Cython cannot find shared objects file
I am trying to link my own C library with Cython following the directions I found online, including this answer:
Using Cython to link Python to a shared library
I am running IPython through Spyder.
My setup.py looks like this:
from distutils.core import setup
from distutils.extension import Extension
from Cython.Build import cythonize
import numpy as np
setup(
ext_modules = cythonize(
[Extension("*",["*.pyx"],
libraries =["MyLib"],
extra_compile_args = ["-fopenmp","-O3"],
extra_link_args=["-L/path/to/lib"])
]),
include_dirs = [np.get_include()],
)
The file libMyLib.so
is in /path/to/lib
and it compiles just fine.
I have a Python script in the IPython profile startup folder that does this
try:
os.environ["LD_LIBRARY_PATH"] += ":/path/to/lib"
except KeyError:
os.environ["LD_LIBRARY_PATH"] = "/path/to/lib"
I can confirm that this works because if I type os.environ["LD_LIBRARY_PATH"]
into the IPython interpreter it returns/path/to/lib
But when I try to load the Cython module (i.e. import mycythonmodule
) I get:
ImportError: libMyLib.so: cannot open shared object file: No such file or directory
I also tried putting libMyLib.so elsewhere to see if cython finds:
- In the directory where Python is running
- On the Python Path
- In the same folder as the cython module
But it still doesn't find the shared library. The only way to get it to find the library is to dump it in /usr/lib
, but I don't want it there, I want to be able to set the library path.
Did I miss something?
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I answer myself in case anyone is facing the same problem. Looks like the answers are here:
Set LD_LIBRARY_PATH before import in python
Change LD_LIBRARY_PATH at runtime for ctypes
According to these answers (and my experience) the linker reads LD_LIBRARY_PATH when python starts up, so changing it from within python has no beneficial effect, at least not the effect I was hoping for. The only solution is to either wrap python in a wrapper script that sets LD_LIBRARY_PATH, or cut the shared object somewhere in the linker search path.
Kind of pain, but that's what it is.
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