"RuntimeError: Make sure the Graphviz executables are on your system's path" after installing Graphviz 2.38

Question

I downloaded Graphviz 2.38 MSI version and installed under folder C:\Python34, then I run pip install Graphviz, everything went well. In system's path I added C:\Python34\bin. When I tried to run a test script, in line filename=dot.render(filename='test'), I got a message

 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. I tried to uninstall Graphviz and pip uninstall graphviz, then reinstall it and pip install again, but nothing works.

The whole traceback message is:

Traceback (most recent call last):
  File "C:\Python34\lib\site-packages\graphviz\files.py", line 220, in render
    proc = subprocess.Popen(cmd, startupinfo=STARTUPINFO)
  File "C:\Python34\lib\subprocess.py", line 859, in __init__
    restore_signals, start_new_session)
  File "C:\Python34\lib\subprocess.py", line 1112, in _execute_child
    startupinfo)
FileNotFoundError: [WinError 2] The system cannot find the file specified

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "C:\Users\Documents\Kissmetrics\curves and lines\eventNodes.py", line 56, in <module>
    filename=dot.render(filename='test')
  File "C:\Python34\lib\site-packages\graphviz\files.py", line 225, in render
    'are on your systems\' path' % cmd)
RuntimeError: failed to execute ['dot', '-Tpdf', '-O', 'test'], make sure the Graphviz executables are on your systems' path

Does anybody have any experience with it?

Gossipry

Answer 1

You should install the graphviz package in your system (not just the python package). On Ubuntu you should try:

sudo apt-get install graphviz

Whorehouse

If this doesn't work (it says the package is referenced but not there or something like that) run sudo apt-get update in order to update apt-get and tell it what packages are there. – Bombard

If you're in a Docker Container (like I was), I was already at root and only needed apt-get install graphviz – Erebus

Hope I can help someone with this. It did not work the first time for me so I ran sudo apt-get update && sudo apt-get upgrade and it worked afterwards. – Convolution

What if I just want to install graphviz in a virtual environment? – Rattly

Answer 2

This one should solve the problem on MacOS:

brew install graphviz

---

To explain the misconception for new comer who using Conda. When we run conda install graphviz, it install the binary of Graphviz (this is not executable in Phyton yet).

And then we usually will also install conda install python-graphviz, this install the wrapper for phyton to run the binary of graphviz, the problem is we might get errors with message "graphviz" not exececuteable.

Thus why better use homebrew to install Graphviz binary and then install python-graphviz. Homebrew will guarantee the binary executeable.

Agrimony

For mac, it seem this is best option. Unless you want to use MacPorts and install graphviz from here: graphviz.org/Download_macos.php. – Insentient

How do I find my bin folder where I have graphviz. I am having this problem and is really killing right now. Just checked I have graphviz 2.38. – Lita

Before brew install graphviz worked I had to run: xcode-select --install – Erythrocytometer

Thank you. I installed graphviz with pip but only worked when I installed it with homebrew. – Purapurblind

No brew does not. – Deviltry

This is what did it for my (mac os) – Chequer

Answer 3

import os
os.environ["PATH"] += os.pathsep + 'D:/Program Files (x86)/Graphviz2.38/bin/'

In windows just add these 2 lines in the beginning, where 'D:/Program Files (x86)/Graphviz2.38/bin/' is replaced by the address of where your bin file is.

That solves the problem.

Horeb

worked in windows, I downloaded graphviz-2.38.zip from here graphviz.gitlab.io/_pages/Download/Download_windows.html. Unzip it and place it the mentioned folder – Ginder

This works for me. I tried to add this to user and system environment variables, but that doesn't work, only your solution works for me. – Krystlekrystyna

this worked for me as well, but it threw another error before working. For some reason It gave me a side-by-side configuration....-error. I had to additionally reinstall the Microsoft Visual C++ 2008 Redistributable Package (x86). If someone has the same problem, here's the link: [microsoft.com/de-DE/download/details.aspx?id=29] – Recalesce

I used chocolatey to install graphviz choco install -y graphviz – Inhumation

Yep this worked. make sure to download the right graphviz. I also placed the graphviz bins on both user and system paths. – Cleanup

This worked for me; downloaded zip files, and used this code snippet to point to unzipped contents. Did not have to use the Environment Variables menu to state the path. – Threequarter

Answer 4

For Windows:

1. Install windows package from: https://graphviz.gitlab.io/_pages/Download/Download_windows.html
2. Install python graphviz package
3. Add C:\Program Files (x86)\Graphviz2.38\bin to User path
4. Add C:\Program Files (x86)\Graphviz2.38\bin\dot.exe to System Path

This worked for me!

Washin

Also Close your "cmd" in which jupyter notebook is running. Existing running CMD dont catch the new changes in Environment variables. – Masto

It didn't work for me until I restarted the system – Waggish

This worked perfectly. Just had to restart the notebook again. Thanks. – Norvil

You don't need to restart the entire system, but just the python kernel. – Carlo

@Carlo - didn't work - I had to restart the entire system. – Abib

If you are using chocolatey, you can use choco install graphviz – Northwester

Answer 5

Try using:

conda install python-graphviz

The graphviz executable sit on a different path from your conda directory, if you use pip install graphviz.

Groats

Conda install graphviz worked on windows! nothing else seems to work :\ – Gamma

pygraphviz have a nice big warning against using conda, Not clear why, though. – Priapism

I ran conda install python-graphviz in my Anaconda prompt and once the execution is done, just restart the Jupyter notebook kernel. It worked for me. – Westerfield

I ran conda install python-graphviz in my Anaconda prompt and once the execution is done, just restart the Jupyter notebook kernel. It worked for me. Worked on Windows as well. – Gerthagerti

Answer 6

Step 1: Install Graphviz binary

Windows:

1. Download Graphviz from http://www.graphviz.org/download/
2. Add below to PATH environment variable (mention the installed graphviz version):
   • C:\Program Files (x86)\Graphviz2.38\bin
   • C:\Program Files (x86)\Graphviz2.38\bin\dot.exe
3. Close any opened Juypter notebook and the command prompt
4. Restart Jupyter / cmd prompt and test

Linux:

1. sudo apt-get update
2. sudo apt-get install graphviz
3. or build it manually from http://www.graphviz.org/download/

Step 2: Install graphviz module for python

pip:

• pip install graphviz

conda:

• conda install graphviz

Aiden

Solved for me on winzoz – Charqui

Excellent explanation! Thank you~ – Riproaring

Others also answered the question, but this "takes you by the hand". 🌟 – Brier

Answer 7

This is showing some path issue:

pip install graphviz

So this worked for me:

sudo apt-get install graphviz

Outface

sudo apt-get install graphviz is not alternative of pip install – Deviltry

Answer 8

OSX Sierra, Python 2.7, Graphviz 2.38

Using pip install graphviz and conda install graphviz BOTH resolves the problem.

pip only gets path problem same as yours and conda only gets import error.

Convolve

ONLY this worked for me. after trying everything. thanks. – Anarchism

Conda install graphviz worked on windows! nothing else seems to work :\ – Gamma

Answer 9

Using conda install graphviz and conda install python-graphviz to install GraphViz on Windows10 the path needed was C:/ProgramData/Anaconda3/Library/bin/graphviz/ for me. I.e. adding

import os
os.environ["PATH"] += os.pathsep + 'C:/ProgramData/Anaconda3/Library/bin/graphviz/'

solved the issue for me.

Ladew

This def solved the issue... thanks – Luddite

Answer 10

Just add below to your Environmental Variable(system) PATH on Windows

C:\Program Files (x86)\Graphviz2.38\bin

there, you can find .exe files

If not work

Find Graphviz2.38/bin folder in your Program Files not in python lib

Then, add to your PATH

It's important to find a folder where .exe files exist

Sterlingsterlitamak

it seems only your post can solve my problem...win10 enterprise edition, jupyter notebook, py 3.6 – Asclepiadaceous

You will have to restart the jupyter notebook/annaconda for the environmental variables (PATH) to be re-cached. – Carlo

Answer 11

Try conda install graphviz. I had the same problem, I resolved it by mentioned command in MacOS.

Rainfall

Conda install graphviz worked on windows! nothing else seems to work :\ – Gamma

Answer 12

On Ubuntu Linux this solved it for me:

pip install graphviz
sudo apt-get install graphviz

You could also try conda install -c conda-forge graphviz instead of pip if using Anaconda.

Thaumaturge

This worked for me in WSL in Windows 10 as well. Installation using pip was not enough. – Uriah

Answer 13

conda install python-graphviz

For Windows, install the Python Graphviz which will include the executables in the path.

Van

Conda install graphviz worked on windows! nothing else seems to work :\ – Gamma

Answer 14

When solving this issue for myself, I used this GitHub tutorial, which analysed the cause of this issue. If we read in between the lines, it says it needs system as well as python graph viz. In addition to conda install, we would need to run:

conda install -c conda-forge python-graphviz

Then restart the kernel; it works like a charm.

Weak

Answer 15

I'm on macOS Catalina 10.15.3, and I had a similar error: ExecutableNotFound: failed to execute ['dot', '-Tsvg'], make sure the Graphviz executables are on your systems' PATH

Fixed it with:

pip3 install graphviz AND brew install graphviz

Note the pip3 install will only return the success message Successfully installed graphviz-0.13.2 so we still need to run brew install to get graphviz 2.42.3 (as of 10 Mar 2020, 6PM).

Wildlife

Answer 16

I am using windows10 , I tried installing graphwiz in program files and setting the path: Didn't worked for me

Tried

conda install -c anaconda graphviz

doesn't work.

Then tried

conda install python-graphviz

It worked, It seems our python compiler is not able to access the Graphwiz. Hence python-graphwize worked. pip install graphviz also didn't work.

Gillispie

Answer 17

1) Graphviz – download unzip in a particular place in the system (pip does not work in windows ) and include the bin folder in the path (‘set environment variables in windows’ OR) set manually in each program

import os
os.environ["PATH"] += os.pathsep + 'C:/GraphViz/bin'

2) Then put the model to plot

clf = xgb.train(params, d_train, 1000, evals=evallist, early_stopping_rounds=10)
xgb.plot_tree(clf)
plt.rcParams['figure.figsize'] = [50, 10]
plt.show()

Ensepulcher

Answer 18

I had the same issue on Linux with Jupyter.

To solve it I've added the dot library to python sys.path

First: check if dot is installed,

Then:
find his path whereis dot -> /local/notebook/miniconda2/envs/ik2/bin/dot

Finally in python script : sys.path.append("/local/notebook/miniconda2/envs/ik2/bin/dot")

Devitalize

On linux I just did sudo apt-get install graphviz (after doing pip install graphviz) and after that it worked. – Thaumaturge

@Thaumaturge Your comment should be an answer. Solved the problem for me – Khania

@Thaumaturge that's the answer! – Ballflower

Answer 19

1- first downlaod it(graphviz 2.38).

2- install org.graphviz.Graphviz-2.38-graphviz-2.38.

3- now add "C:\Program Files (x86)\Graphviz2.38\bin" and "C:\Program Files (x86)\Graphviz2.38\bin\dot.exe" to path like this video
note:in windows 8 you must use ; for path example: C:\Program Files;D:\Users;E:\file\

Kipper

Answer 20

I had the same error message on Mac OS (El Capitan), using the PyCharm IDE. I had installed Graphviz using brew, as recommended in RZK's answer, and installed the graphviz python package using PyCharm (I could check Graphviz was installed correctly by trying dot -V in a terminal and getting: dot - graphviz version 2.40.1 (20161225.0304)). Yet I was still getting the error message when trying to call Graphviz from PyCharm.

I had to add the path /usr/local/bin in PyCharm options, as recommended in the answer to this question to resolve the problem.

Recipient

Answer 21

After you've installed the package (link if you haven't), add the path to dot.exe as a new system variable.

Default path is:

C:\Program Files (x86)\Graphviz2.38\bin\dot.exe

Dore

i don't have this dot.exe file – Mosquito

Answer 22

In Windows environment, use chocolately to install, it will ensure the environmental vars are set correctly.

choco install graphviz

Pleader

this worked for me. Make sure to run it in administrator mode. – Gillard

Answer 23

When I first installed pydot and graphviz it showed me the error, but the command below worked for me:

import os
os.environ["PATH"] += os.pathsep + r'C:\Users\vivek\Downloads\graphviz-2.44.1-win32\Graphviz\bin'

Tedford

Answer 24

First, you should use pip install, and then download another package in http://www.graphviz.org/Download_windows.php and add the install location into the environmental path, then it works.

Welldefined

Answer 25

OS Mojave 10.14., Python 3.6

Using pip install graphviz had good feedback in terminal, but lead to this error when I tried to make a graph in a Jupyter notebook. I then ran brew install graphviz, which gave an error in terminal. Then I ran conda install graphviz and the graph worked.

From @Leighton's comment: pip only gets path problem same as yours and conda only gets import error.

Mitchelmitchell

Answer 26

Add graphviz to the System Path

1. Windows - Edit the System Environment Variables.
2. Choose Environment Variables.
3. Select Path - New
4. Add the Path of graphviz

Ex: C:\Users\AppData\Local\Continuum\anaconda3\Library\bin\graphviz

Lactalbumin

Answer 27

try typing the following code in anaconda prompt one by one.

this worked for me.

Source: https://anaconda.org/conda-forge/python-graphviz

conda install -c conda-forge python-graphviz
conda install -c conda-forge/label/broken python-graphviz
conda install -c conda-forge/label/cf201901 python-graphviz
conda install -c conda-forge/label/cf202003 python-graphviz 

Restart the kernel afterwards!

Mightily

Answer 28

For Linux users who don't have root access and hence can't use sudo command as suggested in other answers...

First, activate your conda virtual-environment (if you want to use one) by:

source activate virtual-env-name

Then install graphviz, even if you have already done it using pip:

conda install graphviz

then copy the result of the following command:

whereis dot

In my case, its output is:

/home/nader/anaconda2/bin/dot

and add it to your PATH variable. Just run the command below

nano ~/.bashrc

and add these lines to the end of the opened file:

PATH="/home/username/anaconda2/bin/dot:$PATH"
export PATH

now press Ctrl+O and then Ctrl+X to save and exit.

Problem should be solved by now.

Pycharm users, please note: Pycharm does not always see the PATH variable the same as your terminal. This solution does not work for Pycharm, and maybe other IDEs. But you can fix this by adding this line of code:

os.environ["PATH"] += os.pathsep + '/home/nader/anaconda2/bin'

to your python program. Do not forget to

import os

first :)

Edit: If you don't want to use conda, you can still install graphviz from here without any root permissions and add the bin folder to your PATH variable. I didn't test this.

Marqueritemarques

what if whereis dot outputs nothing but dot:? I am using PyCharm on Windows to connect to Ubuntu 16.04 server and can't seem to find necessary bin folder to add os.environ["PATH"] += os.pathsep + '...' – Stoltz

Rather refer to this issue of mine posted here – Stoltz

Answer 29

1.install windows package from: https://graphviz.gitlab.io/_pages/Download/Download_windows.html and download msi file

Add in Environmental variables 2. Add C:\Program Files (x86)\Graphviz2.38\bin to User path

3. Add C:\Program Files (x86)\Graphviz2.38\bin\dot.exe to System Path

4. Restart your python notebook.

It will work.

Ilion

Answer 30

#Write this on anaconda prompt in admin mode
conda install -c anaconda graphviz
conda install -c conda-forge python-graphviz
conda install -c conda-forge/label/broken python-graphviz
conda install -c conda-forge/label/cf201901 python-graphviz
conda install -c conda-forge/label/cf202003 python-graphviz

#check dot -v in window's cmd prompt
C:\WINDOWS\system32>dot -V
dot - graphviz version 2.38.0 (20140413.2041)
(this means graphviz installed successfully)

#Add path to sys and user eve variables
PATH
C:\Anaconda3\pkgs\graphviz-2.38-hfd603c8_2\Library\bin
(search bin folder of graphviz and then copy n paste path in env variables)

#Re-run all cmds in jyupter notebook
#if error occurs (less chances)
#then 
#Restart anaconda and again run all cmds in jyupter notebook
eg.
import graphviz as gp
with open("tree.dot") as f:
    dot_read=f.read()
display(gp.Source(dot_read))

Frizette

Answer 31

import os
os.environ["PATH"] += os.pathsep + "/Macintosh HD⁩/anaconda3⁩/lib⁩/⁨python3.7⁩/site-packages⁩/sphinx⁩/templates⁩/graphviz"

This solved the PATH issue on MAC for me!

Peso

Answer 32

If you are not using Conda but vanilla Python, 'brew install graphviz' works.

Munitions

Answer 33

Mac & Big Sur. Python 3.8.6 w/vs code. While it should have been included in diagrams package, I had to manually install graphviz.

(mymltools) ➜  infrastructure git:(master) pip list
Package    Version
---------- -------
diagrams   0.18.0
graphviz   0.13.2
Jinja2     2.11.2
MarkupSafe 1.1.1
pip        20.3.2
setuptools 51.0.0
wheel      0.36.2

Running diagrams failed. Then manually ran

pipenv install graphviz

Works like a charm.

Misty

Answer 34

MACOS - Solution for Monterey

1. Open: Terminal
2. Run: pip install graphviz
3. Run: brew install graphviz
4. Close: Terminal
5. Open: Anaconda (Jupyter or Spyder)
6. Run: import os
7. os.environ["PATH"] += os.pathsep + "/usr/local/Cellar/graphviz/2.49.3/bin/dot"

(You'll have to run this EACH time until the bug is fixed.) The tricky part is finding the dot file. It is the location where brew installs the package. (But it should be something similar to the path that I gave.) Test by running:

import mglearn as mglearn
mglearn.plots.plot_animal_tree()

Hopefully, you are good to go now!

Portal

Answer 35

you can use the following command in Anaconda prompt :

conda install python-graphviz

and make sure to install pm4py in Anaconda prompt :

pip install pm4py

and in the end you have to try running your python code with Anaconda propmpt.

Dexterdexterity

Answer 36

For Mac users (this worked for me):

# not required for graphviz but required for running the below command
pip3 install pipdeptree

pip3 install graphviz
brew install graphviz

# You could include in the .bashrc or .zshrc file to make it permanent. 
# As it may not save when you close the current terminal session!
export PATH="$PATH:/usr/local/Cellar/graphviz/8.1.0/bin";

Then I can run:

pipdeptree --graph-output png > dependencies.png

FYI I used this in a virtual env with python3.8

Unwary

Answer 37

On my end, as suggested in top response here, using conda, first I installed graphviz

conda install graphviz

followed by python-graphviz

conda install python-graphviz

And then it worked for me.

Wallford

Answer 38

For MACOS the problem is mostly because that its installed in the wrong environment:

In a cell run:

!pip uninstall graphviz -y
!pip install graphviz

Take

Answer 39

For windows, these 2 commands work for me, in the power shell running as administrator.

1. pip install graphviz

2. choco install graphviz

Hedve

Please make an effort to tailor your answer to the system of the asker. – Greyson

Answer 40

choco install -y graphviz

Solved the issue for me. Windows

Appendage

There's already an answer for that https://mcmap.net/q/99971/-quot-runtimeerror-make-sure-the-graphviz-executables-are-on-your-system-39-s-path-quot-after-installing-graphviz-2-38 – Gyp

Answer 41

trying doing this in python import sys !conda install --yes --prefix {sys.prefix} graphviz import graphviz

Ilion

Please add more details to your answer, such as why this would fix the issue – Facet