliore M, Cavarretta F, Hines ML, Shepherd GM (2014) Distributed organization of a brain microcircuit analysed by three-dimensional modeling: the olfactory bulb Front. Comput. Neurosci. 8:50 [Journal]

   3D model of the olfactory bulb (Migliore et al. 2014) [Model]

(18 refs)