"Modern asynchronous runtime systems allow the re-thinking of large-scale scientific applications. With the example of a simulator of morphologically detailed neural networks, we show how detaching from the commonly used bulk-synchronous parallel (BSP) execution allows for the increase of prefetching capabilities, better cache locality, and a overlap of computation and communication, consequently leading to a lower time to solution. Our strategy removes the operation of collective synchronization of ODEs’ coupling information, and takes advantage of the pairwise time dependency between equations, leading to a fully-asynchronous exhaustive yet not speculative stepping model. Combined with fully linear data structures, communication reduce at compute node level, and an earliest equation steps first scheduler, we perform an acceleration at the cache level that reduces communication and time to solution by maximizing the number of timesteps taken per neuron at each iteration. Our methods were implemented on the core kernel of the NEURON scientific application. Asynchronicity and distributed memory space are provided by the HPX runtime system for the ParalleX execution model. Benchmark results demonstrate a superlinear speed-up that leads to a reduced runtime compared to the bulk synchronous execution, yielding a speed-up between 25% to 65% across different compute architectures, and in the order of 15% to 40% for distributed executions."
Model Type: Realistic Network
Model Concept(s): Methods
Simulation Environment: NEURON (web link to model)
Implementer(s): Magalhães, Bruno [brunomaga at gmail.com]
References:
Magalhães BR, Sterling T, Hines M, Schürmann F. (2019). Fully-Asynchronous Cache-Efficient Simulation of Detailed Neural Networks Computational Science -- ICCS 2019.
Magalhães BRC, Sterling T, Hines M, Schürmann F. (2019). Asynchronous Branch-Parallel Simulation of Detailed Neuron Models. Frontiers in neuroinformatics. 13 [PubMed]
Magalhães B, Hines M, Sterling T, Schüermann F. (2019). Exploiting Flow Graph of System of ODEs to Accelerate the Simulation of Biologically-Detailed Neural Networks 2019 IEEE International Parallel and Distributed Processing Symposium (IPDPS).