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Unable to import numpy in notebook in new environment #7

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ChristopherHogan opened this issue Feb 12, 2019 · 4 comments
Closed

Unable to import numpy in notebook in new environment #7

ChristopherHogan opened this issue Feb 12, 2019 · 4 comments

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@ChristopherHogan
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This is on Ubuntu 16.04

conda info

  active environment : None
            shell level : 0
       user config file : /home/chris/.condarc
 populated config files : 
          conda version : 4.6.1
    conda-build version : 3.17.8
         python version : 3.6.8.final.0
       base environment : /home/chris/miniconda3  (writable)
           channel URLs : https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/free/linux-64
                          https://repo.anaconda.com/pkgs/free/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /home/chris/miniconda3/pkgs
                          /home/chris/.conda/pkgs
       envs directories : /home/chris/miniconda3/envs
                          /home/chris/.conda/envs
               platform : linux-64
             user-agent : conda/4.6.1 requests/2.18.4 CPython/3.6.8 Linux/4.15.0-45-generic ubuntu/16.04.5 glibc/2.23
                UID:GID : 1000:1000
             netrc file : None
           offline mode : False

Reproducer

$ conda create -n jup -c conda-forge numpy jupyter
$ conda activate jup
$ jupyter notebook

Next, create a new notebook and type import numpy in the first cell, and run. A box pops up with

Kernel Restarting
The kernel appears to have died. It will restart automatically.

The console messages:

[NotebookApp] Creating new notebook in 
[NotebookApp] Kernel started: xxx
[NotebookApp] Adapting to protocol v5.1 for kernel xxx
[NotebookApp] KernelRestarter: restarting kernel (1/5), keep random ports
WARNING:root:kernel xxx restarted

conda list --show-channel-urls

# packages in environment at /home/chris/miniconda3/envs/jup:
#
# Name                    Version                   Build  Channel
atk                       2.25.90           hb9dd440_1002    conda-forge
attrs                     18.2.0                     py_0    conda-forge
backcall                  0.1.0                      py_0    conda-forge
blas                      1.1                    openblas    conda-forge
bzip2                     1.0.6             h14c3975_1002    conda-forge
ca-certificates           2018.11.29           ha4d7672_0    conda-forge
cairo                     1.16.0            ha4e643d_1000    conda-forge
certifi                   2018.11.29            py37_1000    conda-forge
dbus                      1.13.0            h4e0c4b3_1000    conda-forge
decorator                 4.3.2                      py_0    conda-forge
entrypoints               0.3                   py37_1000    conda-forge
expat                     2.2.5             hf484d3e_1002    conda-forge
fontconfig                2.13.1            h2176d3f_1000    conda-forge
freetype                  2.9.1             h94bbf69_1005    conda-forge
gdk-pixbuf                2.36.12           h49783d7_1002    conda-forge
gettext                   0.19.8.1          h9745a5d_1001    conda-forge
glib                      2.58.2            hf63aee3_1001    conda-forge
gobject-introspection     1.58.2          py37h2da5eee_1000    conda-forge
graphite2                 1.3.13            hf484d3e_1000    conda-forge
gstreamer                 1.14.4            h66beb1c_1001    conda-forge
gtk2                      2.24.31           hb68c50a_1001    conda-forge
harfbuzz                  2.3.1                h6824563_0    conda-forge
icu                       58.2              hf484d3e_1000    conda-forge
ipykernel                 5.1.0           py37h24bf2e0_1002    conda-forge
ipython                   7.2.0           py37h24bf2e0_1000    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
ipywidgets                7.4.2                      py_0    conda-forge
jedi                      0.13.2                py37_1000    conda-forge
jinja2                    2.10                       py_1    conda-forge
jpeg                      9c                h14c3975_1001    conda-forge
jsonschema                3.0.0a3               py37_1000    conda-forge
jupyter                   1.0.0                      py_1    conda-forge
jupyter_client            5.2.4                      py_1    conda-forge
jupyter_console           6.0.0                      py_0    conda-forge
jupyter_core              4.4.0                      py_0    conda-forge
libffi                    3.2.1             hf484d3e_1005    conda-forge
libgcc-ng                 7.3.0                hdf63c60_0    conda-forge
libgfortran-ng            7.2.0                hdf63c60_3    conda-forge
libiconv                  1.15              h14c3975_1004    conda-forge
libpng                    1.6.36            h84994c4_1000    conda-forge
libsodium                 1.0.16            h14c3975_1001    conda-forge
libstdcxx-ng              7.3.0                hdf63c60_0    conda-forge
libtiff                   4.0.10            h648cc4a_1001    conda-forge
libuuid                   2.32.1            h14c3975_1000    conda-forge
libxcb                    1.13              h14c3975_1002    conda-forge
libxml2                   2.9.8             h143f9aa_1005    conda-forge
markupsafe                1.1.0           py37h14c3975_1000    conda-forge
mistune                   0.8.4           py37h14c3975_1000    conda-forge
nbconvert                 5.3.1                      py_1    conda-forge
nbformat                  4.4.0                      py_1    conda-forge
ncurses                   6.1               hf484d3e_1002    conda-forge
notebook                  5.7.4                 py37_1000    conda-forge
numpy                     1.16.1          py37_blas_openblash1522bff_0  [blas_openblas]  conda-forge
openblas                  0.3.3             h9ac9557_1001    conda-forge
openssl                   1.0.2p            h14c3975_1002    conda-forge
pandoc                    2.6                           1    conda-forge
pandocfilters             1.4.2                      py_1    conda-forge
pango                     1.40.14           h4ea9474_1004    conda-forge
parso                     0.3.3                      py_0    conda-forge
pcre                      8.41              hf484d3e_1003    conda-forge
pexpect                   4.6.0                 py37_1000    conda-forge
pickleshare               0.7.5                 py37_1000    conda-forge
pip                       19.0.2                   py37_0    conda-forge
pixman                    0.34.0            h14c3975_1003    conda-forge
prometheus_client         0.5.0                      py_0    conda-forge
prompt_toolkit            2.0.8                      py_0    conda-forge
pthread-stubs             0.4               h14c3975_1001    conda-forge
ptyprocess                0.6.0                 py37_1000    conda-forge
pygments                  2.3.1                      py_0    conda-forge
pyqt                      5.6.0           py37h13b7fb3_1008    conda-forge
pyrsistent                0.14.10          py37h14c3975_0    conda-forge
python                    3.7.1             hd21baee_1000    conda-forge
python-dateutil           2.8.0                      py_0    conda-forge
pyzmq                     17.1.2          py37h6afc9c9_1001    conda-forge
qt                        5.6.2             hce4f676_1013    conda-forge
qtconsole                 4.4.3                      py_0    conda-forge
readline                  7.0               hf8c457e_1001    conda-forge
send2trash                1.5.0                      py_0    conda-forge
setuptools                40.8.0                   py37_0    conda-forge
sip                       4.18.1          py37hf484d3e_1000    conda-forge
six                       1.12.0                py37_1000    conda-forge
sqlite                    3.26.0            h67949de_1000    conda-forge
terminado                 0.8.1                 py37_1001    conda-forge
testpath                  0.4.2                 py37_1000    conda-forge
tk                        8.6.9             h84994c4_1000    conda-forge
tornado                   5.1.1           py37h14c3975_1000    conda-forge
traitlets                 4.3.2                 py37_1000    conda-forge
wcwidth                   0.1.7                      py_1    conda-forge
webencodings              0.5.1                      py_1    conda-forge
wheel                     0.33.0                   py37_0    conda-forge
widgetsnbextension        3.4.2                 py37_1000    conda-forge
xorg-kbproto              1.0.7             h14c3975_1002    conda-forge
xorg-libice               1.0.9             h14c3975_1004    conda-forge
xorg-libsm                1.2.3             h4937e3b_1000    conda-forge
xorg-libx11               1.6.7             h14c3975_1000    conda-forge
xorg-libxau               1.0.9                h14c3975_0    conda-forge
xorg-libxdmcp             1.1.2             h14c3975_1007    conda-forge
xorg-libxext              1.3.3             h14c3975_1004    conda-forge
xorg-libxrender           0.9.10            h14c3975_1002    conda-forge
xorg-libxt                1.1.5             h14c3975_1002    conda-forge
xorg-renderproto          0.11.1            h14c3975_1002    conda-forge
xorg-xextproto            7.3.0             h14c3975_1002    conda-forge
xorg-xproto               7.0.31            h14c3975_1007    conda-forge
xz                        5.2.4             h14c3975_1001    conda-forge
zeromq                    4.2.5             hf484d3e_1006    conda-forge
zlib                      1.2.11            h14c3975_1004    conda-forge
@minrk
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minrk commented Feb 13, 2019

Can you import numpy in an IPython session in the same env?

@ChristopherHogan
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Can you import numpy in an IPython session in the same env?

No, I get Illegal instruction (core dumped). Running the import through gdb the stack trace shows

Thread 1 "python" received signal SIGILL, Illegal instruction.
0x00007ffff5d16fd8 in sdot_k_SKYLAKEX ()
   from /home/chris/miniconda3/envs/jup/lib/python3.7/site-packages/numpy/core/../../../../libopenblas.so.0

This happens with the normal Python interpreter too, not just IPython. I guess this issue belongs in the numpy or openblas feedstock.

@minrk
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minrk commented Feb 13, 2019

There's something funky going on with an update to libgfortran. My guess is this is related.

@ChristopherHogan
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Transferred to conda-forge/openblas-feedstock#60.

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@minrk @ChristopherHogan