03_01_autoencoder_train.ipynb and 03_03_vae_digits_train.ipynb both crash with GraphViz error

[jtiscione]

I set up the conda environment according to instructions; all notebooks in chapter 2 work, but as soon as I get to chapter 3 I'm stopped by this error in 03_01_autoencoder_train.ipynb and 03_03_vae_digits_train.ipynb:

---------------------------------------------------------------------------
FileNotFoundError                         Traceback (most recent call last)
~/anaconda3/envs/generative/lib/python3.6/site-packages/pydot.py in create(self, prog, format, encoding)
   1914                 arguments=arguments,
-> 1915                 working_dir=tmp_dir,
   1916             )

~/anaconda3/envs/generative/lib/python3.6/site-packages/pydot.py in call_graphviz(program, arguments, working_dir, **kwargs)
    135         stdout=subprocess.PIPE,
--> 136         **kwargs
    137     )

~/anaconda3/envs/generative/lib/python3.6/subprocess.py in __init__(self, args, bufsize, executable, stdin, stdout, stderr, preexec_fn, close_fds, shell, cwd, env, universal_newlines, startupinfo, creationflags, restore_signals, start_new_session, pass_fds, encoding, errors)
    728                                 errread, errwrite,
--> 729                                 restore_signals, start_new_session)
    730         except:

~/anaconda3/envs/generative/lib/python3.6/subprocess.py in _execute_child(self, args, executable, preexec_fn, close_fds, pass_fds, cwd, env, startupinfo, creationflags, shell, p2cread, p2cwrite, c2pread, c2pwrite, errread, errwrite, restore_signals, start_new_session)
   1363                             err_msg += ': ' + repr(err_filename)
-> 1364                     raise child_exception_type(errno_num, err_msg, err_filename)
   1365                 raise child_exception_type(err_msg)

FileNotFoundError: [Errno 2] No such file or directory: 'dot': 'dot'

During handling of the above exception, another exception occurred:

FileNotFoundError                         Traceback (most recent call last)
~/anaconda3/envs/generative/lib/python3.6/site-packages/keras/utils/vis_utils.py in _check_pydot()
     25         # to check the pydot/graphviz installation.
---> 26         pydot.Dot.create(pydot.Dot())
     27     except OSError:

~/anaconda3/envs/generative/lib/python3.6/site-packages/pydot.py in create(self, prog, format, encoding)
   1921                     prog=prog)
-> 1922                 raise OSError(*args)
   1923             else:

FileNotFoundError: [Errno 2] "dot" not found in path.

During handling of the above exception, another exception occurred:

OSError                                   Traceback (most recent call last)
<ipython-input-4-2cbc3320019b> in <module>
     11 
     12 if MODE == 'build':
---> 13     AE.save(RUN_FOLDER)
     14 else:
     15     AE.load_weights(os.path.join(RUN_FOLDER, 'weights/weights.h5'))

~/repo/GDL_code/models/AE.py in save(self, folder)
    153                 ], f)
    154 
--> 155         self.plot_model(folder)
    156 
    157 

~/repo/GDL_code/models/AE.py in plot_model(self, run_folder)
    182 
    183     def plot_model(self, run_folder):
--> 184         plot_model(self.model, to_file=os.path.join(run_folder ,'viz/model.png'), show_shapes = True, show_layer_names = True)
    185         plot_model(self.encoder, to_file=os.path.join(run_folder ,'viz/encoder.png'), show_shapes = True, show_layer_names = True)
    186         plot_model(self.decoder, to_file=os.path.join(run_folder ,'viz/decoder.png'), show_shapes = True, show_layer_names = True)

~/anaconda3/envs/generative/lib/python3.6/site-packages/keras/utils/vis_utils.py in plot_model(model, to_file, show_shapes, show_layer_names, rankdir)
    130             'LR' creates a horizontal plot.
    131     """
--> 132     dot = model_to_dot(model, show_shapes, show_layer_names, rankdir)
    133     _, extension = os.path.splitext(to_file)
    134     if not extension:

~/anaconda3/envs/generative/lib/python3.6/site-packages/keras/utils/vis_utils.py in model_to_dot(model, show_shapes, show_layer_names, rankdir)
     53     from ..models import Sequential
     54 
---> 55     _check_pydot()
     56     dot = pydot.Dot()
     57     dot.set('rankdir', rankdir)

~/anaconda3/envs/generative/lib/python3.6/site-packages/keras/utils/vis_utils.py in _check_pydot()
     27     except OSError:
     28         raise OSError(
---> 29             '`pydot` failed to call GraphViz.'
     30             'Please install GraphViz (https://www.graphviz.org/) '
     31             'and 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.

I did some searching and people are saying to fix it by running conda install graphviz followed by conda install python-graphviz, but I tried that and it doesn't change anything. The book doesn't mention GraphViz anywhere.

[jtiscione]

This is on an Ubuntu system, so I tried running sudo apt-get install -y graphviz libgraphviz-dev in a separate terminal, and that appears to have nailed it.

I'm not sure whether or not the conda install graphviz and conda install python-graphviz were necessary for this to work.

[soundpoet]

conda install pydot and then proceeding installation of the suggested packages fixed it for me.