`pydot` failed to call GraphViz.Please install GraphViz and ensure that its executables are in the $PATH

My jupyter server is running in a gcp deep learning vm.

I'm trying to print the model in a Jupyter notebook cell.

import os, sys
from utils.models.alexnet import alexnet
from keras.utils.vis_utils import plot_model
from keras.optimizers import SGD

model = alexnet(len(class_names))
model.summary()
plot_model(model, to_file="alexnet_model.png", show_shapes=True)

I get this error

`pydot` failed to call GraphViz.Please install GraphViz ([https://www.graphviz.org/](https://www.graphviz.org/)) and ensure that its executables are in the $PATH.

I have correctly installed Graphviz in my machine with

apt-get install graphviz

stat /usr/bin/dot
  File: /usr/bin/dot
  Size: 10568       Blocks: 24         IO Block: 4096   regular file
Device: 801h/2049d  Inode: 142872      Links: 1
Access: (0755/-rwxr-xr-x)  Uid: (    0/    root)   Gid: (    0/    root)
Access: 2020-02-10 11:48:19.416617639 +0000
Modify: 2017-02-19 10:32:17.000000000 +0000
Change: 2019-12-13 01:47:41.084977709 +0000

The python packages pydot, pydot-ng, pydotplus are also installed.

This is my path variable

echo $PATH
/usr/local/cuda/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games

/user/bin is included here.

EDIT

When executed in a jupyter notebook shell.

print(os.environ["PATH"])

/usr/local/cuda/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games

Another wierd thing

I have a simple image dataset with 3 classes and altogether around 2000 images. In my jupyter notebook I first process and load the images into memory. Creating the model and printing it comes next. With the simple dataset it works without error. This happens when I work with large datasets.

I was also getting the same thing so i install conda install python-graphviz after conda install pydot

Failed to import pydot. You must install pydot and graphviz for, I have Python 3.5 installed. Both pydot and graphviz are installed in the proper environment. This is the error I get. ensure that its executables are in the $ PATH.') OSError: pydot failed to call GraphViz.Please install GraphViz (https:// www.graphviz.org/) and ensure that its executables are in the $PATH. Dismiss Join GitHub today. GitHub is home to over 50 million developers working together to host and review code, manage projects, and build software together.

conda installs only binary files of graphviz, but you need to install Python dependencies also. So install both of them with:

conda install graphviz    

conda install python-graphviz

ImportError: You must install pydot and graphviz for `pydotprint` to , You must install pydot and graphviz for pydotprint to work. Compare plans � Contact Sales GitHub is home to over 50 million developers working together to host ImportError: Failed to import pydot. And add the software bin directory to the system's path. So in windows, assign it to be an .exe file. pip install graphviz; conda install graphviz; Downloading graphviz on my system and manually adding its path to environment variable in my script; Adding downloaded graphviz's bin folder to the environment variable; Nothing worked for me. If someone can please help out would be really helpful. Thanks!

I have the same problem, I solved it by following the Answer of Prerna Verma. By the way, there are three steps for using graphviz in Linux Envs:

  1. sudo apt-get install graphviz (download and install graphviz, if you are a Windows User)

  2. conda install pydot

  3. conda install python-graphviz

then, you can use it!

Solve pydot failed to call GraphViz, Please install GraphViz (https://www.graphviz.org/) and ensure that its executables are in the $PATH. I am a law-abiding person. Before this error occurred, I have� I installed the graphviz executable in the path "C:\anaconda3\Lib\site-pac kages\grap hviz-2.38" and for pydot, I did pip install pydot in the command prompt. Also, downloaded the tar files of pydot and put in the path "C:\anaconda3\Lib\site-pac kages\pydo t-1.2.4" I will try with wingraphinstaller. Many Thanks. output.PNG

OSError: `pydot` failed to call GraphViz.Please install GraphViz , If the problem still pops up: OSError: pydot failed to call GraphViz.Please install GraphViz (https://www.http /graphviz.org/) and ensure that its executables are in the Path = r'path/to/your/dot/exe/file'# For example my: C:/Program Files� pydot-ng was a fork of pydot, but (as can be seen later on in that same pydot/pydot-ng#52), the pydot repository was transferred to the same maintainer as pydot-ng . He then archived pydot-ng and added parts of the .bat -code discussed in pydot/pydot-ng#52 to pydot/pydot instead ( 8c55fe5 ).

Solution: Failed to import pydot and Graphviz. Pydot can not find , You must install pydot' ' and graphviz for `pydotprint` to work. Pydot Download add the Duration: 4:08 Posted: Mar 18, 2018 RuntimeError: failed to execute ['dot', '-Tpdf', '-O', 'test'], make sure the Graphviz executables are on your systems' path I tried to put "C:\Python34\bin\dot.exe" in system's path, but it didn't work, and I even created a new environment variable "GRAPHVIZ_DOT" with value "C:\Python34\bin\dot.exe" , still not working.

HOW TO: Add folder to PATH ('GraphViz's executables not found , HOW TO: Add folder to PATH ('GraphViz's executables not found' Fixed). 32,302 views32K Duration: 2:22 Posted: Feb 9, 2018 conda install graphviz installs the C graphviz executables and libraries (e.g. the dot executable). pip install graphviz installs one of the Python bindings for Graphviz (the one used by Dask). conda install python-graphviz installs the same package as pip install graphviz, but patched to work with conda's Graphviz C package.

Comments
  • You installed locally the dot tool, but shouldn't this be on the cloud server? Is it 100% sure that the path that is used in jupyter is having the /usr/bin in its path (check inside the place where you want to use it)?
  • What does os.path.exists('/usr/bin/dot') emit when executed in Jupyter Notebook?
  • @CharlesDuffy It returns True
  • Thank you -- that affirms that dot is installed on your GCP node, not just your local client.