Seg fault importing numpy on fresh conda environment

[stogey25]

Hi all,

With a fresh install of Anaconda3 on my machine running Ubuntu 18.10, I created an Intel python environment using the instructions here.

After switching to the environment, I can open run intel python and confirm it's the Intel distro:

Python 3.6.8 |Intel Corporation| (default, Mar  1 2019, 00:10:45) 
[GCC 4.8.2 20140120 (Red Hat 4.8.2-15)] on linux
Type "help", "copyright", "credits" or "license" for more information.
Intel(R) Distribution for Python is brought to you by Intel Corporation.
Please check out: https://software.intel.com/en-us/python-distribution
>>> 

Upon importing numpy I immediately get a segmentation fault, and I have no idea why:

>>> import numpy as np
Segmentation fault (core dumped)

Below is the output of conda list:

# packages in environment at /home/steve/anaconda3/envs/idp:
#
# Name                    Version                   Build  Channel
absl-py                   0.7.1                    py36_0  
asn1crypto                0.24.0                   py36_3    intel
astor                     0.7.1                    py36_0  
bzip2                     1.0.6                        17    intel
c-ares                    1.15.0               h7b6447c_1  
certifi                   2018.1.18                py36_2    intel
cffi                      1.11.5                   py36_3    intel
chardet                   3.0.4                    py36_3    intel
cryptography              2.3                      py36_1    intel
cycler                    0.10.0                   py36_7    intel
cython                    0.29.3                   py36_1    intel
daal                      2019.3                intel_199    intel
daal4py                   2019.3           py36h7b7c402_6    intel
freetype                  2.9                           3    intel
funcsigs                  1.0.2                    py36_7    intel
gast                      0.2.2                    py36_0  
grpcio                    1.14.1           py36h9ba97e2_0  
h5py                      2.8.0            py36h989c5e5_3  
hdf5                      1.10.2                        2    intel
icc_rt                    2019.3                intel_199    intel
idna                      2.6                      py36_3    intel
impi_rt                   2019.3                intel_201    intel
intel-openmp              2019.3                intel_199    intel
intelpython               2019.3                        0    intel
intelpython3_core         2019.3                        0    intel
intelpython3_full         2019.3                        0    intel
ipp                       2019.3                intel_199    intel
keras-applications        1.0.7                      py_0  
keras-preprocessing       1.0.9                      py_0  
kiwisolver                1.0.1                    py36_2    intel
libffi                    3.2.1                        11    intel
libgcc-ng                 8.2.0                hdf63c60_1  
libpng                    1.6.36                        2    intel
libprotobuf               3.7.1                hd408876_0  
libstdcxx-ng              8.2.0                hdf63c60_1  
llvmlite                  0.27.1                   py36_0    intel
markdown                  3.1                      py36_0  
matplotlib                3.0.1                    py36_1    intel
mkl                       2019.3                intel_199    intel
mkl-service               1.0.0                    py36_7    intel
mkl_fft                   1.0.11           py36h7b7c402_0    intel
mkl_random                1.0.2            py36h7b7c402_4    intel
mpi4py                    3.0.0                    py36_3    intel
numba                     0.42.1              np116py36_0    intel
numexpr                   2.6.8                    py36_2    intel
numpy                     1.16.1           py36h7b7c402_3    intel
numpy-base                1.16.1                   py36_3    intel
openssl                   1.0.2r                        0    intel
pandas                    0.24.1                   py36_3    intel
pip                       10.0.1                   py36_0    intel
protobuf                  3.7.1            py36he6710b0_0  
pycosat                   0.6.3                    py36_3    intel
pycparser                 2.18                     py36_2    intel
pyeditline                2.0.0                    py36_0    intel
pyopenssl                 17.5.0                   py36_2    intel
pyparsing                 2.2.0                    py36_2    intel
pysocks                   1.6.7                    py36_1    intel
python                    3.6.8                         6    intel
python-dateutil           2.6.0                   py36_12    intel
pytz                      2018.4                   py36_3    intel
pyyaml                    4.1                      py36_3    intel
requests                  2.20.1                   py36_1    intel
ruamel_yaml               0.11.14                  py36_4    intel
scikit-learn              0.20.2           py36h7b7c402_2    intel
scipy                     1.2.0                    py36_3    intel
setuptools                39.0.1                   py36_0    intel
six                       1.11.0                   py36_3    intel
smp                       0.1.4                    py36_0    intel
sqlite                    3.27.2                        2    intel
tbb                       2019.4                intel_199    intel
tbb4py                    2019.4             py36_intel_0    intel
tcl                       8.6.4                        22    intel
tensorboard               1.12.2           py36he6710b0_0  
tensorflow                1.12.0                   py36_0    intel
termcolor                 1.1.0                    py36_1  
tk                        8.6.4                        28    intel
urllib3                   1.24.1                   py36_2    intel
werkzeug                  0.14.1                   py36_0    intel
wheel                     0.31.0                   py36_3    intel
xgboost                   0.81                     py36_0    intel
xz                        5.2.3                         2    intel
yaml                      0.1.7                         2    intel
zlib                      1.2.11                        5    intel

Anyone know how to resolve this? I should note that I can follow the same procedure in Windows 10 and get no errors.

Thanks,

Steve

[Oleksandr_P_Intel · Accepted solution]

Hi,

This crash is caused by an issue in GLIBC version 2.28, used in Ubuntu 18.10

It is fixed in glibc 2.29 though:  https://bugs.launchpad.net/ubuntu/+source/glibc/+bug/1821677 

Sasha