Test suite segfault on Linux/x86_64/Python 3.7 with old GCC #12483
Description
Description
In the conda-forge project, we see a segfault in the test suite when building scikit-learn packages against Python 3.7 using an older GCC. Here is the related issue report.
Steps/Code to Reproduce
This failure comes up in our CI-based automated build system. Here is the build info and here is the relevant log file.
My reproduction of the build environment isolates the segfault to this test:
test_common.py::test_non_meta_estimators[AgglomerativeClustering-AgglomerativeClustering-check_clustering(readonly_memmap=True)] <- $PREFIX/lib/python3.7/site-packages/sklearn/tests/test_common.py
The bit involving a memmap seems to me like it could potentially be fragile, but I see that there are other tests with the same flag that succeed.
Running in a debugger, I don't have any debug symbols, but the backtrace lands in scipy:
(gdb) bt
#0 0x00007fffcc189f3e in pdist_euclidean_double_wrap ()
from /a/TEMP37/lib/python3.7/site-packages/scipy/spatial/_distance_wrap.cpython-37m-x86_64-linux-gnu.so
#1 0x0000000000431f3d in cfunction_call_varargs ()
#2 0x0000000000431fee in PyCFunction_Call ()
#3 0x00000000004ef5df in do_call_core ()
(Then the backtrace continues for many frames inside the Python interpreter.)
We do not see this failure on other versions of Python, or when building with GCC7, or on macOS.
I can upload the Conda package made out of the build that exhibits this problem, but since it doesn't have debugging symbols I think it would be a challenge to do much investigation with it.
Versions
System
------
python: 3.7.0 | packaged by conda-forge | (default, Sep 30 2018, 14:56:18) [GCC 4.8.2 20140120 (Red Hat 4.8.2-15)]
executable: /a/TEMP37/bin/python
machine: Linux-4.18.16-200.fc28.x86_64-x86_64-with-fedora-28-Twenty_Eight
BLAS
----
macros: HAVE_CBLAS=None
lib_dirs: /a/TEMP37/lib
cblas_libs: openblas, openblas
Python deps
-----------
pip: 18.1
setuptools: 40.5.0
sklearn: 0.20.0
numpy: 1.15.3
scipy: 1.1.0
Cython: None
pandas: None