akuesters authored 5 years ago and Benjamin Cumming committed 5 years ago

Add docs for Python wrapper to ReadTheDocs:

- Overview, Common Types, Hardware Management, Recipes, Domain Decomposition, Simulations, Metering
- Installing Arbor: Optional Requirements (Python), Buidling and Installing (Python Frontend), and Installation (Python Module)

Missing (, since not implemented yet): 

- probes
- arbor-sup 
- hint maps in domain_decomposition
- reset, events, empty schedule in event_generator
Also does not cover unit testing (since doc is user-centric).

Makes also defaults and units in wrapper consistent.

Fixes  #766

Add citation information to the readme.

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

Add gap junctions and improve general model overview in docs.

* Replace Arbor Model::Common Types with Arbor Model::Concepts, that introduces the concept of cells, connections and gap junctions. 
* Add gap junction documentation to cpp:recipe
* Document the implicit rule forcing cells connected by gap junctions to be in the same cell group.
* Add documentation that discusses core concepts in Arbor models.

Update Hardware API documentation

* split the domain decomposition and hardware API docs into separate pages
* update hardware API to reflect new *libarbor* and *libarborenv*
* add basic documentation for `optional`, `any` and `unique_any` types.

Update the installation guide to reflect the latest supported tool,
compiler and library versions.

Remove the Python docs, because they documented features that have not
been implemented yet. The Python docs can be added incrementally as
features are implemented.

Start work on oupdating the documenetation for hardware interfaces and
domain decomposition.

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

Update documentation for Python.

    splits the conceptual model ideas from the C++ docs into their own section
    has C++ and Python docs for recipes, domain decomposition, etc.

fixes #667

Added the following documentation (structure):

GETTING STARTED:

    Installing Arbor/Requirements/Optional Requirements/Python
    Installing Arbor/Building and Installing Arbor/Python Front End

MODEL BASICS:

    Overview
    Common Types
    Recipes
    Domain Decomposition
    Simulations

PYTHON:

    Overview
    Common Types
    Recipes
    Domain Decomposition
    Simulations

DEVELOPERS:

    Python Profiler
    Python Unit Testing

GETTING STARTED has two added sections of optional requirements using python and how to build the python front end.

MODEL BASICS describes Arbor's concepts in general (independent of programming language), thus general information on concepts in C++ API was moved here/ added.

PYTHON describes Arbor's python frontend in the same structure as MODEL BASICS and C++ API ( needs updates as soon as features are added/changed in new python PR).

DEVELOPERS section has two added sections for meter management and unit testing with python front end.

Further, some corrections in existing documentation (for obvious errors, e.g. duplicate text, not ending sentences) and referencing sections were done.

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

Dry-run mode: 
* An implementation of distributed_context that is used to mimic the performance of running an MPI distributed simulation with n ranks.
* Verifiable against an MPI run with the same parameters. 

Implementation: 
* Describe the model on a single domain (tile) and translate it to however many domains we want to mimic using arb::tile and arb::symmetric_recipe. This allows us to know the exact behavior of the entire system by only running the simulation on a single node.
* Mimic communication between domains using arb::dry_run_context

Example: 
* dryrun in example/ is a verifiable example of using dry-run mode with mc_cells

Other:
* Documentation of dry-run mode 
* unit test for dry_run_context 

Make the execution context presented to users an opaque handle, moving all implementation of the gpu, thread and distributed contexts into the back end.

* move `execution_context` and `distributed_context` definitions to the back end
* create `execution_context` handle called `context` in the public API
* provide `make_context` helper functions that build different context configurations (default, user-specified local resources, with MPI)
* update documentation for all parts of the public API that touch contexts
* move `distributed_context` docs to the developer documentation (from the public API docs)

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

Move from choosing the distributed communication model from a compile time choice (the old `arb::communication::communication_policy` type) to a run time decision.

* Add `arb::distributed_context` class that provides the required interface for distributed communication implementations, using type-erasure to provide value semantics.
* Add two implementations for the distributed context: `arb::mpi_context` and `arb::local_context`.
* Allow distribution over a user-supplied MPI communicator by providing it as an argument to `arb::mpi_context`.
* Add `mpi_error` exception type to wrap MPI errors.
* Move contents of the `arb::communication` namespace to the `arb` namespace.
* Add preprocessor for-each utility `ARB_PP_FOREACH`.
* Rewrite all examples and tests to use the new distributed context interface.
* Add documentation for distributed context class and semantics, and update documentation for load balancer and simulation classes accordingly.

Fixes #472

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

Add two new documentation pages for the C++ API

* Add domain decomposition page that covers `domain_decomposition`, `node_info` and `partition_load_balance`.
* Add simulation page that describes `arb::simulation` API interface.
* Fix some small typos elsewhere in the docs.
* Use `std::move` when adding spike callbacks to `arb::simulation` (useful if callbacks are stateful).

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

Add some C++ API documentation.

* Create C++ API section in docs.
* Document `arb::recipe`: both a class reference along with more explanatory text and best practices guide.
* Add some class documentation of basic types required to understand recipe definition.
* Some in-code comment clean up.
* Change `arb::cell_kind` from a vanilla enum to a scoped enum.

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

Put all the SIMD docs in a single topic, to simplify the documentation tree.

Added an installation guide to the Read The Docs
Removed the outdated build/install information from README.md
Link from README to Read The Docs
Updated the splash page for Read The Docs

This provides a bunch of SIMD intrinsic wrappers as a precursor to the SIMD printers.

The aim is that the SIMD printer can be agnostic regarding the particular vector architecture.

The design is based rather loosely on the proposal P0214R6 for C++ Parallelism TS 2. The transcendental function implementations are adapted from the existing SIMD architecture-specific code, which in turn are based on the Cephes library algorithms.

The custom CSS for the html documentation have been tweaked.

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

Replace the profiler with a simpler design that works for nested multi-threaded regions.

* Replace hierarchical profiler accounting with strictly exclusive regions.
* Make tree grouping of profile data a presentation concern.
* Uncouple profiler semantics from Arbor classes such as `model`.
* Add thorough documentation for the new profiler to the library documentation.

Towards resolution of issue #283.

* Replace probe/sample infrastructure with new API as outlined in the `sampling_api.rst` documentation.
* Separate `cell` probe information from `cell` description object.
* Add `--list` option to `tsplot`, to summarize available time series for plotting together with their metadata.
* Add `--sample-dt` option to validation tests.
* Change validation time series comparison behaviour: linf distance metric now estimated by comparing reference data points against linearly interpreted simulation samples, rather than the other way around.
* Add utility class `any_ptr` which allows lightweight and type-checked access to a type-erased pointer.
* Replace `singleton_recipe` with two simple recipe base classes used for unit and validation tests, in `tests/simple_recipes.hpp`.
* Simplify RSS cell implementation.
* Add statistical functions for testing of probabilistic methods in `tests/unit/stats.hpp` (and .cpp):
   * simple summary stats class;
   * Kolmogorov–Smirnov one-sided statistic and CDF;
   * approximate Poisson CDF.
* Simplify and refactor miniapp `sample_trace` code.
* Add new utility class `handle_set` for managing a collection of integer handles. (Near-simplest implementation.)
* Relax const-ness constraints on `transform_iterator`.

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.