[Matplotlib-users] TkAgg won't plot - how to debug?

Andrew Z formisc at gmail.com
Mon Nov 6 18:33:40 EST 2017 

this is what i have installed:
[az at hp src]$ rpm -qa | grep tkint
python3-tkinter-3.5.3-6.fc24.x86_64
tkinter-2.7.13-2.fc24.x86_64
[az at hp src]$


[az at hp src]$ pip3 list | grep tk
DEPRECATION: The default format will switch to columns in the future. You
can use --format=(legacy|columns) (or define a format=(legacy|columns) in
your pip.conf under the [list] section) to disable this warning.


rpm -qa | grep matplot
python-matplotlib-data-fonts-1.5.2-0.1.rc2.fc24.noarch
python3-matplotlib-1.5.2-0.1.rc2.fc24.x86_64
python3-matplotlib-tk-1.5.2-0.1.rc2.fc24.x86_64
python-matplotlib-data-1.5.2-0.1.rc2.fc24.noarch

basically i removed the pip3 installed matplot and felt back to rpm
provided in hope to have that config working.

Copy/paste from
https://matplotlib.org/gallery/pyplots/pyplot_simple.html#sphx-glr-gallery-pyplots-pyplot-simple-py
[az at hp src]$ which python3.5
/usr/bin/python3.5
[az at hp src]$ file /usr/bin/python3.5
/usr/bin/python3.5: ELF 64-bit LSB shared object, x86-64, version 1 (SYSV),
dynamically linked, interpreter /lib64/ld-linux-x86-64.so.2, for GNU/Linux
2.6.32, BuildID[sha1]=cc90b759ab34ba1043b3a96779f17eba4c0baf7a, stripped
[az at hp src]$
[az at hp src]$ python3.5
Python 3.5.3 (default, May 11 2017, 09:10:41)
[GCC 6.3.1 20161221 (Red Hat 6.3.1-1)] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import matplotlib.pyplot as plt
>>> plt.plot([1,2,3,4])
<hangs with one core 100% busy>
Terminated
[az at hp src]$
[az at hp src]$
[az at hp src]$ python3.5
Python 3.5.3 (default, May 11 2017, 09:10:41)
[GCC 6.3.1 20161221 (Red Hat 6.3.1-1)] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import matplotlib.pyplot as plt
>>> import matplotlib
>>> matplotlib.get_backend()
'TkAgg'
>>> exit
Use exit() or Ctrl-D (i.e. EOF) to exit

removing TKagg from config:
[az at hp src]$ find / -name matplotlibrc* 2>>/dev/null
/etc/matplotlibrc
[az at hp src]$ grep -v ^# /etc/matplotlibrc
backend      : TkAgg

changing to Agg and running the same code:

[az at hp src]$ python3.5
Python 3.5.3 (default, May 11 2017, 09:10:41)
[GCC 6.3.1 20161221 (Red Hat 6.3.1-1)] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import matplotlib
>>> matplotlib.get_backend()
'agg'
>>> import matplotlib.pyplot as plt
>>> plt.ylabel('some numbers')
^C^Z
[1]+  Stopped                 python3.5

[az at hp src]$ python3.5
Python 3.5.3 (default, May 11 2017, 09:10:41)
[GCC 6.3.1 20161221 (Red Hat 6.3.1-1)] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import matplotlib.pyplot as plt
>>> plt.plot([1,2,3,4])
<Hangs>

I'll stop making any changes to the env now, since i don't want to bring
any confusion into the matter.
thank you for helping out!








On Mon, Nov 6, 2017 at 4:48 PM, Andrew Z <formisc at gmail.com> wrote:

>
> >backend in your matplotlibrc file to "agg" and it still hung on you?
>
> Yes. I can confirm that
>
> >Some possibilities are
> >...."matplotlib.py" or "pylab.py" or some such, and then start to wonder
> why their code doesn't work properly.
>
> I used pycharms "scratch files" and typed directly in the interpreter-
> always same result. I saw this naming issue whileresearching my problem. My
> file is plot.py and works perfectly fine on any other machine but
> this.(drives me mad, honestly). Directory is /home/az/work/nja/src. Also
> consistent across machines (minus username)
>
> >Have you looked to see if there are other programs that are running
> during the import stage?
>
> Im not sure what do you mean?
> I have a xwindow terminal , nothing but Firefox is up.(well a tons of
> regular background processes).
>
>
>
>
> On Nov 6, 2017 16:18, "Benjamin Root" <ben.v.root at gmail.com> wrote:
>
>> Just to make absolutely clear, you set the default backend in your
>> matplotlibrc file to "agg" and it still hung on you? If that is the case,
>> then the problem isn't tkinter.
>>
>> Some possibilities are
>>
>> 1) a massive font database that matplotlib is trying to build a cache for
>> 2) import of matplotlib from somewhere else unexpected (which would
>> explain pycharm's behavior), and that file/module is misbehaving. We have
>> seen instances in the past where users would name their plotting porting of
>> their code "matplotlib.py" or "pylab.py" or some such, and then start to
>> wonder why their code doesn't work properly.
>>
>> Have you looked to see if there are other programs that are running
>> during the import stage? One thing matplotlib does for the first import is
>> to create a font cache, and it does this by using some fc-list program,
>> iirc. This can take a long time on some machines that have adobe's font
>> collection installed, for example, but that is usually a Windows thing....
>>
>> Ben Root
>>
>>
>> On Mon, Nov 6, 2017 at 4:09 PM, Andrew Z <formisc at gmail.com> wrote:
>>
>>> Tkinter was most likely installed as part of rpm install.
>>> Backends - not really. I do know that with mpld3and agg  the scripts
>>> hang.
>>> Ihave reinstalled matplot using rpm ( rpm comes only in 1.5 version) and
>>> with pip3.
>>> Today i tried on the office machine (fedora 25). Rpm brings only
>>> matplot1.5.
>>>
>>> maybe 2 installed locally using pip3 messes with 1.5 leftover or
>>> libraries.
>>> Not sure how to validate this idea though..
>>> Probably unrelated:
>>> In pycharm pyplot is not been recognized as part of matplotlib when i
>>> "import matplotlib.pyplot. yet the script doesnt crash on import
>>> statement...
>>>
>>>
>>>
>>>
>>>
>>> On Nov 6, 2017 15:13, "Benjamin Root" <ben.v.root at gmail.com> wrote:
>>>
>>> How did you install Tkinter? Have you tested any other backends? Does
>>> this happen for just the head-less "Agg" backend set as default?
>>>
>>> On Sat, Nov 4, 2017 at 3:35 PM, Andrew Z <formisc at gmail.com> wrote:
>>>
>>>> more relevant information:
>>>> [az at hp src]$ python3.5
>>>> Python 3.5.3 (default, May 11 2017, 09:10:41)
>>>> [GCC 6.3.1 20161221 (Red Hat 6.3.1-1)] on linux
>>>> Type "help", "copyright", "credits" or "license" for more information.
>>>> >>> import matplotlib
>>>> >>> matplotlib.__file__
>>>> '/home/az/.local/lib/python3.5/site-packages/matplotlib/__init__.py'
>>>> >>> matplotlib.get_configdir()
>>>> '/home/az/.config/matplotlib'
>>>> >>> print(matplotlib.__version__)
>>>> 2.1.0
>>>>
>>>> now if i get the simplest plot :
>>>>
>>>> [az at hp src]$ more ./main1.py
>>>> import matplotlib.pyplot as plt
>>>> print("imported")
>>>> plt.plot([1,2,4,1])
>>>> print("plot is done")
>>>> plt.show()
>>>> print("show is done")
>>>>
>>>> [az at hp src]$ python3.5 main1.py --verbose-debug
>>>> $HOME=/home/az
>>>> matplotlib data path /home/az/.local/lib/python3.5/
>>>> site-packages/matplotlib/mpl-data
>>>> loaded rc file /home/az/.local/lib/python3.5/
>>>> site-packages/matplotlib/mpl-data/matplotlibrc
>>>> matplotlib version 2.1.0
>>>> verbose.level debug
>>>> interactive is False
>>>> platform is linux
>>>> loaded modules: ['_locale', 'urllib.request', 'numpy.lib.shape_base',
>>>> 'numpy.matrixlib', 'ipaddress', 'hashlib', 'collections',
>>>> 'numpy.lib.financial', 'atexit', 'numpy.lib._iotools',
>>>> '_frozen_importlib_external', 'numpy.polynomial.chebyshev', 'six',
>>>> 'unittest.runner', '_sitebuiltins', 'numpy.compat', 'numpy.ma.core',
>>>> 'abrt_exception_handler3', 'codecs', 'sre_constants', 'calendar',
>>>> 'matplotlib.cbook', 'contextlib', 'heapq', 'ssl', 'dis', 'binascii',
>>>> 'posixpath', 'cython_runtime', 'traceback', 'numpy.polynomial.laguerre',
>>>> '_hashlib', 'zipimport', 'email.utils', '_functools', 'copyreg', 'sys',
>>>> '_sre', 'matplotlib.cbook._backports', 'numpy.lib.arraysetops', 'random',
>>>> 'email.parser', 'numpy.fft.helper', '_collections', 'difflib',
>>>> 'numpy.lib.scimath', 'unittest', '_sysconfigdata', 'numpy', 'site', '_ast',
>>>> 'json.scanner', 'os', 'http', 'functools', 'unittest.main', '
>>>> numpy.linalg.info', '_heapq', 'token', 'pathlib', 'tokenize',
>>>> 'cycler', 'encodings.cp437', 'numpy.polynomial.polynomial',
>>>> 'numpy.polynomial._polybase', 'numpy.lib.mixins', 'ctypes._endian',
>>>> 'numpy.lib.arraypad', 'numpy.matrixlib.defmatrix', 'distutils.version',
>>>> '_signal', 'marshal', 'stat', 'pprint', 'base64', 'logging', 'enum',
>>>> 'selectors', 'numpy.core', 'json.encoder', 'operator',
>>>> 'numpy.testing.nosetester', 'matplotlib._version', 'numpy.ctypeslib',
>>>> 'numpy.add_newdocs', 'unittest.util', '_weakref', 'select',
>>>> 'importlib._bootstrap_external', 'mtrand', 'importlib._bootstrap',
>>>> 'matplotlib.rcsetup', 'matplotlib.colors', 'numpy.testing.decorators',
>>>> 'json', 'numpy.core.machar', 'email.encoders', 'six.moves.urllib',
>>>> 'matplotlib', 'keyword', 'errno', 'numpy.lib.stride_tricks', '_socket',
>>>> 'email.quoprimime', 'numpy.ma.extras', 'numbers', 'numpy.version',
>>>> '_bisect', '_string', 'numpy.lib.arrayterator', 'numpy.core.umath',
>>>> 'numpy.lib', '_thread', 'time', '_frozen_importlib', 'numpy.core.info',
>>>> 'numpy.core.multiarray', 'math', '_opcode', 'urllib.parse',
>>>> 'distutils.sysconfig', 'ntpath', 'argparse', 'types', 'sre_compile',
>>>> 'glob', '__main__', 'email._encoded_words', 'socket', '_struct', '
>>>> numpy.fft.info', 'unittest.signals', 'numpy.lib.npyio', 'grp',
>>>> 'urllib.error', '_io', 'numpy._globals', 'gettext', 'numpy.compat.py3k',
>>>> 'distutils', 'email.charset', 'ast', 'numpy.lib.function_base', 'uu',
>>>> 'encodings', 'urllib', 'numpy.lib.twodim_base', 'encodings.latin_1',
>>>> 'tempfile', 'numpy.lib._version', 'numpy.polynomial.polyutils', 'quopri',
>>>> 'os.path', '_imp', 'email.base64mime', 'email.message', 'email.header',
>>>> 'opcode', 'encodings.utf_8', 'reprlib', '_stat', '_warnings',
>>>> 'email.feedparser', 'numpy.testing.utils', 'numpy.lib.utils',
>>>> 'genericpath', 'numpy.polynomial.hermite', '_compat_pickle', 'bz2',
>>>> '_compression', 'subprocess', '_json', 'numpy.lib.nanfunctions', 'inspect',
>>>> 'sysconfig', '_operator', 'shutil', 'pwd', 'warnings', '_ctypes',
>>>> '_random', 'email.iterators', '_collections_abc', '__future__', 'email',
>>>> 'numpy._distributor_init', 'unittest.loader', '_bootlocale',
>>>> 'numpy.core.records', 'fnmatch', '_posixsubprocess', 'numpy._import_tools',
>>>> 'numpy.lib.format', '_lzma', 'numpy.core.arrayprint', 'json.decoder',
>>>> 'signal', 'gzip', 'posix', 'textwrap', 'numpy.fft.fftpack',
>>>> 'importlib.machinery', 'lzma', 'struct', 'pickle', '_codecs',
>>>> 'numpy.core.einsumfunc', 'itertools', 'numpy.core.shape_base',
>>>> 'encodings.aliases', 'numpy.lib.index_tricks', 'numpy.random.info',
>>>> 'numpy.linalg._umath_linalg', 'matplotlib.fontconfig_pattern',
>>>> 'six.moves.urllib.request', '_weakrefset', 'distutils.errors', 'io',
>>>> 'locale', 'email.errors', 'numpy.core.numerictypes',
>>>> 'numpy.compat._inspect', 'zlib', 'numpy.polynomial.hermite_e',
>>>> 'numpy.lib.type_check', 'mpl_toolkits', 'numpy.fft.fftpack_lite', 'bisect',
>>>> 'dateutil', 'numpy.polynomial', 'collections.abc', '_bz2', 'weakref',
>>>> 'numpy.lib.ufunclike', 'numpy.core.function_base', 'abc', 'six.moves',
>>>> 'numpy.linalg', 'numpy.polynomial.legendre', 'numpy.core.defchararray',
>>>> 'numpy.linalg.lapack_lite', 'numpy.core._internal', 'importlib',
>>>> 'unittest.suite', 'unittest.case', 'numpy.core.memmap', 'email._parseaddr',
>>>> '_pickle', '_ssl', 'matplotlib.compat.subprocess', 'numpy.random',
>>>> 'datetime', 'email._policybase', 'sre_parse', 'numpy.linalg.linalg',
>>>> 'copy', 'numpy.lib._datasource', 'numpy.core._methods', 'linecache',
>>>> 'matplotlib.compat', 'numpy.testing', 'numpy.__config__',
>>>> 'unittest.result', 're', 'http.client', 'numpy.lib.info',
>>>> 'numpy.core.fromnumeric', 'numpy.core.getlimits', 'matplotlib._color_data',
>>>> 'urllib.response', 'pyparsing', 'numpy.lib.polynomial', 'threading',
>>>> 'string', 'numpy.core.numeric', 'numpy.ma', 'numpy.fft', 'ctypes',
>>>> 'numpy.random.mtrand', 'matplotlib.cbook.deprecation', '_datetime',
>>>> 'builtins']
>>>> CACHEDIR=/home/az/.cache/matplotlib
>>>> Using fontManager instance from /home/az/.cache/matplotlib/fon
>>>> tList.json
>>>> backend TkAgg version 8.6
>>>> imported
>>>> ^C
>>>> Hangs at this point with CPU @ 100%
>>>>
>>>> grep -v '#' /home/az/.local/lib/python3.5/
>>>> site-packages/matplotlib/mpl-data/matplotlibrc
>>>>
>>>> The only line is :
>>>> backend      : TkAgg
>>>>
>>>>
>>>> [az at hp src]$ gcc --version
>>>> gcc (GCC) 6.3.1 20161221 (Red Hat 6.3.1-1)
>>>>
>>>> I installed using pip3 into --user directory.
>>>> but i also remember that i used dnf to get tkInnter installed:
>>>> rpm -qa | grep tkin
>>>> python3-tkinter-3.5.3-6.fc24.x86_64
>>>> tkinter-2.7.13-2.fc24.x86_64
>>>> tix-1:8.4.3-17.fc24.x86_64
>>>> if i were to compare "pip3 list" between system (root) and the user
>>>> (az):
>>>> diff -u /tmp/root_pip /tmp/usr_pip
>>>> --- /tmp/root_pip    2017-11-04 15:26:09.612643559 -0400
>>>> +++ /tmp/usr_pip    2017-11-04 15:25:52.396473226 -0400
>>>> @@ -1,39 +1,65 @@
>>>>  astroid (1.4.5)
>>>>  beautifulsoup4 (4.6.0)
>>>> +bleach (2.1)
>>>>  blivet (1.20.3)
>>>>  chardet (2.2.1)
>>>>  coverage (4.4.1)
>>>>  cssselect (0.9.1)
>>>>  cupshelpers (1.0)
>>>> +cx-Oracle (6.0.2)
>>>>  cycler (0.10.0)
>>>>  decorator (4.0.11)
>>>>  distro (1.0.2)
>>>>  dnf-langpacks (0.15.1)
>>>> +entrypoints (0.2.3)
>>>>  fros (1.1)
>>>> -html5lib (0.999)
>>>> +html5lib (1.0b10)
>>>>  humanize (0.5.1)
>>>>  ib-insync (0.8.5)
>>>> +ibapi (9.73.2)
>>>>  iniparse (0.4)
>>>>  initial-setup (0.3.40)
>>>>  IPy (0.81)
>>>> +ipykernel (4.6.1)
>>>> +ipython (6.2.0)
>>>> +ipython-genutils (0.2.0)
>>>>  ipywidgets (7.0.0)
>>>>  isc (1.0)
>>>>  javapackages (4.6.0)
>>>> +jedi (0.11.0)
>>>> +Jinja2 (2.9.6)
>>>> +jsonschema (2.6.0)
>>>>  jupyter (1.0.0)
>>>> +jupyter-client (5.1.0)
>>>> +jupyter-console (5.2.0)
>>>> +jupyter-core (4.3.0)
>>>>  langtable (0.0.35)
>>>>  lazy-object-proxy (1.2.1)
>>>>  lxml (3.7.2)
>>>> +MarkupSafe (1.0)
>>>> +matplotlib (2.1.0)
>>>> +mistune (0.7.4)
>>>> +nbconvert (5.3.1)
>>>> +nbformat (4.4.0)
>>>> +notebook (5.1.0)
>>>>  ntplib (0.3.3)
>>>>  numpy (1.13.3)
>>>>  ordered-set (2.0.0)
>>>>  pandas (0.20.3)
>>>> +pandocfilters (1.4.2)
>>>> +parso (0.1.0)
>>>> +pexpect (4.2.1)
>>>> +pickleshare (0.7.4)
>>>>  pid (2.0.1)
>>>>  Pillow (3.2.0)
>>>>  pip (9.0.1)
>>>> +prompt-toolkit (1.0.15)
>>>> +ptyprocess (0.5.2)
>>>>  pwquality (1.3.0)
>>>>  pycups (1.9.72)
>>>>  pycurl (7.43.0)
>>>>  pyenchant (1.6.8)
>>>> +Pygments (2.2.0)
>>>>  pygobject (3.20.1)
>>>>  pygpgme (0.3)
>>>>  pyinotify (0.9.6)
>>>> @@ -42,6 +68,7 @@
>>>>  pylint (1.5.6)
>>>>  pyparsing (2.2.0)
>>>>  pyparted (3.10.7)
>>>> +PyQt5 (5.9)
>>>>  PySocks (1.5.6)
>>>>  python-augeas (0.5.0)
>>>>  python-dateutil (2.6.1)
>>>> @@ -50,6 +77,9 @@
>>>>  pytz (2017.2)
>>>>  pyudev (0.21.0)
>>>>  pyxdg (0.25)
>>>> +pyzmq (16.0.2)
>>>> +qtconsole (4.3.1)
>>>> +Quamash (0.5.5)
>>>>  requests (2.10.0)
>>>>  requests-file (1.4)
>>>>  requests-ftp (0.3.1)
>>>> @@ -60,11 +90,21 @@
>>>>  sepolicy (1.1)
>>>>  setroubleshoot (1.1)
>>>>  setuptools (20.1.1)
>>>> +simplegeneric (0.8.1)
>>>> +sip (4.19.3)
>>>>  six (1.11.0)
>>>>  slip (0.6.4)
>>>>  slip.dbus (0.6.4)
>>>>  sos (3.2)
>>>>  SSSDConfig (1.15.3)
>>>>  systemd-python (232)
>>>> +terminado (0.6)
>>>> +testpath (0.3.1)
>>>> +tornado (4.5.2)
>>>> +traitlets (4.3.2)
>>>> +tws-async (0.5.5)
>>>>  urllib3 (1.15.1)
>>>> +wcwidth (0.1.7)
>>>> +webencodings (0.5.1)
>>>> +widgetsnbextension (3.0.3)
>>>>  wrapt (1.10.10)
>>>>
>>>>
>>>> I just removed html5lib from system(root) , but tha made no difference
>>>> to the plotting..
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> On Sat, Nov 4, 2017 at 11:09 AM, Andrew Z <formisc at gmail.com> wrote:
>>>>
>>>>> hello,
>>>>>  the issue i'm experiencing is local to my laptop ( the other machines
>>>>> i have run examples just fine).
>>>>> I described it here https://www.mail-archive.com/p
>>>>> ython-list at python.org/msg432343.html in details.
>>>>> i searched around, but none of the proposed workarounds helped.
>>>>>
>>>>> Is there a  way to enable some-kind of debugging or verbose output to
>>>>> see what exactly is happening behind the scene?
>>>>>
>>>>> Thank you.
>>>>> AZ
>>>>>
>>>>>
>>>>
>>>> _______________________________________________
>>>> Matplotlib-users mailing list
>>>> Matplotlib-users at python.org
>>>> https://mail.python.org/mailman/listinfo/matplotlib-users
>>>>
>>>>
>>>
>>>
>>
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