1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254
|
#!/usr/bin/env bash
set -xe
# A script to loop over the available pythons installed
# on Linux/OSX and build wheels
#
# Note: It should be invoked from nrn directory
#
# PREREQUESITES:
# - cmake (>=3.5)
# - flex
# - bison
# - python >= 3.7
# - cython
# - MPI
# - X11
# - C/C++ compiler
# - ncurses
set -e
if [ ! -f setup.py ]; then
echo "Error: setup.py not found. Please launch $0 from the nrn root dir"
exit 1
fi
py_ver=""
setup_venv() {
local py_bin="$1"
py_ver=$("$py_bin" -c "import sys; print('%d%d' % tuple(sys.version_info)[:2])")
suffix=$("$py_bin" -c "print(str(hash(\"$py_bin\"))[0:8])")
local venv_dir="nrn_build_venv${py_ver}_${suffix}"
echo " - Creating $venv_dir: $py_bin -m venv $venv_dir"
"$py_bin" -m venv "$venv_dir"
. "$venv_dir/bin/activate"
if ! pip install -U pip setuptools wheel; then
curl https://raw.githubusercontent.com/pypa/get-pip/20.3.4/get-pip.py | python
pip install -U setuptools wheel
fi
}
pip_numpy_install() {
# numpy is special as we want the minimum wheel version
numpy_ver="numpy"
case "$py_ver" in
36) numpy_ver="numpy==1.12.1" ;;
37) numpy_ver="numpy==1.14.6" ;;
38) numpy_ver="numpy==1.17.5" ;;
39) numpy_ver="numpy>=2" ;;
310) numpy_ver="numpy>=2" ;;
311) numpy_ver="numpy>=2" ;;
312) numpy_ver="numpy>=2" ;;
313) numpy_ver="numpy>=2" ;;
*) echo "Error: numpy version not specified for this python!" && exit 1;;
esac
# older version for apple m1 as building from source fails
if [[ `uname -m` == 'arm64' ]] && [[ $py_ver -le 311 ]] ; then
numpy_ver="numpy==1.21.3"
fi
echo " - pip install $numpy_ver"
pip install $numpy_ver
}
build_wheel_linux() {
echo "[BUILD WHEEL] Building with interpreter $1"
local skip=
setup_venv "$1"
(( $skip )) && return 0
echo " - Installing build requirements"
pip install auditwheel
pip install -r packaging/python/build_requirements.txt
pip_numpy_install
echo " - Building..."
rm -rf dist build
CMAKE_DEFS="NRN_MPI_DYNAMIC=$3"
if [ "$USE_STATIC_READLINE" == "1" ]; then
CMAKE_DEFS="$CMAKE_DEFS,NRN_WHEEL_BUILD=ON,NRN_WHEEL_STATIC_READLINE=ON"
fi
if [ "$2" == "coreneuron" ]; then
setup_args="--enable-coreneuron"
elif [ "$2" == "coreneuron-gpu" ]; then
setup_args="--enable-coreneuron --enable-gpu"
# nvhpc is required for GPU support but make sure
# CC and CXX are unset for building python extensions
source ~/.bashrc
module load nvhpc
unset CC CXX
# make the NVIDIA compilers default to targeting haswell CPUs
# the default is currently 70;80, partly because NVHPC does not
# support OpenMP target offload with 60. Wheels use mod2c and
# OpenACC for now, so we can be a little more generic.
CMAKE_DEFS="${CMAKE_DEFS},CMAKE_CUDA_ARCHITECTURES=60;70;80,CMAKE_C_FLAGS=-tp=haswell,CMAKE_CXX_FLAGS=-tp=haswell"
fi
# Workaround for https://github.com/pypa/manylinux/issues/1309
git config --global --add safe.directory "*"
python setup.py build_ext --cmake-prefix="/nrnwheel/ncurses;/nrnwheel/readline" --cmake-defs="$CMAKE_DEFS" $setup_args bdist_wheel
# For CI runs we skip wheelhouse repairs
if [ "$SKIP_WHEELHOUSE_REPAIR" = true ] ; then
echo " - Skipping wheelhouse repair ..."
mkdir wheelhouse && cp dist/*.whl wheelhouse/
else
echo " - Auditwheel show"
auditwheel show dist/*.whl
echo " - Repairing..."
# TODO: still need work to make sure this robust and usable
# currently this will break when coreneuron is used and when
# dev environment is not installed.
auditwheel repair dist/*.whl --exclude "libgomp.so.1"
fi
deactivate
}
build_wheel_osx() {
echo "[BUILD WHEEL] Building with interpreter $1"
local skip=
setup_venv "$1"
(( $skip )) && return 0
echo " - Installing build requirements"
pip install -U delocate -r packaging/python/build_requirements.txt
pip_numpy_install
echo " - Building..."
rm -rf dist build
if [ "$2" == "coreneuron" ]; then
setup_args="--enable-coreneuron"
elif [ "$2" == "coreneuron-gpu" ]; then
echo "Error: GPU support on MacOS is not available!"
exit 1
fi
CMAKE_DEFS="NRN_MPI_DYNAMIC=$3"
if [ "$USE_STATIC_READLINE" == "1" ]; then
CMAKE_DEFS="$CMAKE_DEFS,NRN_WHEEL_BUILD=ON,NRN_WHEEL_STATIC_READLINE=ON"
fi
# We need to "fix" the platform tag if the Python installer is universal2
# See:
# * https://github.com/pypa/setuptools/issues/2520
# * https://github.com/neuronsimulator/nrn/pull/1562
py_platform=$(python -c "import sysconfig; print('%s' % sysconfig.get_platform());")
echo " - Python platform: ${py_platform}"
if [[ "${py_platform}" == "macosx"-*"-arm64" ]]; then
# This is a shortcut to have a successful delocate-wheel. See:
# https://github.com/matthew-brett/delocate/issues/153
python -c "import os,delocate; print(os.path.join(os.path.dirname(delocate.__file__), 'tools.py'));quit()" | xargs -I{} sed -i."" "s/first, /input.pop('i386',None); first, /g" {}
python -c "import os,delocate; print('LOOK HERE'); print(os.path.join(os.path.dirname(delocate.__file__), 'tools.py'));quit()"
fi
if [[ "${py_platform}" == *"-universal2" ]]; then
if [[ `uname -m` == 'arm64' ]]; then
export _PYTHON_HOST_PLATFORM="${py_platform/universal2/arm64}"
echo " - Python installation is universal2 and we are on arm64, setting _PYTHON_HOST_PLATFORM to: ${_PYTHON_HOST_PLATFORM}"
export ARCHFLAGS="-arch arm64"
echo " - Setting ARCHFLAGS to: ${ARCHFLAGS}"
# This is a shortcut to have a successful delocate-wheel. See:
# https://github.com/matthew-brett/delocate/issues/153
python -c "import os,delocate; print(os.path.join(os.path.dirname(delocate.__file__), 'tools.py'));quit()" | xargs -I{} sed -i."" "s/first, /input.pop('i386',None); first, /g" {}
python -c "import os,delocate; print('LOOK HERE'); print(os.path.join(os.path.dirname(delocate.__file__), 'tools.py'));quit()"
else
export _PYTHON_HOST_PLATFORM="${py_platform/universal2/x86_64}"
echo " - Python installation is universal2 and we are on x84_64, setting _PYTHON_HOST_PLATFORM to: ${_PYTHON_HOST_PLATFORM}"
export ARCHFLAGS="-arch x86_64"
echo " - Setting ARCHFLAGS to: ${ARCHFLAGS}"
fi
fi
python setup.py build_ext --cmake-prefix="/opt/nrnwheel/ncurses;/opt/nrnwheel/readline;/usr/x11" --cmake-defs="$CMAKE_DEFS" $setup_args bdist_wheel
echo " - Calling delocate-listdeps"
delocate-listdeps dist/*.whl
echo " - Repairing..."
delocate-wheel -w wheelhouse -v dist/*.whl # we started clean, there's a single wheel
deactivate
}
# platform for which wheel to be build
platform=$1
# python version for which wheel to be built; 3* (default) means all python 3 versions
python_wheel_version=
if [ ! -z "$2" ]; then
python_wheel_version=$2
fi
# enable coreneuron support: "coreneuron" or "coreneuron-gpu"
# this should be removed/improved once wheel is stable
coreneuron=$3
# MAIN
case "$1" in
linux)
MPI_INCLUDE_HEADERS="/nrnwheel/openmpi/include;/nrnwheel/mpich/include"
# Check for MPT headers. On Azure, we extract them from a secure file and mount them in the docker image in:
MPT_INCLUDE_PATH="/nrnwheel/mpt/include"
if [ -d "$MPT_INCLUDE_PATH" ]; then
MPI_INCLUDE_HEADERS="${MPI_INCLUDE_HEADERS};${MPT_INCLUDE_PATH}"
fi
USE_STATIC_READLINE=1
python_wheel_version=${python_wheel_version//[-._]/}
for py_bin in /opt/python/cp${python_wheel_version}*/bin/python; do
build_wheel_linux "$py_bin" "$coreneuron" "$MPI_INCLUDE_HEADERS"
done
;;
osx)
BREW_PREFIX=$(brew --prefix)
MPI_INCLUDE_HEADERS="${BREW_PREFIX}/opt/openmpi/include;${BREW_PREFIX}/opt/mpich/include"
USE_STATIC_READLINE=1
for py_bin in /Library/Frameworks/Python.framework/Versions/${python_wheel_version}*/bin/python3; do
build_wheel_osx "$py_bin" "$coreneuron" "$MPI_INCLUDE_HEADERS"
done
;;
CI)
if [ "$CI_OS_NAME" == "osx" ]; then
BREW_PREFIX=$(brew --prefix)
MPI_INCLUDE_HEADERS="${BREW_PREFIX}/opt/openmpi/include;${BREW_PREFIX}/opt/mpich/include"
build_wheel_osx $(which python3) "$coreneuron" "$MPI_INCLUDE_HEADERS"
else
MPI_INCLUDE_HEADERS="/usr/lib/x86_64-linux-gnu/openmpi/include;/usr/include/x86_64-linux-gnu/mpich"
build_wheel_linux $(which python3) "$coreneuron" "$MPI_INCLUDE_HEADERS"
fi
ls wheelhouse/
;;
*)
echo "Usage: $(basename $0) < linux | osx > [python version 36|37|38|39|3*] [coreneuron | coreneuron-gpu]"
exit 1
;;
esac
|