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v0.9.0

** 2023 08 09 **

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

  • 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.
  • 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.
  • 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.
  • 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.
  • 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.

Breaking changes since v0.8.1

  • It is no longer possible to set binning and sampling policies, due to Arbor now having a fixed timestep. Removing exact delivery increases the speed of the simulation due to elimination of small steps, makes the numerics independent of presence of sampling, and also leads to a number of code simplifications.
  • Contexts are now constructed kwargs-only. So, arbor.context(12, None) is now arb.context(threads=12, gpu=None). In the case no arguments are supplied, the context initialized to default_allocation, which means it will use the total number of threads and first GPU that are locally available. arbor.simulation constructed without an explicit arbor.context also initializes a default_allocation.
  • Version bumps:
    • CUDA 11 or higher is required for GPU builds.

Full commit log

Neuroscience, documentation

Core

  • Better handling of powers in modcc. by @thorstenhater in arbor-sim#2061
  • Silence spurious unused variable warnings in generated code by @bcumming in arbor-sim#2073
  • BluePyOpt API updates by @lukasgd in arbor-sim#2045
  • Add some missing #include directives by @musicinmybrain in arbor-sim#2080
  • Remove redundant sample events structure. by @thorstenhater in arbor-sim#2079
  • 🧹 Re-factor FVM lowered cell implementation and shared state by @thorstenhater in arbor-sim#2082
  • Take less locks for shorter times when sampling. by @thorstenhater in arbor-sim#2093
  • Fix LIF oversampling. by @thorstenhater in arbor-sim#2091
  • 📊 Pin threads by @thorstenhater in arbor-sim#2094
  • Add zero'ing by @thorstenhater in arbor-sim#2107
  • Add an error on NET_RECEIVE w/ > 1 args. by @thorstenhater in arbor-sim#2127
  • Update busyring to generate rings by @bcumming in arbor-sim#2144
  • Apply some polish to model construction. by @thorstenhater in arbor-sim#2134
  • SVE backend by @boeschf in arbor-sim#2148
  • Exit sup::path stage left; enter std::filesystem::path stage right by @thorstenhater in arbor-sim#2165
  • gtest dependency by @boeschf in arbor-sim#2163

Build, testing, CI

Fixes, optimization

New Contributors

Full Changelog: https://github.com/arbor-sim/arbor/compare/v0.8.1...v0.9.0

v0.8.1

** 2022 12 22 **

A 🎄 holiday release! Not much has changed in a month, but we'd like to share it all the same. Notably, the Arbor GUI is co-released as of Arbor v0.8, and v0.8.1 will be no different.

Major new features

  • Voltage Processes: add the VOLTAGE_PROCESS mechanism kind to modcc, allowing for direct writing to the membrane voltage (#2033)
  • Spack gpu option: added conditional variant for cuda builds to enable GPU-based random number generation (#2043)
  • SDE Tutorial (#2044)

Breaking changes since v0.8

  • None 💃!

Bug fixed

  • Fix ornstein_uhlenbeck example on gpu (#2039)
  • Setting ARB_MODCC was broken and nunfunctional. Fixed. (#2029)
  • The --cxx flag in arbor-build-catalogue is now properly used; falls back to c++. (#2051)

Full commit log

  • Post release: add Zenodo entry, add Spack entry, update docs and scripts by @brenthuisman in arbor-sim#2036
  • BUGFIX: add ARB_CUDA flag to example catalogue by @boeschf in arbor-sim#2039
  • Additional builtin functions to Arbor's NMODL dialect by @boeschf in arbor-sim#2035
  • Throw better errors when we cannot look up ion diffusivity by @thorstenhater in arbor-sim#2040
  • ⚡ Voltage Processes by @thorstenhater in arbor-sim#2033
  • simplify make catalogue by @boeschf in arbor-sim#2042
  • spack gpu option by @boeschf in arbor-sim#2043
  • Remove deprecated spike_detector. by @thorstenhater in arbor-sim#2041
  • make ARB_MODCC functional again by @brenthuisman in arbor-sim#2029
  • Yank v0.5 from Spack file, it does not build due to change in setting arch by @brenthuisman in arbor-sim#2037
  • Use pugixml instead of libxml2 by @thorstenhater in arbor-sim#2048
  • [BUGFIX] a-b-c: actually set compiler, improved default by @brenthuisman in arbor-sim#2051
  • Sde Tutorial by @boeschf in arbor-sim#2044
  • Set Python to known version for all CI workflows by @brenthuisman in arbor-sim#2058
  • consistent mechanism ids by @boeschf in arbor-sim#2057
  • Fix docs about exprelr. by @thorstenhater in arbor-sim#2064
  • Allow __ in profiler names. by @thorstenhater in arbor-sim#2065
  • CI fixes for wheel building, prep for musllinux, Spack by @brenthuisman in arbor-sim#2069

v0.8

** 2022 11 15 **

Welcome to another installment of the Arbor simulator!

In this release we add a CHANGELOG, where major new features and breaking changes will be mentioned specifically.

Major new features

  • Stochastic Differential Equations. Introduces sources of white noise to arbor (and nmodl). Both point and density mechanisms may now use white noise as part of the state updates, turning the ODEs effectively into SDEs. The noise sources are provided per connection end point (point mech.) or control volume (density mech.) and are uncorrelated (spatially, temporally and across different mechanism instantiations). arbor-sim#1884
  • Mutable connection table. Add functionality, docs, and examples on editing the connection table. This is a first, small PR on the topic, further functionality will come as requested. arbor-sim#1919
  • Allow editing morphologies. Supported operations: join_at, split_at, equivalence, equality, apply isometry. arbor-sim#1957
  • Arbor cable cell exporter and backend support in BluePyOpt. arbor-sim#1959
  • Make LIF cells probeable. arbor-sim#2021

Breaking changes since v0.7:

  • A change in decor API: arbor.cable_cell has the labels and decor arguments swapped. I.e.: (tree, labels, decor) -> (tree, decor, label). Labels are now optional. arbor-sim#1978
  • Remove the generate-catalogue script. modcc accepts now a list of NMODL files and is able to spit out a catalogue.cpp file. arbor-sim#1975
  • Mechanism ABI version is bumped to 0.3.1. arbor-sim#1884
  • Rename spike detector -> threshold detector. arbor-sim#1976
  • Remove access to time t in NMODL. arbor-sim#1967
  • Major dependency version bumps:
    • GCC: 9 and up
    • CUDA: 11 and up
    • Clang: 10 and up

Full commit log

Neuroscience, documentation

Core

Build, testing, CI

Fixes, optimization

New Contributors

Full Changelog: https://github.com/arbor-sim/arbor/compare/v0.7...v0.8-rc

v0.7

** 2022 07 20 **

What's Changed

Neuroscience/documentation

  • prep extracellular potentials tutorial. Updated corresponding example by @espenhgn in arbor-sim#1825
  • Add documentation on faster NMODL. by @thorstenhater in arbor-sim#1840
  • Add tstop doc in recipe API doc by @schmitts in arbor-sim#1852
  • Use list comprehension to speed up creation of connections by @schmitts in arbor-sim#1864
  • Support markers in neurolucida ascii files by @bcumming in arbor-sim#1867
  • simplified create_polygon function in lfpykit example by @espenhgn in arbor-sim#1881
  • Better key for the lfpykit intersphinx mapping by @Helveg in arbor-sim#1878
  • Sort (in python) the mechanism names (for convenience). by @thorstenhater in arbor-sim#1882
  • Always emit weight expression. by @thorstenhater in arbor-sim#1875
  • Add support for epoch callbacks by @bcumming in arbor-sim#1873
  • Add introspection for global properties. by @thorstenhater in arbor-sim#1890
  • Add point probes to demo by @schmitts in arbor-sim#1891
  • Tut/use avail threads by @brenthuisman in arbor-sim#1900
  • Allen tutorial by @brenthuisman in arbor-sim#1781
  • New policy 'round_robin_halt' by @jlubo in arbor-sim#1868
  • Axial Diffusion by @thorstenhater in arbor-sim#1729
  • Add some convenience to simulation creation. by @thorstenhater in arbor-sim#1904
  • Predefine SWC Regions. by @thorstenhater in arbor-sim#1911
  • Diffusion Example Improvements (and a bit of clean-up) by @thorstenhater in arbor-sim#1914
  • Inhomogeneous parameters by @AdhocMan in arbor-sim#1887
  • Fix line numbers in tutorials and assorted doc corrections by @brenthuisman in arbor-sim#1917

Core

  • 🐍 Be more lenient when accepting args to file I/O by @thorstenhater in arbor-sim#1819
  • modcc: generate missing node_index read needed for reading time t in the mechanisms by @noraabiakar in arbor-sim#1866
  • Add Developer Documentation by @thorstenhater in arbor-sim#1639
  • Isolate external catalogues from libarbor.a. by @thorstenhater in arbor-sim#1837

Build, testing, CI

Fixes, optimization

New Contributors

Full Changelog: https://github.com/arbor-sim/arbor/compare/v0.6...v0.7

v0.6

** 2022 01 26 **

What's Changed

Core API:

  • Add S-Exp for CV Policies by @thorstenhater in arbor-sim#1511
  • Clean-up and extend mech cat iterator interface. by @thorstenhater in arbor-sim#1564
  • Mech ABI: The final step. by @thorstenhater in arbor-sim#1452
  • Add dim3 to gridDim constructor in generated mechanism code by @noraabiakar in arbor-sim#1630
  • Added an empty catalogue by @Helveg in arbor-sim#1677
  • Allow to limit Poisson schedule with a stop time (closes #1617) by @schmitts in arbor-sim#1684
  • Expose profiler to Python by @Helveg in arbor-sim#1688
  • Added a debug mode to build-catalogue by @Helveg in arbor-sim#1686
  • Write build-catalogue (c)make errors to stdout and stderr by @Helveg in arbor-sim#1679
  • Makejobs arg by @Helveg in arbor-sim#1673
  • Feature/python clean memory by @max9901 in arbor-sim#1670
  • Feature/label dict by @apeyser in arbor-sim#1711
  • Add locset expressions for proximal and distal translation of locations by @bcumming in arbor-sim#1671
  • Gap Junction mechanisms by @noraabiakar in arbor-sim#1682
  • Solve non-linear systems that are not kinetic schemes. by @noraabiakar in arbor-sim#1724
  • Add cos and sin SVE implementations by @noraabiakar in arbor-sim#1744
  • Deal with zero radius points in a morphology by @halfflat in arbor-sim#1719
  • Simplify default proc_allocation generation. by @halfflat in arbor-sim#1725
  • Find morphology location from a coordinate by @bcumming in arbor-sim#1751
  • resurrect lmorpho by @schmitts in arbor-sim#1746
  • Expose information about the CV discretization to the public inteface by @noraabiakar in arbor-sim#1758
  • Allow the use of string s-expression CV-policies in pyarb by @noraabiakar in arbor-sim#1799
  • Construct domain_decomposition given a list of group_descriptions. by @noraabiakar in arbor-sim#1788
  • Profile externally loaded mechanisms by @noraabiakar in arbor-sim#1691
  • Have option to set thread count to local maximum by @brenthuisman in arbor-sim#1716

CI/build/testing:

Documentation:

  • arbor.mechanism_catalogue.extend() documentation added. by @brenthuisman in arbor-sim#1597
  • zenodo 0.5.2 entry by @brenthuisman in arbor-sim#1598
  • mpi.py updated for new synapse labelling by @brenthuisman in arbor-sim#1602
  • Tutorial structure: remove deduplication, includify by @brenthuisman in arbor-sim#1575
  • Docs mechabi by @brenthuisman in arbor-sim#1610
  • Improved documentation about weights by @brenthuisman in arbor-sim#1620
  • Adapt to changes in Pandas requiring unique indices by @brenthuisman in arbor-sim#1625
  • Add implies default license by @kanzl in arbor-sim#1635
  • Update Slack to Gitter by @brenthuisman in arbor-sim#1637
  • Better Python installation instructions by @brenthuisman in arbor-sim#1622
  • Add example based on LFPykit example Example_Arbor_swc.ipynb by @espenhgn in arbor-sim#1652
  • Name and describe arguments to constructors where ambiguous. by @brenthuisman in arbor-sim#1678
  • improved Github Issue templates by @brenthuisman in arbor-sim#1698
  • Add some comments about units to network ring examples by @schmitts in arbor-sim#1697
  • Fix link (closes #1664) by @schmitts in arbor-sim#1701
  • Fix class members in cable example by @schmitts in arbor-sim#1641
  • Correctify and seabornize dendrite tutorial by @brenthuisman in arbor-sim#1706
  • Polish GJ example readme by @thorstenhater in arbor-sim#1726
  • Completed the docs with more config() flags by @Helveg in arbor-sim#1708
  • Make connectivity example more complete by @brenthuisman in arbor-sim#1721
  • Add description of arbor and NEURON's nernst application rules to the docs. by @noraabiakar in arbor-sim#1638
  • Show docs version info more prominently on RTD by @brenthuisman in arbor-sim#1737
  • Update/fix tinyopt README.md by @halfflat in arbor-sim#1747
  • Add python gap junction example by @kanzl in arbor-sim#1750
  • Documentation: add expected nmodl units by @noraabiakar in arbor-sim#1756
  • Fixed broken link from get_probes to probes by @Helveg in arbor-sim#1763
  • Removed double preposition by @Helveg in arbor-sim#1762
  • Fixed MD to RST typo by @Helveg in arbor-sim#1760
  • Fix broken links in probe_sample.rst by @Helveg in arbor-sim#1761
  • Docs/contrib updates by @brenthuisman in arbor-sim#1736
  • Add Release procedure to docs by @brenthuisman in arbor-sim#1738
  • Example and tutorial for two cells connected via a gap junction by @schmitts in arbor-sim#1771
  • Have single source for citation info, compatible with Github citation UI by @brenthuisman in arbor-sim#1791
  • Advertise GH Discussions for modelling by @brenthuisman in arbor-sim#1793
  • Add release cycle info to docs by @brenthuisman in arbor-sim#1798
  • Added a warning when users are reading latest docs. by @Helveg in arbor-sim#1800

Fixes/optimization:

  • Fix GPU compile. by @thorstenhater in arbor-sim#1601
  • Compile all arbor source files with -fvisibility=hidden by @noraabiakar in arbor-sim#1599
  • Bug/assorted static analysis by @thorstenhater in arbor-sim#1615
  • Fix ambiguous Region/Locset expressions by @thorstenhater in arbor-sim#1629
  • Clean-up AVX routine and global def [EOM] by @thorstenhater in arbor-sim#1618
  • Categorise ASSIGNED RANGE variables as STATE-ish. by @thorstenhater in arbor-sim#1624
  • Check that mechanisms have the right kind by @noraabiakar in arbor-sim#1633
  • Resolve uninitialised values. by @thorstenhater in arbor-sim#1616
  • Correctly parse diameter in ASCII files by @bcumming in arbor-sim#1640
  • Attempt fixing a64fx build by @bcumming in arbor-sim#1636
  • Fix simulation::add_sampler cell_group dispatch by @noraabiakar in arbor-sim#1654
  • Fix on-components on empty cable bug by @halfflat in arbor-sim#1658
  • Fix cv_policy parse and write in ACC by @noraabiakar in arbor-sim#1665
  • Fixed MRO and code duplication in setup.py by @Helveg in arbor-sim#1672
  • Rephrase exception message in case of missing segment by @schmitts in arbor-sim#1659
  • Fix modcc simd generation by @noraabiakar in arbor-sim#1681
  • Segfault on instantiating mechanisms on empty regions by @thorstenhater in arbor-sim#1657
  • Add missing closing bracket to mechanism repr (closes #1667) by @schmitts in arbor-sim#1699
  • Better handling of errors during dynamic catalogue loading by @thorstenhater in arbor-sim#1702
  • Swap && and || operator precedence in modcc by @noraabiakar in arbor-sim#1710
  • Remove use of removed INSTRUMENT_MALLOC symbols from Glibc 2.34 by @brenthuisman in arbor-sim#1730
  • Generate correct simd code for reading peer_index and v_peer by @noraabiakar in arbor-sim#1735
  • fixes for non-standard code by @boeschf in arbor-sim#1769
  • Modcc: Forward declare procedure kernels in generated GPU code by @noraabiakar in arbor-sim#1787
  • modcc: exit solvers early if errors encountered. by @noraabiakar in arbor-sim#1755
  • Fix cmake configuration of out-of-core fmt library by @bcumming in arbor-sim#1796
  • Bug fix: properly partition networks containing one-sided gap-junction connections by @noraabiakar in arbor-sim#1774
  • Remove footgun: Catalogue Lifetimes by @thorstenhater in arbor-sim#1807

New Contributors

Full Changelog: https://github.com/arbor-sim/arbor/compare/v0.5.2...v0.6

v0.5.2

** 2021 06 24 **

This release fixes an error in the CI generated Python wheels, which are as of this release available on PyPI. Other than those fixes, this release is identical to v0.5.1.

v0.5.1

** 2021 06 22 **

Since v0.5 there have been some major features, and many small fixes and improvements.

Core API features:

  • [C++/Python] Labels instead of indices for placeable item identification.
  • [C++/Python] Morphology file format support: Arbor Cable-Cell Format.
  • [C++/Python] Morphology file format support: Neurolucida ASCII format.
  • [C++/Python] Morphology file format improvements: SWC.
  • [C++/Python] Simplified connections and junctions.
  • [C++/Python] Enable simulation resume/restart.
  • [C++/Python] Add post events functionality to support models with STDP synapses
  • [C++/Python] Allow dynamically creating and loading of mechanism catalogue

Documentation:

  • Documentation URL changed to docs.arbor-sim.org
  • New Python examples and tutorials
  • Ever more complete documentation
  • Added Code of Conduct

Build / CI:

  • Spack distribution
  • CI generated binary Python wheels
  • Apple M1 compatibility
  • CI moved from Travis to Github Actions
  • Improved Python and C++ unit testing
  • ARM CI
  • Sanitizer CI

Contributions by, in no specific order, @haampie, @clinssen, @espenhgn, @Helveg, @brenthuisman, @noraabiakar, @thorstenhater, @halfflat, @schmitts and @bcumming

v0.5

** 2021 01 07 **

Since v0.4 there have been some major features, and many small fixes and improvements.

Core API features:

  • [C++/Python] Numerous small bug fixes, optimizations and improvements.
  • [C++/Python] Refactor cable cell interface to be read only, and be constructed from
    descriptions of morphology, labels, and decorations.
  • [C++/Python]Expose diverse probes and rich interface for describing where and what to sample on cable cells.
  • [C++/Python] Support for querying names in mechanism catalogues
  • [Python] Wrapper for existing C++ pw_lin functionality
  • [C++] Improved validation of recipe definitions during model building

Documentation:

  • Added new Python examples
  • Many small fixes for links, spelling, grammar and clarity.
  • Add extensive guide for contributions and coding polices.

Build:

  • Allow CMake configuration to use system copies of C++ dependencies (nlohmann/json and pybind11), and makes this the default option.
  • Added GitHub Actions support for automated testing of a wider range of tests and features than are run on our Travis CI (which will be removed soon)
  • More robust Python detection and consistent use of the same Python interpreter in CMake configure and build steps.

Contributions by, in no specific order, @brenthuisman, @noraabiakar, @thorstenhater, @halfflat, @schmitts and @bcumming

v0.4

** 2019 10 15 **

Release notes

Library

  • Moved from C++14 to C++17
    • Removed our hand-rolled versions of any, optional and variant.
  • Added std::expected equivalent for error handling.

Features

  • Added mechanism catalogues with mechanisms used by Allen and BBP models.
  • Removed support for spherical segments at the root of cable morphologies, and replaced the sample-based representation with a segment-based representation:
    • Morphologies are defined in terms of two-point segments.
    • Gaps are allowed between segments anywhere in a morphology.
  • Exposed the current time inside mechanisms.
  • Added support for NeuroML2 morphology descriptions.
  • Added a "stitch" morphology builder for constructing morphologies with cable sections that can connect to any location on their parent cable.
  • Replaced recipe probe API with more flexible API that allows for sampling not only voltages at single locations, but currents, ion species properties, and mechanism state variables at single locations or across an entire cell.
  • Added support for querying probe metadata from the simulation object.
  • Added new 'place_pwlin' C++ API for cell geometry queries.
  • Added support for loading Allen SDK cell model morphologies from SWC.
  • Added support for composing policies for creating compartments over sub-regions.

Documentation

  • Restructured documentation to have cleaner separation between high level descriptions of concepts and the C++ and Python APIs.
  • Added high level documentation for morphology descriptions, labels and cable cell construction.

Optimizations

  • Implemented memory optimizations for GPU matrix solver.
  • Added support for ARM SVE intrinsics in the vectorized CPU back end.

Bug Fixes

  • Fixed various modcc code generation errors.

v0.3

** 2020 04 01 **

Arbor library version 0.3, tagged as v0.3

Arbor is a library for implementing performance portable network simulations of multi-compartment neuron models.

An installation guide and library documentation are available online at Read the Docs.

Submit a ticket if you have any questions or want help.

Change Log

Changes since v0.2:

  • Python wrapper with pip installation.
  • Replace the morphology specification API for more flexible cell building.
  • Flat descriptions of ion channel distribution and synapse placement.
  • Multi-compartment back end support for sub-branch mechanism distributions.
  • Improved NMODL support:
    • nonlinear kinetic schemes
    • linear system solution in initial conditions
    • many small features and bug fixes
  • Generic ion species.
  • Many optimizations and bug fixes.

v0.2.1

** 2019 08 26 **

Arbor library version 0.2.1, tagged as v0.2.1

Arbor is a library for implementing performance portable network simulations of multi-compartment neuron models.

An installation guide and library documentation are available online at Read the Docs.

Submit a ticket if you have any questions or want help.

Release Notes.

Minor Update.

v0.2

** 2019 03 04 **

Arbor library version 0.2, tagged as v0.2

Arbor is a library for implementing performance portable network simulations of multi-compartment neuron models.

An installation guide and library documentation are available online at Read the Docs.

Submit a ticket if you have any questions or want help.

Some key features include:

  • Optimized back ends for CUDA, KNL, AVX2, ARM NEON intrinsics.
  • Asynchronous spike exchange that overlaps compute and communication.
  • Efficient sampling of voltage and current on all back ends.
  • Efficient implementation of all features on GPU.
  • Reporting of memory and energy consumption (when available on platform).
  • An API for addition of new cell types, e.g. LIF and Poisson spike generators.

Change Log

Changes since v0.1:

  • A new Hines matrix solver back end for the GPU that parallelises over cell branches, not cells, to increase the amount of parallelism. See #631.
  • Support for describing and simulating electrical gap junctions. See #661 #686.
  • An additional library libarborenv is now installed with useful helper functionality for managing the environment (e.g. detecting the number of available CPU cores). See #679.
  • Detection and allocation of GPUs to MPI ranks on systems with more than one GPU per node in libarborenv. See #659 and #654.
  • The miniapp example was removed and replaced with a simple single cell model that shows how to use morphologies. See #703 and #710.
  • Support for ARM NEON intrinsics. See #698.
  • Basic Python support. Full Python support is slated for v0.3. See #668.

Contributors

Nora Abi Akar John Biddiscombe Benjamin Cumming Felix Huber Marko Kabic Vasileios Karakasis Wouter Klijn Anne Küsters Alexander Peyser Stuart Yates

Citation

DOI

Nora Abi Akar, John Biddiscombe, Benjamin Cumming, Felix Huber, Marko Kabic, Vasileios Karakasis, Wouter Klijn, Anne Küsters, Alexander Peyser, Stuart Yates. (2019, March 4). arbor-sim/arbor: Arbor Library v0.2 (Version v0.2). Zenodo. http://doi.org/10.5281/zenodo.2583709

v0.1

** 2018 10 18 **

Arbor Library

Arbor library version 0.1, tagged as v0.1

Arbor is a library for implementing performance portable network simulations of multi-compartment neuron models.

An installation guide and library documentation are available online at Read the Docs.

Submit a ticket if you have any questions or want help.

Some key features include:

* Optimized back ends for CUDA, KNL and AVX2 intrinsics.
* Asynchronous spike exchange that overlaps compute and communication.
* Efficient sampling of voltage and current on all back ends.
* Efficient implementation of all features on GPU.
* Reporting of memory and energy consumption (when available on platform).
* An API for addition of new cell types, e.g. LIF and Poisson spike generators.
* Validation tests against numeric/analytic models and NEURON.

Contributors

Nora Abi Akar John Biddiscombe Benjamin Cumming Marko Kabic Vasileios Karakasis Wouter Klijn Anne Küsters Ivan Martinez Alexander Peyser Stuart Yates

Citation

DOI

If you use this version of Arbor, please cite it as Nora Abi Akar, John Biddiscombe, Benjamin Cumming, Marko Kabic, Vasileios Karakasis, Wouter Klijn, Anne Küsters, Ivan Martinez, Alexander Peyser, Stuart Yates. (2018, October 12). arbor-sim/arbor: Version 0.1: First release (Version v0.1). Zenodo. http://doi.org/10.5281/zenodo.1459679. The full citation is available in different formats on Zenodo.