Merged master.

Merge remote-tracking branch 'upstream/master' into spack_improvements

.github/workflows/benchmarks.yml

@@ -3,6 +3,7 @@ name: Benchmarks
 on:
  pull_request:
  branches: [ master ]
+ paths-ignore: 'doc/**'
 
 jobs:
  build:

.github/workflows/lint.yml

@@ -7,14 +7,15 @@ on:
 jobs:
  build:
  name: Lint
- runs-on: ubuntu-20.04
+ runs-on: ubuntu-22.04
  strategy:
  fail-fast: false
  steps:
+ - uses: actions/checkout@v3
  - name: Set up Python
  uses: actions/setup-python@v4
  with:
- python-version: 3.7
+ python-version: '3.10'
  - name: Get packages
  run: |
  python -m pip install --upgrade pip

.github/workflows/sanitize.yml

@@ -3,6 +3,7 @@ name: Sanitize
 on:
  pull_request:
  branches: [ master ]
+ paths-ignore: 'doc/**'
 
 jobs:
  build:

.github/workflows/test-docs.yaml

@@ -0,0 +1,41 @@
+name: Test docs
+
+on:
+ push:
+ branches: [ master ]
+ paths: 'doc/**'
+ pull_request:
+ branches: [ master ]
+ paths: 'doc/**'
+
+jobs:
+ testdocs:
+ name: "Docs build test"
+ runs-on: ${{ matrix.os }}
+ strategy:
+ matrix:
+ os: [ubuntu-20.04]
+ python-version: [3.7]
+ steps:
+ - name: Set up cmake
+ uses: jwlawson/[email protected]
+ with:
+ cmake-version: ${{ matrix.config.cmake }}
+ - name: Set up Python
+ uses: actions/setup-python@v4
+ with:
+ python-version: ${{ matrix.python-version }}
+ - name: Update pip and setup venv
+ run: python -m pip install --upgrade pip && python -m venv ~/env && . ~/env/bin/activate && echo "PATH=$PATH" >> $GITHUB_ENV
+ - name: Clone w/ submodules
+ uses: actions/checkout@v3
+ with:
+ submodules: recursive
+ - name: Install Python packages
+ run: python -m pip install -r doc/requirements.txt -U
+ - name: Build Arbor Docs
+ run: |
+ mkdir build
+ cd build
+ cmake .. -DARB_WITH_PYTHON=ON -DPython3_EXECUTABLE=`which python` -DARB_USE_BUNDLED_LIBS=ON
+ make html

.github/workflows/test-everything.yml → .github/workflows/test-matrix.yml

@@ -1,10 +1,12 @@
-name: Test Everything
+name: Test Matrix
 
 on:
  push:
  branches: [ master ]
+ paths-ignore: 'doc/**'
  pull_request:
  branches: [ master ]
+ paths-ignore: 'doc/**'
 
 jobs:
  testallconfigs:
@@ -191,67 +193,3 @@ jobs:
  # run: scripts/run_python_examples.sh
  - name: Test executables
  run: ./scripts/test_executables.sh
- testpip:
- name: "Pip build test + Python examples test"
- runs-on: ${{ matrix.os }}
- strategy:
- matrix:
- os: [ubuntu-20.04]
- python-version: [3.7]
- steps:
- - uses: actions/setup-python@v4
- with:
- python-version: ${{ matrix.python-version }}
- - name: Clone w/ submodules
- uses: actions/checkout@v3
- with:
- submodules: recursive
- - name: Update pip and setup venv
- run: python -m pip install --upgrade pip && python -m venv ~/env && . ~/env/bin/activate && echo PATH=$PATH >> $GITHUB_ENV
- - name: Debug info Python
- run: |
- which python
- python --version
- pip --version
- - name: Build and install Arbor using pip + build flags
- run: CMAKE_ARGS="-DARB_VECTORIZE=ON -DARB_ARCH=native" pip install . --user
- - name: Check that build flags match
- run: |
- python -c "import arbor; print(arbor.config())" | grep -q "'arch': 'native'"
- - name: Run Python tests
- run: python -m unittest discover -v -s python
- - name: Run Python examples
- run: scripts/run_python_examples.sh
- - name: Test executables
- run: scripts/test_executables.sh
- testdocs:
- name: "Docs build test"
- runs-on: ${{ matrix.os }}
- strategy:
- matrix:
- os: [ubuntu-20.04]
- python-version: [3.7]
- steps:
- - name: Set up cmake
- uses: jwlawson/[email protected]
- with:
- cmake-version: ${{ matrix.config.cmake }}
- - name: Set up Python
- uses: actions/setup-python@v4
- with:
- python-version: ${{ matrix.python-version }}
- - name: Update pip and setup venv
- run: python -m pip install --upgrade pip && python -m venv ~/env && . ~/env/bin/activate && echo "PATH=$PATH" >> $GITHUB_ENV
- - name: Clone w/ submodules
- uses: actions/checkout@v3
- with:
- submodules: recursive
- - name: Install Python packages
- run: python -m pip install -r doc/requirements.txt -U
- - name: Build Arbor Docs
- run: |
- mkdir build
- cd build
- cmake .. -DARB_WITH_PYTHON=ON -DPython3_EXECUTABLE=`which python` -DARB_USE_BUNDLED_LIBS=ON
- make html
- 

.github/workflows/test-pip.yaml

@@ -0,0 +1,44 @@
+name: Test pip
+
+on:
+ push:
+ branches: [ master ]
+ paths-ignore: 'doc/**'
+ pull_request:
+ branches: [ master ]
+ paths-ignore: 'doc/**'
+
+jobs:
+ testpip:
+ name: "Pip build test + Python examples test"
+ runs-on: ${{ matrix.os }}
+ strategy:
+ matrix:
+ os: [ubuntu-20.04]
+ python-version: [3.7]
+ steps:
+ - uses: actions/setup-python@v4
+ with:
+ python-version: ${{ matrix.python-version }}
+ - name: Clone w/ submodules
+ uses: actions/checkout@v3
+ with:
+ submodules: recursive
+ - name: Update pip and setup venv
+ run: python -m pip install --upgrade pip && python -m venv ~/env && . ~/env/bin/activate && echo PATH=$PATH >> $GITHUB_ENV
+ - name: Debug info Python
+ run: |
+ which python
+ python --version
+ pip --version
+ - name: Build and install Arbor using pip + build flags
+ run: CMAKE_ARGS="-DARB_VECTORIZE=ON -DARB_ARCH=native" pip install . --user
+ - name: Check that build flags match
+ run: |
+ python -c "import arbor; print(arbor.config())" | grep -q "'arch': 'native'"
+ - name: Run Python tests
+ run: python -m unittest discover -v -s python
+ - name: Run Python examples
+ run: scripts/run_python_examples.sh
+ - name: Test executables
+ run: scripts/test_executables.sh

.github/workflows/spack.yml → .github/workflows/test-spack.yml

@@ -3,8 +3,10 @@ name: Spack
 on:
  push:
  branches: [ master ]
+ paths-ignore: 'doc/**'
  pull_request:
  branches: [ master ]
+ paths-ignore: 'doc/**'
 
 jobs:
  build:

CMakeLists.txt

@@ -19,11 +19,13 @@ set(CMAKE_POSITION_INDEPENDENT_CODE ON)
 
 # Have LTO where possible, ie add -flto
 check_ipo_supported(RESULT HAVE_LTO OUTPUT ERR_LTO)
-if(HAVE_LTO AND NOT DEFINED CMAKE_INTERPROCEDURAL_OPTIMIZATION)
- message (STATUS "LTO support found, enabling")
- set(CMAKE_INTERPROCEDURAL_OPTIMIZATION TRUE)
-else()
- message(STATUS "No LTO: ${ERR_LTO}")
+if(NOT DEFINED CMAKE_INTERPROCEDURAL_OPTIMIZATION)
+ if(HAVE_LTO)
+ message (STATUS "LTO support found, enabling")
+ set(CMAKE_INTERPROCEDURAL_OPTIMIZATION TRUE)
+ else()
+ message(STATUS "No LTO: ${ERR_LTO}")
+ endif()
 endif()
 
 # Turn on this option to force the compilers to produce color output when output is

README.md

@@ -1,5 +1,7 @@
-[![ci](https://github.com/arbor-sim/arbor/actions/workflows/test-everything.yml/badge.svg)](https://github.com/arbor-sim/arbor/actions/workflows/test-everything.yml)
-[![pythonwheels](https://github.com/arbor-sim/arbor/actions/workflows/release.yml/badge.svg)](https://github.com/arbor-sim/arbor/actions/workflows/release.yml)
+[![ci](https://github.com/arbor-sim/arbor/actions/workflows/test-matrix.yml/badge.svg)](https://github.com/arbor-sim/arbor/actions/workflows/test-matrix.yml)
+[![spack](https://github.com/arbor-sim/arbor/actions/workflows/test-spack.yml/badge.svg)](https://github.com/arbor-sim/arbor/actions/workflows/test-spack.yml)
+[![pip](https://github.com/arbor-sim/arbor/actions/workflows/test-pip.yml/badge.svg)](https://github.com/arbor-sim/arbor/actions/workflows/test-pip.yml)
+[![pythonwheels](https://github.com/arbor-sim/arbor/actions/workflows/build-pip-wheels.yml/badge.svg)](https://github.com/arbor-sim/arbor/actions/workflows/build-pip-wheels.yml)
 [![gitpod](https://img.shields.io/badge/Gitpod-Ready--to--Code-blue?logo=gitpod)](https://gitpod.io/#https://github.com/arbor-sim/arbor)
 [![docs](https://readthedocs.org/projects/arbor/badge/?version=latest)](https://docs.arbor-sim.org/en/latest/)
 [![gitter](https://badges.gitter.im/arbor-sim/community.svg)](https://gitter.im/arbor-sim/community)

arbor/backends/gpu/forest.hpp

@@ -58,6 +58,8 @@ struct ARB_ARBOR_API forest {
 
 
 struct level_iterator {
+ constexpr static unsigned npos = unsigned(-1);
+
  level_iterator(tree* t, unsigned level) {
  tree_ = t;
  only_on_level = level;
@@ -94,16 +96,15 @@ struct level_iterator {
  next_children = index + 1;
  } else {
  // we are done with the iteration
- current_level = -1;
- current_node = -1;
- next_children = -1;
+ current_level = npos;
+ current_node = npos;
+ next_children = npos;
  }
 
  }
  }
 
  unsigned next() {
- constexpr unsigned npos = unsigned(-1);
  if (!valid()) {
  // we are done
  return npos;

arbor/backends/gpu/shared_state.cpp

@@ -43,8 +43,7 @@ std::pair<arb_value_type, arb_value_type> minmax_value_impl(arb_size_type n, con
 
 // Ion state methods:
 
-ion_state::ion_state(int charge,
- const fvm_ion_config& ion_data,
+ion_state::ion_state(const fvm_ion_config& ion_data,
  unsigned, // alignment/padding ignored.
  solver_ptr ptr):
  write_eX_(ion_data.revpot_written),
@@ -62,7 +61,7 @@ ion_state::ion_state(int charge,
  reset_Xi_(make_const_view(ion_data.reset_iconc)),
  reset_Xo_(make_const_view(ion_data.reset_econc)),
  init_eX_(make_const_view(ion_data.init_revpot)),
- charge(1u, charge),
+ charge(1u, static_cast<arb_value_type>(ion_data.charge)),
  solver(std::move(ptr)) {
  arb_assert(node_index_.size()==init_Xi_.size());
  arb_assert(node_index_.size()==init_Xo_.size());

arbor/backends/gpu/shared_state.hpp

@@ -64,11 +64,9 @@ struct ARB_ARBOR_API ion_state {
 
  ion_state() = default;
 
- ion_state(
- int charge,
- const fvm_ion_config& ion_data,
- unsigned align,
- solver_ptr ptr);
+ ion_state(const fvm_ion_config& ion_data,
+ unsigned align,
+ solver_ptr ptr);
 
  // Set ion concentrations to weighted proportion of default concentrations.
  void init_concentration();

arbor/communication/communicator.cpp

@@ -36,21 +36,21 @@ communicator::communicator(const recipe& rec,
 constexpr inline
 bool is_external(cell_gid_type c) {
  // index of the MSB of cell_gid_type in bits
- constexpr auto msb = 1 << (std::numeric_limits<cell_gid_type>::digits - 1);
+ constexpr auto msb = static_cast<cell_gid_type>(1 << (std::numeric_limits<cell_gid_type>::digits - 1));
  // If set, we are external
  return bool(c & msb);
 }
 
 constexpr inline
 cell_member_type global_cell_of(const cell_remote_label_type& c) {
- constexpr auto msb = 1 << (std::numeric_limits<cell_gid_type>::digits - 1);
+ constexpr auto msb = static_cast<cell_gid_type>(1 << (std::numeric_limits<cell_gid_type>::digits - 1));
  // set the MSB
  return {c.rid | msb, c.index};
 }
 
 constexpr inline
 cell_member_type global_cell_of(const cell_member_type& c) {
- constexpr auto msb = 1 << (std::numeric_limits<cell_gid_type>::digits - 1);
+ constexpr auto msb = static_cast<cell_gid_type>(1 << (std::numeric_limits<cell_gid_type>::digits - 1));
  // set the MSB
  return {c.gid | msb, c.index};
 }

arbor/cv_policy.cpp

@@ -57,7 +57,7 @@ struct cv_policy_bar_: cv_policy_base {
  }
 
  locset cv_boundary_points(const cable_cell& c) const override {
- return unique_sum(ls::restrict(lhs_.cv_boundary_points(c), complement(rhs_.domain())), rhs_.cv_boundary_points(c));
+ return unique_sum(ls::restrict_to(lhs_.cv_boundary_points(c), complement(rhs_.domain())), rhs_.cv_boundary_points(c));
  }
 
  region domain() const override { return join(lhs_.domain(), rhs_.domain()); }
@@ -82,7 +82,7 @@ locset cv_policy_explicit::cv_boundary_points(const cable_cell& cell) const {
  ls::support(
  util::foldl(
  [this](locset l, const auto& comp) {
- return sum(std::move(l), ls::restrict(locs_, comp));
+ return sum(std::move(l), ls::restrict_to(locs_, comp));
  },
  ls::boundary(domain_),
  components(cell.morphology(), thingify(domain_, cell.provider()))));
@@ -190,7 +190,7 @@ locset cv_policy_every_segment::cv_boundary_points(const cable_cell& cell) const
 
  return unique_sum(
  ls::cboundary(domain_),
- ls::restrict(ls::segment_boundaries(), domain_));
+ ls::restrict_to(ls::segment_boundaries(), domain_));
 }
 cv_policy_base_ptr cv_policy_every_segment::clone() const {
  return cv_policy_base_ptr(new cv_policy_every_segment(*this));

arbor/fvm_lowered_cell.hpp

@@ -185,7 +185,9 @@ struct probe_association_map {
  }
 
  // Return range of fvm_probe_data values associated with probeset_id.
- auto data_on(cell_member_type probeset_id) const {
+ // Trailing return type added here to avoid warnings about ODR violations when building shared
+ // lib together with LTO - needs to be re-checked in the future
+ auto data_on(cell_member_type probeset_id) const -> decltype(util::transform_view(util::make_range(data.equal_range(probeset_id)), util::second)) {
  return util::transform_view(util::make_range(data.equal_range(probeset_id)), util::second);
  }
 };