Theano breaks on new numpy

[ColCarroll]

Running pip install pymc3 in a fresh environment today installs numpy==1.16.0, which throws an error (via theano) for pretty much any input. We should pin numpy to below 1.16 for now, until we can get a fix into theano.

Here's one reproducible example along with the traceback:

with pm.Model():
    pm.Normal('x')
    pm.sample()

Traceback (most recent call last):
  File "<stdin>", line 2, in <module>
  File "/Users/rustrulz/miniconda3/envs/pymc3_bug3.6/lib/python3.6/site-packages/pymc3/distributions/distribution.py", line 41, in __new__
    dist = cls.dist(*args, **kwargs)
  File "/Users/rustrulz/miniconda3/envs/pymc3_bug3.6/lib/python3.6/site-packages/pymc3/distributions/distribution.py", line 52, in dist
    dist.__init__(*args, **kwargs)
  File "/Users/rustrulz/miniconda3/envs/pymc3_bug3.6/lib/python3.6/site-packages/pymc3/distributions/continuous.py", line 432, in __init__
    self.variance = 1. / self.tau
  File "/Users/rustrulz/miniconda3/envs/pymc3_bug3.6/lib/python3.6/site-packages/theano/tensor/var.py", line 203, in __rtruediv__
    return theano.tensor.basic.true_div(other, self)
  File "/Users/rustrulz/miniconda3/envs/pymc3_bug3.6/lib/python3.6/site-packages/theano/gof/op.py", line 670, in __call__
    no_recycling=[])
  File "/Users/rustrulz/miniconda3/envs/pymc3_bug3.6/lib/python3.6/site-packages/theano/gof/op.py", line 955, in make_thunk
    no_recycling)
  File "/Users/rustrulz/miniconda3/envs/pymc3_bug3.6/lib/python3.6/site-packages/theano/gof/op.py", line 858, in make_c_thunk
    output_storage=node_output_storage)
  File "/Users/rustrulz/miniconda3/envs/pymc3_bug3.6/lib/python3.6/site-packages/theano/gof/cc.py", line 1217, in make_thunk
    keep_lock=keep_lock)
  File "/Users/rustrulz/miniconda3/envs/pymc3_bug3.6/lib/python3.6/site-packages/theano/gof/cc.py", line 1157, in __compile__
    keep_lock=keep_lock)
  File "/Users/rustrulz/miniconda3/envs/pymc3_bug3.6/lib/python3.6/site-packages/theano/gof/cc.py", line 1609, in cthunk_factory
    key = self.cmodule_key()
  File "/Users/rustrulz/miniconda3/envs/pymc3_bug3.6/lib/python3.6/site-packages/theano/gof/cc.py", line 1300, in cmodule_key
    c_compiler=self.c_compiler(),
  File "/Users/rustrulz/miniconda3/envs/pymc3_bug3.6/lib/python3.6/site-packages/theano/gof/cc.py", line 1379, in cmodule_key_
    np.core.multiarray._get_ndarray_c_version())
AttributeError: module 'numpy.core.multiarray' has no attribute '_get_ndarray_c_version'

[ColCarroll]

Oh hai -- looks like it is fixed on theano master: Theano/Theano#6671

[nouiz]

We just released Theano 1.0.4 that added support for numpy 1.16 on the CPU. We didn't test on the GPU.

[twiecki]

Seems like we should pin to theano >= 1.0.4

[poiuwn]

@ColCarroll I am a newbie to PyMC and Bayesian. I installed Anaconda 3 and PyMC3 yesterday [Apr 13, 2019], but when I try to run code similar to your code snippet, I also have this error:
AttributeError: module 'numpy.core.multiarray' has no attribute '_get_ndarray_c_version'

I believe you people are talking about a workaround. But when you say pin to higher theano, what does that mean? And what should I do exactly? I also went to the URL of Pin to higher theano #3342 but I did not find out what to do.
Here is my environment:
np.version
Out[234]: '1.16.2'
pm.version
Out[235]: '3.6'

thank you for your attention

[ericmjl]

@poiuwn, to pin to a higher version of theano means to ensure that you are using at least theano version >=1.0.4.

You can do this in your environment.yml file (if you are using conda environments), or your requirements.txt file (if you are using a virtual env (venv)). I would refer to their respective documentation to specify how to pin a dependency to a particular version.

[poiuwn]

@ericmjl Thanks so much for your prompt reply. I am using Anaconda 3.
I downloaded environment.yml following the instruction at https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#creating-an-environment-from-an-environment-yml-file . The downloaded file has an entry that reads: - theano=1.0.3=py37_0.
Do I need to do something about it?
The downloaded file is attached for your convenience.

environmentExported.zip

[ericmjl]

Do I need to do something about it?

@poiuwn yes, I would change that line to:

- theano>=1.0.4

You can remove the py37_0.

[poiuwn]

@ericmjl Thanks for your reply. Indeed I have never dealth with environment.yml file, so I find it easier to upgrade the Theano to 1.0.4, which i did by pip install --upgrade theano. After that the error disappears.

Thanks again for your help.

[reemlores]

Hi everyone
I got the same error :" AttributeError: module 'numpy.core.multiarray' has no attribute '_get_ndarray_c_version'"
even after upgrading Theano to 1.0.4.
Python version 3.7
numpy version 1.16.2

[ericmjl]

@reemlores can you paste here the output of the following?

$ which pip
$ which python
$ conda env list 

My first hunch is environment mismatch.