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Getting undefined reference when trying to build a pybind11 project using gcc

由 Deadly 提交于 2021-02-08 06:40:54

问题


I am trying to build a C++ static library in Linux (Ubuntu 18.04 in my case) using GCC using a Makefile. I noticed the issue is not with the makefile itself but the way I'm trying to compile and build with GCC. Before I explain a bit more on the GCC side, here is how my current project hierarchy looks like.

The project uses Pybind11 header only library which resides in the External_Libraries directory.

My class definition and implementation, naming Core.h and Core.cpp reside in Internal_libraries along with py_utilities.h and any.hpp which contain some utility functions. (These two files are not used though). and finally test_lib.cpp which uses Core.h resides in the root.

This is how it looks :

📦MainDirectory  
 ┣ 📂External_Libraries  
 ┃ ┗ 📂Pybind11    
 ┃   ┗ 📂Pybind11    
 ┃     ┗ 📂Include      
 ┃ 
 ┣ 📂Internal_Libraries  
 ┃ ┣📜Core.h  
 ┃ ┣📜Core.cpp  
 ┃ ┣📜py_utilities.h  
 ┃ ┣📜any.hpp  
 ┃
 ┗📜test_lib.cpp

Now, the project as you can see, depends on Pybind11 include directories and also <Python.h> plus pythons lib directories. I face the same undefined errors both when I try to build the static library or the normal executable. I include the needed search paths (include and library) to the GCC like this :

  • Building Core.o:
g++ -I./External_Libraries/pybind11/pybind11/include -I/home/rika/anaconda3/include/python3.7m -L/home/rika/anaconda3/lib -L/home/rika/anaconda3/lib/python3.7/site-packages -c ./Internal_Libraries/Core.cpp -o Core.o
  • Building test_lib.o:
g++ -I./External_Libraries/pybind11/pybind11/include -I/home/rika/anaconda3/include/python3.7m -L/home/rika/anaconda3/lib -L/home/rika/anaconda3/lib/python3.7/site-packages -c test_lib.cpp -o test_lib.o

and finally :

  • Building test_lib executable:
g++ -I./External_Libraries/pybind11/pybind11/include -I/home/rika/anaconda3/include/python3.7m -L/home/rika/anaconda3/lib -L/home/rika/anaconda3/lib/python3.7/site-packages test_lib.o Core.o -o test_lib

This is where it fails and I get lots of undefined errors which I guess is related to the linker, however I provided the needed paths, so I'm at a loss what's gone wrong here!

These are the errors I get:

g++ -I./External_Libraries/pybind11/pybind11/include -I/home/rika/anaconda3/include/python3.7m -L/home/rika/anaconda3/lib -L/home/rika/anaconda3/lib/python3.7/site-packages test_lib.o Core.o -o test_lib
test_lib.o: In function `pybind11::cast_error::set_error() const':
test_lib.cpp:(.text._ZNK8pybind1110cast_error9set_errorEv[_ZNK8pybind1110cast_error9set_errorEv]+0x29): undefined reference to `PyExc_RuntimeError'
test_lib.cpp:(.text._ZNK8pybind1110cast_error9set_errorEv[_ZNK8pybind1110cast_error9set_errorEv]+0x34): undefined reference to `PyErr_SetString'
test_lib.o: In function `pybind11::error_scope::error_scope()':
test_lib.cpp:(.text._ZN8pybind1111error_scopeC2Ev[_ZN8pybind1111error_scopeC5Ev]+0x27): undefined reference to `PyErr_Fetch'
test_lib.o: In function `pybind11::error_scope::~error_scope()':

...

Core.o: In function `std::enable_if<((!std::is_floating_point<int>::value)&&std::is_signed<int>::value)&&((sizeof (int))<=(sizeof (long))), pybind11::handle>::type pybind11::detail::type_caster<int, void>::cast<int>(int, pybind11::return_value_policy, pybind11::handle)':
Core.cpp:(.text._ZN8pybind116detail11type_casterIivE4castIiEENSt9enable_ifIXaaaantsrSt17is_floating_pointIT_E5valuesrSt9is_signedIS6_E5valuelestS6_stlENS_6handleEE4typeES6_NS_19return_value_policyESA_[_ZN8pybind116detail11type_casterIivE4castIiEENSt9enable_ifIXaaaantsrSt17is_floating_pointIT_E5valuesrSt9is_signedIS6_E5valuelestS6_stlENS_6handleEE4typeES6_NS_19return_value_policyESA_]+0x2c): undefined reference to `PyLong_FromSsize_t'
Core.o: In function `pybind11::array_t<unsigned char, 16>::ensure(pybind11::handle)':
Core.cpp:(.text._ZN8pybind117array_tIhLi16EE6ensureENS_6handleE[_ZN8pybind117array_tIhLi16EE6ensureENS_6handleE]+0x70): undefined reference to `PyErr_Clear'
Core.o: In function `pybind11::array_t<unsigned char, 16>::raw_array_t(_object*)':
Core.cpp:(.text._ZN8pybind117array_tIhLi16EE11raw_array_tEP7_object[_ZN8pybind117array_tIhLi16EE11raw_array_tEP7_object]+0x26): undefined reference to `PyExc_ValueError'
Core.cpp:(.text._ZN8pybind117array_tIhLi16EE11raw_array_tEP7_object[_ZN8pybind117array_tIhLi16EE11raw_array_tEP7_object]+0x35): undefined reference to `PyErr_SetString'
collect2: error: ld returned 1 exit status

here is the link to the full error log : error log

In case the contents of Core.h is important here it is :

#ifndef CORE_H

#define CORE_H



/* If we are we on Windows, we want a single define for it.*/

#if !defined(_WIN32) && (defined(__WIN32__) || defined(WIN32) || defined(__MINGW32__))

 #define _WIN32

#endif /* _WIN32 */


#if defined(_WIN32) && defined(_CORE_BUILD_DLL)

/* We are building CORE as a Win32 DLL */

 #define CORE_API __declspec(dllexport)

#elif defined(_WIN32) && defined(CORE_DLL)

/* We are calling CORE as a Win32 DLL */

 #define CORE_API __declspec(dllimport)

#elif defined(__GNUC__) && defined(_CORE_BUILD_DLL)

/* We are building CORE as a shared / dynamic library */

#define CORE_API __attribute__((visibility("default")))

#else

/* We are building or calling CORE as a static library */

 #define CORE_API

#endif


#include <iostream>
#include <string>
#include <vector>
#include <functional>
#include <memory>
#include <pybind11/pybind11.h>
#include <pybind11/embed.h>
#include <pybind11/numpy.h>
#include <pybind11/stl.h>
#include <pybind11/functional.h>

namespace py = pybind11;
using namespace py::literals;

typedef void(*CallbackFn)(bool, std::string, py::array_t<uint8_t>&);
typedef std::function<void(std::string)> LogFunction;
typedef void * HANDLE;


class CORE_API Core

{
private:
    py::scoped_interpreter guard{};
    py::object serviceUtilsModule;
    py::object cls;
    py::object obj;
    py::object startFunc;
...



public:

    Core();
    Core(bool showFeed);
    Core(LogFunction logInfo);
    Core(LogFunction logInfo, LogFunction logWarning);
    Core(LogFunction logInfo, LogFunction logWarning, LogFunction logDebug);
    Core(LogFunction logInfo, LogFunction logWarning, LogFunction logDebug, std::vector<CallbackFn> callbackList);
...
    ~Core();


    void Start(bool async= false);
    py::list GetCallbacks(void);
...
    static void DefaultLoger(std::string str);
};



extern "C"

{
    //COREAPI wchar_t** GetResults(wchar_t* word, int* length, int threshold = 9);
    CORE_API void Start(bool);
    CORE_API void Stop(void);
    CORE_API void SetCpuAffinity(int mask);
    CORE_API void AddCallback(CallbackFn callback);
    CORE_API void RemoveCallback(CallbackFn callback);
    CORE_API void* GetCallbacks(void);
    CORE_API void DefaultLoger(char* str);

    CORE_API void*  CreateHandle();
    CORE_API void*  GetCurrentHandle();
    CORE_API void   DisposeCurrentHandle();
    CORE_API void   SetCurrentHandle(void* handle);
    CORE_API void*  GetHandle();
    CORE_API void   DisposeHandle(void*);

}



#endif // !CORE_H

The project works fine under Windows and Visual C++ v14 (VS2015) and now I'm trying to do the same thing in Linux using GCC. It seems I'm doing something wrong obviously but I can't seem to know where I have gone wrong. What am I missing here?

Update

After following this link on manually compile pybind11, I ended up doing :

g++ -O3 -Wall -std=c++11 -fPIC -I./External_Libraries/pybind11/pybind11/include -I/home/rika/anaconda3/include/python3.7m -L/home/rika/anaconda3/lib -L/home/rika/anaconda3/lib/python3.7/site-packages -c ./Internal_Libraries/Core.cpp -o Core.o
g++ -O3 -Wall -std=c++11 -fPIC -I./External_Libraries/pybind11/pybind11/include -I/home/rika/anaconda3/include/python3.7m -L/home/rika/anaconda3/lib -L/home/rika/anaconda3/lib/python3.7/site-packages -c test_lib.cpp -o test_lib.o
g++ -O3 -Wall -std=c++11 -fPIC -I./External_Libraries/pybind11/pybind11/include -I/home/rika/anaconda3/include/python3.7m -L/home/rika/anaconda3/lib -L/home/rika/anaconda3/lib/python3.7/site-packages test_lib.o Core.o -o test_lib

Please note that, I removed the shared keyword from the commands above so it doesn't create the shared library! Having said that the last command still gives linker errors:

 g++ -O3 -Wall -std=c++11 -fPIC -I./External_Libraries/pybind11/pybind11/include -I/home/rika/anaconda3/include/python3.7m -L/home/rika/anaconda3/lib -L/home/rika/anaconda3/lib/python3.7/site-packages test_lib.o -o test_lib
test_lib.o: In function `pybind11_static_get':
test_lib.cpp:(.text.pybind11_static_get[pybind11_static_get]+0x3): undefined reference to `PyProperty_Type'
test_lib.o: In function `pybind11_static_set':
test_lib.cpp:(.text.pybind11_static_set[pybind11_static_set]+0x12): undefined reference to `PyProperty_Type'
test_lib.o: In function `pybind11::cast_error::set_error() const':
test_lib.cpp:(.text._ZNK8pybind1110cast_error9set_errorEv[_ZNK8pybind1110cast_error9set_errorEv]+0x10): undefined reference to `PyExc_RuntimeError'
test_lib.cpp:(.text._ZNK8pybind1110cast_error9set_errorEv[_ZNK8pybind1110cast_error9set_errorEv]+0x1c): undefined reference to `PyErr_SetString'
test_lib.o: In function `pybind11::detail::translate_exception(std::__exception_ptr::exception_ptr)':

...


test_lib.cpp:(.text._ZN8pybind116detail5printENS_5tupleENS_4dictE[_ZN8pybind116detail5printENS_5tupleENS_4dictE]+0x9a): undefined reference to `PyTuple_Size'
test_lib.cpp:(.text._ZN8pybind116detail5printENS_5tupleENS_4dictE[_ZN8pybind116detail5printENS_5tupleENS_4dictE]+0xaa): undefined reference to `PyTuple_GetItem'
test_lib.cpp:(.text._ZN8pybind116detail5printENS_5tupleENS_4dictE[_ZN8pybind116detail5printENS_5tupleENS_4dictE]+0xd3): undefined reference to `PyObject_Str'
test_lib.cpp:(.text._ZN8pybind116detail5printENS_5tupleENS_4dictE[_ZN8pybind116detail5printENS_5tupleENS_4dictE]+0x1cc): undefined reference to `PyDict_Contains'
test_lib.cpp:(.text._ZN8pybind116detail5printENS_5tupleENS_4dictE[_ZN8pybind116detail5printENS_5tupleENS_4dictE]+0x3c1): undefined reference to `PyDict_Contains'
test_lib.cpp:(.text._ZN8pybind116detail5printENS_5tupleENS_4dictE[_ZN8pybind116detail5printENS_5tupleENS_4dictE]+0x518): undefined reference to `PyImport_ImportModule'
test_lib.o: In function `void pybind11::print<(pybind11::return_value_policy)1, pybind11::list>(pybind11::list&&)':
test_lib.cpp:(.text._ZN8pybind115printILNS_19return_value_policyE1EJNS_4listEEEEvDpOT0_[_ZN8pybind115printILNS_19return_value_policyE1EJNS_4listEEEEvDpOT0_]+0x21): undefined reference to `PyDict_New'
test_lib.o: In function `main':
test_lib.cpp:(.text.startup+0x34): undefined reference to `Core::Core(bool)'
test_lib.cpp:(.text.startup+0x41): undefined reference to `Core::SetCpuAffinity(int)'
test_lib.cpp:(.text.startup+0x4b): undefined reference to `Core::Start(bool)'
test_lib.cpp:(.text.startup+0x5b): undefined reference to `Core::GetCallbacks()'
test_lib.cpp:(.text.startup+0x85): undefined reference to `Core::GetCallbacks()'
test_lib.cpp:(.text.startup+0x107): undefined reference to `PyObject_Str'
collect2: error: ld returned 1 exit status

Update 2

Looking at the errors, it seems to me the issue isnot pybind11 itself, but the Python libraries. PyObject_Str,PyObject_Str, PyImport_ImportModule, PyProperty_Type ,etc are all Python C APIs. However I'm providing the Python include and especially the libs directory, so g++ should be able to find the libs and link them. I'm at a loss here why this doesn't work. What is missing here?

I even made a bash file and tried all paths I've found to no avail:

#!/bin/bash  

PYBIND_INCL_DIR=-I/home/rika/Documents/cpp/External_Libraries/pybind11/pybind11/include
PYTHON_INCL_DIR=-I/home/rika/anaconda3/include/python3.7m
PYTHON_INCL_DIR2=-I/home/rika/anaconda3/pkgs/python-3.7.4-h265db76_1/include/python3.7m

PYTHON_LIB_DIRS=-L/home/rika/anaconda3/lib/
PYTHON_LIB_DIRS2=-L/home/rika/anaconda3/lib/python3.7/site-packages/
PYTHON_LIB_DIRS3=-L/home/rika/anaconda3/pkgs/python-3.7.4-h265db76_1/lib/

# echo $PYBIND_INCL_DIR
# echo $PYTHON_INCL_DIR

g++ $PYBIND_INCL_DIR  $PYTHON_INCL_DIR  $PYTHON_LIB_DIRS $PYTHON_LIB_DIRS2 $PYTHON_LIB_DIRS3 -c Core.cpp -o Core.o
g++ $PYBIND_INCL_DIR  $PYTHON_INCL_DIR  $PYTHON_LIB_DIRS $PYTHON_LIB_DIRS2 $PYTHON_LIB_DIRS3 test_lib.cpp Core.o -o test_lib

回答1:


Short answer:
As I said, the linker errors were related to the Python library not being found. In order to have a successful build, thus one, needed to only include that library, so the final build command would be : 

PYBIND_INCL_DIR=-I/home/rika/Documents/mahsan_FV/cpp/External_Libraries/pybind11/pybind11/include
PYTHON_INCL_DIR=-I/home/rika/anaconda3/include/python3.7m
PYTHON_LIB_DIRS=-L/home/rika/anaconda3/lib/

g++ $PYBIND_INCL_DIR  $PYTHON_INCL_DIR  $PYTHON_LIB_DIRS -c Core.cpp -o Core.o 
g++ $PYBIND_INCL_DIR  $PYTHON_INCL_DIR  $PYTHON_LIB_DIRS test_lib.cpp Core.o -lpython3.7m -o test_lib

This simply compiles and links all the object files together and solves the issue.

More Explanation:

You can get this either by navigating to the Python lib directory or simply executing python3-config --ldflags or python3.7-config --ldflags (depending on your version of python if you have several installations) in your terminal.(Thank you @ChrisD)

However, in order for the executable to be run properly, the lib folder needs to be in PATH or one could also use ldconfig to load the needed library. : I had to also do : 

sudo ldconfig /home/rika/anaconda3/lib/

Side note:
I also found this website very helpful on the linking procedure. I also tried to directly use the library which was:

home/hossein/anaconda3/pkgs/python-3.7.4-h265db76_1/lib/libpython3.7m.a

which resulted in the error : 

lto1: fatal error: bytecode stream in file ‘/home/rika/anaconda3/pkgs/python-3.7.4-h265db76_1/lib/libpython3.7m.a’ generated with LTO version 6.0 instead of the expected 6.2
compilation terminated.
lto-wrapper: fatal error: g++ returned 1 exit status

proving the only way to get the linking right was to use -lpython3.7m!



来源：https://stackoverflow.com/questions/61064801/getting-undefined-reference-when-trying-to-build-a-pybind11-project-using-gcc

标签
c++
g++
python-c-api
pybind11
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