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Parallel algorithms for simulating interacting carriers in nanocommunication

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Abstract
Diffusion-based molecular communication (DMC) with interacting carrier molecules allows exploring a variety of new communication paradigms. Simulating these interactions on a network scale is however hard from an analytic point of view, and continuous detection of which couples of particles may interact is a computationally expensive task. This work proposes different algorithms that allow detecting which particles are interacting. Hierarchical grid based approaches are explored and designed to maximally exploit the parallelism offered by multiple-graphics processing units (multi-GPU) systems. An implementation of the proposed algorithm is compared to some of our previous work in this domain and to a state-of-the-art collision detection library and nanosimulator. Performance tests indicate a speedup of up to a factor 100 compared to the collision detection algorithm implemented in the nanosimulator, and a factor 77 relative to the collision detection library. (C) 2019 Elsevier B.V. All rights reserved.
Keywords
DIFFUSION, Collision detection, Multi-level grids, Nanocommunication, Molecular, communications (MolCom), Multi-GPU system

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Please use this url to cite or link to this publication:

MLA
Stroobant, Pieter, et al. “Parallel Algorithms for Simulating Interacting Carriers in Nanocommunication.” NANO COMMUNICATION NETWORKS, vol. 20, Elsevier, 2019, pp. 20–30.
APA
Stroobant, P., Felicetti, L., Colle, D., Tavernier, W., Femminella, M., Reali, G., & Pickavet, M. (2019). Parallel algorithms for simulating interacting carriers in nanocommunication. NANO COMMUNICATION NETWORKS, 20, 20–30.
Chicago author-date
Stroobant, Pieter, Luca Felicetti, Didier Colle, Wouter Tavernier, Mauro Femminella, Gianluca Reali, and Mario Pickavet. 2019. “Parallel Algorithms for Simulating Interacting Carriers in Nanocommunication.” NANO COMMUNICATION NETWORKS 20: 20–30.
Chicago author-date (all authors)
Stroobant, Pieter, Luca Felicetti, Didier Colle, Wouter Tavernier, Mauro Femminella, Gianluca Reali, and Mario Pickavet. 2019. “Parallel Algorithms for Simulating Interacting Carriers in Nanocommunication.” NANO COMMUNICATION NETWORKS 20: 20–30.
Vancouver
1.
Stroobant P, Felicetti L, Colle D, Tavernier W, Femminella M, Reali G, et al. Parallel algorithms for simulating interacting carriers in nanocommunication. NANO COMMUNICATION NETWORKS. 2019;20:20–30.
IEEE
[1]
P. Stroobant et al., “Parallel algorithms for simulating interacting carriers in nanocommunication,” NANO COMMUNICATION NETWORKS, vol. 20, pp. 20–30, 2019.
@article{8617629,
  abstract     = {Diffusion-based molecular communication (DMC) with interacting carrier molecules allows exploring a variety of new communication paradigms. Simulating these interactions on a network scale is however hard from an analytic point of view, and continuous detection of which couples of particles may interact is a computationally expensive task. This work proposes different algorithms that allow detecting which particles are interacting. Hierarchical grid based approaches are explored and designed to maximally exploit the parallelism offered by multiple-graphics processing units (multi-GPU) systems. An implementation of the proposed algorithm is compared to some of our previous work in this domain and to a state-of-the-art collision detection library and nanosimulator. Performance tests indicate a speedup of up to a factor 100 compared to the collision detection algorithm implemented in the nanosimulator, and a factor 77 relative to the collision detection library. (C) 2019 Elsevier B.V. All rights reserved.},
  author       = {Stroobant, Pieter and Felicetti, Luca and Colle, Didier and Tavernier, Wouter and Femminella, Mauro and Reali, Gianluca and Pickavet, Mario},
  issn         = {1878-7789},
  journal      = {NANO COMMUNICATION NETWORKS},
  keywords     = {DIFFUSION,Collision detection,Multi-level grids,Nanocommunication,Molecular,communications (MolCom),Multi-GPU system},
  language     = {eng},
  pages        = {20--30},
  publisher    = {Elsevier},
  title        = {Parallel algorithms for simulating interacting carriers in nanocommunication},
  url          = {http://dx.doi.org/10.1016/j.nancom.2019.02.002},
  volume       = {20},
  year         = {2019},
}

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