Optimizing NEURON Simulation Environment Using Remote Memory Access with Recursive Doubling on Distributed Memory Systems
Joint Authors
Source
Computational Intelligence and Neuroscience
Issue
Vol. 2016, Issue 2016 (31 Dec. 2015), pp.1-10, 10 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2016-06-20
Country of Publication
Egypt
No. of Pages
10
Main Subjects
Abstract EN
Increase in complexity of neuronal network models escalated the efforts to make NEURON simulation environment efficient.
The computational neuroscientists divided the equations into subnets amongst multiple processors for achieving better hardware performance.
On parallel machines for neuronal networks, interprocessor spikes exchange consumes large section of overall simulation time.
In NEURON for communication between processors Message Passing Interface (MPI) is used.
MPI_Allgather collective is exercised for spikes exchange after each interval across distributed memory systems.
The increase in number of processors though results in achieving concurrency and better performance but it inversely affects MPI_Allgather which increases communication time between processors.
This necessitates improving communication methodology to decrease the spikes exchange time over distributed memory systems.
This work has improved MPI_Allgather method using Remote Memory Access (RMA) by moving two-sided communication to one-sided communication, and use of recursive doubling mechanism facilitates achieving efficient communication between the processors in precise steps.
This approach enhanced communication concurrency and has improved overall runtime making NEURON more efficient for simulation of large neuronal network models.
American Psychological Association (APA)
Shehzad, Danish& Bozkuş, Zeki. 2016. Optimizing NEURON Simulation Environment Using Remote Memory Access with Recursive Doubling on Distributed Memory Systems. Computational Intelligence and Neuroscience،Vol. 2016, no. 2016, pp.1-10.
https://search.emarefa.net/detail/BIM-1099663
Modern Language Association (MLA)
Shehzad, Danish& Bozkuş, Zeki. Optimizing NEURON Simulation Environment Using Remote Memory Access with Recursive Doubling on Distributed Memory Systems. Computational Intelligence and Neuroscience Vol. 2016, no. 2016 (2015), pp.1-10.
https://search.emarefa.net/detail/BIM-1099663
American Medical Association (AMA)
Shehzad, Danish& Bozkuş, Zeki. Optimizing NEURON Simulation Environment Using Remote Memory Access with Recursive Doubling on Distributed Memory Systems. Computational Intelligence and Neuroscience. 2016. Vol. 2016, no. 2016, pp.1-10.
https://search.emarefa.net/detail/BIM-1099663
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-1099663