Segmentation Fault 11 when running jupyter on Mac OS X

[EmmanuelJeanBriand]

Solution to issue cannot be found in the documentation.

• I checked the documentation.

Issue

Since april 30, 2023, with Mac OS X 10.14.6 and jupyter installed from conda-forge, I cannot start anymore jupyter lab nor jupyter notebook; I get Segmentation fault: 11.

Other users report the same issue at:

• https://stackoverflow.com/questions/76124633/jupyterlab-packaging-jlpm-segmentation-fault
• https://discourse.jupyter.org/t/trying-to-run-jupyter-lab-from-prompt-yields-segmentation-fault-11/19173
• https://community.anaconda.cloud/t/cannot-using-anaconda-to-launch-juypter-notebook/54566
• jupyterlab from conda-forge seg faults on mac jupyterlab/jupyterlab#14495

Installed packages

# Name                    Version                   Build  Channel
alabaster                 0.7.13             pyhd8ed1ab_0    conda-forge
anaconda-clean            1.1.0            py39hecd8cb5_1  
anyio                     3.6.2              pyhd8ed1ab_0    conda-forge
appnope                   0.1.3              pyhd8ed1ab_0    conda-forge
argon2-cffi               21.3.0             pyhd8ed1ab_0    conda-forge
argon2-cffi-bindings      21.2.0           py39ha30fb19_3    conda-forge
asttokens                 2.2.1              pyhd8ed1ab_0    conda-forge
async-lru                 2.0.2              pyhd8ed1ab_0    conda-forge
attrs                     23.1.0             pyh71513ae_1    conda-forge
babel                     2.12.1             pyhd8ed1ab_1    conda-forge
backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
backports                 1.0                pyhd8ed1ab_3    conda-forge
backports.functools_lru_cache 1.6.4              pyhd8ed1ab_0    conda-forge
beautifulsoup4            4.12.2             pyha770c72_0    conda-forge
bleach                    6.0.0              pyhd8ed1ab_0    conda-forge
boltons                   23.0.0             pyhd8ed1ab_0    conda-forge
brotli                    1.0.9                hb7f2c08_8    conda-forge
brotli-bin                1.0.9                hb7f2c08_8    conda-forge
bzip2                     1.0.8                h0d85af4_4    conda-forge
c-ares                    1.19.1               h0dc2134_0    conda-forge
ca-certificates           2023.5.7             h8857fd0_0    conda-forge
certifi                   2023.5.7           pyhd8ed1ab_0    conda-forge
cffi                      1.15.1           py39h131948b_3    conda-forge
charset-normalizer        3.1.0              pyhd8ed1ab_0    conda-forge
colorama                  0.4.6              pyhd8ed1ab_0    conda-forge
comm                      0.1.3              pyhd8ed1ab_0    conda-forge
conda                     23.3.1           py39h6e9494a_0    conda-forge
conda-package-handling    2.0.2              pyh38be061_0    conda-forge
conda-package-streaming   0.7.0              pyhd8ed1ab_1    conda-forge
cryptography              40.0.2           py39hbeae22c_0    conda-forge
debugpy                   1.6.7            py39h7a8716b_0    conda-forge
decorator                 5.1.1              pyhd8ed1ab_0    conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
docutils                  0.17.1           py39h6e9494a_2    conda-forge
entrypoints               0.4                pyhd8ed1ab_0    conda-forge
et_xmlfile                1.1.0              pyhd8ed1ab_0    conda-forge
executing                 1.2.0              pyhd8ed1ab_0    conda-forge
flit-core                 3.9.0              pyhd8ed1ab_0    conda-forge
fmt                       9.1.0                hb8565cd_0    conda-forge
freetype                  2.12.1               h3f81eb7_1    conda-forge
icu                       70.1                 h96cf925_0    conda-forge
idna                      3.4                pyhd8ed1ab_0    conda-forge
imagesize                 1.4.1              pyhd8ed1ab_0    conda-forge
importlib-metadata        6.6.0              pyha770c72_0    conda-forge
importlib_metadata        6.6.0                hd8ed1ab_0    conda-forge
importlib_resources       5.12.0             pyhd8ed1ab_0    conda-forge
ipycanvas                 0.13.1             pyhd8ed1ab_0    conda-forge
ipykernel                 6.23.1             pyh736e0ef_0    conda-forge
ipython                   8.13.2             pyhd1c38e8_0    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
ipywidgets                8.0.2              pyhd8ed1ab_1    conda-forge
jedi                      0.18.2             pyhd8ed1ab_0    conda-forge
jinja2                    3.1.2              pyhd8ed1ab_1    conda-forge
json5                     0.9.5              pyh9f0ad1d_0    conda-forge
jsonpatch                 1.32               pyhd8ed1ab_0    conda-forge
jsonpointer               2.0                        py_0    conda-forge
jsonschema                4.17.3             pyhd8ed1ab_0    conda-forge
jupyter-lsp               2.1.0              pyhd8ed1ab_0    conda-forge
jupyter_client            8.2.0              pyhd8ed1ab_0    conda-forge
jupyter_core              5.3.0            py39h6e9494a_0    conda-forge
jupyter_events            0.6.3              pyhd8ed1ab_0    conda-forge
jupyter_server            2.5.0              pyhd8ed1ab_0    conda-forge
jupyter_server_terminals  0.4.4              pyhd8ed1ab_1    conda-forge
jupyterlab                4.0.0              pyhd8ed1ab_1    conda-forge
jupyterlab_pygments       0.2.2              pyhd8ed1ab_0    conda-forge
jupyterlab_server         2.22.1             pyhd8ed1ab_0    conda-forge
jupyterlab_widgets        3.0.7              pyhd8ed1ab_1    conda-forge
krb5                      1.20.1               h049b76e_0    conda-forge
lcms2                     2.15                 h2dcdeff_1    conda-forge
lerc                      4.0.0                hb486fe8_0    conda-forge
libarchive                3.6.2                h6d8d9f1_0    conda-forge
libblas                   3.9.0           16_osx64_openblas    conda-forge
libbrotlicommon           1.0.9                hb7f2c08_8    conda-forge
libbrotlidec              1.0.9                hb7f2c08_8    conda-forge
libbrotlienc              1.0.9                hb7f2c08_8    conda-forge
libcblas                  3.9.0           16_osx64_openblas    conda-forge
libcurl                   7.88.1               h6df9250_1    conda-forge
libcxx                    16.0.4               hd57cbcb_0    conda-forge
libdeflate                1.18                 hac1461d_0    conda-forge
libedit                   3.1.20191231         h0678c8f_2    conda-forge
libev                     4.33                 haf1e3a3_1    conda-forge
libffi                    3.4.2                h0d85af4_5    conda-forge
libgfortran               5.0.0           11_3_0_h97931a8_31    conda-forge
libgfortran5              12.2.0              he409387_31    conda-forge
libiconv                  1.17                 hac89ed1_0    conda-forge
libjpeg-turbo             2.1.5.1              hb7f2c08_0    conda-forge
liblapack                 3.9.0           16_osx64_openblas    conda-forge
libmamba                  1.3.1                h9d281b0_1    conda-forge
libmambapy                1.3.1            py39he664332_1    conda-forge
libnghttp2                1.52.0               he2ab024_0    conda-forge
libopenblas               0.3.21          openmp_h429af6e_3    conda-forge
libpng                    1.6.39               ha978bb4_0    conda-forge
libsodium                 1.0.18               hbcb3906_1    conda-forge
libsolv                   0.7.23               hbc0c0cd_0    conda-forge
libsqlite                 3.42.0               h58db7d2_0    conda-forge
libssh2                   1.10.0               h47af595_3    conda-forge
libtiff                   4.5.0                hedf67fa_6    conda-forge
libuv                     1.44.2               hac89ed1_0    conda-forge
libwebp-base              1.3.0                hb7f2c08_0    conda-forge
libxcb                    1.15                 hb7f2c08_0    conda-forge
libxml2                   2.10.3               h201ad9d_4    conda-forge
libzlib                   1.2.13               hfd90126_4    conda-forge
llvm-openmp               16.0.4               hff08bdf_0    conda-forge
lz4-c                     1.9.4                hf0c8a7f_0    conda-forge
lzo                       2.10              haf1e3a3_1000    conda-forge
mamba                     1.3.1            py39h412838c_1    conda-forge
markupsafe                2.1.2            py39ha30fb19_0    conda-forge
matplotlib-inline         0.1.6              pyhd8ed1ab_0    conda-forge
mistune                   2.0.5              pyhd8ed1ab_0    conda-forge
nbclassic                 1.0.0              pyhb4ecaf3_1    conda-forge
nbclient                  0.7.4              pyhd8ed1ab_0    conda-forge
nbconvert                 7.3.1              pyhd8ed1ab_0    conda-forge
nbconvert-core            7.3.1              pyhd8ed1ab_0    conda-forge
nbconvert-pandoc          7.3.1              pyhd8ed1ab_0    conda-forge
nbformat                  5.8.0              pyhd8ed1ab_0    conda-forge
nbstripout                0.5.0              pyhd8ed1ab_0    conda-forge
ncurses                   6.3                  h96cf925_1    conda-forge
nest-asyncio              1.5.6              pyhd8ed1ab_0    conda-forge
nodejs                    18.12.1              hd0c9b3c_0    conda-forge
notebook                  6.5.4              pyha770c72_0    conda-forge
notebook-shim             0.2.3              pyhd8ed1ab_0    conda-forge
numpy                     1.24.3           py39h892e69a_0    conda-forge
openjpeg                  2.5.0                h13ac156_2    conda-forge
openpyxl                  3.0.9              pyhd3eb1b0_0  
openssl                   3.1.0                h8a1eda9_3    conda-forge
packaging                 23.1               pyhd8ed1ab_0    conda-forge
pandas                    1.5.3            py39hecff1ad_0    conda-forge
pandoc                    2.19.2               h694c41f_1    conda-forge
pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge
parso                     0.8.3              pyhd8ed1ab_0    conda-forge
pexpect                   4.8.0              pyh1a96a4e_2    conda-forge
pickleshare               0.7.5                   py_1003    conda-forge
pillow                    9.5.0            py39he6683de_1    conda-forge
pip                       23.1.2             pyhd8ed1ab_0    conda-forge
pkgutil-resolve-name      1.3.10             pyhd8ed1ab_0    conda-forge
platformdirs              3.5.1              pyhd8ed1ab_0    conda-forge
pluggy                    1.0.0              pyhd8ed1ab_5    conda-forge
prometheus_client         0.16.0             pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.38             pyha770c72_0    conda-forge
prompt_toolkit            3.0.38               hd8ed1ab_0    conda-forge
psutil                    5.9.5            py39ha30fb19_0    conda-forge
pthread-stubs             0.4               hc929b4f_1001    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
pure_eval                 0.2.2              pyhd8ed1ab_0    conda-forge
pybind11-abi              4                    hd8ed1ab_3    conda-forge
pycosat                   0.6.4            py39ha30fb19_1    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pygments                  2.15.1             pyhd8ed1ab_0    conda-forge
pyobjc-core               9.1.1            py39h0504f80_0    conda-forge
pyobjc-framework-cocoa    9.1.1            py39h0504f80_0    conda-forge
pyopenssl                 23.1.1             pyhd8ed1ab_0    conda-forge
pyparsing                 3.0.9              pyhd8ed1ab_0    conda-forge
pyrsistent                0.19.3           py39ha30fb19_0    conda-forge
pysocks                   1.7.1              pyha2e5f31_6    conda-forge
python                    3.9.12          h1cc4136_1_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-fastjsonschema     2.17.1             pyhd8ed1ab_0    conda-forge
python-json-logger        2.0.7              pyhd8ed1ab_0    conda-forge
python.app                3                py39hca72f7f_0  
python_abi                3.9                      3_cp39    conda-forge
pytz                      2023.3             pyhd8ed1ab_0    conda-forge
pyyaml                    6.0              py39ha30fb19_5    conda-forge
pyzmq                     25.0.2           py39hed8f129_0    conda-forge
readline                  8.2                  h9e318b2_1    conda-forge
reproc                    14.2.4               hb7f2c08_0    conda-forge
reproc-cpp                14.2.4               hf0c8a7f_0    conda-forge
requests                  2.31.0             pyhd8ed1ab_0    conda-forge
rfc3339-validator         0.1.4              pyhd8ed1ab_0    conda-forge
rfc3986-validator         0.1.1              pyh9f0ad1d_0    conda-forge
rise                      5.7.1            py39h6e9494a_2    conda-forge
ruamel.yaml               0.17.26          py39hdc70f33_0    conda-forge
ruamel.yaml.clib          0.2.7            py39ha30fb19_1    conda-forge
send2trash                1.8.2              pyhd1c38e8_0    conda-forge
setuptools                67.7.2             pyhd8ed1ab_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
sniffio                   1.3.0              pyhd8ed1ab_0    conda-forge
snowballstemmer           2.2.0              pyhd8ed1ab_0    conda-forge
soupsieve                 2.3.2.post1        pyhd8ed1ab_0    conda-forge
sphinx                    4.4.0              pyhd3eb1b0_0  
sphinxcontrib-applehelp   1.0.4              pyhd8ed1ab_0    conda-forge
sphinxcontrib-devhelp     1.0.2                      py_0    conda-forge
sphinxcontrib-htmlhelp    2.0.1              pyhd8ed1ab_0    conda-forge
sphinxcontrib-jsmath      1.0.1                      py_0    conda-forge
sphinxcontrib-qthelp      1.0.3                      py_0    conda-forge
sphinxcontrib-serializinghtml 1.1.5              pyhd8ed1ab_2    conda-forge
sqlite                    3.42.0               h2b0dec6_0    conda-forge
stack_data                0.6.2              pyhd8ed1ab_0    conda-forge
terminado                 0.17.1             pyhd1c38e8_0    conda-forge
tinycss2                  1.2.1              pyhd8ed1ab_0    conda-forge
tk                        8.6.12               h5dbffcc_0    conda-forge
tomli                     2.0.1              pyhd8ed1ab_0    conda-forge
toolz                     0.12.0             pyhd8ed1ab_0    conda-forge
tornado                   6.3.2            py39hdc70f33_0    conda-forge
tqdm                      4.65.0             pyhd8ed1ab_1    conda-forge
traitlets                 5.9.0              pyhd8ed1ab_0    conda-forge
typing-extensions         4.5.0                hd8ed1ab_0    conda-forge
typing_extensions         4.5.0              pyha770c72_0    conda-forge
tzdata                    2023c                h71feb2d_0    conda-forge
urllib3                   2.0.2              pyhd8ed1ab_0    conda-forge
wcwidth                   0.2.6              pyhd8ed1ab_0    conda-forge
webencodings              0.5.1                      py_1    conda-forge
websocket-client          1.5.2              pyhd8ed1ab_0    conda-forge
wheel                     0.40.0             pyhd8ed1ab_0    conda-forge
widgetsnbextension        4.0.3              pyhd8ed1ab_0    conda-forge
xorg-libxau               1.0.11               h0dc2134_0    conda-forge
xorg-libxdmcp             1.1.3                h35c211d_0    conda-forge
xz                        5.2.6                h775f41a_0    conda-forge
yaml                      0.2.5                h0d85af4_2    conda-forge
yaml-cpp                  0.7.0                hf0c8a7f_2    conda-forge
zeromq                    4.3.4                he49afe7_1    conda-forge
zipp                      3.15.0             pyhd8ed1ab_0    conda-forge
zlib                      1.2.13               hfd90126_4    conda-forge
zstandard                 0.19.0           py39h5bcbcff_1    conda-forge
zstd                      1.5.2                hbc0c0cd_6    conda-forge

Environment info

active environment : base
    active env location : /Users/gibus/miniconda3
            shell level : 1
       user config file : /Users/gibus/.condarc
 populated config files : /Users/gibus/.condarc
          conda version : 23.3.1
    conda-build version : not installed
         python version : 3.9.12.final.0
       virtual packages : __archspec=1=x86_64
                          __osx=10.14.6=0
                          __unix=0=0
       base environment : /Users/gibus/miniconda3  (writable)
      conda av data dir : /Users/gibus/miniconda3/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/osx-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/osx-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/osx-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /Users/gibus/miniconda3/pkgs
                          /Users/gibus/.conda/pkgs
       envs directories : /Users/gibus/miniconda3/envs
                          /Users/gibus/.conda/envs
               platform : osx-64
             user-agent : conda/23.3.1 requests/2.31.0 CPython/3.9.12 Darwin/18.7.0 OSX/10.14.6
                UID:GID : 503:20
             netrc file : None
           offline mode : False

[bollwyvl]

Thanks for reporting. Unfortunately, I have no machine on which to test this (and we're not adding 10x the builds just to get tests on the platform where this is ocurring), so will have to defer to a suitably equipped member of @conda-forge/jupyterlab to debug further.

[jasongrout]

Since april 30, 2023, with Mac OS X 10.14.6

FYI, according to https://endoflife.date/macos (not official, but informative), OS X 10.14 was end-of-life about 1.5 years ago (Oct 2021). I'm not sure what the conda-forge policy is towards end-of-life OS versions, but I wouldn't be surprised if support was dropped.

[marcbernot]

Hello I got the same issue with macOS Mojave 10.14.6.
Since I still have some not updated working environments I was able to track this down to a change of libffi version (and other related differences).

You can recover a working environment with last jupyterlab version by pinning libffi to 3.3.
micromamba create -f https://prefix.dev/envs/marcbernot/mojave/conda-lock.yml -n mojave
or
conda create -n testmojave python=3.9 libffi=3.3 notebook jupyterlab

If someone wants to investigate further, these are two environments with python=3.9.7. The first one is ok (libffi=3.3), the second one gives the segmentation fault (libffi>3.3).

micromamba create -f https://prefix.dev/envs/marcbernot/mojave/conda-lock.yml -n mojave
micromamba create -f https://prefix.dev/envs/marcbernot/mojave_nok/conda-lock.yml -n mojave_nok

A conda compare of the two environments yields

cffi found but mismatch. Specification pkg: cffi==1.15.1=py39h131948b_3, Running pkg: cffi==1.14.6=py39hb71fe58_0
libffi found but mismatch. Specification pkg: libffi==3.4.2=h0d85af4_5, Running pkg: libffi==3.3=h046ec9c_2
openssl found but mismatch. Specification pkg: openssl==3.1.1=h8a1eda9_1, Running pkg: openssl==1.1.1u=h8a1eda9_0
pyobjc-core found but mismatch. Specification pkg: pyobjc-core==9.1.1=py39h0504f80_0, Running pkg: pyobjc-core==7.3=py39h89e85a6_2
pyobjc-framework-cocoa found but mismatch. Specification pkg: pyobjc-framework-cocoa==9.1.1=py39h0504f80_0, Running pkg: pyobjc-framework-cocoa==7.3=py39h6e9494a_1
python found but mismatch. Specification pkg: python==3.9.7=h38b4d05_3_cpython, Running pkg: python==3.9.7=hd187cdc_0_cpython

[fcollonval]

@marcbernot thanks for sharing your workaround

[EmmanuelJeanBriand]

@marcbernot a big thank you!

[marcbernot]

I investigated a little further. The pyobjc-core package from conda-forge seems to be the culprit.

Indeed if you pin the pyobjc-core version to 8.2 everything is ok.
conda create -n mojave_py310_pyobjc82 python=3.10 pyobjc-core=8.2 notebook

It is starting to fail at 8.4
conda create -n mojave_py310_pyobjc84 python=3.10 pyobjc-core=8.4 notebook

However you can fix a failing environment (like mojave_py310_pyobjc84) with
pip install pyobjc-core pyobjc-framework-cocoa --force-reinstall

So the package from pypi works where the one from conda-forge does not. All this looks related to this issue in the feedstock of the conda-forge pyobjc-core package.

I think this issue can be closed as it is not related to jupyterlab feedstock.

[fcollonval]

I relabelled the issue as question instead of closing it. So it is easier to discover in case an user hit this.

[aadejare]

I investigated a little further. The pyobjc-core package from conda-forge seems to be the culprit.

Indeed if you pin the pyobjc-core version to 8.2 everything is ok. conda create -n mojave_py310_pyobjc82 python=3.10 pyobjc-core=8.2 notebook

It is starting to fail at 8.4 conda create -n mojave_py310_pyobjc84 python=3.10 pyobjc-core=8.4 notebook

However you can fix a failing environment (like mojave_py310_pyobjc84) with pip install pyobjc-core pyobjc-framework-cocoa --force-reinstall

So the package from pypi works where the one from conda-forge does not. All this looks related to this issue in the feedstock of the conda-forge pyobjc-core package.

I think this issue can be closed as it is not related to jupyterlab feedstock.

Yep that was the issue for me. Thanks!