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

* Make global parameters and ion rebindings part of the instantiate interface, rather than insist that all concrete mechanisms implement these as methods.
* Mechanism catalogue instance() returns a pair, comprising the concrete mechanism for the requested backend, together with the override data.
* Extend catalgoue derive() method to take a list of old ion name -> new ion name remappings for a mechanism.
* Add exceptions for ion remapping errors, and check for these errors.
* Add convenience function for reparameterizing a mechanism with a single ion dependency over other ions. (This will be used for the future nernst pre-supplied mechanism.)
* Add unit tests for: chained renamings of ion names across multiple derivations; correct shared state ion assignment after renamings; ion remapping exceptions; parameterize_over_ion.

Eric Müller authored 5 years ago and Benjamin Cumming committed 5 years ago

* cmake/FindUnwind.cmake used the wrong variable (caused by commit ad1c78ab)
* CMakeLists.txt seems to use wrong syntax for providing a compiler define
  of `WITH_UNWIND` (used in `arbor/util/unwind.cpp`)

Fixes #782 
* consistent formatting of strings returned by `__repr__` and `__str__` for wrapped types
* rename enum wrappers to be less verbose, where it makes sense.

Add full wrappers for

- `lif_cell`
- `spike_source_cell`
- `benchmark_cell

And an opaque wrapper for cable_cell with a helper function that generates a random morphology identical to the ones in the nsuite benchmarks.

Fixes #767.

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

Wrap `arb::simulation` type and interface for running `run()`, resetting `reset()`, and `set_binning_policy(policy, bin_interval)`. 

Wrap `enum binning_kind`, used to set event binning on `simulation` API.

Fixes #763 

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

Extended USEION VALENCE support.

* Augment modcc parser to accept identifier or signed integer after VALENCE.
* Treat identifer after VALENCE as global scalar, tied to ionic charge.
* Add ionic charge field to mechanism ion parameter pointers, replacing scalar in shared state with a length-1 array.
* Verify presence of ion name and check ion charge against numeric valence in mechanism info when discretizing in `fvm_build_mechanism_data`.
* Pass ion info, coalesce_synapse global state to `fvm_build_mechanism_data` just via cable cell global properties.
* Add more unit-test only mechanisms (test_ca_read_valence, test_cl_valence).
* Add unit tests for valence verification and reading into mechanism state (multicore only).
* Update existing unit tests for new interfaces.

Implements #780.

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

* Change occurances of 'ionKind' to corresponding string values in test_parser.cpp.
* Add unit-modcc to travis script.

Fixes #775.

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.