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

Domain decomposition in python wrapper
* functions: `partition_load_balance`
*  types: `group_description` and `domain_decomposition`

Also includes
* remove comment that `gid` in a `group_description` must be sorted.
* a host of small clean ups of python wrapper

Fixes #761

clean up stringification in python wrappers

move python wrapper for schedules to their own files

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

Fixes #760

Wraps arbor recipe (without probes, i.e. num_probes, probe_info, get_probe) including 

- cell_connection, 
- gap_junction_connection, 
- recipe with
  - num_cells
  - cell_description
  - cell_kind
  - num_sources
  - num_targets
  - num_gap_junctions_sites
  - event_generators
  - connections_on
  - gap_junctions_on
  - global_properties
- enum cell_kind in `identifiers.cpp`

Addresses #757.

* Check if the multiplicity vector is empty before trying to use its contents. 
* Add unit test to catch the problem

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

Fix a memory error triggered on the GPU when assertions were enabled. An assertion was testing a value in shared memory, that should have been stored in host memory.

Python: mpi4py communicators as first class citizens

Sam Yates authored 5 years ago and Benjamin Cumming committed 5 years ago

* Replace ionKind enumerations with corresponding string values.
* Rename `ion.hpp` as `ion_info.hpp`.
* Re-jig 'nonspecific' current handling in modcc: make explicit the external source of the corresponding current variable, and treat as non-indexed those locals with an external variable that has no data source, as opposed to special-casing the `ionKind::nonspecific` value.
* Add another field in ion dependency information that captures a write to an ionic reversal potential.

Fixes #748.

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

 + Included conversion from `pybind11::object()` to `arb::util::optional` for `arbor.proc_allocation().gpu_id` and exception handling for `arbor.context(mpi=comm)`.

+ cleaned-up `test_event_generator.py`

+ for discussion: How do we want to handle the strings? Include them in appropriate `.cpp` or collect them in `strings.c/hpp`?

Fixes #746.

* Make `one_probe` an `inline` function rather than `static inline` in order to work around a linker issue (see issue #746).

* Fixes segmentation faults; output compiler errors instead.
* Consume units if provided in function/procedure prototypes or after function prototype.
* Consume UNITSON/UNITSOFF.
* Consume and store VALENCE as an ion property.

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

Wrapped the following C++ features in Python: 
- Identifiers (`cell_member`) + according tests
- `event_generator` and schedules (`regular_schedule`, `explicit_schedule`, `poisson_schedule`) + according tests

Sam Yates authored 5 years ago and Benjamin Cumming committed 5 years ago

Changes implicit solve step from:
> solve (c/δt + L) v' = c/δt v - J

to
> solve (c/δt + g + L)v' = (c/δt +g) v - J

where _c_ is capacitance, _g_ is membrane conductance, _J_ is membrane current.

* Compute conductivity contribution for mechanisms from symbolic d/dv of current contribution (extracted from linearity test.)
* Add new modcc 'source kind' for conductivity; tie to `vec_g_`.
* Add conductivity field to fvm shared state.
* Include conductivity in matrix assemblies for solution.

Fixes #633.

Add citation information to the readme.

Fix bug in CUDA reduce_by_key implementation on V100 or later GPUs.
The bug was not triggered for current use cases of the algorithm in Arbor, though it will be a problem when more than one reduction is to be performed in a single kernel invocation, which is required for ac
cumulating both current and conductance values.
* Use warp-synchronous aware operations to avoid problems on V100.
* Simplify reduction kernel.
* Rename `run_length` ancillary data structure to `key_set_pos`.
* Add unit tests that trigger the incorrect behaviour observed in #736.

Fixes #736.

* Add value_type and emplace method to the optional class to support automatic conversion of arb::util::optional in python.
* Add unit test for arb::util::optional::emplace.

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

Python 3.6 is tested (serial and mpi), in particular: 
- 3.6.3 on linux with a virtualenv, 
- 3.6.5 as downgrade from 3.7 on osx as in https://stackoverflow.com/questions/52584907/how-to-downgrade-python-from-3-7-to-3-6?rq=1 (other solutions did not work)

Fixes #715

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

* Rename `arb:simd::simd_detail` namespace to `arb::simd::detail`.
* Update SIMD documentation to suit.

Fixes #468.

Fixes #717.

* Move time interval update step after threshold check.

Rename mc_cell to cable_cell, cable1d_neuron to cable, and lif_neuron to lif in public API.

Fixes #701 

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.

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

* Remove data/ directory, contents as they are not used now in Arbor.

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

Remove the miniapp example.

* Remove the miniapp source from example/miniapp.
* Remove references to miniapp from CMake files.
* Remove miniapp from the travis tests.
* Fix unused variable warning in brunel miniapp.

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

Adds a small self contained example demonstrating the use of SWC and morphology specifications, to fill a void that will be left when the miniapp is removed.

* Adds `single-cell` example, together with short README and example SWC file.
* Removes redundant constructors for context objects.
* Corrects and simplifies some of the context comments.
* Add a method to `mc_segment` for calculating (approximately) a lower bound on the length constant of that segment for a given frequency, for use with a NEURON 'd-lambda' style discretization rule.

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

Remove old code and comments from Python config code.

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

Fixes #700

Usage in python as: 

```
>>>import arbor
>>>arbor.config()
{'mpi': True, 'mpi4py': True, 'gpu': False, 'version': '0.1.1-dev'}
>>>d = arbor.config()
>>>arbor.print_config(d)
Arbor's configuration:
     mpi    :       True
     mpi4py :       True
     gpu    :      False
     version:  0.1.1-dev
```

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.

noraabiakar authored 6 years ago and Sam Yates committed 6 years ago

* Add SIMD neon implementation for aarch64.
* Update unit tests to suit.

noraabiakar authored 6 years ago and Sam Yates committed 6 years ago

Allow distinct point processes with the same linear dynamics to be combined if they reside in the same CV after discretization.

* Add `linear` flag to `mechinfo` struct.
* Add a linearity test to `modcc` that determines if a point process is a suitable candidate for coalescing: state and current updates must be linear, homogeneous functions of the state variables; state change on an event arrival (`net_receive`) must be independent of current state values.
* Add `mechanism_state_table()` inquiry function to backend mechanism interface.
* Add a field `multiplicity` to `fvm_mechanism_config` that accounts for merged synapse instances, and a corresponding `multiplicity` field in `mechanism::layout`.
* Merge linear synapses of the same type  in `fvm_build_mechanism_data` if they have the same parameters.
* Add global mc_cell property `coalesce_synapses` which enables or disables the merging of linear synapses at run time.
* Rename virtual `nrn_init()` interface funct...

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.