Implements #1376.

* Provide a common C linkage ABI for externally compiled mechanisms, for both CPU and GPU.
* Remove mechanism type hierarchy (`concrete_mechanism` etc.), and move corresponding functionality to the back-end shared state objects. Mechanism catalogue is no longer indexed by type id.
* Distinguish between SIMD optimal alignment and SIMD width with new `min_align` attribute. Mechanisms provide both pieces of information via ABI.

`/doc/scripts/divio_docs_theme` has the contents of the tarball from PyPI, slightly modified (custom fonts removed, font-awesome reduced to woff2, logo enabled, divio banner/analytics removed.).

* Adapt to moved readthedocs account

* Move .gitlab-ci.yml inside the repo
* Remove submodule with gitlab pipeline

Combine badges on readme and move ci git submodule to `ext/`

* Add Dockerfiles for MPI + CUDA test builds on Daint
* Add bors.toml for CI on Daint
* Add the separate ci repo as submodule for convenience
* Add a CI badge for master to the top of the readme

akuesters authored 6 years ago and Benjamin Cumming committed 6 years ago

First step towards the Python front end.

This commit sets up the structure of the python implementation
* directory structure
* git submodule for pybind11
* best practices for making bindings with pybind11
* unit testing for the python front end

It implements the following features in the Python front end
* execution contexts
* gpu detection
* thread count detection
* MPI initialization helpers.

Fixes #667.

noraabiakar authored 6 years ago and Benjamin Cumming committed 6 years ago

- Task system is no longer a single system private to the implementation of the threading backend and used everywhere. A separate task_system can be used (with a specified number of threads) for every simulation.
- arb::execution_context is the interface to task_system  and the previously defined distributed_context
- TBB and serial support has been removed. Cthreads is the only threading backend available. 

Sam Yates authored 6 years ago and Benjamin Cumming committed 6 years ago

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...

This replaces the CMake templates provided by TBB with a much more sane alternative!

The TBB CMake templates had a very strange workflow, that involved downloading the TBB source and compiling it, which made it impossible to configure the TBB build, and caused problems on systems without connection to the internet.

We replace this with a fork of the TBB repository maintained by Github user @wjakob:
https://github.com/wjakob/tbb
This fork provides a sane CMakeLists.txt that can be configured from our CMake setup.
It is added as a git submodule, so it can be downloaded with the rest of the repository, hence not requiring connection to the internet during CMake configuration.

It could be extended to use a user-provided build of TBB to use instead of building it.

fixes #332.

Ben Cumming authored 7 years ago and Sam Yates committed 7 years ago

Adds support for building documentation with Sphinx from reStructuredText-formatted files in the `doc` subdirectory. Automatic building has been verified with ReadTheDocs.

* Add basic documentation to the `doc` path.
* Use a git submodule and associated CMake to pull in ReadTheDocs theme at configuration time.

* Use git submodule for incorporating Google benchmark library.
* Add one microbenchmark for comparing `util::transform_view` performance.

Note that the microbenchmarks are not built by default; they can be built with `make ubenches`, and then run individually. The microbenchmarks will be built in `tests/ubench/`, relative to the build directory.

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...

* only the source has been moved over and the cmake rules updated
* the tests still have to be moved

* add header only library TCLAP for parsing command line arguments
    - added as git submodule
    - update CMakeLists to include headers
* remove the ring model from miniapp
* add support for user supplied parameters for miniapp
    - arguments for cell counts etc can be command line flags
    - or in a user-defined json input file
* the all-to-all model supports synapses-per-cell is less than
  the total number of cells
    - in this case a random set of sources is selected