Exception in example NB

[twiecki]

I'm up-to-date on pymc3 and gelato.

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
/Users/twiecki/anaconda/lib/python3.6/site-packages/theano/gof/op.py in __call__(self, *inputs, **kwargs)
    624                 try:
--> 625                     storage_map[ins] = [self._get_test_value(ins)]
    626                     compute_map[ins] = [True]

/Users/twiecki/anaconda/lib/python3.6/site-packages/theano/gof/op.py in _get_test_value(cls, v)
    580         detailed_err_msg = utils.get_variable_trace_string(v)
--> 581         raise AttributeError('%s has no test value %s' % (v, detailed_err_msg))
    582 

AttributeError: Softmax.0 has no test value  
Backtrace when that variable is created:

  File "/Users/twiecki/anaconda/lib/python3.6/site-packages/ipykernel/zmqshell.py", line 533, in run_cell
    return super(ZMQInteractiveShell, self).run_cell(*args, **kwargs)
  File "/Users/twiecki/anaconda/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2717, in run_cell
    interactivity=interactivity, compiler=compiler, result=result)
  File "/Users/twiecki/anaconda/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2821, in run_ast_nodes
    if self.run_code(code, result):
  File "/Users/twiecki/anaconda/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2881, in run_code
    exec(code_obj, self.user_global_ns, self.user_ns)
  File "<ipython-input-18-7dd01309b711>", line 37, in <module>
    prediction = gelato.layers.get_output(network)
  File "/Users/twiecki/anaconda/lib/python3.6/site-packages/lasagne/layers/helper.py", line 190, in get_output
    all_outputs[layer] = layer.get_output_for(layer_inputs, **kwargs)
  File "/Users/twiecki/anaconda/lib/python3.6/site-packages/lasagne/layers/dense.py", line 124, in get_output_for
    return self.nonlinearity(activation)
  File "/Users/twiecki/anaconda/lib/python3.6/site-packages/lasagne/nonlinearities.py", line 44, in softmax
    return theano.tensor.nnet.softmax(x)


During handling of the above exception, another exception occurred:

ValueError                                Traceback (most recent call last)
<ipython-input-18-7dd01309b711> in <module>()
     44                    prediction,
     45                    observed=target_var,
---> 46                    total_size=total_size)

/Users/twiecki/working/projects/pymc/pymc3/distributions/distribution.py in __new__(cls, name, *args, **kwargs)
     35                 raise TypeError("observed needs to be data but got: {}".format(type(data)))
     36             total_size = kwargs.pop('total_size', None)
---> 37             dist = cls.dist(*args, **kwargs)
     38             return model.Var(name, dist, data, total_size)
     39         else:

/Users/twiecki/working/projects/pymc/pymc3/distributions/distribution.py in dist(cls, *args, **kwargs)
     46     def dist(cls, *args, **kwargs):
     47         dist = object.__new__(cls)
---> 48         dist.__init__(*args, **kwargs)
     49         return dist
     50 

/Users/twiecki/working/projects/pymc/pymc3/distributions/discrete.py in __init__(self, p, *args, **kwargs)
    429         super(Categorical, self).__init__(*args, **kwargs)
    430         try:
--> 431             self.k = tt.shape(p)[-1].tag.test_value
    432         except AttributeError:
    433             self.k = tt.shape(p)[-1]

/Users/twiecki/anaconda/lib/python3.6/site-packages/theano/gof/op.py in __call__(self, *inputs, **kwargs)
    637                         raise ValueError(
    638                             'Cannot compute test value: input %i (%s) of Op %s missing default value. %s' %
--> 639                             (i, ins, node, detailed_err_msg))
    640                     elif config.compute_test_value == 'ignore':
    641                         # silently skip test

ValueError: Cannot compute test value: input 0 (Softmax.0) of Op Shape(Softmax.0) missing default value.  
Backtrace when that variable is created:

  File "/Users/twiecki/anaconda/lib/python3.6/site-packages/ipykernel/zmqshell.py", line 533, in run_cell
    return super(ZMQInteractiveShell, self).run_cell(*args, **kwargs)
  File "/Users/twiecki/anaconda/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2717, in run_cell
    interactivity=interactivity, compiler=compiler, result=result)
  File "/Users/twiecki/anaconda/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2821, in run_ast_nodes
    if self.run_code(code, result):
  File "/Users/twiecki/anaconda/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2881, in run_code
    exec(code_obj, self.user_global_ns, self.user_ns)
  File "<ipython-input-18-7dd01309b711>", line 37, in <module>
    prediction = gelato.layers.get_output(network)
  File "/Users/twiecki/anaconda/lib/python3.6/site-packages/lasagne/layers/helper.py", line 190, in get_output
    all_outputs[layer] = layer.get_output_for(layer_inputs, **kwargs)
  File "/Users/twiecki/anaconda/lib/python3.6/site-packages/lasagne/layers/dense.py", line 124, in get_output_for
    return self.nonlinearity(activation)
  File "/Users/twiecki/anaconda/lib/python3.6/site-packages/lasagne/nonlinearities.py", line 44, in softmax
    return theano.tensor.nnet.softmax(x)

[twiecki]

@ferrine any idea?

[ferrine]

I think that can be caused by our changing flags in context. You can try to set compute_test_value='raise'

[twiecki]

@ferrine that didn't help.

[ferrine]

Ok I'll rerun it on weekends

[ferrine]

It worked

[twiecki]

Now getting a different error:

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
~/anaconda/lib/python3.6/site-packages/theano/gof/op.py in __call__(self, *inputs, **kwargs)
    624                 try:
--> 625                     storage_map[ins] = [self._get_test_value(ins)]
    626                     compute_map[ins] = [True]

~/anaconda/lib/python3.6/site-packages/theano/gof/op.py in _get_test_value(cls, v)
    580         detailed_err_msg = utils.get_variable_trace_string(v)
--> 581         raise AttributeError('%s has no test value %s' % (v, detailed_err_msg))
    582 

AttributeError: AdvancedSubtensor1.0 has no test value  
Backtrace when that variable is created:

  File "/Users/twiecki/anaconda/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 235, in dispatch_shell
    handler(stream, idents, msg)
  File "/Users/twiecki/anaconda/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 399, in execute_request
    user_expressions, allow_stdin)
  File "/Users/twiecki/anaconda/lib/python3.6/site-packages/ipykernel/ipkernel.py", line 196, in do_execute
    res = shell.run_cell(code, store_history=store_history, silent=silent)
  File "/Users/twiecki/anaconda/lib/python3.6/site-packages/ipykernel/zmqshell.py", line 533, in run_cell
    return super(ZMQInteractiveShell, self).run_cell(*args, **kwargs)
  File "/Users/twiecki/anaconda/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2698, in run_cell
    interactivity=interactivity, compiler=compiler, result=result)
  File "/Users/twiecki/anaconda/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2802, in run_ast_nodes
    if self.run_code(code, result):
  File "/Users/twiecki/anaconda/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2862, in run_code
    exec(code_obj, self.user_global_ns, self.user_ns)
  File "<ipython-input-3-d01dfc616598>", line 6, in <module>
    target_var = target_var[ridx]


During handling of the above exception, another exception occurred:

ValueError                                Traceback (most recent call last)
<ipython-input-18-7dd01309b711> in <module>()
     44                    prediction,
     45                    observed=target_var,
---> 46                    total_size=total_size)

~/working/projects/pymc/pymc3/distributions/distribution.py in __new__(cls, name, *args, **kwargs)
     37             total_size = kwargs.pop('total_size', None)
     38             dist = cls.dist(*args, **kwargs)
---> 39             return model.Var(name, dist, data, total_size)
     40         else:
     41             raise TypeError("Name needs to be a string but got: {}".format(name))

~/working/projects/pymc/pymc3/model.py in Var(self, name, dist, data, total_size)
    543                 var = ObservedRV(name=name, data=data,
    544                                  distribution=dist,
--> 545                                  total_size=total_size, model=self)
    546             self.observed_RVs.append(var)
    547             if var.missing_values:

~/working/projects/pymc/pymc3/model.py in __init__(self, type, owner, index, name, data, distribution, total_size, model)
    958         if type is None:
    959             data = pandas_to_array(data)
--> 960             type = TensorType(distribution.dtype, data.shape)
    961 
    962         self.observations = data

~/anaconda/lib/python3.6/site-packages/theano/tensor/var.py in <lambda>(self)
    273             return theano.tensor.basic.transpose(self, axes)
    274 
--> 275     shape = property(lambda self: theano.tensor.basic.shape(self))
    276 
    277     size = property(lambda self: self.shape[0] if self.ndim == 1 else

~/anaconda/lib/python3.6/site-packages/theano/gof/op.py in __call__(self, *inputs, **kwargs)
    637                         raise ValueError(
    638                             'Cannot compute test value: input %i (%s) of Op %s missing default value. %s' %
--> 639                             (i, ins, node, detailed_err_msg))
    640                     elif config.compute_test_value == 'ignore':
    641                         # silently skip test

ValueError: Cannot compute test value: input 0 (AdvancedSubtensor1.0) of Op Shape(AdvancedSubtensor1.0) missing default value.  
Backtrace when that variable is created:

  File "/Users/twiecki/anaconda/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 235, in dispatch_shell
    handler(stream, idents, msg)
  File "/Users/twiecki/anaconda/lib/python3.6/site-packages/ipykernel/kernelbase.py", line 399, in execute_request
    user_expressions, allow_stdin)
  File "/Users/twiecki/anaconda/lib/python3.6/site-packages/ipykernel/ipkernel.py", line 196, in do_execute
    res = shell.run_cell(code, store_history=store_history, silent=silent)
  File "/Users/twiecki/anaconda/lib/python3.6/site-packages/ipykernel/zmqshell.py", line 533, in run_cell
    return super(ZMQInteractiveShell, self).run_cell(*args, **kwargs)
  File "/Users/twiecki/anaconda/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2698, in run_cell
    interactivity=interactivity, compiler=compiler, result=result)
  File "/Users/twiecki/anaconda/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2802, in run_ast_nodes
    if self.run_code(code, result):
  File "/Users/twiecki/anaconda/lib/python3.6/site-packages/IPython/core/interactiveshell.py", line 2862, in run_code
    exec(code_obj, self.user_global_ns, self.user_ns)
  File "<ipython-input-3-d01dfc616598>", line 6, in <module>
    target_var = target_var[ridx]

[ferrine]

what is your theano.config.compute_test_value?

[twiecki]

On Sun, Jun 25, 2017 at 12:41 PM, Maxim Kochurov ***@***.***> wrote: theano.config.compute_test_value

'raise'

[ferrine]

Could you please git pull and rerun?

[ferrine]

seems like get_output is called without computing test value. Try to set warn in the NB header and rerun

[twiecki]

That did the trick (just pulling), thanks!

[ferrine]

Closed the issue as it seems to be solved