Parallel network simulations with NEURON (Migliore et al 2006)

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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]
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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).