[Matplotlib-users] TkAgg won't plot - how to debug?
Jody Klymak
jklymak at uvic.ca
Wed Nov 8 17:00:43 EST 2017
https://conda.io/docs/index.html <https://conda.io/docs/index.html>
> On 8 Nov 2017, at 13:53 PM, Andrew Z <formisc at gmail.com> wrote:
>
> Jody,
> what do i need to use ? i've been using either dnf or pip3 depending on the situation ( if i want to install in to user's env - > pip3 ir system wide - dnf ).
>
> On Wed, Nov 8, 2017 at 4:50 PM, Jody Klymak <jklymak at uvic.ca <mailto:jklymak at uvic.ca>> wrote:
> Andrew,
>
> Can I *strongly* suggest you just use anaconda, unless you have some compelling reason not to?
>
> It takes care of most of these packaging headaches. I guess I’m ignorant about pycharm, but I’m pretty sure people use it w/ pycharm.
>
> Cheers, Jody
>
>
>> On 8 Nov 2017, at 13:41 PM, Andrew Z <formisc at gmail.com <mailto:formisc at gmail.com>> wrote:
>>
>> I tried PyQT5 with the same unhappy results:
>>
>> First, i verified that pyqt5 works -
>>
>> PyQt5 (5.9.1) - Python bindings for the Qt cross platform UI and application toolkit
>> INSTALLED: 5.9
>> LATEST: 5.9.1
>>
>> ran http://www.thehackeruniversity.com/2014/01/23/pyqt5-beginner-tutorial/ <http://www.thehackeruniversity.com/2014/01/23/pyqt5-beginner-tutorial/> - exampled worked with no issues. Everything got resolved in pycharm.
>>
>> next installed the matplot backend:
>> python3-matplotlib-qt5.x86_64
>>
>> ran examples from here https://pythonspot.com/en/pyqt5-matplotlib/ <https://pythonspot.com/en/pyqt5-matplotlib/> - and it hanged.
>> pycharm is complaining about :
>> from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
>> from matplotlib.figure import Figure
>> import matplotlib.pyplot as plt
>> "can not find reference 'backends' in __init__.py'
>> ' unresolved reference backend_qt5agg'
>> 'cant reference 'figure' '
>> 'no module named pyplot'
>>
>>
>>
>>
>>
>> On Mon, Nov 6, 2017 at 6:33 PM, Andrew Z <formisc at gmail.com <mailto:formisc at gmail.com>> wrote:
>> 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 <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 <mailto: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 <mailto: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 <mailto: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 <mailto: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 <mailto: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 <http://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 <http://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 <http://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 <http://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 <http://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 <http://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/fontList.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 <mailto: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/python-list@python.org/msg432343.html <https://www.mail-archive.com/python-list@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
>>
>>
>>
>> _______________________________________________
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>>
>>
>>
>>
>>
>>
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>
> --
> Jody Klymak
> http://web.uvic.ca/~jklymak/ <http://web.uvic.ca/~jklymak/>
>
>
>
>
>
>
--
Jody Klymak
http://web.uvic.ca/~jklymak/
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