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HPC parallel implementation combining NEST Simulator and Python modules

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Abstract

The paper presents a supercomputer parallel implementation of a brain inspired model combining a Python module simulating a layer of retina ganglion cells and NEST Simulator for a layer of spike timing neurons of Lateral geniculate nucleus (LGN) in the brain. Since the Python module appeared to be the bottleneck in the developed hierarchical model of human visual system, the proposed two parallel implementations of that module were combined with NEST Simulator in a single module. Simulations of developed module on different number of nodes and varying number of parallel processes were investigated and compared with respect to their time consumption.

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Data availability

Not applicable.

Code availability

We will provide the code of our software on github after acceptance of the manuscript for publication.

Notes

  1. https://www.nest-simulator.org/.

  2. http://www.opensourcebrain.org/projects/111.

  3. https://mpi4py.readthedocs.io/en/stable/index.html.

  4. http://www.hpc.acad.bg/system-1/.

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Acknowledgements

We acknowledge the provided access to the e-infrastructure of the NCHDC—part of the Bulgarian National Roadmap on RIs, with the financial support by the Grant No. DO\(1-387/18.12.2020\). It is a significantly extended version of our work presented at the International Conference INISTA'2020.

Funding

Simona Nedelcheva was supported by the Bulgarian National Scientific Program Young Scientists and Postdocs, Module Young Scientists.

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Authors and Affiliations

  1. Institute of Information and Communication Technologies, Bulgarian Academy of Sciences, Acad. G. Bonchev str. bl.25A, 1113, Sofia, Bulgaria

    Simona Nedelcheva, Sofiya Ivanovska, Mariya Durchova & Petia Koprinkova-Hristova

Authors
  1. Simona Nedelcheva
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  2. Sofiya Ivanovska
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  3. Mariya Durchova
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  4. Petia Koprinkova-Hristova
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Contributions

SN and PK-H developed the Python and NEST modules and conducted their parallel implementation and simulation experiments. MD and SI supported HPC implementation and software installation on Avitohol supercomputer.

Corresponding author

Correspondence to Petia Koprinkova-Hristova.

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The authors declare that they have no conflict of interest.

Research involving human and animal participants

The conducted research did not include humans or animal participants.

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Nedelcheva, S., Ivanovska, S., Durchova, M. et al. HPC parallel implementation combining NEST Simulator and Python modules. Cluster Comput 25, 1637–1644 (2022). https://doi.org/10.1007/s10586-021-03422-0

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  • DOI: https://doi.org/10.1007/s10586-021-03422-0

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