diff --git a/.github/workflows/ciwheel.yml b/.github/workflows/ciwheel.yml
new file mode 100644
index 0000000000000000000000000000000000000000..44dd204b18454345ff0f74b5c8dc208e13b73afb
--- /dev/null
+++ b/.github/workflows/ciwheel.yml
@@ -0,0 +1,89 @@
+name: Arbor on Wheels
+
+on:
+ push:
+ branches: [ ciwheel ]
+ tags:
+ - v*
+
+jobs:
+ build_binary_wheels:
+ name: Build wheels on ${{ matrix.os }}
+ runs-on: ${{ matrix.os }}
+ strategy:
+ matrix:
+ os: [ubuntu-latest, macos-latest]
+
+ steps:
+ - uses: actions/checkout@v2
+ with:
+ fetch-depth: 0
+ submodules: recursive
+
+ - name: Build wheels Linux
+ if: ${{ startsWith(matrix.os, 'ubuntu') }}
+ uses: joerick/cibuildwheel@v1.9.0
+ with:
+ output-dir: dist
+ env:
+ CIBW_BEFORE_BUILD: python -m pip install numpy setuptools
+ CIBW_BUILD: "cp3?-manylinux_x86_64"
+ CIBW_SKIP: "cp35-*"
+ CIBW_MANYLINUX_X86_64_IMAGE: manylinux2014
+ # CIBW_TEST_COMMAND: TODO
+
+ - name: Build wheels macos
+ if: ${{ startsWith(matrix.os, 'macos') }}
+ uses: joerick/cibuildwheel@v1.9.0
+ with:
+ output-dir: dist
+ env:
+ MACOSX_DEPLOYMENT_TARGET: "10.15" #needed to undo some CIBW settings
+ CIBW_BEFORE_BUILD: python -m pip install numpy setuptools
+ CIBW_BUILD: "cp3?-macosx_x86_64"
+ CIBW_SKIP: "cp35-*"
+ CIBW_ARCHS_MACOS: x86_64 universal2
+ # CIBW_TEST_COMMAND: TODO
+
+ # this action runs auditwheel automatically with the following args:
+ # https://cibuildwheel.readthedocs.io/en/stable/options/#repair-wheel-command
+
+ - uses: actions/upload-artifact@v2
+ with:
+ name: dist
+ path: dist/*.whl
+
+ build_sdist:
+ name: Build sdist
+ runs-on: ubuntu-latest
+
+ steps:
+ - name: Set up Python
+ uses: actions/setup-python@v2
+ - uses: actions/checkout@v2
+ with:
+ fetch-depth: 0
+ submodules: recursive
+ - name: Make sdist
+ run: python setup.py sdist
+ - uses: actions/upload-artifact@v2
+ with:
+ name: dist
+ path: dist/*.tar.gz
+
+# TODO
+ # upload_test_pypi:
+ # name: upload to test pypi
+ # runs-on: ubuntu-latest
+ # needs: [build_binary_wheels, build_sdist]
+ # steps:
+ # - uses: actions/download-artifact@v2
+ # with:
+ # name: dist
+ # - name: Publish distribution 📦 to Test PyPI
+ # run: |
+ # pip install twine
+ # twine upload -r testpypi dist/*
+ # env:
+ # TWINE_USERNAME: __token__
+ # TWINE_PASSWORD: ${{ secrets.ciwheeltest }}
diff --git a/.github/workflows/ebrains.yml b/.github/workflows/ebrains.yml
index 7a527e91f95624162de35e1c2e3ac14613c46323..60932fa6b11dc6a97c87af3d01954ffd0c826e46 100644
--- a/.github/workflows/ebrains.yml
+++ b/.github/workflows/ebrains.yml
@@ -1,6 +1,8 @@
name: Mirror to Ebrains
-on: push
+on:
+ push:
+ branches: [ master ]
jobs:
to_ebrains:
diff --git a/CMakeLists.txt b/CMakeLists.txt
index a71711d952a7708e796bc249bdf1ad0f50a39216..b3b0618e1fcf668cbe07b93d11a8444fed62678b 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -259,7 +259,11 @@ endif()
if(ARB_WITH_PYTHON)
cmake_dependent_option(ARB_USE_BUNDLED_PYBIND11 "Use bundled pybind11" ON "ARB_WITH_PYTHON;ARB_USE_BUNDLED_LIBS" OFF)
- find_package(Python3 ${arb_py_version} COMPONENTS Interpreter Development REQUIRED)
+ if(DEFINED ENV{CIBUILDWHEEL})
+ find_package(Python3 ${arb_py_version} COMPONENTS Interpreter Development.Module REQUIRED)
+ else()
+ find_package(Python3 ${arb_py_version} COMPONENTS Interpreter Development REQUIRED)
+ endif()
# Required to link the dynamic libraries for python modules.
# Effectively adds '-fpic' flag to CXX_FLAGS.
diff --git a/doc/install/build_install.rst b/doc/install/build_install.rst
index 7181512c400ba5c03c833a99852637511510947c..9de38d00ed9a9870844dfbe5f77b37102e948d03 100644
--- a/doc/install/build_install.rst
+++ b/doc/install/build_install.rst
@@ -359,6 +359,9 @@ to implement these kernels. Arbor currently has vectorization support for x86 ar
with AVX, AVX2 or AVX512 ISA extensions; and for AArch64 ARM architectures with NEON and SVE
(first available on ARMv8-A).
+.. note::
+ Note that on x86-64 platforms compilation will fail if you enable vectorization, but the CPU or ``-DARB_ARCH`` does not support any form of AVX.
+
.. _install-gpu:
GPU backend
diff --git a/doc/install/python.rst b/doc/install/python.rst
index ad2066a62b9925bdd3ffeb7c2b895ac497716746..0ecfafd76eb9d832d3f8dbec62a1f2e1f006cfc6 100644
--- a/doc/install/python.rst
+++ b/doc/install/python.rst
@@ -21,9 +21,9 @@ Every point release of Arbor is pushed to the Python Package Index. The easiest
.. note::
You will need to have some development packages installed in order to build Arbor this way.
- * Ubuntu/Debian: `sudo apt install git build-essential python3-dev python3-pip`
- * Fedora/CentOS/Red Hat: `sudo yum install git @development-tools python3-devel python3-pip`
- * macOS: get `brew` `here <https://brew.sh>`_ and run `brew install cmake clang python3`
+ * Ubuntu/Debian: `sudo apt install git build-essential python3-dev python3-pip libxml2-dev`
+ * Fedora/CentOS/Red Hat: `sudo yum install git @development-tools python3-devel python3-pip libxml2-devel`
+ * macOS: get `brew` `here <https://brew.sh>`_ and run `brew install cmake clang python3 libxml2`
* Windows: the simplest way is to use `WSL <https://docs.microsoft.com/en-us/windows/wsl/install-win10>`_ and then follow the instructions for Ubuntu.
If you wish to get the latest Arbor straight from
@@ -73,7 +73,7 @@ be used to configure the installation:
* ``--mpi``: Enable MPI support (requires MPI library).
* ``--gpu``: Enable GPU support for NVIDIA GPUs with nvcc using ``cuda``, or with clang using ``cuda-clang`` (both require cudaruntime).
Enable GPU support for AMD GPUs with hipcc using ``hip``. By default set to ``none``, which disables gpu support.
-* ``--vec``: Enable vectorization. This might require choosing an appropriate architecture using ``--arch``.
+* ``--vec``: Enable vectorization. This might require choosing an appropriate architecture using ``--arch``. Note that on x86-64 platforms compilation will fail if you enable vectorization, but the CPU or ``--arch`` does not support any form of AVX.
* ``--arch``: CPU micro-architecture to target. By default this is set to ``native``.
If calling ``setup.py`` the flags must come after ``install`` on the command line,
diff --git a/setup.py b/setup.py
index 48f1108766ecd93d154a58cb10a4dc9581cead5a..ac92bf81513d9190e5f41277a52dc4ae5ea05a50 100644
--- a/setup.py
+++ b/setup.py
@@ -6,6 +6,13 @@ from setuptools import Extension
from setuptools.command.build_ext import build_ext
from setuptools.command.install import install
import subprocess
+try:
+ from wheel.bdist_wheel import bdist_wheel
+ WHEEL_INSTALLED = True
+except:
+ #wheel package not installed.
+ WHEEL_INSTALLED = False
+ pass
# Singleton class that holds the settings configured using command line
# options. This information has to be stored in a singleton so that it
@@ -19,7 +26,7 @@ class CL_opt:
'gpu': 'none',
'vec': False,
'arch': 'native',
- 'neuroml': False,
+ 'neuroml': True,
'bundled': True}
def settings(self):
@@ -28,6 +35,17 @@ class CL_opt:
def cl_opt():
return CL_opt().settings()
+# extend user_options the same way for all Command()s
+user_options_ = [
+ ('mpi', None, 'enable mpi support (requires MPI library)'),
+ ('gpu=', None, 'enable nvidia cuda support (requires cudaruntime and nvcc) or amd hip support. Supported values: '
+ 'none, cuda, cuda-clang, hip'),
+ ('vec', None, 'enable vectorization'),
+ ('arch=', None, 'cpu architecture, e.g. haswell, skylake, armv8.2-a+sve, znver2 (default native).'),
+ ('neuroml', None, 'enable parsing neuroml morphologies in Arbor (requires libxml)'),
+ ('sysdeps', None, 'don\'t use bundled 3rd party C++ dependencies (pybind11 and json). This flag forces use of dependencies installed on the system.')
+ ]
+
# VERSION is in the same path as setup.py
here = os.path.abspath(os.path.dirname(__file__))
with open(os.path.join(here, 'VERSION')) as version_file:
@@ -49,15 +67,7 @@ def check_cmake():
# python3 setup.py install --mpi --arch=skylake
# pip3 install --install-option '--mpi' --install-option '--arch=skylake' .
class install_command(install):
- user_options = install.user_options + [
- ('mpi', None, 'enable mpi support (requires MPI library)'),
- ('gpu=', None, 'enable nvidia cuda support (requires cudaruntime and nvcc) or amd hip support. Supported values: '
- 'none, cuda, cuda-clang, hip'),
- ('vec', None, 'enable vectorization'),
- ('arch=', None, 'cpu architecture, e.g. haswell, skylake, armv8.2-a+sve, znver2 (default native).'),
- ('neuroml', None, 'enable parsing neuroml morphologies in Arbor (requires libxml)'),
- ('sysdeps', None, 'don\'t use bundled 3rd party C++ dependencies (pybind11 and json). This flag forces use of dependencies installed on the system.')
- ]
+ user_options = install.user_options + user_options_
def initialize_options(self):
install.initialize_options(self)
@@ -90,6 +100,41 @@ class install_command(install):
install.run(self)
+if WHEEL_INSTALLED:
+ class bdist_wheel_command(bdist_wheel):
+ user_options = bdist_wheel.user_options + user_options_
+
+ def initialize_options(self):
+ bdist_wheel.initialize_options(self)
+ self.mpi = None
+ self.gpu = None
+ self.arch = None
+ self.vec = None
+ self.neuroml = None
+ self.sysdeps = None
+
+ def finalize_options(self):
+ bdist_wheel.finalize_options(self)
+
+ def run(self):
+ # The options are stored in global variables:
+ opt = cl_opt()
+ # mpi : build with MPI support (boolean).
+ opt['mpi'] = self.mpi is not None
+ # gpu : compile for AMD/NVIDIA GPUs and choose compiler (string).
+ opt['gpu'] = "none" if self.gpu is None else self.gpu
+ # vec : generate SIMD vectorized kernels for CPU micro-architecture (boolean).
+ opt['vec'] = self.vec is not None
+ # arch : target CPU micro-architecture (string).
+ opt['arch'] = "native" if self.arch is None else self.arch
+ # neuroml : compile with neuroml support for morphologies.
+ opt['neuroml'] = self.neuroml is not None
+ # bundled : use bundled/git-submoduled 3rd party libraries.
+ # By default use bundled libs.
+ opt['bundled'] = self.sysdeps is None
+
+ bdist_wheel.run(self)
+
class cmake_extension(Extension):
def __init__(self, name):
Extension.__init__(self, name, sources=[])
@@ -163,8 +208,12 @@ setuptools.setup(
zip_safe=False,
ext_modules=[cmake_extension('arbor')],
cmdclass={
- 'build_ext': cmake_build,
- 'install': install_command,
+ 'build_ext': cmake_build,
+ 'install': install_command,
+ 'bdist_wheel': bdist_wheel_command,
+ } if WHEEL_INSTALLED else {
+ 'build_ext': cmake_build,
+ 'install': install_command,
},
author='The Arbor dev team.',