-
Notifications
You must be signed in to change notification settings - Fork 113
/
build_wheels.bash
executable file
·268 lines (222 loc) · 9.14 KB
/
build_wheels.bash
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
255
256
257
258
259
260
261
262
263
264
265
266
267
268
#!/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 (>=3.15.0)
# - flex
# - bison
# - python >= 3.8
# - 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=""
clone_install_nmodl_requirements() {
git config --global --add safe.directory /root/nrn
git submodule update --init --recursive --force --depth 1 -- external/nmodl
pip install -r external/nmodl/requirements.txt
}
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 "$py_ver" in
36) numpy_ver="numpy==1.12.1" ;;
37) numpy_ver="numpy==1.14.6" ;;
38) numpy_ver="numpy==1.17.5" ;;
39) numpy_ver="numpy==1.19.3" ;;
310) numpy_ver="numpy==1.21.3" ;;
311) numpy_ver="numpy==1.23.5" ;;
312) numpy_ver="numpy==1.26.0" ;;
*) echo "Error: numpy version not specified for this python!" && exit 1;;
esac
# older version for apple m1 as building from source fails
if [[ `uname -m` == 'arm64' && "$py_ver" == "39" ]]; 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_BINARY_DIST_BUILD=ON,NRN_WHEEL_STATIC_READLINE=ON"
fi
if [ "$2" == "coreneuron" ]; then
setup_args="--enable-coreneuron"
clone_install_nmodl_requirements
CMAKE_DEFS="${CMAKE_DEFS},LINK_AGAINST_PYTHON=OFF"
fi
# Workaround for https://github.com/pypa/manylinux/issues/1309
git config --global --add safe.directory "*"
if [ -n "${setup_args}" ]; then
python -m build --wheel --no-isolation \
--config-setting="--global-option=build_ext" \
--config-setting="--global-option=${setup_args}" \
--config-setting="--global-option=--cmake-defs=${CMAKE_DEFS}" \
--config-setting='--global-option=--cmake-prefix="/nrnwheel/ncurses;/nrnwheel/readline"'
else
python -m build --wheel --no-isolation \
--config-setting="--global-option=build_ext" \
--config-setting="--global-option=--cmake-defs=${CMAKE_DEFS}" \
--config-setting='--global-option=--cmake-prefix="/nrnwheel/ncurses;/nrnwheel/readline"'
fi
# 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..."
# NOTE:
# libgomp: 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. Note that on aarch64 we have
# seen issue with libgomp.so and hence we started excluding it.
# libnrniv: we ship precompiled version of neurondemo containing libnrnmech.so
# which is linked to libnrniv.so. auditwheel manipulate rpaths and
# ships an extra copy of libnrniv.so and hence exclude it here.
auditwheel -v repair dist/*.whl --exclude "libgomp.so.1" --exclude "libnrniv.so"
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"
clone_install_nmodl_requirements
fi
CMAKE_DEFS="NRN_MPI_DYNAMIC=$3"
if [ "$USE_STATIC_READLINE" == "1" ]; then
CMAKE_DEFS="$CMAKE_DEFS,NRN_BINARY_DIST_BUILD=ON,NRN_WHEEL_STATIC_READLINE=ON"
fi
# We need to "fix" the platform tag if the Python installer is universal2
# See:
# * https://github.com/pypa/setuptools/issues/2520
# * https://github.com/neuronsimulator/nrn/pull/1562
py_platform=$(python -c "import sysconfig; print('%s' % sysconfig.get_platform());")
echo " - Python platform: ${py_platform}"
if [[ "${py_platform}" == *"-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: ${ARCHFLAGS}"
# This is a shortcut to have a successful delocate-wheel. See:
# https://github.com/matthew-brett/delocate/issues/153
python -c "import os,delocate; print(os.path.join(os.path.dirname(delocate.__file__), 'tools.py'));quit()" | xargs -I{} sed -i."" "s/first, /input.pop('i386',None); first, /g" {}
else
export _PYTHON_HOST_PLATFORM="${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: ${ARCHFLAGS}"
fi
fi
if [ -n "${setup_args}" ]; then
python -m build --wheel --no-isolation \
--config-setting="--global-option=build_ext" \
--config-setting="--global-option=${setup_args}" \
--config-setting="--global-option=--cmake-defs=${CMAKE_DEFS}" \
--config-setting='--global-option=--cmake-prefix="/opt/nrnwheel/ncurses;/opt/nrnwheel/readline;/usr/x11"'
else
python -m build --wheel --no-isolation \
--config-setting="--global-option=build_ext" \
--config-setting="--global-option=--cmake-defs=${CMAKE_DEFS}" \
--config-setting='--global-option=--cmake-prefix="/opt/nrnwheel/ncurses;/opt/nrnwheel/readline;/usr/x11"'
fi
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"
# 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]"
exit 1
;;
esac