ImportError: Symbol not found: _PyModule_Create2 about annoy HOT 10 CLOSED

What's pip2?

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pip2 is python package manager pip. I rename pip as pip2 for reminding of this is python2.x packages manager.

from annoy.

Seems like something broken with your Python environment.

For example: http://stackoverflow.com/questions/32152166/python-2-7-suddenly-not-working-symbol-not-found-pyerr-replaceexception-wh

Did you try to install it in a virtual environment? Might work better

from annoy.

Works on my mac:

$ virtualenv venv
$ venv/bin/pip2 install annoy
$ venv/bin/python2
>>> import annoy
>>> 

(a bunch of output removed)

from annoy.

I tried as following.

• step 1, pip install virutalenv venv
• step 2, follow your recommendation

_It did not work._
Maybe I should reinstall Python and try it again. Personally, I am curious about how to locate the _PyModule_Create2. There is not such symbol in file annoymodule.cc and annoylib.so

readelf -a annoylib.so | grep PyModule
00000020e028  000500000007 R_X86_64_JUMP_SLO 0000000000000000 PyModule_AddObject + 0
     5: 0000000000000000     0 FUNC    GLOBAL DEFAULT  UND PyModule_AddObject
    83: 0000000000000000     0 FUNC    GLOBAL DEFAULT  UND PyModule_AddObject

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pretty sure _PyModule_Create2 is defined in /usr/lib/libpython

I think your problem is that libpython isn't found in runtime

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I actually noticed I have this problem on my work computer so will try to repro & fix

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Interestingly, I have begun to see the same linker error on an unrelated package, and this was the only Google hit for the exact exception string.

# tox -e py27
GLOB sdist-make: /Users/amcgregor/Projects/marrow/src/libsass-python/setup.py
py27 inst-nodeps: /Users/amcgregor/Projects/marrow/src/libsass-python/.tox/dist/libsass-0.9.2.zip
py27 installed: flake8==2.5.0,libsass==0.9.2,mccabe==0.3.1,pep8==1.5.7,pyflakes==1.0.0,six==1.10.0,Werkzeug==0.11.2,wheel==0.24.0
py27 runtests: PYTHONHASHSEED='3228397935'
py27 runtests: commands[0] | python -c from shutil import *; rmtree("build", True)
py27 runtests: commands[1] | python -m unittest sasstests
Traceback (most recent call last):
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/runpy.py", line 162, in _run_module_as_main
    "__main__", fname, loader, pkg_name)
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/runpy.py", line 72, in _run_code
    exec code in run_globals
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/unittest/__main__.py", line 12, in <module>
    main(module=None)
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/unittest/main.py", line 94, in __init__
    self.parseArgs(argv)
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/unittest/main.py", line 149, in parseArgs
    self.createTests()
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/unittest/main.py", line 158, in createTests
    self.module)
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/unittest/loader.py", line 130, in loadTestsFromNames
    suites = [self.loadTestsFromName(name, module) for name in names]
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/unittest/loader.py", line 91, in loadTestsFromName
    module = __import__('.'.join(parts_copy))
  File "sasstests.py", line 23, in <module>
    import sass
  File "sass.py", line 26, in <module>
    from _sass import OUTPUT_STYLES, compile_filename, compile_string
ImportError: dlopen(./_sass.so, 2): Symbol not found: _PyModule_Create2
  Referenced from: ./_sass.so
  Expected in: flat namespace
 in ./_sass.so
ERROR: InvocationError: '/Users/amcgregor/Projects/marrow/src/libsass-python/.tox/py27/bin/python -m unittest sass tests'

Running using a brew-installed pypy or pypy3 does not exhibit this problem, but the both CPython 2 runs do. The py27 compiled module similarly does not contain a reference to that symbol:

# symbols .tox/py27/lib/python2.7/site-modules/_sass.so | grep PyModule
                0x000fad92 (     0x6) DYLD-STUB$$PyModule_AddObject [DYLD-STUB, LENGTH, NameNList, MangledNameNList, NList]

Weird.

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@Edonym what happens if you clone the repository and run python setup.py install? Does it also give the same error? If so – can you send the command line options for the compiler? Mine look like this:

cc -fno-strict-aliasing -fno-common -dynamic -arch x86_64 -arch i386 -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch x86_64 -arch i386 -pipe -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c src/annoymodule.cc -o build/temp.macosx-10.10-intel-2.7/src/annoymodule.o -O3 -march=native -ffast-math

See the -dynamic flag here – that one is key

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@Edonym were you able to find out a solution to the error that you talked about,
>>> import annoy Traceback (most recent call last): File "<input>", line 1, in <module> File "/usr/local/lib/python2.7/site-packages/annoy/__init__.py", line 15, in <module> from .annoylib import * ImportError: dlopen(/usr/local/lib/python2.7/site-packages/annoy/annoylib.so, 2): Symbol not found: _PyModule_Create2 Referenced from: /usr/local/lib/python2.7/site-packages/annoy/annoylib.so Expected in: flat namespace in /usr/local/lib/python2.7/site-packages/annoy/annoylib.so
I am getting the same error while I am working on Python 2.7 on HPC.

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