Software

FZJ-2023-03030

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Arbor Library (v0.9.0)

Akar, N. A. ; Biddiscombe, J. ; Cumming, B. ; Kabic, M. ; Karakasis, V. ; Klijn, W.FZJ* ; Küsters, A.FZJ* ; Peyser, A.FZJ* ; Yates, S. ; Hater, T.FZJ* ; Huisman, B. (Corresponding author)FZJ* ; Hagen, E. ; Schepper, R. D. ; Linssen, C.FZJ* ; Stoppels, H. ; Schmitt, S. ; Huber, F. ; Engelen, M. ; Bösch, F. ; Luboeinski, J. ; Frasch, S. ; Drescher, L. ; Landsmeer, L.

2023

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Please use a persistent id in citations: doi:10.5281/ZENODO.8233847

Abstract: After much more delay than anticipated, we are very happy to present a new Arbor release. Nearly 8 months of work is in it, much of which focussed on speed, optimisation, fixes and build system changes. This release includes Python 3.12 wheels as probably one of the first packages on PyPI.Major new features:(1) External Connectivity: Arbor can now interface with other simulators or processes through MPI. Contexts now accept a second MPI communicator and Recipes can implement a  external_connections_on  method to specify how simulations might be interacting.  See documentation for more. (2) Arbor now supports checkpointing and resume from a previously stored checkpoint. Useful when a certain point in time needs to be explored in multiple directions, when you want to rewind to a previous state, etc.  See documentation for more.(3) More painted parameters are now scalable through  iexpr : temperature, capacitance, resistivity, membrane potential and the following ionic parameters: internal and external concentration, diffusivity, and reversal potential.  See documentation.(4) A set of ANN activation functions for NMODL have been added:  sigmoid(x) ,  relu(x)  and  tanh(x) . Control volume  area  is exposed through NMODL.(5) A revamped backend for ARM CPU's that support Scalable Vector Extension (SVE). Arbor and modcc are now fully compatible, so users who have access to A64FX-based HPC can take full advantage of that hardware.

Keyword(s): neuroscience ; computational neuroscience ; morpholically detailed simulator

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Contributing Institute(s):

1. Jülich Supercomputing Center (JSC)

Research Program(s):

1. 5111 - Domain-Specific Simulation & Data Life Cycle Labs (SDLs) and Research Groups (POF4-511) (POF4-511)
2. HBP SGA3 - Human Brain Project Specific Grant Agreement 3 (945539) (945539)
3. SLNS - SimLab Neuroscience (Helmholtz-SLNS) (Helmholtz-SLNS)

Appears in the scientific report 2023

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