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Keras installation, problem to install graphviz package

luc_bartkowskiluc_bartkowski Member Posts: 46  Maven
edited September 2019 in Help

I want to start with the Keras extension. So I followed the install script at https://community.rapidminer.com/t5/RapidMiner-Studio-Knowledge-Base/Keras-Deep-Learning-extension/ta-p/40839

I'm using a new MacBook. So I followed the MacOS/OSX Annaconda install script. The results are:

conda create –n keras (successfully executed)
source activate keras (successfully executed)
conda install pandas (successfully executed)
conda install scikit-learn (successfully executed)
conda install -c conda-forge keras (successfully executed)
conda install –c anaconda graphviz (unsuccessful but successful using Anaconda Navigator)
conda install –c conda-forge pydotplus (unsuccessful but successful using Anaconda Navigator)
The last install step states "In RapidMiner Studio Keras and Python Scripting panels in preferences, specify the path to your new conda environment Python executable." I set it to: /Users/luc/anaconda3/envs/keras/bin/python


Still RapidMiner Preferences is complaining about graphviz:





I tried to change my path in .bash_profile to: export PATH="/Users/luc/anaconda3/envs/keras/bin:$PATH"

Such does not bring a solution. What could be the problem?

Best Answer

  • luc_bartkowskiluc_bartkowski Member Posts: 46  Maven
    Solution Accepted

    By installing graphviz using 'pip install graphviz' I solved my problem.



  • sgenzersgenzer 12Administrator, Moderator, Employee, RapidMiner Certified Analyst, Community Manager, Member, University Professor, PM Moderator Posts: 2,952  Community Manager

    tagging @pschlunder and @jpuente





  • GottfriedGottfried Member Posts: 17  Maven

    I had the same issue with graphviz and pydot. I followed your recommendation and used pip to install both. Then indeed the keras test in RapiMiner's preferences returned an Ok installation. Yet, now when running a keras sample example (SP 500 regression), I get an error message: "Pydot failed to call GraphViz. Please install GraphViz and ensure that its executablesare in $PATH. (Script line 197)". Anyone a clue how to fix this?Pydot failed Graphviz.png

  • pschlunderpschlunder Employee, RapidMiner Certified Analyst, RapidMiner Certified Expert, RMResearcher, Member Posts: 84  RM Research

    Hi @Gottfried,

    please check if the PATH set for the Python extension and the one for the Keras extension match. Therefore open the RapidMiner settings and open the respective tabs. My guess is, that your Python extension points to another path, than Keras. The Keras extension relies on the python extension for somethings, hence the need to set both path alike.


    Hope this helps.



  • GottfriedGottfried Member Posts: 17  Maven

    I have been setting up these two extension paths manually and systematically to the same values after each of my trials of installing Keras. It helped me check whether RapidMiner detected missing python modules etc. Now following exactly the procedure found on RapidMiner’s pages through Anaconda environment plus launching a pip command for installing graphviz and pydot, RM’s extension checks both send back “all clear” messages. Just, when actually running a Keras script example, I get this “pydot could not call graphviz” error. It happens after quite a long processing time as if Keras had really computed the neural network and just had a problem to report results...



  • pschlunderpschlunder Employee, RapidMiner Certified Analyst, RapidMiner Certified Expert, RMResearcher, Member Posts: 84  RM Research

    Hi @Gottfried,

    could you share your process xml please? And if possible a reduced data set for testing?




  • GottfriedGottfried Member Posts: 17  Maven
    Hello @pschlunder,
    I just ran any of the examples coming with the Keras extension setup, e.g. the SP500 regression example. I did no change to neither the proposed process nor the dataset. Do I really need to paste a copy here?
  • lbookmanlbookman Member Posts: 5 Contributor I

    I encountered the same problem. Has anyone solved it yet?

  • lbookmanlbookman Member Posts: 5 Contributor I

    Did you ever get a resolution to this problem?

  • M_MartinM_Martin RapidMiner Certified Analyst, Member Posts: 125   Unicorn
    Hi Colleagues: I ran into the exact same problem with Graphviz and pydot under OS X - under Windows, the set-up worked after installing the Windows version of Graphviz and setting the PATH statement to include the path to the Graphviz executeble file.  Would be grateful for any other suggestions.  Best wishes, Michael Martin
  • pblack476pblack476 Member Posts: 83  Maven
    @GottfriedI have the exact same issue. First through anaconda I got a Graphviz was not installed error when testing. Then I switched to the bin directory installation and the test ran fine. Both Python Scripting and Keras tests.

    Now I get the same error you do. "pydot could not call graphviz".

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