- Jul 05, 2021
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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 cell according to a user-selected policy. Changes to the model-initialization: * The `communicator` now needs `label_resolution_maps` constructed from the cell group data in order to build the `connections` vectors. * The `simulation_state` object handles the transfer of the information when it is constructed. * Spike exchange at runtime remains unchanged, because `communicator::connections` remains unchanged. Changes to cells, cell_groups and recipe: * `decor::place` expects a third label parameter, no longer returns an `lid_range`. * `lif`, `source`, and `benchmark` cells need source/target labels in their constructors. * A `cell_group` needs to save data about the gid/labels/lid_ranges of each cell, to propagate back to the `communicator` constructor. * Connections/gap junction connections are formed between {label, policy} pairs on cells instead of indices. * `num_sources`, `num_targets`, `num_gap_junction_sites` deleted from `recipe`. Additional changes: * Add MPI wrapper for exchanging vectors of strings. * Corresponding updates to unit tests, Python wrapper, C++ and Python examples, documentation. Fixes #1394
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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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- May 31, 2021
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Brent Huisman authored
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Robin De Schepper authored
* Delete symlinks from repository for Windows devs * Dropped extension of executable scripts to follow shell convention * set executable bits in scripts/ Co-authored-by: Robin De Schepper <robin.deschepper93gmail.com> Co-authored-by:
Brent Huisman <brent@huisman.pl>
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Nora Abi Akar authored
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thorstenhater authored
* Raise KeyError in catalogue. * Raise KeyError in label_dict.
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- May 27, 2021
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Benjamin Cumming authored
The C++ label parse code was returning the error type in the value part of a `parse_hopefully<std::any>`, and not in the error slot.
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- May 26, 2021
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Robin De Schepper authored
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Sebastian Schmitt authored
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Benjamin Cumming authored
The `label_dict` Python wrapper caches label strings and their descriptions in order to provide a convenient Python iterator interface and `[]` access. These were not being properly updated or set when the label_dict was constructed from a C++ label_dict.
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Brent Huisman authored
* Update URLs to arbor-sim.org * update badge links
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- May 19, 2021
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Benjamin Cumming authored
Add a CI test for ARM-SVE - compiles and runs the unit tests with vectorization enabled for the `armv8.2-a+sv` architecture - uses a dedicated gitlab runner on ault.cscs.ch Fixes #1498
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- May 18, 2021
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Sebastian Schmitt authored
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Nora Abi Akar authored
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Sam Yates authored
Fixes issue #1529.
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Brent Huisman authored
* Adapt CSS for the HTML5 transition in docutils 0.17 * Fix some reST markup errors * Add meta-tag to enable indexation control at Google (current indexation appears at least a year old).
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- May 17, 2021
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Nora Abi Akar authored
Fix mistakes reported by @Helveg in the Python tutorial docs.
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- May 10, 2021
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thorstenhater authored
* Add a GH workflow to build and run Arbor tests and examples with Clang sanitizers. * Fix some uninitialized struct members; missing `override` qualifiers.
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