- Aug 31, 2020
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Sam Yates authored
* Add `equal_range()` method to `pw_elements`. * Simplify `embed_pwlin`, `place_pwlin` implementations, in particular the handling of zero-length branches. * Scale segment positions in `embed_pwlin` by divding by branch_length, instead of multiplying by the reciprocal, as the latter is a false economy after all the caveats that need to be checked to preserve ordering and bounds. * Add new method `place_pwlin::all_at()`, which gives all the points that correspond to a single `mlocation`. * Add new method `place_pwlin::all_segments()`, providing the set of segments and/or partial-segments that correspond to an extent. * Add new method `place_pwlin::segments()`, which provides a minimal set of segments and/or partial-segments that map onto an extent. * Extend unit tests to suit. Fixes #1116 and #1068.
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- Aug 27, 2020
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Benjamin Cumming authored
This PR adds a bunch of high-level docs for concepts related to single cell models. * morphologies * labels (region and locset expressions) * mechanisms * cable cells It adds some python scripts to the `doc` path, which are called during documentation building to generate images of cell morphologies, regions and locsets that are generated in a separate script that uses the Arbor Python API. The docs are not complete: the cable cell and mechanism docs are unfinished, and the tutorial section needs to build on these concepts to give more detailed step by step examples.
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Sam Yates authored
New PR post master rollback; squashed and rebased, but reprises #1111. * Add (forward) ordered forest implementation, tests. * Add `segment` region expression; to ease implementation, `msegment` now also knows its own id. * Add `stitch_builder` and `stitched_morphology`. A stitch corresponds to a labelled, linearly-interpolated segment which can be attached at any point along a parent stitch. A `stitched_morphology` takes a `stitch_builder` object and constructs a segment tree and morphology, and provides a dictionary of stitch labels to segment indices and region expressions. * Add `import` method for `label_dict`, so that the label dictionary returned by `stitched_morphology` can be merged with an existing dictionary. * Add section on stitch builder etc. to cable cell docs. * Update cable cell docs to remove out of date info and to provide some context. * Describe ordered forest datastructure and interface in a long comment at the...
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Sam Yates authored
* Add `get_probe_metadata` method to `simulator` that forwards probe metadata queries to appropriate cell group, via new interface method in cell group base class. * Replace `gid_to_local_` map in simulator implementation with a map that takes gid to local cell index _and_ local cell group index. * Move scheduler association map mutex into the cell group where it is being used (i.e. `mc_cell_group`). * Add generic (`visit`-able) interface to specifc fvm-probe types for accessing metadata via `any_ptr`. * Implement (override) `get_probe_metadata` method for `mc_cell_group`. * Use new cv policy API for LFP example discretization. * Use new probe metadata API to simplify LFP example sampler callback. * Add `on_components` locset expression that gives points a relative distance from the head of each component of a region. * Simplify implementation of thingification of `ls::boundary`. Fixes #1079
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- Aug 26, 2020
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Brent Huisman authored
Update the docs landing page and add pip install from git. Fixes #1118
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- Aug 20, 2020
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Nora Abi Akar authored
The `vec_t_` time vector is already available to the mechanisms, but not exposed. It is indexed by `cell_index` instead of directly by the `node_index` (`vec_t[vec_ci_[node_index_[i]]]`). This kind of indexing was previously unavailble. It has not been added to the printers. This PR also includes some cleanup in the vectorized code printer. Address #1109
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- Aug 13, 2020
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Brent Huisman authored
Guide Python users to the Python installation steps early in the installation guide.
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- Aug 10, 2020
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Brent Huisman authored
Added Issue templates to help guide usage-related questions towards 'Discussions'.
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Brent Huisman authored
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- Aug 06, 2020
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Brent Huisman authored
Update all Python scripts used during build/testing/running Arbor to explicitly use Python 3.
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thorstenhater authored
* Check for self-assignment in `device_reference::operator=(const device_reference&)`. * Return reference to self in ` device_reference::operator=(const device_reference&)`. * Prohibit default construction of `device_reference` and clarify copy semantics.
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- Aug 05, 2020
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Brent Huisman authored
The tiniest of fixes: mechanisms/generate_catalogue had a bang line incompatible with newer Linux platforms without python.
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- Jul 28, 2020
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Sam Yates authored
* Correct hash implementation. * Add ==, != comparisons. Fixes #1093
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Brent Huisman authored
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- Jul 24, 2020
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thorstenhater authored
Rename import method to avoid Python keyword collision.
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- Jul 23, 2020
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Harmen Stoppels authored
This is copied from DLA Future. It should set the CI status on the commit from the PR instead of just on the Bors commit. This way the gitlab CI status also appears in the checks section below the PR.
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Nora Abi Akar authored
Fix a Python example that was out of date.
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thorstenhater authored
Make all pointer arguments to kernels `__restrict__` to avoid unnecessary loads. The effect on the busyring benchmark (swapped pas -> hh) with 8192 cells on a V100 GPU (time for model-run in seconds): ``` |----------+-------| | Baseline | After | |----------+-------| | 2.347 | 2.268 | | 2.345 | 2.262 | | 2.321 | 2.276 | | 2.323 | 2.267 | | 2.330 | 2.249 | |----------+-------| | 2.321 | 2.249 | |----------+-------| ```
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- Jul 21, 2020
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Benjamin Cumming authored
* add parse_swc_allen method * small fixes and clean up * add test for incomplete branches and make error messages more consistent * add extra swc assertion, and remove single sample special case
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- Jul 13, 2020
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Benjamin Cumming authored
* Remove spherical root/soma from morphology representations and logic. * Replace `sample_tree` with `segment_tree`, which represents sample points in pairs and allows the representation of detached branches and cable segments. * Remove sample point properties and predicates. * Remove `cv_policy_flag::single_root_cv` as somata with a single attached dendrite will have a representation in the morphology of a single branch. * Remove `arb::math::{volume/area}_sphere`, which are no longer being used. * Remove spherical root special cases from `embed_pwlin` and `place_pwlin` objects. * Add textual representation of `mnpos` in morphology exception text. * Rename `sample_tree_from_swc` to `segement_tree_from_swc` and remove any special casing for one point somata. * Remove `msample` and `mbranch` types. * Update unit tests and python wrapper to reflect the changes.
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thorstenhater authored
* Add import method for mechanism catalogues, allowing mechanisms from a second catalogue to be incorporated with a prefix, together with Python interface. * Expose `global_allen_catalogue`. * Extend unit tests to cover mechanism catalogue import and check for name collision error cases.
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- Jul 08, 2020
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Nora Abi Akar authored
* Use assign when reading memory in simd mode. * Expand assign to work for numbers and other simd_impls. * Don't expose detail namespace in simd.hpp.
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- Jul 07, 2020
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Nora Abi Akar authored
* Add zero assignments to local variables in modcc output.
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Harmen Stoppels authored
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- Jul 02, 2020
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Sam Yates authored
* Move `cv_policy` classes to new source files. * Remove `cv_policy_flag::single_root_cv`. * Allow all supplied `cv_policy` makers to be restricted a domain specified by a region: the policy is then applied per component, with the boundary points of the completion of the components included. * Expose `cv_policy` domain in public interface. * Add `components` function for splitting an extent into disconnected components. Add comment describing what is meant by connected in this context. * Rename `super` region function to `complete`. * Add region expression functions `complement` and `difference`. * Add new locset expression function `boundary` which returns the extrmal points of each component of a region. * Add new locset expression `cboundary` which returns the extremal points of the completion of each component of the region, which is what we need to close off CVs generated by region-restricted CV policies. * Add locset expression `supp...
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- Jun 25, 2020
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Nora Abi Akar authored
* Add new API for the SIMD library that is compatible with the ARM 'sizeless' SVE vectors. Language restrictions prevent the use of the operator overload interface used up to this point for SIMD. * Add `indirect_expressions` and `indirect_indexed_expressions` for describing memory reads/writes. `where_expressions` control masked access to simd vectors. * Implement the SVE SIMD back-end in accordance with the alternate SIMD API. * Retrieve vector width information from compiled mechanisms. * Use alternate SIMD API in modcc-generated mechanisms. * Add assertion in generated mechanism code that checks runtime vector width compatibility. Fixess #1021.
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Sam Yates authored
* Add C++ analogue to simple NEURON demo provided by LFPy project under example/lfp. * Add plot script for rending example output to match that from NEURON demo.
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- Jun 24, 2020
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thorstenhater authored
Remove a redundant copy in favor of a swap operation for a gain in performance; especially on GPU since copies are synchronous. Similarly, instead of solving the linear system into an intermediate array, write output directly into the target. Here is the effect on the busyring benchmark (swapped pas -> hh) with 8192 cells on a V100 GPU (time for model-run in seconds). ``` |----------+--------------------------------+------------------------------------| | Baseline | fvm_lowered_cell: copy -> swap | matrix: solve + copy -> solve_into | |----------+--------------------------------+------------------------------------| | 2.230 | 2.199 | 2.129 | | 2.231 | 2.209 | 2.132 | | 2.225 | 2.209 | 2.136 | | 2.227 | 2.186 | 2.130 | | 2.220 | ...
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thorstenhater authored
Add a new catalogue comprising optimised version of some of the mechanisms commonly used in models of the Allen Cell Types Database, eg http://celltypes.brain-map.org/mouse/experiment/electrophysiology/323535089. This made required extending modcc to some new NMODL features, as well as to expose some optimisations. In addition clean up the default catalogue by moving test mechanisms to their proper place in the unit tests.
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Benjamin Cumming authored
Update core library: * support derivation of named mechanisms in catalogue from a string description of the parent. * fix bug in radois_ge region expression that was finding region_lt. * fix test for radius_ge region expression Add support for mechanism, global properties and catalogue shenanigans to python wrapper
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- Jun 23, 2020
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Sam Yates authored
* Guard `event_generator` implicit constructor with type test. * Fix linking error from use of `empty_generator` by replacing pointers to `no_event` with nullptr. * Clarify `regular_generator` semantics in comment. * Add unit test for checking. Fixes #1066
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- Jun 22, 2020
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Sam Yates authored
* Add new `isometry` class representing a direct Euclidean isometry comprising a rotation and translation. Translations are always taken with respect to absolute coordinates, but rotations are composed with respect to intrinsic coordinates. * Add new `place_pwlin` class, that takes a morphology and an isometry, and answers location queries: where in space does a particular `mlocation` lie? * Split out (some of) the common code between `place_pwlin` and `embed_pwlin`. * Add equality operator to `mpoint`. This functionality is added to aid the presentation of the local field potential example.
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- Jun 16, 2020
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Nora Abi Akar authored
Update `mech_vec.cpp` to work with the new API Print profiler summary in the ring example
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thorstenhater authored
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- Jun 12, 2020
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Sam Yates authored
* Make recipe return probes as a vector. * Remove `probe_id` from `probe_info`. * Rename `fvm_probe_info` to `fvm_probe_data` (everything was being called info, and it was getting confusing). * Make `probe_association_map` specific to `mc_cell_group`/`fvm_lowered_cell`. * Change probe_association_map representation: unordered map for probe_id -> tag; unordered multimap for probe_id -> fvm_probe_data. This allows multiple probes to be associated with the same probe id. * Call sampler callback separately for each probe with the same probe_id. * Replace location-based probes with locset equivalents. * Add index for probes sharing a probe id. * Bundle all probe metadata (id, tag, index, probe-specific meta) into `probe_metadata` struct for passing to sampler callbacks. * Change simple_sampler to work on `trace_vector`, a vector of `trace_data`. The _i_th element is the data from probe with index i. * Consolidate hash composition and `std::hash` specialization code in new header. * Update python lib for new API. * Update tests and examples for new recipe, internal probe, and simple_sampler APIs. * Update docs to suit.
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- Jun 04, 2020
- May 28, 2020
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thorstenhater authored
* Add ranges in STATE blocks of the form FROM ... TO ... * Unit test for the above * Add type check for <..., ...> ranges * Add units in procedure argument lists * Unit test for the above.
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- May 26, 2020
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Sam Yates authored
Fixes #1037. * Add fake unmatchable spike events to event queue for each exact sample request, so that integration boundaries align with exact sample times. * Update probe-demo for exact sampling. * Add copy assignment for `cable_cell`. * Extend max args for ARB_PP_FOREACH to 20. * Add unit test for ARB_PP_FOREACH. * Use ARB_PP_FOREACH to instantiate backend-specific probe unit tests. This also fixes the GPU probe tests that were using multicore backend. * Add unit test that exercises exact sampling requests combined with regular events in a gap junction context.
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Harmen Stoppels authored
This is a bit experimental. It builds arbor with `-fprofile-arcs -ftest-coverage` and creates a docker image with just the project binaries, lcov, gcov and generated `.gcno` files. This should still be reasonably small since there are no object files etc. When run on daint, `.gcna` files are produced (should be thread / process safe according to gcc's manual) inside of the container, and `lcov` is used to combine all those things into a single file with a random name in the mounted git project folder (hopefully this solves clashes with multiple nodes). After all tests are run, the combined reports are uploaded to codecov.io.
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