Arbor Library v0.9.0 Article Swipe

<strong>v0.9.0</strong> ** 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 😄. <strong>Major new features</strong> 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 <code>external_connections_on</code> 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 <code>iexpr</code>: 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: <code>sigmoid(x)</code>, <code>relu(x)</code> and <code>tanh(x)</code>. Control volume <code>area</code> 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. <strong>Breaking changes since v0.8.1</strong> 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, <code>arbor.context(12, None)</code> is now <code>arb.context(threads=12, gpu=None)</code>. In the case no arguments are supplied, the context initialized to <code>default_allocation</code>, which means it will use the total number of threads and first GPU that are locally available. <code>arbor.simulation</code> constructed without an explicit <code>arbor.context</code> also initializes a <code>default_allocation</code>. Version bumps: CUDA 11 or higher is required for GPU builds. <strong>Full commit log</strong> <strong>Neuroscience, documentation</strong> Emit better warning. by @thorstenhater in https://github.com/arbor-sim/arbor/pull/2071 ANN activation functions for NMODL: <code>sigmoid(x)</code>, <code>relu(x)</code> and <code>tanh(x)</code> by @llandsmeer in https://github.com/arbor-sim/arbor/pull/2052 📊 Make profiler output a bit nicer. by @thorstenhater in https://github.com/arbor-sim/arbor/pull/2078 Merge GUI tutorial by @brenthuisman in https://github.com/arbor-sim/arbor/pull/2088 Busyring example by @boeschf in https://github.com/arbor-sim/arbor/pull/2100 Feature: External Connectivity by @thorstenhater in https://github.com/arbor-sim/arbor/pull/2001 FEATURE: fixed dt by @boeschf in https://github.com/arbor-sim/arbor/pull/2053 mention Matrix, GUI, Playground in docs by @brenthuisman in https://github.com/arbor-sim/arbor/pull/2113 Document presets by @thorstenhater in https://github.com/arbor-sim/arbor/pull/2126 Doc updates by @brenthuisman in https://github.com/arbor-sim/arbor/pull/2119 CV area exposed to NMODL. by @thorstenhater in https://github.com/arbor-sim/arbor/pull/2110 Fix enumeration in docs by @thorstenhater in https://github.com/arbor-sim/arbor/pull/2140 Docs: corrections. by @brenthuisman in https://github.com/arbor-sim/arbor/pull/2135 Fix documentation by @boeschf in https://github.com/arbor-sim/arbor/pull/2152 Address missing logo on all but front page by @brenthuisman in https://github.com/arbor-sim/arbor/pull/2155 Document features by @brenthuisman in https://github.com/arbor-sim/arbor/pull/2158 Make (most) painted parameters scalable. by @thorstenhater in https://github.com/arbor-sim/arbor/pull/2141 Add better (helpful?) errors on mechanism semantic misuse. by @thorstenhater in https://github.com/arbor-sim/arbor/pull/2171 Checkpoint/Resume by @thorstenhater in https://github.com/arbor-sim/arbor/pull/2081 <strong>Core</strong> Better handling of powers in modcc. by @thorstenhater in https://github.com/arbor-sim/arbor/pull/2061 Silence spurious unused variable warnings in generated code by @bcumming in https://github.com/arbor-sim/arbor/pull/2073 BluePyOpt API updates by @lukasgd in https://github.com/arbor-sim/arbor/pull/2045 Add some missing #include directives by @musicinmybrain in https://github.com/arbor-sim/arbor/pull/2080 Remove redundant sample events structure. by @thorstenhater in https://github.com/arbor-sim/arbor/pull/2079 🧹 Re-factor FVM lowered cell implementation and shared state by @thorstenhater in https://github.com/arbor-sim/arbor/pull/2082 Take less locks for shorter times when sampling. by @thorstenhater in https://github.com/arbor-sim/arbor/pull/2093 Fix LIF oversampling. by @thorstenhater in https://github.com/arbor-sim/arbor/pull/2091 📊 Pin threads by @thorstenhater in https://github.com/arbor-sim/arbor/pull/2094 Add zero'ing by @thorstenhater in https://github.com/arbor-sim/arbor/pull/2107 Add an error on NET_RECEIVE w/ &gt; 1 args. by @thorstenhater in https://github.com/arbor-sim/arbor/pull/2127 Update busyring to generate rings by @bcumming in https://github.com/arbor-sim/arbor/pull/2144 Apply some polish to model construction. by @thorstenhater in https://github.com/arbor-sim/arbor/pull/2134 SVE backend by @boeschf in https://github.com/arbor-sim/arbor/pull/2148 Exit <code>sup::path</code> stage left; enter <code>std::filesystem::path</code> stage right by @thorstenhater in https://github.com/arbor-sim/arbor/pull/2165 gtest dependency by @boeschf in https://github.com/arbor-sim/arbor/pull/2163 <strong>Build, testing, CI</strong> v0.8.1 by @brenthuisman in https://github.com/arbor-sim/arbor/pull/2072 v0.8.1 postrelease by @brenthuisman in https://github.com/arbor-sim/arbor/pull/2074 Enable Spack tests by @brenthuisman in https://github.com/arbor-sim/arbor/pull/2098 Python/pip strikes again: execute <code>pip install</code> in venvs by @brenthuisman in https://github.com/arbor-sim/arbor/pull/2111 Scikit build core by @brenthuisman in https://github.com/arbor-sim/arbor/pull/2121 Spack: add dev version by @brenthuisman in https://github.com/arbor-sim/arbor/pull/2150 Break out pip and doc tests, exclude doc-change from eating up precious runner cycles by @brenthuisman in https://github.com/arbor-sim/arbor/pull/2160 rename test-pip.yml by @boeschf in https://github.com/arbor-sim/arbor/pull/2166 cscs-ci by @boeschf in https://github.com/arbor-sim/arbor/pull/2149 gtest in CI containers by @boeschf in https://github.com/arbor-sim/arbor/pull/2170 Spack-solvable versions, add tests to Spack workflow by @brenthuisman in https://github.com/arbor-sim/arbor/pull/2156 Fudge version in pyproject.toml for ci by @brenthuisman in https://github.com/arbor-sim/arbor/pull/2200 enable remote example by @boeschf in https://github.com/arbor-sim/arbor/pull/2173 <strong>Fixes, optimization</strong> [BUGFIX] a-b-c: actually set compiler, improved default by @brenthuisman in https://github.com/arbor-sim/arbor/pull/2051 🐙 Optimise PPACK by @thorstenhater in https://github.com/arbor-sim/arbor/pull/2067 Silence flake8 and appease black. by @thorstenhater in https://github.com/arbor-sim/arbor/pull/2086 BUGFIX: add missing functions to sve backend by @boeschf in https://github.com/arbor-sim/arbor/pull/2096 BUGFIX gpu ppack declarations by @boeschf in https://github.com/arbor-sim/arbor/pull/2087 BUGFIX: gpu mechanism init by @boeschf in https://github.com/arbor-sim/arbor/pull/2095 The Initialisation Optimisation by @thorstenhater in https://github.com/arbor-sim/arbor/pull/2097 Fix crash in FindId Visitor. by @thorstenhater in https://github.com/arbor-sim/arbor/pull/2115 Add LTO and M1 arch to CMake by @thorstenhater in https://github.com/arbor-sim/arbor/pull/2106 Fix crash on probing non-existent mechanism state. by @thorstenhater in https://github.com/arbor-sim/arbor/pull/2112 Python/concurrency defaults by @brenthuisman in https://github.com/arbor-sim/arbor/pull/1979 Add faster merge events. by @thorstenhater in https://github.com/arbor-sim/arbor/pull/2108 Fix a typo in python bindings. by @thorstenhater in https://github.com/arbor-sim/arbor/pull/2125 Fix incorrect mention of attribute <code>catalogue</code> in <code>single_cell_model</code> by @Helveg in https://github.com/arbor-sim/arbor/pull/2122 Avoid crash when integrating over empty branch. by @thorstenhater in https://github.com/arbor-sim/arbor/pull/2124 fix lint pipleine by @boeschf in https://github.com/arbor-sim/arbor/pull/2151 Ward against probing the void. by @thorstenhater in https://github.com/arbor-sim/arbor/pull/2139 Fix GPU/NVC problems by @thorstenhater in https://github.com/arbor-sim/arbor/pull/2143 fix ODR violation by @boeschf in https://github.com/arbor-sim/arbor/pull/2154 <strong>New Contributors</strong> @musicinmybrain made their first contribution in https://github.com/arbor-sim/arbor/pull/2080 <strong>Full Changelog</strong>: https://github.com/arbor-sim/arbor/compare/v0.8.1...v0.9.0