- Jun 25, 2018
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CMake and build refactoring * Use CUDA as first-class language (leading to CMake 3.9 minimum version requirement). * Use 'modern CMake' interface libraries for compiler options, include file and library dependency tracking. Interface library targets: * `arbor-deps`: compiler options and library requirements for the `libarbor.a` static library, as governed by configure-time options and environment. * `arbor-private-headers`: include path for non-installed headers, as required by unit tests and arbor itself. * `arbor-aux`: helper classes and utilities used across tests and examples. * `ext-json`, `ext-tclap`, `ext-tbb`, `ext-benchmark`, `ext-sphinx_rtd_theme`: externally maintained software that we include (directly or via submodule) in the `ext/` subdirectory. * Single static library `libarbor.a` includes all built-in modules and CUDA objects. * Simply configuration options: * `ARB_WITH_TRACE`, `ARB_AUTORUN_MODCC_ON_CHA...
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- May 09, 2018
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Sam Yates authored
First commit of two for mechanism refactor work (refer to PR #484 and PR #483). FVM/mechanism code: * Refactor mechanism data structures to decouple backend-specific implementations and mechanism metadata. * Add mechanism catalogue for managing mechanism metadata and concrete implementation prototypes. * Add fingerprint-checking to mechanism metadata and implementations to confirm they come from the same NMODL source (fingerprint is not yet computed, but tests are in place). * Split FVM discretization work out from FVM integrator code. * Use abstract base class over backend-templated FVM integrator class `fvm_lowered_cell_impl` to allow separate compilation of `mc_cell_group` and to remove the dummy backend code. * Add a new FVM-specific scalar type `fvm_index_type` that is an alias for `int` to replace `fvm_size_type` in fvm layouts and mechanisms. This was chosen as an alternative to making `unsigned` versions of all our SIMD implementation classes. * Exte...
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- Sep 28, 2017
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Sam Yates authored
Change nest::mc namespaces to arb
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- Apr 21, 2017
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Sam Yates authored
Fixes #232. * Try `NMC_DATADIR` environment variable for validation data path, or else if the #defined `NMC_DATADIR` does not point to a directory, try `./validation/data` and `../validation/data`. * Don't define `NMC_DATADIR` if CMake version 3.7 or 3.8. * Extend C++17 filesystem emulation with (POSIX) implementation of `is_directory` and supporting classes, functions and enums `filesystem_error`, `file_status`, `status(..)`, `file_type` and `perms`.
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- Nov 14, 2016
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Ben Cumming authored
This PR is part of the gpu feature merge. The GPU implementation is not implemented here. Instead, we focus on refactoring of the original "multicore" back end so that it is ready for adding the GPU back end. This is a big and messy change, for which I am sorry. ## build System - A `WITH_CUDA` option has been added to the main CMakeLists. This finds the CUDA toolkit, and sets CUDA compiler flags, and will build unit tests for the gpu back end. - The CMakeLists that generates mechanisms with modcc has been updated to generate CUDA mechanisms. - the library is now named `libnestmc` instead of `libcellalgo` - merge the external libraries that are optionally linked againts (tbb, libunwind, etc) into a single `EXTERNAL_LIBRARIES` list for ease of linking ## modcc - the cprinter and cudaprinter have had small changes to generate mechanism files that are compatible with the refactored library. ## algorithms - the indexes into algorithm was "rangified". An algori...
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- Oct 11, 2016
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Sam Yates authored
Validation of simulation results by comparing L-infinity distance and maximum peak displacement in voltage traces taken at mid-points and end-points of sections. Note that these tests will broadly _fail_ at this point. Reference data generation and visualization: * Use voltage traces as validation data from NEURON; refactor generation scripts. * Generate validation data as a dependency of `validation.exe`. * Store validation data in a `tsplot`-compatible format. * Extend `tsplot` to handle multiple time series per file, a non-time 'time' axis (see `-A` option), filtering of time series by meta data queries (see `-s` option). * Remove pre-generated spike-time validation data files. Core extensions: * Add a single-cell `singleton_recipe` recipe wrapper. * Allow cell descriptions to be cloned (explicitly) for use with this wrapper. * Add `simple_sampler` which maintains a trace of scalar observables as a vector of (time, value) pairs. * Allow cell groups to be exposed from `mode...
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