GCC 8: Undefined _ZGVbN2v___log_finite when using -Ofast, missing -lm

[archboy87]

I'm getting a failure when importing numpy 1.13.3 compiled with GCC 8:

Traceback (most recent call last):
File "", line 1, in
File "/usr/lib/python3.6/site-packages/numpy/init.py", line 166, in
from . import random
File "/usr/lib/python3.6/site-packages/numpy/random/init.py", line 99, in
from .mtrand import *
ImportError: /usr/lib/python3.6/site-packages/numpy/random/mtrand.cpython-36m-x86_64-linux-gnu.so: undefined symbol: _ZGVbN2v___log_finite

I've tried with both openblas 0.2.20 and lapack / cblas 3.8.0. I've recompiled cython, cblas & lapack with GCC 8, but this didn't change the result.

I've compiled my whole system (Arch) with gcc-libs 8.0.0 so I can't just use the working GCC 7 version:

ImportError: /usr/lib/libgfortran.so.5: version `GFORTRAN_7' not found (required by /usr/lib/python3.6/site-packages/scipy/special/_ufuncs.cpython-36m-x86_64-linux-gnu.so)

I don't demand to support GCC 8 from you, but rather asking for the root causing this mutual incompatibility. Any ideas?

No, we need to support GCC 8. It looks like -lm needs to be passed to the linker command for mtrand (add m to the libraries). Would you mind submitting a PR with this fix?

Try adding it here:

numpy/numpy/random/setup.py

Line 43 in f1d81d8

libs = []

[juliantaylor]

_ZGVbN2v___log_finite is a a function from the glibc vectorized math library, numpy isn't using this.
With which flags are you compiling numpy? that function should only be used with -ffast-math

[eigenwillig]

Yes, I'm using -march=native -Ofast. I know, that ffast-math leads to some rounding, but I never had a single problem with this.

[rgommers]

This should be fixed, numpy/random/setup.py contains:

mtrand_libs = ['m', 'npymath'] if os.name != 'nt' else ['npymath']

Closing, thanks everyone.