- Aug 24, 2021
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kanzl authored
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thorstenhater authored
* Categorise ASSIGNED RANGE variables as STATE-ish. * Also use the opportunity to clean up the infoprinter. * Accidentaly fix bug in propagating parameter ranges from NMODL
️ `mechinfo` Fixes #1623.
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- Aug 23, 2021
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thorstenhater authored
* Clean-up AVX SIMD mask setting. * Remove redundant global constant in the memory lib. * Fix 'unused variable' warning in `test_probe.cpp`.
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- Aug 20, 2021
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thorstenhater authored
- Add a set of test cases to check the behaviour - Remove the function `(nil)` from the the DSL - Remove `nil` and `()` as literals - Add functions `(region-nil)` and `(locset-nil)` Fixes an issue where `join` (and likely `intersect`) would not work due to the fact that `nil` values could not be coerced to `region` or `locset`. This occurred while loading a NML files. While investigating it was found that certain calls, eg `(join () ())` are ambiguous and cannot be resolved without changes in no proportion to the gain. The cause here is that we can resolve `()` as region or a locset and at the same time `join` maps a list of locsets or regions to a locset or region, consequently `(join () ())` can be both. For future reference, in `label_parse.cpp::eval` we look for the first match in the `eval_map` of a function name that can be successfully evaluated. However, this might not be the best match (and the ordering depends on the internals of `eval_map`). We _could_ check all successful evaluations, but as eval is recursive, this idea has some obvious issues.
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- Aug 19, 2021
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Nora Abi Akar authored
Fixes hipcc rocm-4.0.1 build for AMD GPU Fixes #1628
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Sebastian Schmitt authored
* Run examples via scripts (closes #1566)
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- Aug 17, 2021
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Sebastian Schmitt authored
- make spack ci run use arbor version information - Cache Spack for GH Actions
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- Aug 16, 2021
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Brent Huisman authored
Latest Pandas versions required unique indices, breaking the plotting in the python examples.
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- Aug 10, 2021
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Brent Huisman authored
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- Aug 02, 2021
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thorstenhater authored
* Fix failure to return value in `py_mech_cat_value_iterator `. * String butchered by formatting. * Join unnecessary separation of string literals in `arborio/cabelio.cpp` * Add missing throw in s_expr code. * Return value, not reference, in `merge_iterator::operator++(int)`. * Check for self-assignment in `mechanism_catalogue`. * Initialize all members of `mechanism`. * Fix index check order in `multi_event_stream` debug output. * Use coordinator_ from base class in `memory::array`.
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Brent Huisman authored
* Bit of review on the copy of the mech abi docs. * Convert api/abi docs to C Domain directives.
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- Jul 29, 2021
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Benjamin Cumming authored
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thorstenhater authored
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.
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- Jul 27, 2021
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Brent Huisman authored
* added notes re literal_include to python examples * merged changes in #1504 * deduped and includified (https://github.com/arbor-sim/arbor/pull/1558) tutorials. * First divergence of tutorial and code spotted! * Added some contrib documentation for examples and docs.
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- Jul 23, 2021
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thorstenhater authored
Add clang sanitizer passes to GH CI.
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- Jul 05, 2021
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thorstenhater authored
Closes #1547. - Move `MechCat*Iter` to module instead of catalogue class - Add `keys`, `values`, and `items` - Fix a typo.
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Sebastian Schmitt authored
Run only on Linux and Spack/develop closes #1534
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- Jul 02, 2021
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Nora Abi Akar authored
The visibility of symbols in the python shared library is set to 'hidden'. However, examining the dynamic symbol table of the generated `.so` file revealed that all the symbols of the static arbor libraries are still visible. This causes some issues on the Mac M1. To resolve, all source files are now compiled with `-fvisibility=hidden`.
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Brent Huisman authored
- Minor fixes to python examples. - Fix `mpi.py` to use new label API. - Rename `mpi.py`.
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Brent Huisman authored
- zenodo entry for v0.5.2 - minor formatting update to spack file
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- Jun 29, 2021
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thorstenhater authored
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thorstenhater authored
1. All s-exp parsing has migrated to `arborio` 2. CV policies can now be read from string as per #1334. This is needed for the GUI project. 2. No longer can `arb::locset` and `arb::region` be constructed from mere strings 2. We have `arborio::literals` to construct `region`s, `locset`s, and `cv_policy`s in the form of `_rg`, `_ls`, and `_cvp`. 3. The `_lab` suffix now constructs an object that converts to `named` morphologies, rather than a simple string. 4. Constructors of `region` and `locset` are now properly guarded 5. Consequently, a lot of missing inheritance from `region_tag` and `locset_tag` was retrofitted. Closes #1334 Closes #1419
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- Jun 25, 2021
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Brent Huisman authored
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- Jun 24, 2021
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Brent Huisman authored
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Nora Abi Akar authored
* Remove test_simulator.py. * Add missing python unit test file and fix errors. * Run python unit tests in verbose mode to display which were skipped.
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- Jun 23, 2021
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Brent Huisman authored
Don't pass any architecture by default in setup.py to allow for building binary wheels for targets like x86_64. Build Python package with 'none' arch by default. Bump version to 0.5.2.
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Sebastian Schmitt authored
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Benjamin Cumming authored
- Add an optional CMake option `ARB_CXX_FLAGS_TARGET` for setting target-specific flags to use when compiling for the target architecture (not applied to compilation of modcc). - If `ARB_ARCH=="none"` CMake will not add architecture-specific `mtune/march/mcpu` flags - Remove `ARB_CXXOPT_ARCH` from the installed `arbor-config.cmake`, and replace with more general `ARB_CXX_FLAGS_TARGET`. - Update spack `package.py` to use this feature to pass custom flags. Fixes #1519 Fixes #1522 Replaces PR #1518
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- Jun 22, 2021
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Brent Huisman authored
Bump version for release
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- Jun 21, 2021
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Nora Abi Akar authored
* Turn each task queue in the task system into a finite set of queues of increasing priority. The number of queues is a compile-time constant, currently two. * When a task of priority higher than that of the highest priority queue is scheduled, execute it synchronously. * When scheduling tasks in a task group, use a priority one higher than that of the calling task; when waiting on the task group, work only on tasks with this priority or higher. This is sufficient to avoid the deep recursion issue seen in issue #1570. Fixes #1570. Co-authored-by:
Sam Yates <yates@cscs.ch>
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- Jun 18, 2021
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thorstenhater authored
* Skip relevant corner cases in the matrix solver. * Minor clean-ups in `make_span`. * Add regression test for bug, additional unit tests for `span` and `make_span`. Closes #1540.
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Nora Abi Akar authored
New structs and types: * `cell_tag_type` (std::string): for labelling placeable items on a cell. The label refers to a number of items placed on a locset, equal to the number of locations in a locset. The number of locations in not always known to the user, so the previous way of using indices for items was no longer sufficient. * `lid_selection_policy`: for allowing a user to select a single item from a group of items sharing a label. Currently only `round_robin` and `assert_univalent` are supported. * `cell_local_label_type` and `cell_global_label_type`: for identifying the target and source of a connection or gap_junction connection. * `cell_label_ranges`, and `cell_labels_and_gids`: for propagating information about the labelled items on the cell from the cell groups back to the simulation and communicator. * `label_resolution_map` and `resolver`: for selecting an item (and retaining state) from a labelled group of items on a...
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- Jun 16, 2021
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Sebastian Schmitt authored
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Benjamin Cumming authored
* Sort collected spikes in Python API lfirst by time, then gid, then lid. * Remove redundant old spike handling code from Python lib.
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- Jun 08, 2021
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Sebastian Schmitt authored
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- Jun 02, 2021
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Sebastian Schmitt authored
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Sebastian Schmitt authored
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Brent Huisman authored
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- Jun 01, 2021
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Sebastian Schmitt authored
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Sebastian Schmitt authored
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