I encountered a problem when using openmp in xtensor-python with xtensor-python-cookiecutter.
After executing python setup.py build, I encountered an error when import myLib: undefined symbol: omp_get_thread_num.
And below is my log of python setup.py build
$ py setup.py build
running build
running build_ext
creating tmp
gcc -pthread -B /home/joker/.miniconda3/envs/cpp/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/joker/.miniconda3/envs/cpp/include/python3.8 -c /tmp/tmp8bct6mhu.cpp -o tmp/tmp8bct6mhu.o -std=c++14
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
gcc -pthread -B /home/joker/.miniconda3/envs/cpp/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/joker/.miniconda3/envs/cpp/include/python3.8 -c /tmp/tmpja5ljvir.cpp -o tmp/tmpja5ljvir.o -fvisibility=hidden
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
building 'test' extension
creating build
creating build/temp.linux-x86_64-3.8
creating build/temp.linux-x86_64-3.8/src
gcc -pthread -B /home/joker/.miniconda3/envs/cpp/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/joker/.miniconda3/envs/cpp/include -I/home/joker/.miniconda3/envs/cpp/include -I/home/joker/.miniconda3/envs/cpp/lib/python3.8/site-packages/numpy/core/include -I/home/joker/.miniconda3/envs/cpp/include -I/home/joker/.miniconda3/envs/cpp/Library/include -I/home/joker/.miniconda3/envs/cpp/include/python3.8 -c src/main.cpp -o build/temp.linux-x86_64-3.8/src/main.o -fopenmp -DVERSION_INFO="0.1.0" -std=c++14 -fvisibility=hidden
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
creating build/lib.linux-x86_64-3.8
g++ -pthread -shared -B /home/joker/.miniconda3/envs/cpp/compiler_compat -L/home/joker/.miniconda3/envs/cpp/lib -Wl,-rpath=/home/joker/.miniconda3/envs/cpp/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-3.8/src/main.o -o build/lib.linux-x86_64-3.8/test.cpython-38-x86_64-linux-gnu.so
Check the last command:
g++ -pthread -shared -B /home/joker/.miniconda3/envs/cpp/compiler_compat -L/home/joker/.miniconda3/envs/cpp/lib -Wl,-rpath=/home/joker/.miniconda3/envs/cpp/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-3.8/src/main.o -o build/lib.linux-x86_64-3.8/test.cpython-38-x86_64-linux-gnu.so
It seems that -fopenmp is missing. After I run it mannual with -fopenmp, i.e.
g++ -fopenmp -pthread -shared -B /home/joker/.miniconda3/envs/cpp/compiler_compat -L/home/joker/.miniconda3/envs/cpp/lib -Wl,-rpath=/home/joker/.miniconda3/envs/cpp/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-3.8/src/main.o -o build/lib.linux-x86_64-3.8/test.cpython-38-x86_64-linux-gnu.so
anything is well.
I have added the flag -fopenmp in setup.py, but I don't know why it doesn't work as expected
class BuildExt(build_ext):
"""A custom build extension for adding compiler-specific options."""
c_opts = {
'msvc': ['/EHsc'],
'unix': ['-fopenmp'],
}
Thanks for your reading.
and below is my full setup.py
from setuptools import setup, Extension
from setuptools.command.build_ext import build_ext
import sys
import os
import setuptools
__version__ = '0.1.0'
class get_pybind_include(object):
"""Helper class to determine the pybind11 include path
The purpose of this class is to postpone importing pybind11
until it is actually installed, so that the ``get_include()``
method can be invoked. """
def __init__(self, user=False):
self.user = user
def __str__(self):
import pybind11
return pybind11.get_include(self.user)
class get_numpy_include(object):
"""Helper class to determine the numpy include path
The purpose of this class is to postpone importing numpy
until it is actually installed, so that the ``get_include()``
method can be invoked. """
def __init__(self):
pass
def __str__(self):
import numpy as np
return np.get_include()
ext_modules = [
Extension(
'fold_3d_labelling',
['src/main.cpp'],
include_dirs=[
# Path to pybind11 headers
get_pybind_include(),
get_pybind_include(user=True),
get_numpy_include(),
os.path.join(sys.prefix, 'include'),
os.path.join(sys.prefix, 'Library', 'include')
],
language='c++'
),
]
def has_flag(compiler, flagname):
"""Return a boolean indicating whether a flag name is supported on
the specified compiler.
"""
import tempfile
with tempfile.NamedTemporaryFile('w', suffix='.cpp') as f:
f.write('int main (int argc, char **argv) { return 0; }')
try:
compiler.compile([f.name], extra_postargs=[flagname])
except setuptools.distutils.errors.CompileError:
return False
return True
def cpp_flag(compiler):
"""Return the -std=c++14 compiler flag and errors when the flag is
no available.
"""
if has_flag(compiler, '-std=c++14'):
return '-std=c++14'
else:
raise RuntimeError('C++14 support is required by xtensor!')
class BuildExt(build_ext):
"""A custom build extension for adding compiler-specific options."""
c_opts = {
'msvc': ['/EHsc'],
'unix': ['-fopenmp'],
}
if sys.platform == 'darwin':
c_opts['unix'] += ['-stdlib=libc++', '-mmacosx-version-min=10.7']
def build_extensions(self):
ct = self.compiler.compiler_type
opts = self.c_opts.get(ct, [])
if ct == 'unix':
opts.append('-DVERSION_INFO="%s"' % self.distribution.get_version())
opts.append(cpp_flag(self.compiler))
if has_flag(self.compiler, '-fvisibility=hidden'):
opts.append('-fvisibility=hidden')
elif ct == 'msvc':
opts.append('/DVERSION_INFO=\\"%s\\"' % self.distribution.get_version())
for ext in self.extensions:
ext.extra_compile_args = opts
build_ext.build_extensions(self)
setup(
name='fold_3d_labelling',
version=__version__,
author='test',
author_email='[email protected]',
url='https://test',
description= '',
long_description='',
ext_modules=ext_modules,
install_requires=['pybind11>=2.0.1', 'numpy'],
cmdclass={'build_ext': BuildExt},
zip_safe=False,
)
Thanks again.