Issue running test_step.py::TestNutsCheckTrace

Questions
1

Hi,

I’m not sure if this question is better suited for discourse or the github repo, so I’m starting here.

I am installing the latest development version of pymc3 on my linux cluster and running the automated tests to verify I have everything running correctly. All the tests are passing except for one.

In test_step.py::TestNutsCheckTrace::()::test_bad_init I am getting a RuntimeError when the test is expecting a ValueError. I think the ValueError is being wrapped by the RuntimeError. I see that the latest build is passing this test, so I am assuming its an issue with my specific installation.

Would someone be able to provide some direction to how I might get this test to pass? Has anyone else seen this issue? Should I post this to the github repo instead of here?

Thanks in advance for your help!

Best regards,

Jeff

Running the test:

py.test pymc3/tests/test_step.py::TestNutsCheckTrace

Test traceback:

_____________________________________________________________________________________________________ TestNutsCheckTrace.test_bad_init ______________________________________________________________________________________________________
pymc3.parallel_sampling.RemoteTraceback:
"""
Traceback (most recent call last):
  File "/home/jdoak/src/pymc3/pymc3/parallel_sampling.py", line 73, in run
    self._start_loop()
  File "/home/jdoak/src/pymc3/pymc3/parallel_sampling.py", line 113, in _start_loop
    point, stats = self._compute_point()
  File "/home/jdoak/src/pymc3/pymc3/parallel_sampling.py", line 139, in _compute_point
    point, stats = self._step_method.step(self._point)
  File "/home/jdoak/src/pymc3/pymc3/step_methods/arraystep.py", line 247, in step
    apoint, stats = self.astep(array)
  File "/home/jdoak/src/pymc3/pymc3/step_methods/hmc/base_hmc.py", line 117, in astep
    'might be misspecified.' % start.energy)
ValueError: Bad initial energy: inf. The model might be misspecified.
"""

The above exception was the direct cause of the following exception:
pymc3.parallel_sampling.RemoteTraceback:
"""
Traceback (most recent call last):
  File "/home/jdoak/src/pymc3/pymc3/parallel_sampling.py", line 73, in run
    self._start_loop()
  File "/home/jdoak/src/pymc3/pymc3/parallel_sampling.py", line 113, in _start_loop
    point, stats = self._compute_point()
  File "/home/jdoak/src/pymc3/pymc3/parallel_sampling.py", line 139, in _compute_point
    point, stats = self._step_method.step(self._point)
  File "/home/jdoak/src/pymc3/pymc3/step_methods/arraystep.py", line 247, in step
    apoint, stats = self.astep(array)
  File "/home/jdoak/src/pymc3/pymc3/step_methods/hmc/base_hmc.py", line 117, in astep
    'might be misspecified.' % start.energy)
ValueError: Bad initial energy: inf. The model might be misspecified.
"""

The above exception was the direct cause of the following exception:

ValueError: Bad initial energy: inf. The model might be misspecified.

The above exception was the direct cause of the following exception:

self = <pymc3.tests.test_step.TestNutsCheckTrace object at 0x7f895a6748d0>

    def test_bad_init(self):
        with Model():
            HalfNormal('a', sd=1, testval=-1, transform=None)
            with pytest.raises(ValueError) as error:
>               sample(init=None)

pymc3/tests/test_step.py:431:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pymc3/sampling.py:440: in sample
    trace = _mp_sample(**sample_args)
pymc3/sampling.py:990: in _mp_sample
    for draw in sampler:
pymc3/parallel_sampling.py:305: in __iter__
    draw = ProcessAdapter.recv_draw(self._active)
pymc3/parallel_sampling.py:223: in recv_draw
    six.raise_from(RuntimeError('Chain %s failed.' % proc.chain), old)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

value = None, from_value = ValueError('Bad initial energy: inf. The model might be misspecified.',)

>   ???
E   RuntimeError: Chain 0 failed.

<string>:3: RuntimeError

System Info:

2

Hmm, the test should give you a ValueError and catch by the test. Not sure why it is not catching it.
But in any case, this is not a big deal and you can probably safely ignore it.

3

Thanks Junpeng!