ModelDB: Cell splitting in neural networks extends strong scaling (Hines et al. 2008)

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

Accession: 97917

Neuron tree topology equations can be split into two subtrees and solved on different processors with no change in accuracy, stability, or computational effort; communication costs involve only sending and receiving two double precision values by each subtree at each time step. Application of the cell splitting method to two published network models exhibits good runtime scaling on twice as many processors as could be effectively used with whole-cell balancing.
Reference: 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 [PubMed]

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Model Information (Click on a link to find other models with that property)

Model Type:	Network;
Brain Region(s)/Organism:	Generic;
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];

Model files

Help downloading and running models Versions

This is the readme for the model from the paper

Hines, Eichner, and Schuermann (2008)
Neuron splitting in compute-bound parallel network simulations enables
runtime scaling with twice as many processors.
J Comput Neurosci (accepted).

The pardentategyrus and nrntraub folders contain splitcell
parallelized versions of the ModelDB models used in fig 3 of the above
paper.

Original serial versions of the models are at
http://senselab.med.yale.edu/modeldb/ShowModel.asp?model=51781
http://senselab.med.yale.edu/modeldb/ShowModel.asp?model=45539
Splitcell modifications to the Santhakumar model began with the
pardentategyrus code at
http://senselab.med.yale.edu/modeldb/ShowModel.asp?model=64229

Note: for autolaunch from ModelDB, after the choice of which of the two
figure 3 models to run, an attempt is made to do the appropriate
nrnivmodl or mknrndll and dynamically load the shared library or dll.
The simulation will stop after setup when launched using the mosinit.hoc
file.

In the pardentgyrus directory, see bg.sh for an example of how
these simulations were run in parallel on the BlueGene.

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