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matplotlib qt/swarst errors with anaconda 5.1.0 python2.7 #9229

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kadrlica opened this issue Apr 24, 2018 · 12 comments
Closed

matplotlib qt/swarst errors with anaconda 5.1.0 python2.7 #9229

kadrlica opened this issue Apr 24, 2018 · 12 comments

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@kadrlica
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Actual Behavior

Several warnings and errors are printed when creating interactive figures with matplotlib using the root of a fresh Anaconda 5.1.0 install. This only happens when the matplotlib backend is set to qt5agg (tkagg yields silent success).

Expected Behavior

Figures should be created silently.

Steps to Reproduce

From the Anaconda 5.1.0 root:

> python -c "import pylab as plt; plt.ion(); plt.figure()"
libGL error: No matching fbConfigs or visuals found
libGL error: failed to load driver: swrast
Anaconda or Miniconda version:

Anaconda 5.1.0

Operating System:

Scientific Linux 6.4

conda info
     active environment : None
       user config file : /home/s1/kadrlica/.condarc
 populated config files : /home/s1/kadrlica/.condarc
          conda version : 4.5.1
    conda-build version : 3.4.1
         python version : 2.7.14.final.0
       base environment : /home/s1/kadrlica/software/anaconda/anaconda2-5.1.0  (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/s1/kadrlica/software/anaconda/anaconda2-5.1.0/pkgs
                          /home/s1/kadrlica/.conda/pkgs
       envs directories : /home/s1/kadrlica/software/anaconda/anaconda2-5.1.0/envs
                          /home/s1/kadrlica/.conda/envs
               platform : linux-64
             user-agent : conda/4.5.1 requests/2.18.4 CPython/2.7.14 Linux/2.6.32-696.20.1.el6.x86_64 scientificfermi/6.4 glibc/2.12
                UID:GID : 47737:9620
             netrc file : /home/s1/kadrlica/.netrc
           offline mode : False
conda list --show-channel-urls
# packages in environment at /home/s1/kadrlica/software/anaconda/anaconda2-5.1.0:
#
# Name                    Version                   Build  Channel
_ipyw_jlab_nb_ext_conf    0.1.0            py27h08a7f0c_0    defaults
alabaster                 0.7.10           py27he5a193a_0    defaults
anaconda                  5.1.0                    py27_2    defaults
anaconda-client           1.6.9                    py27_0    defaults
anaconda-navigator        1.7.0                    py27_0    defaults
anaconda-project          0.8.2            py27h236b58a_0    defaults
asn1crypto                0.24.0                   py27_0    defaults
astroid                   1.6.1                    py27_0    defaults
astropy                   2.0.3            py27h14c3975_0    defaults
attrs                     17.4.0                   py27_0    defaults
babel                     2.5.3                    py27_0    defaults
backports                 1.0              py27h63c9359_1    defaults
backports.functools_lru_cache 1.4              py27he8db605_1    defaults
backports.shutil_get_terminal_size 1.0.0            py27h5bc021e_2    defaults
backports_abc             0.5              py27h7b3c97b_0    defaults
beautifulsoup4            4.6.0            py27h3f86ba9_1    defaults
bitarray                  0.8.1            py27h14c3975_1    defaults
bkcharts                  0.2              py27h241ae91_0    defaults
blaze                     0.11.3           py27h5f341da_0    defaults
bleach                    2.1.2                    py27_0    defaults
bokeh                     0.12.13          py27h5233db4_0    defaults
boto                      2.48.0           py27h9556ac2_1    defaults
bottleneck                1.2.1            py27h21b16a3_0    defaults
bzip2                     1.0.6                h9a117a8_4    defaults
ca-certificates           2017.08.26           h1d4fec5_0    defaults
cairo                     1.14.12              h77bcde2_0    defaults
cdecimal                  2.3              py27h14c3975_3    defaults
certifi                   2018.1.18                py27_0    defaults
cffi                      1.11.4           py27h9745a5d_0    defaults
chardet                   3.0.4            py27hfa10054_1    defaults
click                     6.7              py27h4225b90_0    defaults
cloudpickle               0.5.2                    py27_1    defaults
clyent                    1.2.2            py27h7276e6c_1    defaults
colorama                  0.3.9            py27h5cde069_0    defaults
conda                     4.5.1                    py27_0    defaults
conda-build               3.4.1                    py27_0    defaults
conda-env                 2.6.0                h36134e3_1    defaults
conda-verify              2.0.0            py27hf052a9d_0    defaults
configparser              3.5.0            py27h5117587_0    defaults
contextlib2               0.5.5            py27hbf4c468_0    defaults
cryptography              2.1.4            py27h6697b16_0    defaults
curl                      7.58.0               h84994c4_0    defaults
cycler                    0.10.0           py27hc7354d3_0    defaults
cython                    0.27.3           py27hc56b35e_0    defaults
cytoolz                   0.9.0            py27h14c3975_0    defaults
dask                      0.16.1                   py27_0    defaults
dask-core                 0.16.1                   py27_0    defaults
datashape                 0.5.4            py27hf507385_0    defaults
dbus                      1.12.2               hc3f9b76_1    defaults
decorator                 4.2.1                    py27_0    defaults
distributed               1.20.2                   py27_0    defaults
docutils                  0.14             py27hae222c1_0    defaults
entrypoints               0.2.3            py27h502b47d_2    defaults
enum34                    1.1.6            py27h99a27e9_1    defaults
et_xmlfile                1.0.1            py27h75840f5_0    defaults
expat                     2.2.5                he0dffb1_0    defaults
fastcache                 1.0.2            py27h14c3975_2    defaults
filelock                  2.0.13           py27h61a9c69_0    defaults
flask                     0.12.2           py27h6d5c1cd_0    defaults
flask-cors                3.0.3            py27h1a8a27f_0    defaults
fontconfig                2.12.4               h88586e7_1    defaults
freetype                  2.8                  hab7d2ae_1    defaults
funcsigs                  1.0.2            py27h83f16ab_0    defaults
functools32               3.2.3.2          py27h4ead58f_1    defaults
futures                   3.2.0            py27h7b459c0_0    defaults
get_terminal_size         1.0.0                haa9412d_0    defaults
gevent                    1.2.2            py27h475ea6a_0    defaults
glib                      2.53.6               h5d9569c_2    defaults
glob2                     0.6              py27hcea9cbd_0    defaults
gmp                       6.1.2                h6c8ec71_1    defaults
gmpy2                     2.0.8            py27h4cf3fa8_2    defaults
graphite2                 1.3.10               hf63cedd_1    defaults
greenlet                  0.4.12           py27hac09c53_0    defaults
grin                      1.2.1                    py27_4    defaults
gst-plugins-base          1.12.4               h33fb286_0    defaults
gstreamer                 1.12.4               hb53b477_0    defaults
h5py                      2.7.1            py27h2697762_0    defaults
harfbuzz                  1.7.4                hc5b324e_0    defaults
hdf5                      1.10.1               h9caa474_1    defaults
heapdict                  1.0.0                    py27_2    defaults
html5lib                  1.0.1            py27h5233db4_0    defaults
icu                       58.2                 h9c2bf20_1    defaults
idna                      2.6              py27h5722d68_1    defaults
imageio                   2.2.0            py27hf108a7f_0    defaults
imagesize                 0.7.1            py27hd17bf80_0    defaults
intel-openmp              2018.0.0             hc7b2577_8    defaults
ipaddress                 1.0.19                   py27_0    defaults
ipykernel                 4.8.0                    py27_0    defaults
ipython                   5.4.1                    py27_2    defaults
ipython_genutils          0.2.0            py27h89fb69b_0    defaults
ipywidgets                7.1.1                    py27_0    defaults
isort                     4.2.15           py27hcfa4749_0    defaults
itsdangerous              0.24             py27hb8295c1_1    defaults
jbig                      2.1                  hdba287a_0    defaults
jdcal                     1.3              py27h2cc5433_0    defaults
jedi                      0.11.1                   py27_0    defaults
jinja2                    2.10             py27h4114e70_0    defaults
jpeg                      9b                   h024ee3a_2    defaults
jsonschema                2.6.0            py27h7ed5aa4_0    defaults
jupyter                   1.0.0                    py27_4    defaults
jupyter_client            5.2.2                    py27_0    defaults
jupyter_console           5.2.0            py27hc6bee7e_1    defaults
jupyter_core              4.4.0            py27h345911c_0    defaults
jupyterlab                0.31.5                   py27_0    defaults
jupyterlab_launcher       0.10.2                   py27_0    defaults
lazy-object-proxy         1.3.1            py27h682c727_0    defaults
libcurl                   7.58.0               h1ad7b7a_0    defaults
libedit                   3.1                  heed3624_0    defaults
libffi                    3.2.1                hd88cf55_4    defaults
libgcc-ng                 7.2.0                h7cc24e2_2    defaults
libgfortran-ng            7.2.0                h9f7466a_2    defaults
libpng                    1.6.34               hb9fc6fc_0    defaults
libsodium                 1.0.15               hf101ebd_0    defaults
libssh2                   1.8.0                h9cfc8f7_4    defaults
libstdcxx-ng              7.2.0                h7a57d05_2    defaults
libtiff                   4.0.9                h28f6b97_0    defaults
libtool                   2.4.6                h544aabb_3    defaults
libxcb                    1.12                 hcd93eb1_4    defaults
libxml2                   2.9.7                h26e45fe_0    defaults
libxslt                   1.1.32               h1312cb7_0    defaults
llvmlite                  0.21.0           py27h6dad3f9_0    defaults
locket                    0.2.0            py27h73929a2_1    defaults
lxml                      4.1.1            py27hf71bdeb_1    defaults
lzo                       2.10                 h49e0be7_2    defaults
markupsafe                1.0              py27h97b2822_1    defaults
matplotlib                2.1.2            py27h0e671d2_0    defaults
mccabe                    0.6.1            py27h0e7c7be_1    defaults
mistune                   0.8.3                    py27_0    defaults
mkl                       2018.0.1             h19d6760_4    defaults
mkl-service               1.1.2            py27hb2d42c5_4    defaults
mpc                       1.0.3                hec55b23_5    defaults
mpfr                      3.1.5                h11a74b3_2    defaults
mpmath                    1.0.0            py27h9669132_2    defaults
msgpack-python            0.5.1            py27h6bb024c_0    defaults
multipledispatch          0.4.9            py27h9b5f95a_0    defaults
navigator-updater         0.1.0            py27h0f9cd39_0    defaults
nbconvert                 5.3.1            py27he041f76_0    defaults
nbformat                  4.4.0            py27hed7f2b2_0    defaults
ncurses                   6.0                  h9df7e31_2    defaults
networkx                  2.1                      py27_0    defaults
nltk                      3.2.5            py27hec5f4de_0    defaults
nose                      1.3.7            py27heec2199_2    defaults
notebook                  5.4.0                    py27_0    defaults
numba                     0.36.2          np114py27he2868da_0    defaults
numexpr                   2.6.4            py27hd318778_0    defaults
numpy                     1.14.0           py27h3dfced4_1    defaults
numpydoc                  0.7.0            py27h9647a75_0    defaults
odo                       0.5.1            py27h9170de3_0    defaults
olefile                   0.45.1                   py27_0    defaults
openpyxl                  2.4.10                   py27_0    defaults
openssl                   1.0.2o               h20670df_0    defaults
packaging                 16.8             py27h5e07c7c_1    defaults
pandas                    0.22.0           py27hf484d3e_0    defaults
pandoc                    1.19.2.1             hea2e7c5_1    defaults
pandocfilters             1.4.2            py27h428e1e5_1    defaults
pango                     1.41.0               hd475d92_0    defaults
parso                     0.1.1            py27h718acc2_0    defaults
partd                     0.3.8            py27h4e55004_0    defaults
patchelf                  0.9                  hf79760b_2    defaults
path.py                   10.5             py27hefe4bee_0    defaults
pathlib2                  2.3.0            py27h6e9d198_0    defaults
patsy                     0.5.0                    py27_0    defaults
pcre                      8.41                 hc27e229_1    defaults
pep8                      1.7.1                    py27_0    defaults
pexpect                   4.3.1                    py27_0    defaults
pickleshare               0.7.4            py27h09770e1_0    defaults
pillow                    5.0.0            py27h3deb7b8_0    defaults
pip                       9.0.1            py27ha730c48_4    defaults
pixman                    0.34.0               hceecf20_3    defaults
pkginfo                   1.4.1            py27hee1a9ad_1    defaults
pluggy                    0.6.0            py27h1f4f128_0    defaults
ply                       3.10             py27hd6d9ae5_0    defaults
prompt_toolkit            1.0.15           py27h1b593e1_0    defaults
psutil                    5.4.3            py27h14c3975_0    defaults
ptyprocess                0.5.2            py27h4ccb14c_0    defaults
py                        1.5.2            py27h203d672_0    defaults
pycairo                   1.15.4           py27h1b9232e_1    defaults
pycodestyle               2.3.1            py27h904819d_0    defaults
pycosat                   0.6.3            py27ha4109ae_0    defaults
pycparser                 2.18             py27hefa08c5_1    defaults
pycrypto                  2.6.1            py27h14c3975_7    defaults
pycurl                    7.43.0.1         py27hb7f436b_0    defaults
pyflakes                  1.6.0            py27h904a57d_0    defaults
pygments                  2.2.0            py27h4a8b6f5_0    defaults
pylint                    1.8.2                    py27_0    defaults
pyodbc                    4.0.22           py27hf484d3e_0    defaults
pyopenssl                 17.5.0           py27hcee3be0_0    defaults
pyparsing                 2.2.0            py27hf1513f8_1    defaults
pyqt                      5.6.0            py27h4b1e83c_5    defaults
pysocks                   1.6.7            py27he2db6d2_1    defaults
pytables                  3.4.2            py27h1f7bffc_2    defaults
pytest                    3.3.2                    py27_0    defaults
python                    2.7.14              h1571d57_29    defaults
python-dateutil           2.6.1            py27h4ca5741_1    defaults
pytz                      2017.3           py27h001bace_0    defaults
pywavelets                0.5.2            py27hecda097_0    defaults
pyyaml                    3.12             py27h2d70dd7_1    defaults
pyzmq                     16.0.3           py27hc579512_0    defaults
qt                        5.6.2               h974d657_12    defaults
qtawesome                 0.4.4            py27hd7914c3_0    defaults
qtconsole                 4.3.1            py27hc444b0d_0    defaults
qtpy                      1.3.1            py27h63d3751_0    defaults
readline                  7.0                  ha6073c6_4    defaults
requests                  2.18.4           py27hc5b0589_1    defaults
rope                      0.10.7           py27hfe459b0_0    defaults
ruamel_yaml               0.15.35          py27h14c3975_1    defaults
scandir                   1.6              py27hf7388dc_0    defaults
scikit-image              0.13.1           py27h14c3975_1    defaults
scikit-learn              0.19.1           py27h445a80a_0    defaults
scipy                     1.0.0            py27hf5f0f52_0    defaults
seaborn                   0.8.1            py27h633ea1e_0    defaults
send2trash                1.4.2                    py27_0    defaults
setuptools                38.4.0                   py27_0    defaults
simplegeneric             0.8.1                    py27_2    defaults
singledispatch            3.4.0.3          py27h9bcb476_0    defaults
sip                       4.18.1           py27he9ba0ab_2    defaults
six                       1.11.0           py27h5f960f1_1    defaults
snowballstemmer           1.2.1            py27h44e2768_0    defaults
sortedcollections         0.5.3            py27h135218e_0    defaults
sortedcontainers          1.5.9                    py27_0    defaults
sphinx                    1.6.6                    py27_0    defaults
sphinxcontrib             1.0              py27h1512b58_1    defaults
sphinxcontrib-websupport  1.0.1            py27hf906f22_1    defaults
spyder                    3.2.6                    py27_0    defaults
sqlalchemy                1.2.1            py27h14c3975_0    defaults
sqlite                    3.22.0               h1bed415_0    defaults
ssl_match_hostname        3.5.0.1          py27h4ec10b9_2    defaults
statsmodels               0.8.0            py27hc87d62d_0    defaults
subprocess32              3.2.7            py27h373dbce_0    defaults
sympy                     1.1.1            py27hc28188a_0    defaults
tblib                     1.3.2            py27h51fe5ba_0    defaults
terminado                 0.8.1                    py27_1    defaults
testpath                  0.3.1            py27hc38d2c4_0    defaults
tk                        8.6.7                hc745277_3    defaults
toolz                     0.9.0                    py27_0    defaults
tornado                   4.5.3                    py27_0    defaults
traitlets                 4.3.2            py27hd6ce930_0    defaults
typing                    3.6.2            py27h66f49e2_0    defaults
unicodecsv                0.14.1           py27h5062da9_0    defaults
unixodbc                  2.3.4                hc36303a_1    defaults
urllib3                   1.22             py27ha55213b_0    defaults
wcwidth                   0.1.7            py27h9e3e1ab_0    defaults
webencodings              0.5.1            py27hff10b21_1    defaults
werkzeug                  0.14.1                   py27_0    defaults
wheel                     0.30.0           py27h2bc6bb2_1    defaults
widgetsnbextension        3.1.0                    py27_0    defaults
wrapt                     1.10.11          py27h04f6869_0    defaults
xlrd                      1.1.0            py27ha77178f_1    defaults
xlsxwriter                1.0.2            py27h12cbc6b_0    defaults
xlwt                      1.3.0            py27h3d85d97_0    defaults
xz                        5.2.3                h55aa19d_2    defaults
yaml                      0.1.7                had09818_2    defaults
zeromq                    4.2.2                hbedb6e5_2    defaults
zict                      0.1.3            py27h12c336c_0    defaults
zlib                      1.2.11               ha838bed_2    defaults
@kadrlica
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Author

Follow-up... creating a simple environment for matplotlib yields the same problem, with the addition of a missing XDG_RUNTIME_DIR. I've also turned on LIBGL_DEBUG for more info:

> export LIBGL_DEBUG=verbose
> conda create -n mpl python=2.7 matplotlib=2.2.2
> conda activate mpl
> python -c "import pylab as plt; plt.ion(); plt.figure()"
QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to '/tmp/kadrlica/runtime-kadrlica'
libGL: OpenDriver: trying /usr/lib64/dri/tls/swrast_dri.so
libGL: OpenDriver: trying /usr/lib64/dri/swrast_dri.so
libGL: Can't open configuration file /home/s1/kadrlica/.drirc: No such file or directory.
libGL: Can't open configuration file /home/s1/kadrlica/.drirc: No such file or directory.
libGL error: No matching fbConfigs or visuals found
libGL error: failed to load driver: swrast

@mingwandroid
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Can you test with newer packages please?

To not disrupt your existing stuff:

conda create -n latest qt python=2 matplotlib

@mingwandroid
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mingwandroid commented Apr 24, 2018 •
edited
Loading

Sorry I missed your follow up. Do you have Mesa installed? Can you give me as much details about your distro as possible including installed packages?

Do simple opengl tests work ok (glxgears for example)? Can you install mesa-utils and paste the output of glxinfo please?

@kadrlica
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kadrlica commented Apr 24, 2018 •
edited
Loading

I'll give mesa-utils a try. Is there a preferred channel? Doesn't appear to be available in defaults

conda create -n mpl python=2 matplotlib=2.2.2 mesa-utils
Solving environment: failed
PackagesNotFoundError: The following packages are not available from current channels:
  - mesa-utils

Some basic distro info:

> cat /etc/*-release
SB_VERSION=base-4.0-amd64:base-4.0-noarch:core-4.0-amd64:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-noarch
Scientific Linux Fermi release 6.4 (Ramsey)
Scientific Linux Fermi release 6.4 (Ramsey)
Installed packages:

rpm -qa
gridsite1.7-compat-1.7.29-5.el6.x86_64
jakarta-commons-logging-1.0.4-10.el6.noarch
OpenEXR-libs-1.6.1-8.1.el6.x86_64
dash-0.5.5.1-4.el6.x86_64
gnutls-2.12.23-21.el6.x86_64
librsvg2-2.26.0-14.el6.x86_64
poppler-data-0.4.0-1.el6.noarch
perl-XML-NamespaceSupport-1.10-3.el6.noarch
mingetty-1.08-5.el6.x86_64
mesa-dri-drivers-11.0.7-4.el6.x86_64
boost-program-options-1.41.0-15.el6_4.x86_64
microcode_ctl-1.17-25.4.el6_9.x86_64
ustr-1.0.4-9.1.el6.x86_64
yum-plugin-security-1.1.30-40.el6.noarch
nfs-utils-lib-1.1.5-6.el6.x86_64
joda-time-1.5.2-7.2.tzdata2008d.osg33.el6.noarch
libstdc++-4.4.7-3.el6.x86_64
jakarta-commons-cli-1.1-5.el6.x86_64
libxml2-2.7.6-21.el6_8.1.x86_64
udev-147-2.46.el6.x86_64
libXrender-devel-0.9.10-1.el6.x86_64
libacl-2.2.49-6.el6.x86_64
kernel-firmware-2.6.32-696.20.1.el6.noarch
xcb-util-0.4.0-2.2.el6.x86_64
compat-libgfortran-41-4.1.2-39.el6.x86_64
sed-4.2.1-10.el6.x86_64
tzdata-2018d-1.el6.noarch
libICE-1.0.6-1.el6.i686
libblkid-2.17.2-12.9.el6.x86_64
xrootd-client-libs-4.8.0-2.osg33.el6.x86_64
wireless-tools-29-5.1.1.el6.x86_64
libsysfs-2.1.0-7.el6.x86_64
edg-gridftp-client-1.2.9.2-3.osg.el6.x86_64
python-libs-2.6.6-66.el6_8.x86_64
iptables-ipv6-1.4.7-9.el6.x86_64
check_mk-agent-1.1.10b2-1.noarch
dbus-1.2.24-7.el6_3.x86_64
newt-python-0.52.11-3.el6.x86_64
dmz-cursor-themes-0.4-4.el6.noarch
tar-1.23-11.el6.x86_64
perl-Crypt-SSLeay-0.57-16.el6.x86_64
lynx-2.8.6-27.el6.x86_64
pygpgme-0.1-18.20090824bzr68.el6.x86_64
gnome-terminal-2.31.3-8.el6.x86_64
libtasn1-2.3-6.el6_5.x86_64
pixman-0.32.4-4.el6.x86_64
pycairo-1.8.6-2.1.el6.x86_64
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rfkill-0.3-4.el6.x86_64
smp_utils-0.94-4.el6.x86_64
libfprint-0.1.0-19.pre2.el6.x86_64
perl-Archive-Tar-1.58-130.el6_4.x86_64
finger-0.17-39.el6.x86_64
gnome-utils-libs-2.28.1-10.el6.x86_64
globus-gssapi-error-5.5-1.osg33.el6.x86_64
p11-kit-trust-0.18.5-2.el6.x86_64
cigetcert-1.16-2.el6.noarch
bzip2-devel-1.0.5-7.el6_0.x86_64
tree-1.5.3-2.el6.x86_64
atmel-firmware-1.3-7.el6.noarch
netpbm-progs-10.47.05-11.el6.x86_64
globus-gass-transfer-8.10-1.osg33.el6.x86_64
ql23xx-firmware-3.03.27-3.1.el6.noarch
texlive-texmf-errata-dvips-2007-7.1.el6.noarch
globus-proxy-utils-6.19-1.osg33.el6.x86_64
perl-XML-Parser-2.36-7.el6.x86_64
krb5-devel-1.10.3-42z1.el6_7.x86_64
libyaml-0.1.3-4.el6_6.x86_64
keyutils-libs-1.4-4.el6.i686
tex-preview-11.85-10.el6.noarch
canl-c-2.1.8-1.el6.x86_64
ppl-0.10.2-11.el6.x86_64
libtalloc-2.1.5-1.el6_7.x86_64
libX11-common-1.6.4-3.el6.noarch
libgpg-error-devel-1.7-4.el6.x86_64
ruby-shadow-1.4.1-13.el6.x86_64
cvmfs-config-osg-2.0-1.osg33.el6.noarch
MAKEDEV-3.24-6.el6.x86_64
libX11-1.6.4-3.el6.x86_64
MySQL-python-1.2.3-0.3.c1.1.el6.x86_64
lfc-1.9.2-1.el6.x86_64
pinentry-0.7.6-6.el6.x86_64
m17n-lib-1.5.5-2.el6_1.1.x86_64
java-1.5.0-gcj-1.5.0.0-29.1.el6.x86_64
iftop-1.0-0.14.pre4.el6.x86_64
ed-1.1-3.3.el6.x86_64

@mingwandroid
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mesa is a system package that should be provided with your distribution. It is a software OpenGL renderer (more or less, it also supports some hardware rendering for some GPU and driver combinations).

@kadrlica
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kadrlica commented Apr 24, 2018 •
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Ok, so I see several mesa and dri mentions in the installed package list above. However, glxinfo is not found. Some kind of system configuration issue?

Do simple opengl tests work ok (glxgears for example)? Can you install mesa-utils and paste the output of glxinfo please?

I've tried building the environment with mesa from defaults and mesalib from conda-forge (also explicitly requesting pyopengl). Neither has had a noticeable effect. Also, neither has provided access to glxinfo (command not found).

Aside: While I get the libGL error: the matplotlib figure window does pop up. So while the error is probably symptomatic of some deeper problem, I would be reasonably happy with a hack to silence the error messages.

@kadrlica
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I'm installing on a remote machine and forwarding X windows through an ssh session. Could that be related?

@mingwandroid
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I wouldn't mix conda-forge and Anaconda Distribution defaults packages in the same env.

Yes, doing tricky things with X forwarding can cause additional issues.

So while the error is probably symptomatic of some deeper problem, I would be reasonably happy with a hack to silence the error messages.

Why not just ignore it if it's not harmful?

@mingwandroid
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No, it's probably not symptomatic of very much except perhaps that we try to support a vast range of Linux distributions and there will always be some limits to what we can do. This text is printed because you are using an old distro with some hardware and/or driver mismatch and the text is printed not by the Anaconda Distribution but by your linux distribution.

@kadrlica
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kadrlica commented Apr 24, 2018 •
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I wouldn't mix conda-forge and Anaconda Distribution defaults packages in the same env.

Agreed.

Why not just ignore it if it's not harmful?

This is an install for a group of users. I think these error messages would lead to a lot of confusion, and would add noise to any scripted output. This doesn't seem like an uncommon issue (i.e., openai/gym#509), but I guess the proposed solution is either a distro update or a change to the backend (i.e., tkagg)?

As a followup, the error is not printed with an install of matplotlib=2.0.0. Both are using the same system libraries and the qt5agg backend, so any idea of what has changed?

$ conda create -y -n mpl-2.0.0 python=2 matplotlib=2.0.0
Solving environment: done

## Package Plan ##
  environment location: /home/s1/kadrlica/software/anaconda/anaconda2-5.1.0/envs/mpl-2.0.0

  added / updated specs: 
    - matplotlib=2.0.0
    - python=2

The following NEW packages will be INSTALLED:
    ca-certificates:  2018.03.07-0          
    cairo:            1.14.8-0              
    certifi:          2018.4.16-py27_0      
    cycler:           0.10.0-py27hc7354d3_0 
    dbus:             1.13.2-h714fa37_1     
    expat:            2.2.5-he0dffb1_0      
    fontconfig:       2.12.1-3              
    freetype:         2.5.5-2               
    functools32:      3.2.3.2-py27h4ead58f_1
    glib:             2.56.1-h000015b_0     
    gst-plugins-base: 1.14.0-hbbd80ab_1     
    gstreamer:        1.14.0-hb453b48_1     
    icu:              54.1-0                
    intel-openmp:     2018.0.0-8            
    jpeg:             9b-h024ee3a_2         
    libedit:          3.1-heed3624_0        
    libffi:           3.2.1-hd88cf55_4      
    libgcc:           7.2.0-h69d50b8_2      
    libgcc-ng:        7.2.0-hdf63c60_3      
    libgfortran-ng:   7.2.0-hdf63c60_3      
    libiconv:         1.14-0                
    libpng:           1.6.34-hb9fc6fc_0     
    libstdcxx-ng:     7.2.0-hdf63c60_3      
    libxcb:           1.13-h1bed415_1       
    libxml2:          2.9.4-0               
    matplotlib:       2.0.0-np112py27_0     
    mkl:              2018.0.2-1            
    ncurses:          6.0-h9df7e31_2        
    numpy:            1.12.1-py27h9378851_1 
    openssl:          1.0.2o-h20670df_0     
    pcre:             8.42-h439df22_0       
    pip:              9.0.3-py27_0          
    pixman:           0.34.0-hceecf20_3     
    pycairo:          1.13.3-py27hea6d626_0 
    pyparsing:        2.2.0-py27hf1513f8_1  
    pyqt:             5.6.0-py27h4b1e83c_5  
    python:           2.7.14-h1571d57_31    
    python-dateutil:  2.7.2-py27_0          
    pytz:             2018.4-py27_0         
    qt:               5.6.2-5               
    readline:         7.0-ha6073c6_4        
    setuptools:       39.0.1-py27_0         
    sip:              4.18.1-py27he9ba0ab_2 
    six:              1.11.0-py27h5f960f1_1 
    sqlite:           3.23.1-he433501_0     
    subprocess32:     3.2.7-py27h373dbce_0  
    tk:               8.6.7-hc745277_3      
    wheel:            0.31.0-py27_0         
    xz:               5.2.3-h55aa19d_2      
    zlib:             1.2.11-ha838bed_2     

...

$ conda activate mpl-2.0.0
(mpl-2.0.0) $ python -c "import pylab as plt; plt.ion(); plt.figure()"
(mpl-2.0.0) $

@mingwandroid
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any idea of what has changed?

Yes, we updated qt from 5.6.2 (released 12th October 2016) to 5.9.5 (released 12th April 2018). Such a major update to an application framework with advanced GUI capabilities brings in more complex rendering requirements that your underlying distro may not support very well (and in this case your distro has decided to warn you about that).

Programmers decide based on essentially a completely arbitrary basis what to warn about and what not to warn about and when you have something like this that cuts across developers for distros, graphics drivers and OpenGL drivers there's no way to hope for things to be perfectly silent on all possible combinations.

Maybe you can redirect this output to /dev/null via a script?

Closing as there's nothing for us to do here.

@kadrlica
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kadrlica commented Apr 24, 2018 •
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Thanks for the help and explanation!

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