Cythonize GIL error

[RomainBrault]

Error compiling Cython file:

...

cdef inline DTYPE_t dist(self, DTYPE_t* x1, DTYPE_t* x2,
                         ITYPE_t size) except -1 with gil:
    cdef np.ndarray x1arr
    cdef np.ndarray x2arr
    with gil:
        ^

---

sklearn/neighbors/dist_metrics.pyx:1111:13: Trying to acquire the GIL while it is already held.
Traceback (most recent call last):
File "/home/rbrault/OCRF/build_tools/cythonize.py", line 198, in
main(root_dir_arg)
File "/home/rbrault/OCRF/build_tools/cythonize.py", line 190, in main
check_and_cythonize(root_dir)
File "/home/rbrault/OCRF/build_tools/cythonize.py", line 182, in check_and_cythonize
cythonize_if_unchanged(cur_dir, cython_file, gen_file, hashes)
File "/home/rbrault/OCRF/build_tools/cythonize.py", line 156, in cythonize_if_unchanged
cythonize(full_cython_path, full_gen_file_path)
File "/home/rbrault/OCRF/build_tools/cythonize.py", line 75, in cythonize
raise Exception('Cythonizing %s failed' % cython_file)
Exception: Cythonizing sklearn/neighbors/dist_metrics.pyx failed
Traceback (most recent call last):
File "setup.py", line 315, in
setup_package()
File "setup.py", line 299, in setup_package
generate_cython()
File "setup.py", line 185, in generate_cython
raise RuntimeError("Running cythonize failed!")
RuntimeError: Running cythonize failed!

Need investigation.

Linux-4.10.0-40-generic-x86_64-with-debian-stretch-sid
Python 3.6.3 |Anaconda custom (64-bit)| (default, Oct 16 2017, 15:28:36)
[GCC 4.8.2 20140120 (Red Hat 4.8.2-15)]
NumPy 1.13.3
SciPy 0.19.1
GCC 7.0.1

Related issue:
https://stackoverflow.com/questions/46920490/sklearn-installation-trying-to-acquire-the-gil-while-it-is-already-held

[minoriinoue]

I got the same issue. Thanks for investigating the error.

[RomainBrault]

Related issues:
scikit-learn/scikit-learn#9272

Possible fix:
scikit-learn/scikit-learn#9311

[minoriinoue]

Could fix the issue with the possible fix you mentioned(scikit-learn/scikit-learn#9311). Thanks a lot.

[RomainBrault]

@minoriinoue, thanks for the feedback.

[vinhqdang]

Could you elaborate more on how to fix the bug? It is not clear for me :-(

[RomainBrault]

@vinhqdang you can have a look to

scikit-learn/scikit-learn@95f1bb0

for the exact fix. Just copy-paste the changes to the file sklearn/neighbors/dist_metrics.pyx. I'll try to do a PR later for this bug.

@ngoix we could just fetch master again, see if can still run the benchs? That would avoid incompatibilities due to newer version of cython.