Switch XML parser to pugixml; one less runtime dependency and one less blocker to WASM via emscripten.

- Correct `.gitmodules`
- Update all git submodules to latest released versions, except google-benchmark
- Have CHANGELOG
- Breaking changes since v0.7:
  - A change in API: `arbor.cable_cell` has the labels and decor arguments swapped. I.e.: `(tree, labels, decor)`
-> `(tree, decor, label)`. Labels are now optional.
  - Mechanism ABI version is bumped to 0.3.1. https://github.com/arbor-sim/arbor/pull/1884
  - Remove the `generate-catalogue` script.  `modcc` accepts now a list of NMODL files and is able to spit out a catalogue.cpp file
  - Rename spike detector -> threshold detector
  - Remove access to time `t` in NMODL.
- Major dependency version bumps:
  - GCC: 9 and up
  - CUDA: 11 and up
  - Clang: 10 and up

* Use HTTPS access instead of ssh/git for gtest.

- Bump CI actions to latest (cache, checkout, cmake)
- Bump mimimal compiler versions
- Bump minimal test OS to Ubuntu 20.04 LTS
- gtest as submodule (version 1.12.1)
- fixes heap corruptions
- update gtest macros, include paths

Co-authored-by: Thorsten Hater <24411438+thorstenhater@users.noreply.github.com>

EOM

* Create a script that generates `diff.log` if git submodules have tags more recent that the commit they're currently at.
* A Github Action runs this script monthly.
* _If_ updates found, Github Action creates an Issue like so: https://github.com/brenthuisman/arbor/issues/9
* Actually updating the git submodule and Spack file are still manual

First step in addressing #1731

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 algorithm `index_into_iterator` takes two ranges as inputs to make a range that lazily generates the index of sub into super set.

## backends

- made a new path `src/backends/` for backend specific type and implementation code.
- currently:
  - complete support for the `multicore` and `gpu` backends
  - `gpu` back end is not optimized or validated
- the back end implementations are in `src/backends`
- a single `backend` class, `nest::mc::{multicore,gpu}::backend`, is provides all backend specific type and implementation details fro each backend
  - storage containers
  - Hines matrix assembly for FVM method
  - Hines matrix solver
  - mechanism "factory"

## lowered fvm cells

- removed `fvm_cell` because this can be modelled with an `fvm_multicell` with one cell.
- refactored to use backend type and implementation from `fvm_policy`
- use `std::vector` instead of containers in `nest::mc::memory::` where possible when building cells.

## memory library

Refactor the "memory" library, making it much simpler and better integrated into the rest of the application. However, it is still far from perfect. The `Coordinator` approach needs to be improved, most likely by putting target-specific wisdom into pointers (which could obviate the need for a `const_array_view` type.
1. renaming and moving
   - move from `vector/` to `src/memory`
   - move into the `nest::mc` namespace, i.e. all types and functions are now in `nest::mc::memory`
   - change from camel case nameing scheme to NestMC style naming.
2. simplification
   - remove the CRTP cruft that was used to make operator overloading work for operations like copying from one range into another, and filling a range with a constant value. These have been replaced with `memory::fill()` and `memory::copy()` helper functions. This simplified the code _a lot_, and makes code clearer in user land.
   
   ```
   // before
   vec(0, 5) = other;
   // now
   memory::copy(other, vec(0, 5));
   ```
   - add some wrappers in `src/memory/wrappers.hpp` that help with making views. These are particularly useful for passing `std::vector` through interfaces that expect a view.

## debug backtraces

Added stack traces for debugging.
- support for OSX and Linux via libunwind
- backtraces can be generated manually `nest::mc::util::backtrace().print()`
  - creates a new file and dumps trace into file
  - prints message to `stderr` with file name and instructions on how to analyse
- backtraces are also automatically generated when an assertion `EXPECTS` statement fails
- a python script in `scripts/print_backtrace` pretty prints the output with file name, line number and demangled symbols

## util simplification and consolidation

The `src/util.hpp` file was removed
- much of its contents were dead code and just removed
- useful components like `pprintf` and `make_unique` were moved into the `src/utils` path in standalone files
There was a lot of overlap between functionality provided in `src/memory/util.hpp` and existing functions/types in the `nest::mc::util` namespace. The `memory` implementations were removed, and their `nest::mc::util` counterparts used. There is still some work remaining, namely moving the rest of the `src/memory/util.hpp` into `src/util/...`

* 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