Getting Cython-related error when running Python sampler

[eggplantbren]

Hi Dan,

Am I doing something stupid? Was just trying to run the gaussian.py example and it's complaining that I didn't build the Cython extensions, even though I did.

python gaussian.py Traceback (most recent call last): File "gaussian.py", line 43, in <module> sep=" ")) File "/home/brendon/local/anaconda3/lib/python3.5/site-packages/dnest4-0.1.4-py3.5-linux-x86_64.egg/dnest4/sampler.py", line 17, in __init__ raise ImportError("You must build the Cython extensions to use " ImportError: You must build the Cython extensions to use the Python API

[eggplantbren]

I'm using Anaconda 4.2.0 on Ubuntu 16.10, and the DNest python package was successfully installed with python setup.py install. Let me know what other info might help...

[MichelleLochner]

@eggplantbren I had the same problem with anaconda. It turns out to be a mismatch between the compiler used to compile DNest4 and the compiler used by anaconda when running cythonize. I did the following (after making DNest4):

export CC=/usr/bin/gcc export CXX=/usr/bin/g++ python setup.py install

I'm not sure if setting both compilers is necessary or just the C++ one but after this it worked.

[eggplantbren]

I'm glad this worked for you, but it didn't for me...😕

[eggplantbren]

This was a strange issue with my setup that seems to have been resolved. Closing

[eggplantbren]

This is happening again on two separate fresh installs of Anaconda 5.3.1 for Linux. I have no clue why - I have Cython and I saw it compiling when I installed the package. I've also tried Michelle's suggestion, which didn't help. Let me know of anything that might diagnose this, @dfm. It's a fairly severe problem if this happens to a user.

[dfm]

This normally has to do with trying to run within the directory where the package is installed. It can help to use: python setup.py develop instead of install. You might also try running pip uninstall dnest4 a few times first. Hope this helps!

[eggplantbren]

I just tried all of those suggestions and none of them worked.

[dfm]

What happens when you run:

from dnest4._dnest4 import sample

from Python?

[eggplantbren]

I wasn't expecting this, but it seems like a clue!

Python 3.7.0 (default, Oct  9 2018, 10:31:47) 
[GCC 7.3.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import dnest4
>>> from dnest4._dnest4 import sample
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ImportError: /home/brewer/local/anaconda3/lib/python3.7/site-packages/dnest4-0.2.3-py3.7-linux-x86_64.egg/dnest4/_dnest4.cpython-37m-x86_64-linux-gnu.so: undefined symbol: _ZN6DNest46CauchyC1Edd

[dfm]

Looks like there might be new files that need to be included. Take a look at setup.py in the Python directory and see which files are missing? I'm not sure where Cauchy is defined.

[eggplantbren]

That was exactly it. I just didn't know I had to edit setup.py after adding more features in the C++, but now I do. Thanks heaps. Closed with commit b76065322733a48a34eeca32ade23f3d2750df3c

[dfm]

Excellent.