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%)
 
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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

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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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