Missing `graphviz` - please run `conda install fastbook`

jujubi · August 30, 2020, 12:32am

I am on amazon aws. I cant get past

NameError Traceback (most recent call last)
in
4 #alt Pipeline inputs, program, results
5 gv(’’‘program[shape=box3d width=1 height=0.7]
----> 6 inputs->program->results’’’)

~/anaconda3/envs/python3/lib/python3.6/site-packages/fastbook/init.py in gv(s)
42 if IN_COLAB: return setup_colab()
43
—> 44 def gv(s): return graphviz.Source(‘digraph G{ rankdir=“LR”’ + s + ‘; }’)
45
46 def get_image_files_sorted(path, recurse=True, folders=None):

NameError: name ‘graphviz’ is not defined

How does one remove and reinstall conda environment?

sh-4.2$ conda env list

conda environments:

base /home/ec2-user/anaconda3
JupyterSystemEnv * /home/ec2-user/anaconda3/envs/JupyterSystemEnv
R /home/ec2-user/anaconda3/envs/R
amazonei_mxnet_p27 /home/ec2-user/anaconda3/envs/amazonei_mxnet_p27
amazonei_mxnet_p36 /home/ec2-user/anaconda3/envs/amazonei_mxnet_p36
amazonei_tensorflow2_p27 /home/ec2-user/anaconda3/envs/amazonei_tensorflow2_p27
amazonei_tensorflow2_p36 /home/ec2-user/anaconda3/envs/amazonei_tensorflow2_p36
amazonei_tensorflow_p27 /home/ec2-user/anaconda3/envs/amazonei_tensorflow_p27
amazonei_tensorflow_p36 /home/ec2-user/anaconda3/envs/amazonei_tensorflow_p36
chainer_p27 /home/ec2-user/anaconda3/envs/chainer_p27
chainer_p36 /home/ec2-user/anaconda3/envs/chainer_p36
mxnet_p27 /home/ec2-user/anaconda3/envs/mxnet_p27
mxnet_p36 /home/ec2-user/anaconda3/envs/mxnet_p36
python2 /home/ec2-user/anaconda3/envs/python2
python3 /home/ec2-user/anaconda3/envs/python3
pytorch_latest_p36 /home/ec2-user/anaconda3/envs/pytorch_latest_p36
pytorch_p27 /home/ec2-user/anaconda3/envs/pytorch_p27
pytorch_p36 /home/ec2-user/anaconda3/envs/pytorch_p36
tensorflow2_p36 /home/ec2-user/anaconda3/envs/tensorflow2_p36
tensorflow_p27 /home/ec2-user/anaconda3/envs/tensorflow_p27
tensorflow_p36 /home/ec2-user/anaconda3/envs/tensorflow_p36

cogsci2 · August 30, 2020, 12:42pm

try running

conda install python-graphviz

jujubi · August 31, 2020, 12:34am

No, That does not make a difference, I’m afraid.

vscandeira · September 2, 2020, 6:06pm

Hi there. I’m having the same issue trying to run the first notebooks from my Ubuntu machine at home. But with me, it seems a little bit more awkward. When I try to instal through conda, I receive the message bellow:

Package python conflicts for:
defaults|defaults/linux-64::python==3.7.9=h7579374_0
defaults/linux-64::python==3.7.9=h7579374_0The following specifications were found to be incompatible with your system:

feature:/linux-64::__cuda==10.2=0

Your installed version is: 10.2

But my installed version of Cuda is 10.1.
$ nvcc --version
nvcc: NVIDIA ® Cuda compiler driver
Copyright © 2005-2019 NVIDIA Corporation
Built on Sun_Jul_28_19:07:16_PDT_2019
Cuda compilation tools, release 10.1, V10.1.243

$ conda list | grep cud
cudatoolkit 10.1.243 h6bb024c_0 anaconda
cudnn 7.6.5 cuda10.1_0 anaconda
pytorch 1.6.0 py3.7_cuda10.1.243_cudnn7.6.3_0 pytorch

I followed the step suggested by yelwinsoe, it has been installed, but makes no difference at all. Then, I followed the steps suggested by heraldb and found the same problem: when I run from the notebook the pip install comand and try to import fastbook, I get the message that graphviz is missing. Tried also conda install python-graphs, as long as conda install -c conda-forge python-graphviz and conda install -c anaconda graphviz. To all of these commands I get the same cuda error.

Can anyone give a hand? Thanks a lot.

hannuk · September 4, 2020, 8:24pm

I can second this fix. Works for me now. Running Ubuntu 18.04.

anya · September 11, 2020, 10:55pm

This worked for me in AzureML. Thank you.

jqian · September 13, 2020, 2:57am

Had the same problem after using the guide for Google Cloud https://course.fast.ai/start_gcp

The above solution by @heraldb didn’t work for me as it tried to downgrade to fastai 1.0 for me.

I ended up making it work by creating a new conda environment using fastbook’s environment.yml and then setting jupyter to use that environment. Steps I took:

cd ~/fastbook
conda env create --file environment.yml
conda activate fastbook
python -m ipykernel install --user --name=fastbook
pip install -Uqq fastbook

Then in Google Cloud I clicked on the + in the top right, opened a new Launcher, and selected the “fastbook” Notebook. Everything worked once I was running notebooks through this environment.

Make sure the top right “Kernel” selection says fastbook like in the screenshot:

tech_auto · September 14, 2020, 10:39pm

I had this issue, you need to run conda install -c fastai fastbook and conda will find/install the packages which includes graphviz.

sammy500 · September 19, 2020, 11:33am

Anyone using GCP have a solution? I can’t seem to get graphviz to load?

sammy500 · September 19, 2020, 12:03pm

This worked, running this in the notebook pip install graphviz. Thanks to @immarried post here Seeking help - No module named 'graphviz'

u2fastai · September 26, 2020, 1:50pm

Thanks - pip install graphviz worked for GCP

JakobV · September 30, 2020, 10:41am

Run this jupyter cell:

!pip install -Uqq fastbook
!pip install --user graphviz

This worked for me (and I think it was has worked for most in this thread).

Mukut · October 4, 2020, 4:37pm

Thanks a lot. Installing graphviz using ‘conda install python-graphviz’ worked on my mac.

thetj09 · October 7, 2020, 7:07pm

Had a similar issue. The cuda version you externally installed is not required/doesn’t matter. check the version of cudatoolkit (conda list cudatoolkit). This will get you 10.2 I think.

Looks like you have a cuda mismatch with pytorch and/or python.

Remove pytorch cuda and torchvision and reinstall it together as shown below:

conda remove pytorch torchvision cudatoolkit

conda install pytorch==1.6.0 torchvision==0.7.0 cudatoolkit=10.1.168 -c pytorch

For fast ai2, based on my NVIDIA driver (430) I chose the cuda 10.1, I needed based on table 1.

Does this help?

P.S
I didn’t need to install cuda externally. pytorch “gets compiled” and delivered with it’s own CUDA via conda (look for cudatoolkit)

thetj09 · October 8, 2020, 10:06pm

conda install graphviz also is enough and only modifies your current environment in which you are using it.

zh369437558 · November 8, 2020, 2:29pm

it does work thanks

sanjeevurao · January 12, 2021, 4:30pm

conda install python-graphviz worked for me.

VishnuSubramanian · February 23, 2021, 12:25pm

pip install graphviz Works for me.

hackworth · April 4, 2021, 6:09am

I did essentially what @heraldb recommended, but here are the conda commands (I was less familiar with Conda so had to look this up. BTW, this GCP with Debian:

conda deactivate
conda create -n fastai
conda activate -n fastai
conda install -c fastai fastbook
conda install -c fastai fastbook

This essentially deactivates the current conda environment, creates a new ones and switches over to that and all seems to work as expected in this friendly new environment.

It did complain about another package (not graphviz) after and I installed it with conda install -c fastai

After that echo “import fastbook” | python3 works!

SisengCo · April 8, 2021, 5:36am

This just worked for me too. Thanks for (re) posting it.

Even though I just started getting an error message when I tried run my first image classification that “ImageDataBunch” not defined