ChemPy: clang: error: unsupported option '-fopenmp'
ChemPy: clang: error: unsupported option '-fopenmp'
我正在尝试解决以下问题。当我尝试 运行 this ntb 中的以下行时，我得到：
native = get_native(rsys, odesys, 'cvode')
INFO:pyodesys.native._base:Cythonizing /Users/user/Library/Caches/python3.8-pyodesys-0.13.1/_cvode_wrapper.pyx to ./_cvode_wrapper.cpp
INFO:pyodesys.native._base:In "/var/folders/bx/tb4883l53hdd3zp2y0nyy_4m0000gp/T/tmpt2vuw8pg", executing:
"/usr/bin/g++ -fwrapv -pthread -c -std=c++11 -Wall -Wextra -fPIC -O2 -ffast-math -funroll-loops -fopenmp -fno-strict-aliasing -o ./_cvode_wrapper.o -DPYCVODES_NO_KLU=0 -DPYCVODES_NO_LAPACK=0 -DANYODE_NO_LAPACK=0 -I/Users/user/anaconda3/lib/python3.8/site-packages/numpy/core/include -I/Users/jan/anaconda3/lib/python3.8/site-packages/pyodesys/native/sources -I/Users/jan/anaconda3/lib/python3.8/site-packages/pycvodes/include -I/Users/jan/anaconda3/include/python3.8 ./_cvode_wrapper.cpp"
CompilationError: Error executing '/usr/bin/g++ -fwrapv -pthread -c -std=c++11 -Wall -Wextra -fPIC -O2 -ffast-math -funroll-loops -fopenmp -fno-strict-aliasing -o ./_cvode_wrapper.o -DPYCVODES_NO_KLU=0 -DPYCVODES_NO_LAPACK=0 -DANYODE_NO_LAPACK=0 -I/Users/jan/anaconda3/lib/python3.8/site-packages/numpy/core/include -I/Users/jan/anaconda3/lib/python3.8/site-packages/pyodesys/native/sources -I/Users/jan/anaconda3/lib/python3.8/site-packages/pycvodes/include -I/Users/jan/anaconda3/include/python3.8 ./_cvode_wrapper.cpp' in /var/folders/bx/tb4883l53hdd3zp2y0nyy_4m0000gp/T/tmpt2vuw8pg. Command exited with status 1 after givning the following output: clang: error: unsupported option '-fopenmp
我认为这可能是 fopenmp 和 gcc 的问题，如那些地方所述 (, https://github.com/microsoft/LightGBM/issues/3, https://github.com/velocyto-team/velocyto.R/issues/2) but the proposed solutions (https://github.com/velocyto-team/velocyto.R/issues/2#issuecomment-341165967, https://github.com/microsoft/LightGBM/issues/3#issuecomment-254149689, https://github.com/kharchenkolab/conos/wiki/Installing-Conos-for-Mac-OS) 对我不起作用。我也尝试使用 conda 安装 GCC，但我得到：
conda install gcc
PackagesNotFoundError: The following packages are not available from current channels:
- gcc
Current channels:
- https://repo.anaconda.com/pkgs/main/osx-64
- https://repo.anaconda.com/pkgs/main/noarch
- https://repo.anaconda.com/pkgs/r/osx-64
- https://repo.anaconda.com/pkgs/r/noarch
使用 homebrew 我安装了 gcc...知道发生了什么以及如何修复它吗？我正在 运行ning MacOS 10.15.7。谢谢
homebrew 将安装如下内容：
/usr/local/bin/g++-10
您可以通过以下方式准确检查它安装的内容和位置：
brew ls gcc
示例输出
/usr/local/Cellar/gcc/10.2.0/bin/c++-10
/usr/local/Cellar/gcc/10.2.0/bin/cpp-10
/usr/local/Cellar/gcc/10.2.0/bin/g++-10
/usr/local/Cellar/gcc/10.2.0/bin/gcc-10
/usr/local/Cellar/gcc/10.2.0/bin/gcc-ar-10
/usr/local/Cellar/gcc/10.2.0/bin/gcc-nm-10
/usr/local/Cellar/gcc/10.2.0/bin/gcc-ranlib-10
/usr/local/Cellar/gcc/10.2.0/bin/gcov-10
/usr/local/Cellar/gcc/10.2.0/bin/gcov-dump-10
/usr/local/Cellar/gcc/10.2.0/bin/gcov-tool-10
/usr/local/Cellar/gcc/10.2.0/bin/gfortran
/usr/local/Cellar/gcc/10.2.0/bin/gfortran-10
/usr/local/Cellar/gcc/10.2.0/bin/lto-dump-10
/usr/local/Cellar/gcc/10.2.0/bin/x86_64-apple-darwin19-c++-10
/usr/local/Cellar/gcc/10.2.0/bin/x86_64-apple-darwin19-g++-10
/usr/local/Cellar/gcc/10.2.0/bin/x86_64-apple-darwin19-gcc-10
/usr/local/Cellar/gcc/10.2.0/bin/x86_64-apple-darwin19-gcc-10.2.0
/usr/local/Cellar/gcc/10.2.0/bin/x86_64-apple-darwin19-gcc-ar-10
/usr/local/Cellar/gcc/10.2.0/bin/x86_64-apple-darwin19-gcc-nm-10
/usr/local/Cellar/gcc/10.2.0/bin/x86_64-apple-darwin19-gcc-ranlib-10
/usr/local/Cellar/gcc/10.2.0/bin/x86_64-apple-darwin19-gfortran-10
/usr/local/Cellar/gcc/10.2.0/include/c++/ (770 files)
/usr/local/Cellar/gcc/10.2.0/lib/gcc/ (638 files)
/usr/local/Cellar/gcc/10.2.0/libexec/gcc/ (13 files)
/usr/local/Cellar/gcc/10.2.0/share/gcc-10.2.0/ (4 files)
/usr/local/Cellar/gcc/10.2.0/share/man/ (11 files)
然后你可以找到你应该像这样实际使用的符号链接二进制文件：
cd /usr/local/bin
ls -l | grep gcc
示例输出
lrwxr-xr-x 1 mark admin 31 21 Aug 16:41 c++-10 -> ../Cellar/gcc/10.2.0/bin/c++-10
lrwxr-xr-x 1 mark admin 31 21 Aug 16:41 cpp-10 -> ../Cellar/gcc/10.2.0/bin/cpp-10
lrwxr-xr-x 1 mark admin 31 21 Aug 16:41 g++-10 -> ../Cellar/gcc/10.2.0/bin/g++-10
lrwxr-xr-x 1 mark admin 31 21 Aug 16:41 gcc-10 -> ../Cellar/gcc/10.2.0/bin/gcc-10
lrwxr-xr-x 1 mark admin 34 21 Aug 16:41 gcc-ar-10 -> ../Cellar/gcc/10.2.0/bin/gcc-ar-10
lrwxr-xr-x 1 mark admin 34 21 Aug 16:41 gcc-nm-10 -> ../Cellar/gcc/10.2.0/bin/gcc-nm-10
lrwxr-xr-x 1 mark admin 38 21 Aug 16:41 gcc-ranlib-10 -> ../Cellar/gcc/10.2.0/bin/gcc-ranlib-10
lrwxr-xr-x 1 mark admin 32 21 Aug 16:41 gcov-10 -> ../Cellar/gcc/10.2.0/bin/gcov-10
lrwxr-xr-x 1 mark admin 37 21 Aug 16:41 gcov-dump-10 -> ../Cellar/gcc/10.2.0/bin/gcov-dump-10
lrwxr-xr-x 1 mark admin 37 21 Aug 16:41 gcov-tool-10 -> ../Cellar/gcc/10.2.0/bin/gcov-tool-10
lrwxr-xr-x 1 mark admin 33 21 Aug 16:41 gfortran -> ../Cellar/gcc/10.2.0/bin/gfortran
lrwxr-xr-x 1 mark admin 36 21 Aug 16:41 gfortran-10 -> ../Cellar/gcc/10.2.0/bin/gfortran-10
lrwxr-xr-x 1 mark admin 36 21 Aug 16:41 lto-dump-10 -> ../Cellar/gcc/10.2.0/bin/lto-dump-10
lrwxr-xr-x 1 mark admin 53 21 Aug 16:41 x86_64-apple-darwin19-c++-10 -> ../Cellar/gcc/10.2.0/bin/x86_64-apple-darwin19-c++-10
lrwxr-xr-x 1 mark admin 53 21 Aug 16:41 x86_64-apple-darwin19-g++-10 -> ../Cellar/gcc/10.2.0/bin/x86_64-apple-darwin19-g++-10
lrwxr-xr-x 1 mark admin 53 21 Aug 16:41 x86_64-apple-darwin19-gcc-10 -> ../Cellar/gcc/10.2.0/bin/x86_64-apple-darwin19-gcc-10
lrwxr-xr-x 1 mark admin 57 21 Aug 16:41 x86_64-apple-darwin19-gcc-10.2.0 -> ../Cellar/gcc/10.2.0/bin/x86_64-apple-darwin19-gcc-10.2.0
lrwxr-xr-x 1 mark admin 56 21 Aug 16:41 x86_64-apple-darwin19-gcc-ar-10 -> ../Cellar/gcc/10.2.0/bin/x86_64-apple-darwin19-gcc-ar-10
lrwxr-xr-x 1 mark admin 56 21 Aug 16:41 x86_64-apple-darwin19-gcc-nm-10 -> ../Cellar/gcc/10.2.0/bin/x86_64-apple-darwin19-gcc-nm-10
lrwxr-xr-x 1 mark admin 60 21 Aug 16:41 x86_64-apple-darwin19-gcc-ranlib-10 -> ../Cellar/gcc/10.2.0/bin/x86_64-apple-darwin19-gcc-ranlib-10
lrwxr-xr-x 1 mark admin 58 21 Aug 16:41 x86_64-apple-darwin19-gfortran-10 -> ../Cellar/gcc/10.2.0/bin/x86_64-apple-darwin19-gfortran-10
因此，一旦确定了要使用的编译器，就需要告诉构建工具如何使用它。我不熟悉你提到的包，但是你的 post 的第四行暗示它正在使用 /usr/bin/g++ 如果你想使用 homebrew 这是不正确的/usr/local/bin/g++-10.
指定不同编译器的常用方法是：
- 对于 CMake:
CXX=/usr/local/bin/g++-10 cmake ..
- 对于 make:
make CXX=/usr/local/bin/g++-10
- 对于 autoconf:
./configure CXX=/usr/local/bin/g++-10
我花了很长时间，最终有两个主要问题我认为可能对其他人有用。
ChemPy 仅在 Linux 上受支持，所以即使我让我的编译器工作，我也没有在 Mac 和 [=27 上实现 运行 =].有关更多信息，请参阅 Github 上的 issue。
编译器一团糟。最后有效的是使用来自 Anaconda 环境的 clang v10 而不是 v12:
export CC=/usr/bin/clang
export CXX=/usr/bin/clang++
只是为了使它完整，在这里它是什么和工作：
(base) bash-3.2$ clang --version
clang version 10.0.0
Target: x86_64-apple-darwin19.6.0
Thread model: posix
InstalledDir: /Users/user/anaconda3/bin
(base) bash-3.2$ which clang
/Users/user/anaconda3/bin/clang
我正在尝试解决以下问题。当我尝试 运行 this ntb 中的以下行时，我得到：
native = get_native(rsys, odesys, 'cvode')
INFO:pyodesys.native._base:Cythonizing /Users/user/Library/Caches/python3.8-pyodesys-0.13.1/_cvode_wrapper.pyx to ./_cvode_wrapper.cpp
INFO:pyodesys.native._base:In "/var/folders/bx/tb4883l53hdd3zp2y0nyy_4m0000gp/T/tmpt2vuw8pg", executing:
"/usr/bin/g++ -fwrapv -pthread -c -std=c++11 -Wall -Wextra -fPIC -O2 -ffast-math -funroll-loops -fopenmp -fno-strict-aliasing -o ./_cvode_wrapper.o -DPYCVODES_NO_KLU=0 -DPYCVODES_NO_LAPACK=0 -DANYODE_NO_LAPACK=0 -I/Users/user/anaconda3/lib/python3.8/site-packages/numpy/core/include -I/Users/jan/anaconda3/lib/python3.8/site-packages/pyodesys/native/sources -I/Users/jan/anaconda3/lib/python3.8/site-packages/pycvodes/include -I/Users/jan/anaconda3/include/python3.8 ./_cvode_wrapper.cpp"
CompilationError: Error executing '/usr/bin/g++ -fwrapv -pthread -c -std=c++11 -Wall -Wextra -fPIC -O2 -ffast-math -funroll-loops -fopenmp -fno-strict-aliasing -o ./_cvode_wrapper.o -DPYCVODES_NO_KLU=0 -DPYCVODES_NO_LAPACK=0 -DANYODE_NO_LAPACK=0 -I/Users/jan/anaconda3/lib/python3.8/site-packages/numpy/core/include -I/Users/jan/anaconda3/lib/python3.8/site-packages/pyodesys/native/sources -I/Users/jan/anaconda3/lib/python3.8/site-packages/pycvodes/include -I/Users/jan/anaconda3/include/python3.8 ./_cvode_wrapper.cpp' in /var/folders/bx/tb4883l53hdd3zp2y0nyy_4m0000gp/T/tmpt2vuw8pg. Command exited with status 1 after givning the following output: clang: error: unsupported option '-fopenmp
我认为这可能是 fopenmp 和 gcc 的问题，如那些地方所述 (
conda install gcc
PackagesNotFoundError: The following packages are not available from current channels:
- gcc
Current channels:
- https://repo.anaconda.com/pkgs/main/osx-64
- https://repo.anaconda.com/pkgs/main/noarch
- https://repo.anaconda.com/pkgs/r/osx-64
- https://repo.anaconda.com/pkgs/r/noarch
使用 homebrew 我安装了 gcc...知道发生了什么以及如何修复它吗？我正在 运行ning MacOS 10.15.7。谢谢
homebrew 将安装如下内容：
/usr/local/bin/g++-10
您可以通过以下方式准确检查它安装的内容和位置：
brew ls gcc
示例输出
/usr/local/Cellar/gcc/10.2.0/bin/c++-10
/usr/local/Cellar/gcc/10.2.0/bin/cpp-10
/usr/local/Cellar/gcc/10.2.0/bin/g++-10
/usr/local/Cellar/gcc/10.2.0/bin/gcc-10
/usr/local/Cellar/gcc/10.2.0/bin/gcc-ar-10
/usr/local/Cellar/gcc/10.2.0/bin/gcc-nm-10
/usr/local/Cellar/gcc/10.2.0/bin/gcc-ranlib-10
/usr/local/Cellar/gcc/10.2.0/bin/gcov-10
/usr/local/Cellar/gcc/10.2.0/bin/gcov-dump-10
/usr/local/Cellar/gcc/10.2.0/bin/gcov-tool-10
/usr/local/Cellar/gcc/10.2.0/bin/gfortran
/usr/local/Cellar/gcc/10.2.0/bin/gfortran-10
/usr/local/Cellar/gcc/10.2.0/bin/lto-dump-10
/usr/local/Cellar/gcc/10.2.0/bin/x86_64-apple-darwin19-c++-10
/usr/local/Cellar/gcc/10.2.0/bin/x86_64-apple-darwin19-g++-10
/usr/local/Cellar/gcc/10.2.0/bin/x86_64-apple-darwin19-gcc-10
/usr/local/Cellar/gcc/10.2.0/bin/x86_64-apple-darwin19-gcc-10.2.0
/usr/local/Cellar/gcc/10.2.0/bin/x86_64-apple-darwin19-gcc-ar-10
/usr/local/Cellar/gcc/10.2.0/bin/x86_64-apple-darwin19-gcc-nm-10
/usr/local/Cellar/gcc/10.2.0/bin/x86_64-apple-darwin19-gcc-ranlib-10
/usr/local/Cellar/gcc/10.2.0/bin/x86_64-apple-darwin19-gfortran-10
/usr/local/Cellar/gcc/10.2.0/include/c++/ (770 files)
/usr/local/Cellar/gcc/10.2.0/lib/gcc/ (638 files)
/usr/local/Cellar/gcc/10.2.0/libexec/gcc/ (13 files)
/usr/local/Cellar/gcc/10.2.0/share/gcc-10.2.0/ (4 files)
/usr/local/Cellar/gcc/10.2.0/share/man/ (11 files)
然后你可以找到你应该像这样实际使用的符号链接二进制文件：
cd /usr/local/bin
ls -l | grep gcc
示例输出
lrwxr-xr-x 1 mark admin 31 21 Aug 16:41 c++-10 -> ../Cellar/gcc/10.2.0/bin/c++-10
lrwxr-xr-x 1 mark admin 31 21 Aug 16:41 cpp-10 -> ../Cellar/gcc/10.2.0/bin/cpp-10
lrwxr-xr-x 1 mark admin 31 21 Aug 16:41 g++-10 -> ../Cellar/gcc/10.2.0/bin/g++-10
lrwxr-xr-x 1 mark admin 31 21 Aug 16:41 gcc-10 -> ../Cellar/gcc/10.2.0/bin/gcc-10
lrwxr-xr-x 1 mark admin 34 21 Aug 16:41 gcc-ar-10 -> ../Cellar/gcc/10.2.0/bin/gcc-ar-10
lrwxr-xr-x 1 mark admin 34 21 Aug 16:41 gcc-nm-10 -> ../Cellar/gcc/10.2.0/bin/gcc-nm-10
lrwxr-xr-x 1 mark admin 38 21 Aug 16:41 gcc-ranlib-10 -> ../Cellar/gcc/10.2.0/bin/gcc-ranlib-10
lrwxr-xr-x 1 mark admin 32 21 Aug 16:41 gcov-10 -> ../Cellar/gcc/10.2.0/bin/gcov-10
lrwxr-xr-x 1 mark admin 37 21 Aug 16:41 gcov-dump-10 -> ../Cellar/gcc/10.2.0/bin/gcov-dump-10
lrwxr-xr-x 1 mark admin 37 21 Aug 16:41 gcov-tool-10 -> ../Cellar/gcc/10.2.0/bin/gcov-tool-10
lrwxr-xr-x 1 mark admin 33 21 Aug 16:41 gfortran -> ../Cellar/gcc/10.2.0/bin/gfortran
lrwxr-xr-x 1 mark admin 36 21 Aug 16:41 gfortran-10 -> ../Cellar/gcc/10.2.0/bin/gfortran-10
lrwxr-xr-x 1 mark admin 36 21 Aug 16:41 lto-dump-10 -> ../Cellar/gcc/10.2.0/bin/lto-dump-10
lrwxr-xr-x 1 mark admin 53 21 Aug 16:41 x86_64-apple-darwin19-c++-10 -> ../Cellar/gcc/10.2.0/bin/x86_64-apple-darwin19-c++-10
lrwxr-xr-x 1 mark admin 53 21 Aug 16:41 x86_64-apple-darwin19-g++-10 -> ../Cellar/gcc/10.2.0/bin/x86_64-apple-darwin19-g++-10
lrwxr-xr-x 1 mark admin 53 21 Aug 16:41 x86_64-apple-darwin19-gcc-10 -> ../Cellar/gcc/10.2.0/bin/x86_64-apple-darwin19-gcc-10
lrwxr-xr-x 1 mark admin 57 21 Aug 16:41 x86_64-apple-darwin19-gcc-10.2.0 -> ../Cellar/gcc/10.2.0/bin/x86_64-apple-darwin19-gcc-10.2.0
lrwxr-xr-x 1 mark admin 56 21 Aug 16:41 x86_64-apple-darwin19-gcc-ar-10 -> ../Cellar/gcc/10.2.0/bin/x86_64-apple-darwin19-gcc-ar-10
lrwxr-xr-x 1 mark admin 56 21 Aug 16:41 x86_64-apple-darwin19-gcc-nm-10 -> ../Cellar/gcc/10.2.0/bin/x86_64-apple-darwin19-gcc-nm-10
lrwxr-xr-x 1 mark admin 60 21 Aug 16:41 x86_64-apple-darwin19-gcc-ranlib-10 -> ../Cellar/gcc/10.2.0/bin/x86_64-apple-darwin19-gcc-ranlib-10
lrwxr-xr-x 1 mark admin 58 21 Aug 16:41 x86_64-apple-darwin19-gfortran-10 -> ../Cellar/gcc/10.2.0/bin/x86_64-apple-darwin19-gfortran-10
因此，一旦确定了要使用的编译器，就需要告诉构建工具如何使用它。我不熟悉你提到的包，但是你的 post 的第四行暗示它正在使用 /usr/bin/g++ 如果你想使用 homebrew 这是不正确的/usr/local/bin/g++-10.
指定不同编译器的常用方法是：
- 对于 CMake:
CXX=/usr/local/bin/g++-10 cmake .. - 对于 make:
make CXX=/usr/local/bin/g++-10 - 对于 autoconf:
./configure CXX=/usr/local/bin/g++-10
我花了很长时间，最终有两个主要问题我认为可能对其他人有用。
ChemPy 仅在 Linux 上受支持，所以即使我让我的编译器工作，我也没有在 Mac 和 [=27 上实现 运行 =].有关更多信息，请参阅 Github 上的 issue。
编译器一团糟。最后有效的是使用来自 Anaconda 环境的 clang v10 而不是 v12:
export CC=/usr/bin/clang
export CXX=/usr/bin/clang++
只是为了使它完整，在这里它是什么和工作：
(base) bash-3.2$ clang --version
clang version 10.0.0
Target: x86_64-apple-darwin19.6.0
Thread model: posix
InstalledDir: /Users/user/anaconda3/bin
(base) bash-3.2$ which clang
/Users/user/anaconda3/bin/clang