尝试使用pybind11做python的绑定，按照文档操作无果 #2177

KaivnD · 2022-03-18T16:17:58Z

Xmake 版本

v2.6.3+202201242206

操作系统版本和架构

macOS Catalina 10.15.7 (19H15)

描述问题

根据文档尝试使用pybind11

add_rules("mode.release", "mode.debug")
add_requires("pybind11")

target("example")
     add_rules("python.library")
     add_files("src/*.cpp")
     add_packages("pybind11")
     set_languages("c++11")

执行 xmake -vD

[ 25%]: compiling.release src/example.cpp
"/usr/bin/xcrun -sdk macosx clang" -c -Qunused-arguments -arch x86_64 -mmacosx-version-min=10.15 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.1.sdk -fPIC -O3 -std=c++11 -isystem /Users/kaivnd/.xmake/packages/p/pybind11/v2.9.1/a430ad80c311429aaa6c9bb9e36186a5/include -isystem /Users/kaivnd/.xmake/packages/p/python/3.9.10/a1d024625fd7429983211332bf61ed18/include/python3.9 -isystem /Users/kaivnd/.xmake/packages/o/openssl/1.1.1m/e2d70e9cf7bc4473bf897ffef4cbf761/include -DNDEBUG -o build/.objs/example/macosx/x86_64/release/src/example.cpp.o src/example.cpp
[ 50%]: linking.release _example.dylib
"/usr/bin/xcrun -sdk macosx clang++" -o build/macosx/x86_64/release/_example.dylib build/.objs/example/macosx/x86_64/release/src/example.cpp.o -shared -fPIC -arch x86_64 -mmacosx-version-min=10.15 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.1.sdk -stdlib=libc++ -L/Users/kaivnd/.xmake/packages/p/python/3.9.10/a1d024625fd7429983211332bf61ed18/lib -L/Users/kaivnd/.xmake/packages/o/openssl/1.1.1m/e2d70e9cf7bc4473bf897ffef4cbf761/lib -Wl,-x -lpython3.9 -lssl -lcrypto -lz -install_name @rpath/_example.dylib
[100%]: build ok!

得到的结果是一个dylib，尝试使用python导入这个模块

Python 3.9.7 (default, Sep 16 2021, 08:50:36) 
[Clang 10.0.0 ] :: Anaconda, Inc. on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import _example
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ModuleNotFoundError: No module named '_example'

查阅pybind11文档得知此命令行

c++ -O3 -Wall -shared -std=c++17 -fPIC -undefined dynamic_lookup $(python3 -m pybind11 --includes) example.cpp -o example$(python3-config --extension-suffix)

得到文件example.cpython-39-darwin.so，故猜测是后缀名的问题，随后将_example.dylib重命名为_example.cpython-39-darwin.so，再次尝试得到如下错误

Python 3.9.7 (default, Sep 16 2021, 08:50:36) 
[Clang 10.0.0 ] :: Anaconda, Inc. on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import _example
zsh: segmentation fault  python3

然后我就不知道怎么整了，麻烦大神帮忙看一下！万分感谢

期待的结果

希望可以通过xmake使用pybind11进行C++到python的绑定可以正常跨平台使用

工程配置

-- xmake.lua

add_rules("mode.release", "mode.debug")
add_requires("pybind11")

target("example")
     add_rules("python.library")
     add_files("src/*.cpp")
     add_packages("pybind11")
     set_languages("c++11")

// example.cpp
#include <pybind11/pybind11.h>

namespace py = pybind11;

int add(int i, int j) {
    return i + j;
}

PYBIND11_MODULE(_example, m) {
    m.doc() = "pybind11 example plugin"; // optional module docstring

    m.def("add", &add, "A function which adds two numbers");
}

附加信息和错误日志

[ 25%]: compiling.release src/example.cpp
"/usr/bin/xcrun -sdk macosx clang" -c -Qunused-arguments -arch x86_64 -mmacosx-version-min=10.15 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.1.sdk -fPIC -O3 -std=c++11 -isystem /Users/kaivnd/.xmake/packages/p/pybind11/v2.9.1/a430ad80c311429aaa6c9bb9e36186a5/include -isystem /Users/kaivnd/.xmake/packages/p/python/3.9.10/a1d024625fd7429983211332bf61ed18/include/python3.9 -isystem /Users/kaivnd/.xmake/packages/o/openssl/1.1.1m/e2d70e9cf7bc4473bf897ffef4cbf761/include -DNDEBUG -o build/.objs/example/macosx/x86_64/release/src/example.cpp.o src/example.cpp
[ 50%]: linking.release _example.dylib
"/usr/bin/xcrun -sdk macosx clang++" -o build/macosx/x86_64/release/_example.dylib build/.objs/example/macosx/x86_64/release/src/example.cpp.o -shared -fPIC -arch x86_64 -mmacosx-version-min=10.15 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.1.sdk -stdlib=libc++ -L/Users/kaivnd/.xmake/packages/p/python/3.9.10/a1d024625fd7429983211332bf61ed18/lib -L/Users/kaivnd/.xmake/packages/o/openssl/1.1.1m/e2d70e9cf7bc4473bf897ffef4cbf761/lib -Wl,-x -lpython3.9 -lssl -lcrypto -lz -install_name @rpath/_example.dylib
[100%]: build ok!

The text was updated successfully, but these errors were encountered:

xq114 · 2022-03-18T16:22:15Z

用 add_rules("python.library", {soabi = true}) 也不行吗

KaivnD · 2022-03-18T16:32:43Z

是的呢，也不行

Python 3.8.2 (default, Dec 21 2020, 15:06:04) 
[Clang 12.0.0 (clang-1200.0.32.29)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import _example
zsh: segmentation fault  python3

虽然后缀名从dylib变成so了，同样的表现，而且还有另一个问题，with soabi 没有使用conda里的py39，而使用了系统的py38，也挺迷

waruqi · 2022-03-20T14:18:30Z

import _example

看了下，pybind 模块前缀应该是 example.xxx.so 没有下划线，否则 module 导入后报 PyInit__example not found，我刚改进了下，应该可以了

zsh: segmentation fault python3

测试了下，linux 下加载ok，只有 macos 下加载会有这个问题，不过我这系统环境 gdb/lldb 坏了，暂时没环境调试，你可以自己用 gdb/lldb 加载下看下哪里崩溃，贴过来

with soabi 没有使用conda里的py39，而使用了系统的py38

项目编译，用的 xmake-repo 里面的 python 库，所以建议保持一致，用 xmake-repo 里面的 python 来加载

$ xrepo env -b python shell
> cd build/macosx/x86_64/release/
> python
Python 3.9.10 (main, Mar 20 2022, 20:41:15)
[Clang 12.0.5 (clang-1205.0.22.11)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import example

KaivnD · 2022-03-22T15:23:53Z

@waruqi lldb没太用明白，不过在一顿折腾之后，系统弹出个窗口，显示一些错误信息，不知道有没有用，如下

Process:               Python [1372]
Path:                  /Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/Resources/Python.app/Contents/MacOS/Python
Identifier:            Python
Version:               3.8.2 (3.8.2)
Build Info:            python3-73040006000000~129
Code Type:             X86-64 (Native)
Parent Process:        zsh [716]
Responsible:           Terminal [713]
User ID:               501

Date/Time:             2022-03-22 23:21:38.606 +0800
OS Version:            Mac OS X 10.15.7 (19H15)
Report Version:        12
Anonymous UUID:        FE50A71E-8AB6-3656-1780-CBDCBAC2DE6B


Time Awake Since Boot: 590 seconds

System Integrity Protection: enabled

Crashed Thread:        0  Dispatch queue: com.apple.main-thread

Exception Type:        EXC_BAD_ACCESS (SIGSEGV)
Exception Codes:       KERN_INVALID_ADDRESS at 0x0000000000000010
Exception Note:        EXC_CORPSE_NOTIFY

Termination Signal:    Segmentation fault: 11
Termination Reason:    Namespace SIGNAL, Code 0xb
Terminating Process:   exc handler [1372]

VM Regions Near 0x10:
--> 
    __TEXT                 0000000106273000-0000000106277000 [   16K] r-x/r-x SM=COW  /Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/Resources/Python.app/Contents/MacOS/Python

Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0   _example.cpython-38-darwin.so 	0x00000001068debc3 0x1067a5000 + 1285059
1   _example.cpython-38-darwin.so 	0x00000001068df3c3 PyEval_RestoreThread + 19 (ceval.c:469)
2   _example.cpython-38-darwin.so 	0x000000010692d108 PyGILState_Ensure + 104
3   _example.cpython-38-darwin.so 	0x00000001067a94fc 0x1067a5000 + 17660
4   _example.cpython-38-darwin.so 	0x00000001067a92fc PyInit__example + 140
5   com.apple.python3             	0x00000001063b3db5 _PyImport_LoadDynamicModuleWithSpec + 613
6   com.apple.python3             	0x00000001063b3660 _imp_create_dynamic + 336
7   com.apple.python3             	0x00000001062e59b1 cfunction_vectorcall_FASTCALL + 177
8   com.apple.python3             	0x00000001062a7124 PyVectorcall_Call + 100
9   com.apple.python3             	0x0000000106383bf7 _PyEval_EvalFrameDefault + 31095
10  com.apple.python3             	0x0000000106388097 _PyEval_EvalCodeWithName + 3287
11  com.apple.python3             	0x00000001062a790d _PyFunction_Vectorcall + 253
12  com.apple.python3             	0x0000000106387012 call_function + 354
13  com.apple.python3             	0x00000001063836d6 _PyEval_EvalFrameDefault + 29782
14  com.apple.python3             	0x00000001062a778d function_code_fastcall + 237
15  com.apple.python3             	0x0000000106387012 call_function + 354
16  com.apple.python3             	0x00000001063836b9 _PyEval_EvalFrameDefault + 29753
17  com.apple.python3             	0x00000001062a778d function_code_fastcall + 237
18  com.apple.python3             	0x0000000106387012 call_function + 354
19  com.apple.python3             	0x000000010638378a _PyEval_EvalFrameDefault + 29962
20  com.apple.python3             	0x00000001062a778d function_code_fastcall + 237
21  com.apple.python3             	0x0000000106387012 call_function + 354
22  com.apple.python3             	0x000000010638378a _PyEval_EvalFrameDefault + 29962
23  com.apple.python3             	0x00000001062a778d function_code_fastcall + 237
24  com.apple.python3             	0x0000000106387012 call_function + 354
25  com.apple.python3             	0x000000010638378a _PyEval_EvalFrameDefault + 29962
26  com.apple.python3             	0x00000001062a778d function_code_fastcall + 237
27  com.apple.python3             	0x00000001062a91bb object_vacall + 459
28  com.apple.python3             	0x00000001062a93f3 _PyObject_CallMethodIdObjArgs + 227
29  com.apple.python3             	0x00000001063b2548 PyImport_ImportModuleLevelObject + 1800
30  com.apple.python3             	0x0000000106381d2d _PyEval_EvalFrameDefault + 23213
31  com.apple.python3             	0x0000000106388097 _PyEval_EvalCodeWithName + 3287
32  com.apple.python3             	0x000000010637c1e0 PyEval_EvalCode + 48
33  com.apple.python3             	0x00000001063cd933 PyRun_FileExFlags + 291
34  com.apple.python3             	0x00000001063ccd9f PyRun_SimpleFileExFlags + 271
35  com.apple.python3             	0x00000001063ec267 Py_RunMain + 2103
36  com.apple.python3             	0x00000001063ec793 pymain_main + 403
37  com.apple.python3             	0x00000001063ec7eb Py_BytesMain + 43
38  libdyld.dylib                 	0x00007fff6b0eccc9 start + 1

Thread 0 crashed with X86 Thread State (64-bit):
  rax: 0x0000000000000000  rbx: 0x0000000106cc5dc0  rcx: 0x0000000000000000  rdx: 0x0000000000000003
  rdi: 0x0000000106cc5dc0  rsi: 0x0000000106a0b386  rbp: 0x00007ffee998ad50  rsp: 0x00007ffee998acf0
   r8: 0x0000000000000039   r9: 0x00007ffee998adc0  r10: 0x0000000106a25ddd  r11: 0x0000000106a25df0
  r12: 0x000000010676cd70  r13: 0x000000010674d8b0  r14: 0x000000010674d620  r15: 0x000000010674d600
  rip: 0x00000001068debc3  rfl: 0x0000000000010246  cr2: 0x0000000000000010
  
Logical CPU:     0
Error Code:      0x00000004 (no mapping for user data read)
Trap Number:     14


Binary Images:
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       0x106283000 -        0x1064d2ff7  com.apple.python3 (3.8.2 - 3.8.2) <B6FF6B7D-D9D5-3BAF-AEE3-3A8F04133C81> /Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/Python3
       0x1067a5000 -        0x106a38fff +_example.cpython-38-darwin.so (0) <9CED0B51-52E7-3039-92F1-7025328569A9> /Users/USER/*/_example.cpython-38-darwin.so
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       0x106db8000 -        0x10703721b +libcrypto.1.1.dylib (0) <7550BFC6-296C-39A4-8ED7-3BB8C28454D7> /Users/USER/*/libcrypto.1.1.dylib
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VM Region Summary:
ReadOnly portion of Libraries: Total=410.5M resident=0K(0%) swapped_out_or_unallocated=410.5M(100%)
Writable regions: Total=46.1M written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=46.1M(100%)
 
                                VIRTUAL   REGION 
REGION TYPE                        SIZE    COUNT (non-coalesced) 
===========                     =======  ======= 
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shared memory                       12K        3 
===========                     =======  ======= 
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waruqi · 2022-03-22T15:46:57Z

看栈是崩在 python 里面了，感觉跟 xmake 关系不大，要么是 pybind11 问题，要么是 python 的问题，你可以到 pybind11 issues 上去问问。。

或者你可以用 cmake 啥的其他构建工具去构建一个模块，导入下试试，看看是否也会崩，如果 ok，可以对比下两边的 flags 差异。

我看 pybind11 issues 也有人反馈类似的问题

pybind/pybind11#3054
pybind/pybind11#2558

waruqi · 2022-03-22T15:52:22Z

pybind/pybind11#1579 这个似乎跟这个类似，上面说是 python 版本冲突问题

KaivnD · 2022-04-06T06:43:12Z

@waruqi 但是使用c++ -O3 -Wall -shared -std=c++17 -fPIC -undefined dynamic_lookup $(python3 -m pybind11 --includes) example.cpp -o example$(python3-config --extension-suffix) 指令能行

xq114 · 2022-04-06T08:50:55Z

@waruqi 但是使用c++ -O3 -Wall -shared -std=c++17 -fPIC -undefined dynamic_lookup $(python3 -m pybind11 --includes) example.cpp -o example$(python3-config --extension-suffix) 指令能行

对比一下，只有-undefined dynamic_lookup缺了，你试试手动添加这个flag，add_cxxflags("-undefined dynamic_lookup", {force=true})编译试试

KaivnD · 2022-04-06T13:42:00Z

还是不行，🤦‍♂️

waruqi · 2022-04-06T13:43:34Z

@waruqi 但是使用c++ -O3 -Wall -shared -std=c++17 -fPIC -undefined dynamic_lookup $(python3 -m pybind11 --includes) example.cpp -o example$(python3-config --extension-suffix) 指令能行

既然这个可以，那就跟 xmake -vD 做下对比，复制里面的命令，挨个测试下，哪个 flags 有差异

xq114 · 2022-04-06T14:17:47Z

还是不行，🤦‍♂️

我看你之前测试用的python版本都不一样，一下3.9.7一下3.8.2的，能不能用xmake安装的python 3.9.10试试？运行xrepo env -b python3 shell就可以激活虚拟环境，在虚拟环境里面运行python3

KaivnD · 2022-04-06T15:17:43Z

@xq114 不对，build之后得到的后缀是py38的

KaivnD · 2022-04-06T15:18:31Z

@waruqi 这是日志

checkinfo: cannot runv(ccache --version), No such file or directory
checking for ccache ... no
[ 25%]: compiling.release src/example.cpp
"/usr/bin/xcrun -sdk macosx clang" -c -Qunused-arguments -arch x86_64 -mmacosx-version-min=10.15 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.1.sdk -fPIC -O3 -std=c++11 -isystem /Users/kaivnd/.xmake/packages/p/pybind11/v2.9.1/a430ad80c311429aaa6c9bb9e36186a5/include -isystem /Users/kaivnd/.xmake/packages/p/python/3.9.10/a1d024625fd7429983211332bf61ed18/include/python3.9 -isystem /Users/kaivnd/.xmake/packages/o/openssl/1.1.1m/e2d70e9cf7bc4473bf897ffef4cbf761/include -undefined dynamic_lookup -DNDEBUG -o build/.objs/example/macosx/x86_64/release/src/example.cpp.o src/example.cpp
checking for flags (-MMD -MF) ... ok
> xcrun -sdk macosx clang "-MMD" "-MF" "/dev/null"
checking for flags (-fdiagnostics-color=always) ... ok
> xcrun -sdk macosx clang "-fdiagnostics-color=always"
[ 50%]: linking.release _example.cpython-38-darwin.so
"/usr/bin/xcrun -sdk macosx clang++" -o build/macosx/x86_64/release/_example.cpython-38-darwin.so build/.objs/example/macosx/x86_64/release/src/example.cpp.o -shared -fPIC -arch x86_64 -mmacosx-version-min=10.15 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.1.sdk -stdlib=libc++ -L/Users/kaivnd/.xmake/packages/p/python/3.9.10/a1d024625fd7429983211332bf61ed18/lib -L/Users/kaivnd/.xmake/packages/o/openssl/1.1.1m/e2d70e9cf7bc4473bf897ffef4cbf761/lib -Wl,-x -lpython3.9 -lssl -lcrypto -lz -install_name @rpath/_example.cpython-38-darwin.so
[100%]: build ok!

xq114 · 2022-04-08T00:40:31Z

@xq114 不对，build之后得到的后缀是py38的

在虚拟环境里面xmake clean --all 重新build也是py38吗？那样就是find_python的查找有问题了

xq114 · 2022-04-19T11:49:26Z

https://pybind11.readthedocs.io/en/latest/basics.html#creating-bindings-for-a-simple-function

这里的example没有下划线，我试了下windows上原始版本的代码是ok的

KaivnD · 2022-08-08T14:08:21Z

抱歉过了那么长时间才跟进，前一段时间比较忙，昨天把Mac升级到 12.5 (21G72)最新版了，这个版本的内置python被去掉了，干净的系统，用conda做虚拟环境，又做了一次实验，问题依然存在。

waruqi · 2022-08-08T14:21:38Z

这个问题其实我这 mac 下也是一样的问题，但我也不知道为啥。也没时间细看

xq114 · 2022-08-09T13:41:18Z

pybind/pybind11#3907

这里说要加-undefined dynamic_lookup （编译跟链接都要加），而且不能直接链接到python的库

waruqi · 2022-08-09T14:01:52Z

pybind/pybind11#3907
这里说要加-undefined dynamic_lookup （编译跟链接都要加），而且不能直接链接到python的库

确实是这个问题，但跟编译无关，是链接的问题，链接时候加上 -undefined dynamic_lookup ，然后还得去掉 -lpython3.9 的链接

之前 -undefined dynamic_lookup 试过，但是之前没去掉 python 的 links ，所以一直不行。。

我刚改了下，应该可以了，这边测试修复了。。xmake update dev

KaivnD · 2022-08-11T14:55:34Z

@waruqi 亲测有效，给大佬点赞！:smile: 那这个issue需要关掉吗？

KaivnD added the bug label Mar 18, 2022

waruqi added this to the v2.7.1 milestone Aug 9, 2022

waruqi closed this as completed Aug 11, 2022

waruqi mentioned this issue Dec 9, 2024

libxml2: Fix python build & import xmake-io/xmake-repo#5930

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尝试使用pybind11做python的绑定，按照文档操作无果 #2177

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尝试使用pybind11做python的绑定，按照文档操作无果 #2177

尝试使用pybind11做python的绑定，按照文档操作无果 #2177

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