NUMPY_INCLUDE_DIR: /bin/sh: 1: -c: not found about bgslibrary

[andrewssobral]

Hello @Nuwan1654 thanks for reporting this issue.
Can you check please if you have numpy installed ? or send me the output of the following commands:

pip -V
pip list

[Nuwan1654]

Here are the outputs. I installed NumPy but

pip -V:
pip 20.0.2 from /home/dinusha/.virtualenvs/bs/lib/python3.8/site-packages/pip (python 3.8)

pip list:
Package Version

---

numpy 1.24.4
pip 20.0.2
pkg-resources 0.0.0
setuptools 44.0.0
wheel 0.34.2

[andrewssobral]

@Nuwan1654 try this:

cmake -D BGS_PYTHON_SUPPORT=ON \ 
  -D PYTHON_INCLUDE_DIR=$(python3 -c "from distutils.sysconfig import get_python_inc; print(get_python_inc())") \
  -D PYTHON_LIBRARY=$(python3 -c "import distutils.sysconfig as sysconfig; print(sysconfig.get_config_var('LIBDIR'))") ..

[Nuwan1654]

@andrewssobral thanks for looking into this, I tried but still got the same error. I am running this on a virtual python environment. When I try to install in the default python environment with pip install pybgs. it also getting a different error, but I see the NUMPY_INCLUDE_DIR: /home/dinusha/.local/lib/python3.8/site-packages/numpy/core/include

Here is the error for pip install pybgs

-- Found PythonInterp: /usr/bin/python3 (found suitable version "3.8.10", minimum required is "3.8")
      -- Found PythonLibs: /usr/lib/x86_64-linux-gnu/libpython3.8.so
      -- pybind11 v2.3.dev1
      --
      -- Python library status:
      --     executable: /usr/bin/python3
      --     library: /usr/lib/x86_64-linux-gnu/libpython3.8.so
      --     include path: /usr/include/python3.8
      -- NUMPY_INCLUDE_DIR: /home/dinusha/.local/lib/python3.8/site-packages/numpy/core/include
      
      -- Bulding bgslibrary_core STATIC
      --
      -- The bgslibrary python package will be installed at: lib/python3/dist-packages
      
      -- Configuring done
      CMake Error at CMakeLists.txt:223 (add_library):
        No SOURCES given to target: bgslibrary_core
      
      
      CMake Generate step failed.  Build files cannot be regenerated correctly.
      error: command 'cmake' failed with exit status 1
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
error: legacy-install-failure

× Encountered error while trying to install package.
╰─> pybgs

[andrewssobral]

@Nuwan1654
Thanks for those inputs.
I need to check why pybgs is generating this error, it's very strange.
Can you try to build the bgs library by manually setting the NUMPY_INCLUDE_DIR, like:

cmake -D BGS_PYTHON_SUPPORT=ON -D NUMPY_INCLUDE_DIR=/home/dinusha/.local/lib/python3.8/site-packages/numpy/core/include ..

[Nuwan1654]

Hi @andrewssobral thanks for helping me. Now the numpy error is gone, It seems like an issue with cmake.

error left is

CMake Error at CMakeLists.txt:161 (add_subdirectory):
  The source directory

    /home/dinusha/codebase/bs/bgslibrary/modules/pybind11

  does not contain a CMakeLists.txt file.

-- 
-- Python library status:
--     executable: 
--     library: /usr/lib
--     include path: 
-- NUMPY_INCLUDE_DIR: /home/dinusha/.local/lib/python3.8/site-packages/numpy/core/include

-- Bulding bgslibrary_core SHARED
CMake Error at CMakeLists.txt:242 (pybind11_add_module):
  Unknown CMake command "pybind11_add_module".


-- Configuring incomplete, errors occurred!
See also "/home/dinusha/codebase/bs/bgslibrary/build/CMakeFiles/CMakeOutput.log".
See also "/home/dinusha/codebase/bs/bgslibrary/build/CMakeFiles/CMakeError.log".

Here is the content of the CMakeError.log

Performing C SOURCE FILE Test CMAKE_HAVE_LIBC_PTHREAD failed with the following output:
Change Dir: /home/dinusha/codebase/bs/bgslibrary/build/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/make cmTC_3076c/fast && /usr/bin/make -f CMakeFiles/cmTC_3076c.dir/build.make CMakeFiles/cmTC_3076c.dir/build
make[1]: Entering directory '/home/dinusha/codebase/bs/bgslibrary/build/CMakeFiles/CMakeTmp'
Building C object CMakeFiles/cmTC_3076c.dir/src.c.o
/usr/bin/cc   -fPIC -DCMAKE_HAVE_LIBC_PTHREAD -fPIE   -o CMakeFiles/cmTC_3076c.dir/src.c.o   -c /home/dinusha/codebase/bs/bgslibrary/build/CMakeFiles/CMakeTmp/src.c
Linking C executable cmTC_3076c
/usr/bin/cmake -E cmake_link_script CMakeFiles/cmTC_3076c.dir/link.txt --verbose=1
/usr/bin/cc -fPIC -DCMAKE_HAVE_LIBC_PTHREAD    -rdynamic CMakeFiles/cmTC_3076c.dir/src.c.o  -o cmTC_3076c
/usr/bin/ld: CMakeFiles/cmTC_3076c.dir/src.c.o: in function `main':
src.c:(.text+0x46): undefined reference to `pthread_create'
/usr/bin/ld: src.c:(.text+0x52): undefined reference to `pthread_detach'
/usr/bin/ld: src.c:(.text+0x63): undefined reference to `pthread_join'
collect2: error: ld returned 1 exit status
make[1]: *** [CMakeFiles/cmTC_3076c.dir/build.make:87: cmTC_3076c] Error 1
make[1]: Leaving directory '/home/dinusha/codebase/bs/bgslibrary/build/CMakeFiles/CMakeTmp'
make: *** [Makefile:121: cmTC_3076c/fast] Error 2


Source file was:
#include <pthread.h>

void* test_func(void* data)
{
  return data;
}

int main(void)
{
  pthread_t thread;
  pthread_create(&thread, NULL, test_func, NULL);
  pthread_detach(thread);
  pthread_join(thread, NULL);
  pthread_atfork(NULL, NULL, NULL);
  pthread_exit(NULL);

  return 0;
}

Determining if the function pthread_create exists in the pthreads failed with the following output:
Change Dir: /home/dinusha/codebase/bs/bgslibrary/build/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/make cmTC_a7086/fast && /usr/bin/make -f CMakeFiles/cmTC_a7086.dir/build.make CMakeFiles/cmTC_a7086.dir/build
make[1]: Entering directory '/home/dinusha/codebase/bs/bgslibrary/build/CMakeFiles/CMakeTmp'
Building C object CMakeFiles/cmTC_a7086.dir/CheckFunctionExists.c.o
/usr/bin/cc   -fPIC -DCHECK_FUNCTION_EXISTS=pthread_create -fPIE   -o CMakeFiles/cmTC_a7086.dir/CheckFunctionExists.c.o   -c /usr/share/cmake-3.16/Modules/CheckFunctionExists.c
Linking C executable cmTC_a7086
/usr/bin/cmake -E cmake_link_script CMakeFiles/cmTC_a7086.dir/link.txt --verbose=1
/usr/bin/cc -fPIC -DCHECK_FUNCTION_EXISTS=pthread_create    -rdynamic CMakeFiles/cmTC_a7086.dir/CheckFunctionExists.c.o  -o cmTC_a7086  -lpthreads
/usr/bin/ld: cannot find -lpthreads
collect2: error: ld returned 1 exit status
make[1]: *** [CMakeFiles/cmTC_a7086.dir/build.make:87: cmTC_a7086] Error 1
make[1]: Leaving directory '/home/dinusha/codebase/bs/bgslibrary/build/CMakeFiles/CMakeTmp'
make: *** [Makefile:121: cmTC_a7086/fast] Error 2

[andrewssobral]

@Nuwan1654 , perfect!

The new error you encountered is related to the missing submodules of the bgslibrary repository, specifically the pybind11 submodule. Typically, we should clone the bgslibrary using the --recursive option, but you can also run the following command after cloned repo:

git submodule update --init --recursive

After running this command, you can proceed to execute the cmake command.

[Nuwan1654]

@andrewssobral Thank you very much, Now I have built it successfully, but in the guidelines, it says (add 'pybgs.so' to your Python path)

But in the build directory I have pybgs.cpython-38-x86_64-linux-gnu.so How can I add this to the python path

[andrewssobral]

@Nuwan1654 perfect!

To add the bgslibrary build directory to the PYTHONPATH environment variable, you can use the following command:

export PYTHONPATH="${PYTHONPATH}:/root/bgslibrary/build"

Make sure to replace /root/bgslibrary/build with the correct path to your bgslibrary build directory.

[Nuwan1654]

great thanks again for the help