Code runs in PyCharm but not Jupyter

When I run my code in PyCharm, it works fine. But when I copy the same code into a Jupyter notebook, it crashes with the error below:

C:\Users\maria\Anaconda3\envs\PYMC3\lib\site-packages\theano\tensor\subtensor.py:2197: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result.
  rval = inputs[0].__getitem__(inputs[1:])
C:\Users\maria\Anaconda3\envs\PYMC3\lib\site-packages\theano\tensor\subtensor.py:2339: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result.
  out[0][inputs[2:]] = inputs[1]
---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
<ipython-input-8-620e314cdf0c> in <module>()
    797             choices=choices, rewards=rewards, group=group, age=age, n_groups=n_groups,
    798             model_name=model_name, slope_variable=slope_variable, contrast=contrast, fit_individuals=fit_individuals,
--> 799             n_subj=n_subj, n_trials='all', verbose=False, print_logps=False)
    800 
    801         # Fit parameters, calculate model fits, make plots, and save everything

<ipython-input-8-620e314cdf0c> in create_model(choices, rewards, group, age, n_subj, n_trials, model_name, slope_variable, contrast, verbose, print_logps, fitted_data_name, n_groups, fit_individuals, upper)
    636         # Use Bernoulli to sample responses
    637         if n_trials_back < 3:
--> 638             model_choices = pm.Bernoulli('model_choices', p=p_right[:-1], observed=choices[3:])  # predict from trial 3 on; discard last p_right because there is no trial to predict after the last value update
    639         else:
    640             model_choices = pm.Bernoulli('model_choices', p=p_right[:-1], observed=choices[4:])  # predict from trial 4 on; discard last p_right because there is no trial to predict after the last value update

~\Anaconda3\envs\PYMC3\lib\site-packages\pymc3\distributions\distribution.py in __new__(cls, name, *args, **kwargs)
     44                 raise TypeError("observed needs to be data but got: {}".format(type(data)))
     45             total_size = kwargs.pop('total_size', None)
---> 46             dist = cls.dist(*args, **kwargs)
     47             return model.Var(name, dist, data, total_size)
     48         else:

~\Anaconda3\envs\PYMC3\lib\site-packages\pymc3\distributions\distribution.py in dist(cls, *args, **kwargs)
     55     def dist(cls, *args, **kwargs):
     56         dist = object.__new__(cls)
---> 57         dist.__init__(*args, **kwargs)
     58         return dist
     59 

~\Anaconda3\envs\PYMC3\lib\site-packages\pymc3\distributions\discrete.py in __init__(self, p, logit_p, *args, **kwargs)
    310             self._logit_p = tt.as_tensor_variable(logit_p)
    311 
--> 312         self.mode = tt.cast(tround(self.p), 'int8')
    313 
    314     def random(self, point=None, size=None):

~\Anaconda3\envs\PYMC3\lib\site-packages\pymc3\math.py in tround(*args, **kwargs)
    102     """
    103     kwargs['mode'] = 'half_to_even'
--> 104     return tt.round(*args, **kwargs)
    105 
    106 

~\Anaconda3\envs\PYMC3\lib\site-packages\theano\tensor\basic.py in round(a, mode)
   2188         return round_half_away_from_zero(a)
   2189     elif mode == "half_to_even":
-> 2190         return round_half_to_even(a)
   2191     else:
   2192         raise Exception("round mode %s is not implemented." % mode)

~\Anaconda3\envs\PYMC3\lib\site-packages\theano\gof\op.py in __call__(self, *inputs, **kwargs)
    668                 # compute output value once with test inputs to validate graph
    669                 thunk = node.op.make_thunk(node, storage_map, compute_map,
--> 670                                            no_recycling=[])
    671                 thunk.inputs = [storage_map[v] for v in node.inputs]
    672                 thunk.outputs = [storage_map[v] for v in node.outputs]

~\Anaconda3\envs\PYMC3\lib\site-packages\theano\gof\op.py in make_thunk(self, node, storage_map, compute_map, no_recycling, impl)
    953             try:
    954                 return self.make_c_thunk(node, storage_map, compute_map,
--> 955                                          no_recycling)
    956             except (NotImplementedError, utils.MethodNotDefined):
    957                 # We requested the c code, so don't catch the error.

~\Anaconda3\envs\PYMC3\lib\site-packages\theano\gof\op.py in make_c_thunk(self, node, storage_map, compute_map, no_recycling)
    856         _logger.debug('Trying CLinker.make_thunk')
    857         outputs = cl.make_thunk(input_storage=node_input_storage,
--> 858                                 output_storage=node_output_storage)
    859         thunk, node_input_filters, node_output_filters = outputs
    860 

~\Anaconda3\envs\PYMC3\lib\site-packages\theano\gof\cc.py in make_thunk(self, input_storage, output_storage, storage_map, keep_lock)
   1215         cthunk, module, in_storage, out_storage, error_storage = self.__compile__(
   1216             input_storage, output_storage, storage_map,
-> 1217             keep_lock=keep_lock)
   1218 
   1219         res = _CThunk(cthunk, init_tasks, tasks, error_storage, module)

~\Anaconda3\envs\PYMC3\lib\site-packages\theano\gof\cc.py in __compile__(self, input_storage, output_storage, storage_map, keep_lock)
   1155                                             output_storage,
   1156                                             storage_map,
-> 1157                                             keep_lock=keep_lock)
   1158         return (thunk,
   1159                 module,

~\Anaconda3\envs\PYMC3\lib\site-packages\theano\gof\cc.py in cthunk_factory(self, error_storage, in_storage, out_storage, storage_map, keep_lock)
   1622                 node.op.prepare_node(node, storage_map, None, 'c')
   1623             module = get_module_cache().module_from_key(
-> 1624                 key=key, lnk=self, keep_lock=keep_lock)
   1625 
   1626         vars = self.inputs + self.outputs + self.orphans

~\Anaconda3\envs\PYMC3\lib\site-packages\theano\gof\cmodule.py in module_from_key(self, key, lnk, keep_lock)
   1146         """
   1147         # Is the module in the cache?
-> 1148         module = self._get_from_key(key)
   1149         if module is not None:
   1150             return module

~\Anaconda3\envs\PYMC3\lib\site-packages\theano\gof\cmodule.py in _get_from_key(self, key, key_data)
   1045         if name is None:
   1046             return None
-> 1047         return self._get_module(name)
   1048 
   1049     def _get_from_hash(self, module_hash, key, keep_lock=False):

~\Anaconda3\envs\PYMC3\lib\site-packages\theano\gof\cmodule.py in _get_module(self, name)
    718         if name not in self.module_from_name:
    719             _logger.debug('loading name %s', name)
--> 720             self.module_from_name[name] = dlimport(name)
    721             self.stats[1] += 1
    722         else:

~\Anaconda3\envs\PYMC3\lib\site-packages\theano\gof\cmodule.py in dlimport(fullpath, suffix)
    315             warnings.filterwarnings("ignore",
    316                                     message="numpy.ndarray size changed")
--> 317             rval = __import__(module_name, {}, {}, [module_name])
    318         t1 = time.time()
    319         import_time += t1 - t0

ImportError: DLL load failed: The specified procedure could not be found.

I would have loved to use PyMC3 in Jupyter - any insights what might be causing the issue? Thanks!

Not sure why this happens, but maybe try deleting the theano cache and reset your python environment if necessary

Are you sure that jupyter is installed in your environment?

In pycharm and notebook

import os
print(os)

Thanks for your quick responses! I deleted the theano cache and made sure I’m running Jupyter and PyCharm with the same conda environment (and I am), but still no success. I also set n_cores=1, which didn’t help either. A very basic pm example (sampling just one variable) is working fine.
I will just keep working in PyCharm for now. Let me know if anything else comes to mind!