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Anaconda navigator crashes X11 on startup. #10467

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actevlin opened this issue Dec 29, 2018 · 5 comments
Open

Anaconda navigator crashes X11 on startup. #10467

actevlin opened this issue Dec 29, 2018 · 5 comments
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pkg-navigator

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@actevlin
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Actual Behavior

clint@mediaserver ~ $ python
Python 3.7.1 (default, Dec 14 2018, 19:28:38)
[GCC 7.3.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.

quit()
clint@mediaserver ~ $ export PATH=/home/clint/anaconda3/bin:$PATH
clint@mediaserver ~ $ conda --version
conda 4.5.12
clint@mediaserver ~ $ anaconda-navigator
QApplication: invalid style override passed, ignoring it.
The X11 connection broke: Maximum allowed requested length exceeded (code 4)
XIO: fatal IO error 2 (No such file or directory) on X server ":0"
after 426 requests (426 known processed) with 0 events remaining.

Expected Behavior

navigator should start

Steps to Reproduce

just type anaconda-navigator

Anaconda or Miniconda version:

Anaconda 2018.12 For Linux

Operating System:

linux mint 18.3

conda info
     active environment : base
    active env location : /home/clint/anaconda3
            shell level : 1
       user config file : /home/clint/.condarc
 populated config files : 
          conda version : 4.5.12
    conda-build version : 3.17.6
         python version : 3.7.1.final.0
       base environment : /home/clint/anaconda3  (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
                          https://repo.anaconda.com/pkgs/pro/linux-64
                          https://repo.anaconda.com/pkgs/pro/noarch
          package cache : /home/clint/anaconda3/pkgs
                          /home/clint/.conda/pkgs
       envs directories : /home/clint/anaconda3/envs
                          /home/clint/.conda/envs
               platform : linux-64
             user-agent : conda/4.5.12 requests/2.21.0 CPython/3.7.1 Linux/4.15.0-43-generic linuxmint/18.3 glibc/2.23
                UID:GID : 1000:1000
             netrc file : None
           offline mode : False
conda list --show-channel-urls
# packages in environment at /home/clint/anaconda3:
#
# Name                    Version                   Build  Channel
_ipyw_jlab_nb_ext_conf    0.1.0                    py37_0    defaults
alabaster                 0.7.12                   py37_0    defaults
anaconda                  2018.12                  py37_0    defaults
anaconda-client           1.7.2                    py37_0    defaults
anaconda-navigator        1.9.6                    py37_0    defaults
anaconda-project          0.8.2                    py37_0    defaults
asn1crypto                0.24.0                   py37_0    defaults
astroid                   2.1.0                    py37_0    defaults
astropy                   3.1              py37h7b6447c_0    defaults
atomicwrites              1.2.1                    py37_0    defaults
attrs                     18.2.0           py37h28b3542_0    defaults
babel                     2.6.0                    py37_0    defaults
backcall                  0.1.0                    py37_0    defaults
backports                 1.0                      py37_1    defaults
backports.os              0.1.1                    py37_0    defaults
backports.shutil_get_terminal_size 1.0.0                    py37_2    defaults
beautifulsoup4            4.6.3                    py37_0    defaults
bitarray                  0.8.3            py37h14c3975_0    defaults
bkcharts                  0.2                      py37_0    defaults
blas                      1.0                         mkl    defaults
blaze                     0.11.3                   py37_0    defaults
bleach                    3.0.2                    py37_0    defaults
blosc                     1.14.4               hdbcaa40_0    defaults
bokeh                     1.0.2                    py37_0    defaults
boto                      2.49.0                   py37_0    defaults
bottleneck                1.2.1            py37h035aef0_1    defaults
bzip2                     1.0.6                h14c3975_5    defaults
ca-certificates           2018.03.07                    0    defaults
cairo                     1.14.12              h8948797_3    defaults
certifi                   2018.11.29               py37_0    defaults
cffi                      1.11.5           py37he75722e_1    defaults
chardet                   3.0.4                    py37_1    defaults
click                     7.0                      py37_0    defaults
cloudpickle               0.6.1                    py37_0    defaults
clyent                    1.2.2                    py37_1    defaults
colorama                  0.4.1                    py37_0    defaults
conda                     4.5.12                   py37_0    defaults
conda-build               3.17.6                   py37_0    defaults
conda-env                 2.6.0                         1    defaults
conda-verify              3.1.1                    py37_0    defaults
contextlib2               0.5.5                    py37_0    defaults
cryptography              2.4.2            py37h1ba5d50_0    defaults
curl                      7.63.0            hbc83047_1000    defaults
cycler                    0.10.0                   py37_0    defaults
cython                    0.29.2           py37he6710b0_0    defaults
cytoolz                   0.9.0.1          py37h14c3975_1    defaults
dask                      1.0.0                    py37_0    defaults
dask-core                 1.0.0                    py37_0    defaults
datashape                 0.5.4                    py37_1    defaults
dbus                      1.13.2               h714fa37_1    defaults
decorator                 4.3.0                    py37_0    defaults
defusedxml                0.5.0                    py37_1    defaults
distributed               1.25.1                   py37_0    defaults
docutils                  0.14                     py37_0    defaults
entrypoints               0.2.3                    py37_2    defaults
et_xmlfile                1.0.1                    py37_0    defaults
expat                     2.2.6                he6710b0_0    defaults
fastcache                 1.0.2            py37h14c3975_2    defaults
filelock                  3.0.10                   py37_0    defaults
flask                     1.0.2                    py37_1    defaults
flask-cors                3.0.7                    py37_0    defaults
fontconfig                2.13.0               h9420a91_0    defaults
freetype                  2.9.1                h8a8886c_1    defaults
fribidi                   1.0.5                h7b6447c_0    defaults
future                    0.17.1                   py37_0    defaults
get_terminal_size         1.0.0                haa9412d_0    defaults
gevent                    1.3.7            py37h7b6447c_1    defaults
glib                      2.56.2               hd408876_0    defaults
glob2                     0.6                      py37_1    defaults
gmp                       6.1.2                h6c8ec71_1    defaults
gmpy2                     2.0.8            py37h10f8cd9_2    defaults
graphite2                 1.3.12               h23475e2_2    defaults
greenlet                  0.4.15           py37h7b6447c_0    defaults
gst-plugins-base          1.14.0               hbbd80ab_1    defaults
gstreamer                 1.14.0               hb453b48_1    defaults
h5py                      2.8.0            py37h989c5e5_3    defaults
harfbuzz                  1.8.8                hffaf4a1_0    defaults
hdf5                      1.10.2               hba1933b_1    defaults
heapdict                  1.0.0                    py37_2    defaults
html5lib                  1.0.1                    py37_0    defaults
icu                       58.2                 h9c2bf20_1    defaults
idna                      2.8                      py37_0    defaults
imageio                   2.4.1                    py37_0    defaults
imagesize                 1.1.0                    py37_0    defaults
importlib_metadata        0.6                      py37_0    defaults
intel-openmp              2019.1                      144    defaults
ipykernel                 5.1.0            py37h39e3cac_0    defaults
ipython                   7.2.0            py37h39e3cac_0    defaults
ipython_genutils          0.2.0                    py37_0    defaults
ipywidgets                7.4.2                    py37_0    defaults
isort                     4.3.4                    py37_0    defaults
itsdangerous              1.1.0                    py37_0    defaults
jbig                      2.1                  hdba287a_0    defaults
jdcal                     1.4                      py37_0    defaults
jedi                      0.13.2                   py37_0    defaults
jeepney                   0.4                      py37_0    defaults
jinja2                    2.10                     py37_0    defaults
jpeg                      9b                   h024ee3a_2    defaults
jsonschema                2.6.0                    py37_0    defaults
jupyter                   1.0.0                    py37_7    defaults
jupyter_client            5.2.4                    py37_0    defaults
jupyter_console           6.0.0                    py37_0    defaults
jupyter_core              4.4.0                    py37_0    defaults
jupyterlab                0.35.3                   py37_0    defaults
jupyterlab_server         0.2.0                    py37_0    defaults
keyring                   17.0.0                   py37_0    defaults
kiwisolver                1.0.1            py37hf484d3e_0    defaults
krb5                      1.16.1               h173b8e3_7    defaults
lazy-object-proxy         1.3.1            py37h14c3975_2    defaults
libarchive                3.3.3                h5d8350f_5    defaults
libcurl                   7.63.0            h20c2e04_1000    defaults
libedit                   3.1.20170329         h6b74fdf_2    defaults
libffi                    3.2.1                hd88cf55_4    defaults
libgcc-ng                 8.2.0                hdf63c60_1    defaults
libgfortran-ng            7.3.0                hdf63c60_0    defaults
liblief                   0.9.0                h7725739_1    defaults
libpng                    1.6.35               hbc83047_0    defaults
libsodium                 1.0.16               h1bed415_0    defaults
libssh2                   1.8.0                h1ba5d50_4    defaults
libstdcxx-ng              8.2.0                hdf63c60_1    defaults
libtiff                   4.0.9                he85c1e1_2    defaults
libtool                   2.4.6                h7b6447c_5    defaults
libuuid                   1.0.3                h1bed415_2    defaults
libxcb                    1.13                 h1bed415_1    defaults
libxml2                   2.9.8                h26e45fe_1    defaults
libxslt                   1.1.32               h1312cb7_0    defaults
llvmlite                  0.26.0           py37hd408876_0    defaults
locket                    0.2.0                    py37_1    defaults
lxml                      4.2.5            py37hefd8a0e_0    defaults
lz4-c                     1.8.1.2              h14c3975_0    defaults
lzo                       2.10                 h49e0be7_2    defaults
markupsafe                1.1.0            py37h7b6447c_0    defaults
matplotlib                3.0.2            py37h5429711_0    defaults
mccabe                    0.6.1                    py37_1    defaults
mistune                   0.8.4            py37h7b6447c_0    defaults
mkl                       2019.1                      144    defaults
mkl-service               1.1.2            py37he904b0f_5    defaults
mkl_fft                   1.0.6            py37hd81dba3_0    defaults
mkl_random                1.0.2            py37hd81dba3_0    defaults
more-itertools            4.3.0                    py37_0    defaults
mpc                       1.1.0                h10f8cd9_1    defaults
mpfr                      4.0.1                hdf1c602_3    defaults
mpmath                    1.1.0                    py37_0    defaults
msgpack-python            0.5.6            py37h6bb024c_1    defaults
multipledispatch          0.6.0                    py37_0    defaults
navigator-updater         0.2.1                    py37_0    defaults
nbconvert                 5.4.0                    py37_1    defaults
nbformat                  4.4.0                    py37_0    defaults
ncurses                   6.1                  he6710b0_1    defaults
networkx                  2.2                      py37_1    defaults
nltk                      3.4                      py37_1    defaults
nose                      1.3.7                    py37_2    defaults
notebook                  5.7.4                    py37_0    defaults
numba                     0.41.0           py37h962f231_0    defaults
numexpr                   2.6.8            py37h9e4a6bb_0    defaults
numpy                     1.15.4           py37h7e9f1db_0    defaults
numpy-base                1.15.4           py37hde5b4d6_0    defaults
numpydoc                  0.8.0                    py37_0    defaults
odo                       0.5.1                    py37_0    defaults
olefile                   0.46                     py37_0    defaults
openpyxl                  2.5.12                   py37_0    defaults
openssl                   1.1.1a               h7b6447c_0    defaults
packaging                 18.0                     py37_0    defaults
pandas                    0.23.4           py37h04863e7_0    defaults
pandoc                    1.19.2.1             hea2e7c5_1    defaults
pandocfilters             1.4.2                    py37_1    defaults
pango                     1.42.4               h049681c_0    defaults
parso                     0.3.1                    py37_0    defaults
partd                     0.3.9                    py37_0    defaults
patchelf                  0.9                  he6710b0_3    defaults
path.py                   11.5.0                   py37_0    defaults
pathlib2                  2.3.3                    py37_0    defaults
patsy                     0.5.1                    py37_0    defaults
pcre                      8.42                 h439df22_0    defaults
pep8                      1.7.1                    py37_0    defaults
pexpect                   4.6.0                    py37_0    defaults
pickleshare               0.7.5                    py37_0    defaults
pillow                    5.3.0            py37h34e0f95_0    defaults
pip                       18.1                     py37_0    defaults
pixman                    0.34.0               hceecf20_3    defaults
pkginfo                   1.4.2                    py37_1    defaults
pluggy                    0.8.0                    py37_0    defaults
ply                       3.11                     py37_0    defaults
prometheus_client         0.5.0                    py37_0    defaults
prompt_toolkit            2.0.7                    py37_0    defaults
psutil                    5.4.8            py37h7b6447c_0    defaults
ptyprocess                0.6.0                    py37_0    defaults
py                        1.7.0                    py37_0    defaults
py-lief                   0.9.0            py37h7725739_1    defaults
pycodestyle               2.4.0                    py37_0    defaults
pycosat                   0.6.3            py37h14c3975_0    defaults
pycparser                 2.19                     py37_0    defaults
pycrypto                  2.6.1            py37h14c3975_9    defaults
pycurl                    7.43.0.2         py37h1ba5d50_0    defaults
pyflakes                  2.0.0                    py37_0    defaults
pygments                  2.3.1                    py37_0    defaults
pylint                    2.2.2                    py37_0    defaults
pyodbc                    4.0.25           py37he6710b0_0    defaults
pyopenssl                 18.0.0                   py37_0    defaults
pyparsing                 2.3.0                    py37_0    defaults
pyqt                      5.9.2            py37h05f1152_2    defaults
pysocks                   1.6.8                    py37_0    defaults
pytables                  3.4.4            py37ha205bf6_0    defaults
pytest                    4.0.2                    py37_0    defaults
pytest-arraydiff          0.3              py37h39e3cac_0    defaults
pytest-astropy            0.5.0                    py37_0    defaults
pytest-doctestplus        0.2.0                    py37_0    defaults
pytest-openfiles          0.3.1                    py37_0    defaults
pytest-remotedata         0.3.1                    py37_0    defaults
python                    3.7.1                h0371630_7    defaults
python-dateutil           2.7.5                    py37_0    defaults
python-libarchive-c       2.8                      py37_6    defaults
pytz                      2018.7                   py37_0    defaults
pywavelets                1.0.1            py37hdd07704_0    defaults
pyyaml                    3.13             py37h14c3975_0    defaults
pyzmq                     17.1.2           py37h14c3975_0    defaults
qt                        5.9.7                h5867ecd_1    defaults
qtawesome                 0.5.3                    py37_0    defaults
qtconsole                 4.4.3                    py37_0    defaults
qtpy                      1.5.2                    py37_0    defaults
readline                  7.0                  h7b6447c_5    defaults
requests                  2.21.0                   py37_0    defaults
rope                      0.11.0                   py37_0    defaults
ruamel_yaml               0.15.46          py37h14c3975_0    defaults
scikit-image              0.14.1           py37he6710b0_0    defaults
scikit-learn              0.20.1           py37hd81dba3_0    defaults
scipy                     1.1.0            py37h7c811a0_2    defaults
seaborn                   0.9.0                    py37_0    defaults
secretstorage             3.1.0                    py37_0    defaults
send2trash                1.5.0                    py37_0    defaults
setuptools                40.6.3                   py37_0    defaults
simplegeneric             0.8.1                    py37_2    defaults
singledispatch            3.4.0.3                  py37_0    defaults
sip                       4.19.8           py37hf484d3e_0    defaults
six                       1.12.0                   py37_0    defaults
snappy                    1.1.7                hbae5bb6_3    defaults
snowballstemmer           1.2.1                    py37_0    defaults
sortedcollections         1.0.1                    py37_0    defaults
sortedcontainers          2.1.0                    py37_0    defaults
sphinx                    1.8.2                    py37_0    defaults
sphinxcontrib             1.0                      py37_1    defaults
sphinxcontrib-websupport  1.1.0                    py37_1    defaults
spyder                    3.3.2                    py37_0    defaults
spyder-kernels            0.3.0                    py37_0    defaults
sqlalchemy                1.2.15           py37h7b6447c_0    defaults
sqlite                    3.26.0               h7b6447c_0    defaults
statsmodels               0.9.0            py37h035aef0_0    defaults
sympy                     1.3                      py37_0    defaults
tblib                     1.3.2                    py37_0    defaults
terminado                 0.8.1                    py37_1    defaults
testpath                  0.4.2                    py37_0    defaults
tk                        8.6.8                hbc83047_0    defaults
toolz                     0.9.0                    py37_0    defaults
tornado                   5.1.1            py37h7b6447c_0    defaults
tqdm                      4.28.1           py37h28b3542_0    defaults
traitlets                 4.3.2                    py37_0    defaults
unicodecsv                0.14.1                   py37_0    defaults
unixodbc                  2.3.7                h14c3975_0    defaults
urllib3                   1.24.1                   py37_0    defaults
wcwidth                   0.1.7                    py37_0    defaults
webencodings              0.5.1                    py37_1    defaults
werkzeug                  0.14.1                   py37_0    defaults
wheel                     0.32.3                   py37_0    defaults
widgetsnbextension        3.4.2                    py37_0    defaults
wrapt                     1.10.11          py37h14c3975_2    defaults
wurlitzer                 1.0.2                    py37_0    defaults
xlrd                      1.2.0                    py37_0    defaults
xlsxwriter                1.1.2                    py37_0    defaults
xlwt                      1.3.0                    py37_0    defaults
xz                        5.2.4                h14c3975_4    defaults
yaml                      0.1.7                had09818_2    defaults
zeromq                    4.2.5                hf484d3e_1    defaults
zict                      0.1.3                    py37_0    defaults
zlib                      1.2.11               h7b6447c_3    defaults
zstd                      1.3.7                h0b5b093_0    defaults
@kangkang59812
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I have the same question on Mac. Disconnect the wifi , then starting the anaconda will be ok.

@actevlin
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Author

Thanks, I'll play with that in the morning. Curiously, everything works on my machine with wifi but doesn't on my machine with a copper connection...

@Andr1u5
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Andr1u5 commented Jul 6, 2019 •
edited

I had this X11 issue on Ubuntu. I am working on a laptop connected to 32:9 resolution 5120x1440. I only use the external monitor and anaconda-navigator was failing to launch. You have to disable high DPI scaling on anaconda. I had to disconnect the external monitor and just run built-in ---> Launch anaconda-navigator which then launches without any issues go to preferences CTRL+P and de-select Enable high DPI scaling. Hope this resolves your issue.

@drmuelr
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drmuelr commented Jul 8, 2020

I had this X11 issue on Ubuntu. I am working on a laptop connected to 32:9 resolution 5120x1440. I only use the external monitor and anaconda-navigator was failing to launch. You have to disable high DPI scaling on anaconda. I had to disconnect the external monitor and just run built-in ---> Launch anaconda-navigator which then launches without any issues go to preferences CTRL+P and de-select Enable high DPI scaling. Hope this resolves your issue.

I had the exact same issue on RHEL7, also using a 5120x1440 monitor; except I'm on a desktop with no built-in screen. Since disconnecting the external monitor wasn't an option for me, I changed my display resolution to 2560x1440 and tried Anaconda again.

After doing that, the Anaconda navigator started up just fine, and the steps given by @Andr1u5 worked perfectly.

@drmuelr
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drmuelr commented Aug 8, 2020 •
edited

I just encountered an identical error when creating a plot with matplotlib.

I found a comment on a closed issue

After finding this out, I found a closed issue and running with
QT_AUTO_SCREEN_SCALE_FACTOR=0 cantata

It works as expected.

This solution also worked for me, and seems directly related to the 2 previous comments, the latter of which was me.

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@csoja @drmuelr @kangkang59812 @actevlin @Andr1u5