# PyMC v5.0.1 - tutorials in docs page not working from the conda environment (Windows 11)

**URL:** <https://discourse.pymc.io/t/pymc-v5-0-1-tutorials-in-docs-page-not-working-from-the-conda-environment-windows-11/11151>\
**Category:** v5\
**Created:** [January 10, 2023, 3:37am UTC](https://discourse.pymc.io/t/pymc-v5-0-1-tutorials-in-docs-page-not-working-from-the-conda-environment-windows-11/11151 "2023-01-10T03:37:13Z")\
**Posts on this page:** 7\
**Page:** 1

<div class="post-metadata">

**Author:** ![the\_Hypogliph](https://yyz2.discourse-cdn.com/flex036/user_avatar/discourse.pymc.io/the_hypogliph/32/6005_2.png) [@the\_Hypogliph](https://discourse.pymc.io/u/the_Hypogliph)\
**Post date:** [January 10, 2023, 3:37am UTC](https://discourse.pymc.io/t/pymc-v5-0-1-tutorials-in-docs-page-not-working-from-the-conda-environment-windows-11/11151/1 "2023-01-10T03:37:13Z")

</div>

Hello,

I have just installed the new pymc using the installation step in the docs:

```
conda create -c conda-forge -n pymc_env "pymc>=4"
conda activate pymc_env

```

I am trying to run the code in some of the tutorials in the docs page, and always get the same error for all the tutorials. Here’s the code:

```auto
import pymc as pm
print(f"Running on PyMC v{pm. __version__ }") # output : Running on PyMC v5.0.1
import pandas as pd
import numpy as np

# fmt: off
disaster_data = pd.Series(
    [4, 5, 4, 0, 1, 4, 3, 4, 0, 6, 3, 3, 4, 0, 2, 6,
    3, 3, 5, 4, 5, 3, 1, 4, 4, 1, 5, 5, 3, 4, 2, 5,
    2, 2, 3, 4, 2, 1, 3, np.nan, 2, 1, 1, 1, 1, 3, 0, 0,
    1, 0, 1, 1, 0, 0, 3, 1, 0, 3, 2, 2, 0, 1, 1, 1,
    0, 1, 0, 1, 0, 0, 0, 2, 1, 0, 0, 0, 1, 1, 0, 2,
    3, 3, 1, np.nan, 2, 1, 1, 1, 1, 2, 4, 2, 0, 0, 1, 4,
    0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 1]
)
# fmt: on
years = np.arange(1851, 1962)

with pm.Model() as disaster_model:

    switchpoint = pm.DiscreteUniform("switchpoint", lower=years.min(), upper=years.max())

    # Priors for pre- and post-switch rates number of disasters
    early_rate = pm.Exponential("early_rate", 1.0)
    late_rate = pm.Exponential("late_rate", 1.0)

    # Allocate appropriate Poisson rates to years before and after current
    rate = pm.math.switch(switchpoint >= years, early_rate, late_rate)

    disasters = pm.Poisson("disasters", rate, observed=disaster_data)

with disaster_model:
    idata = pm.sample(10000)

```

And the error message I get is the following:

```auto
---------------------------------------------------------------------------
IndexError Traceback (most recent call last)
Cell In[13], line 2
      1 with disaster_model:
----> 2 idata = pm.sample(10000, chains = (2))

File ~\anaconda3\envs\new_pymc\Lib\site-packages\pymc\sampling\mcmc.py:529, in sample(draws, step, init, n_init, initvals, trace, chains, cores, tune, progressbar, model, random_seed, discard_tuned_samples, compute_convergence_checks, callback, jitter_max_retries, return_inferencedata, keep_warning_stat, idata_kwargs, mp_ctx, **kwargs)
    527 _print_step_hierarchy(step)
    528 try:
--> 529 mtrace = _mp_sample( **sample_args,** parallel_args)
    530 except pickle.PickleError:
    531 _log.warning("Could not pickle model, sampling singlethreaded.")

File ~\anaconda3\envs\new_pymc\Lib\site-packages\pymc\sampling\mcmc.py:1005, in _mp_sample(draws, tune, step, chains, cores, random_seed, start, progressbar, trace, model, callback, discard_tuned_samples, mp_ctx, **kwargs)
    992 draws -= tune
    994 traces = [
    995 _init_trace(
    996 expected_length=draws + tune,
   (...)
   1002 for chain_number in range(chains)
   1003 ]
-> 1005 sampler = ps.ParallelSampler(
   1006 draws=draws,
   1007 tune=tune,
   1008 chains=chains,
   1009 cores=cores,
   1010 seeds=random_seed,
   1011 start_points=start,
   1012 step_method=step,
   1013 progressbar=progressbar,
   1014 mp_ctx=mp_ctx,
   1015 )
   1016 try:
   1017 try:

File ~\anaconda3\envs\new_pymc\Lib\site-packages\pymc\sampling\parallel.py:401, in ParallelSampler. __init__ (self, draws, tune, chains, cores, seeds, start_points, step_method, progressbar, mp_ctx)
    399 step_method_pickled = None
    400 if mp_ctx.get_start_method() != "fork":
--> 401 step_method_pickled = cloudpickle.dumps(step_method, protocol=-1)
    403 self._samplers = [
    404 ProcessAdapter(
    405 draws,
   (...)
    414 for chain, seed, start in zip(range(chains), seeds, start_points)
    415 ]
    417 self._inactive = self._samplers.copy()

File ~\anaconda3\envs\new_pymc\Lib\site-packages\cloudpickle\cloudpickle_fast.py:73, in dumps(obj, protocol, buffer_callback)
     69 with io.BytesIO() as file:
     70 cp = CloudPickler(
     71 file, protocol=protocol, buffer_callback=buffer_callback
     72 )
---> 73 cp.dump(obj)
     74 return file.getvalue()

File ~\anaconda3\envs\new_pymc\Lib\site-packages\cloudpickle\cloudpickle_fast.py:602, in CloudPickler.dump(self, obj)
    600 def dump(self, obj):
    601 try:
--> 602 return Pickler.dump(self, obj)
    603 except RuntimeError as e:
    604 if "recursion" in e.args[0]:

File ~\anaconda3\envs\new_pymc\Lib\site-packages\cloudpickle\cloudpickle_fast.py:692, in CloudPickler.reducer_override(self, obj)
    690 return _class_reduce(obj)
    691 elif isinstance(obj, types.FunctionType):
--> 692 return self._function_reduce(obj)
    693 else:
    694 # fallback to save_global, including the Pickler's
    695 # dispatch_table
    696 return NotImplemented

File ~\anaconda3\envs\new_pymc\Lib\site-packages\cloudpickle\cloudpickle_fast.py:565, in CloudPickler._function_reduce(self, obj)
    563 return NotImplemented
    564 else:
--> 565 return self._dynamic_function_reduce(obj)

File ~\anaconda3\envs\new_pymc\Lib\site-packages\cloudpickle\cloudpickle_fast.py:546, in CloudPickler._dynamic_function_reduce(self, func)
    544 """Reduce a function that is not pickleable via attribute lookup."""
    545 newargs = self._function_getnewargs(func)
--> 546 state = _function_getstate(func)
    547 return (types.FunctionType, newargs, state, None, None,
    548 _function_setstate)

File ~\anaconda3\envs\new_pymc\Lib\site-packages\cloudpickle\cloudpickle_fast.py:157, in _function_getstate(func)
    139 def _function_getstate(func):
    140 # - Put func's dynamic attributes (stored in func. __dict__ ) in state. These
    141 # attributes will be restored at unpickling time using
   (...)
    144 # unpickling time by iterating over slotstate and calling setattr(func,
    145 # slotname, slotvalue)
    146 slotstate = {
    147 " __name__": func. __name__ ,
    148 " __qualname__": func. __qualname__ ,
   (...)
    154 " __closure__": func. __closure__ ,
    155 }
--> 157 f_globals_ref = _extract_code_globals(func. __code__ )
    158 f_globals = {k: func. __globals__ [k] for k in f_globals_ref if k in
    159 func. __globals__ }
    161 closure_values = (
    162 list(map(_get_cell_contents, func. __closure__ ))
    163 if func. __closure__ is not None else ()
    164 )

File ~\anaconda3\envs\new_pymc\Lib\site-packages\cloudpickle\cloudpickle.py:334, in _extract_code_globals(co)
    330 names = co.co_names
    331 # We use a dict with None values instead of a set to get a
    332 # deterministic order (assuming Python 3.6+) and avoid introducing
    333 # non-deterministic pickle bytes as a results.
--> 334 out_names = {names[oparg]: None for _, oparg in _walk_global_ops(co)}
    336 # Declaring a function inside another one using the "def ..."
    337 # syntax generates a constant code object corresponding to the one
    338 # of the nested function's As the nested function may itself need
    339 # global variables, we need to introspect its code, extract its
    340 # globals, (look for code object in it's co_consts attribute..) and
    341 # add the result to code_globals
    342 if co.co_consts:

File ~\anaconda3\envs\new_pymc\Lib\site-packages\cloudpickle\cloudpickle.py:334, in <dictcomp>(.0)
    330 names = co.co_names
    331 # We use a dict with None values instead of a set to get a
    332 # deterministic order (assuming Python 3.6+) and avoid introducing
    333 # non-deterministic pickle bytes as a results.
--> 334 out_names = {names[oparg]: None for _, oparg in _walk_global_ops(co)}
    336 # Declaring a function inside another one using the "def ..."
    337 # syntax generates a constant code object corresponding to the one
    338 # of the nested function's As the nested function may itself need
    339 # global variables, we need to introspect its code, extract its
    340 # globals, (look for code object in it's co_consts attribute..) and
    341 # add the result to code_globals
    342 if co.co_consts:

IndexError: tuple index out of range

```

The same error happens when I run other examples as well… I have no clue where this is coming from. Also tried a fresh install twice but no luck.

Thanks.

---

<div class="post-metadata">

**Author:** ![cluhmann](https://yyz2.discourse-cdn.com/flex036/user_avatar/discourse.pymc.io/cluhmann/32/3083_2.png) [@cluhmann](https://discourse.pymc.io/u/cluhmann)\
**Post date:** [January 10, 2023, 3:51am UTC](https://discourse.pymc.io/t/pymc-v5-0-1-tutorials-in-docs-page-not-working-from-the-conda-environment-windows-11/11151/2 "2023-01-10T03:51:27Z")

</div>

Welcome!

A couple of questions. I assume you are Windows. Did you have a previous version of PyMC installed where you were not getting these errors? What happens if you add `chains=1` to the call to `pm.sample()`?

---

<div class="post-metadata">

**Author:** ![the\_Hypogliph](https://yyz2.discourse-cdn.com/flex036/user_avatar/discourse.pymc.io/the_hypogliph/32/6005_2.png) [@the\_Hypogliph](https://discourse.pymc.io/u/the_Hypogliph)\
**Post date:** [January 10, 2023, 4:01am UTC](https://discourse.pymc.io/t/pymc-v5-0-1-tutorials-in-docs-page-not-working-from-the-conda-environment-windows-11/11151/3 "2023-01-10T04:01:21Z")

</div>

Hi, thank you so much for getting back to me.

Yes, I am running on windows 11, and have not had a prior Pymc version that didn’t show these errors on this specific machine.  
Chains = 1 does not throw the error, and it is able to sample.  
Chains = 2 (or 3, 4, 5) still throws the error.

Thanks again for your help.

---

<div class="post-metadata">

**Author:** ![cluhmann](https://yyz2.discourse-cdn.com/flex036/user_avatar/discourse.pymc.io/cluhmann/32/3083_2.png) [@cluhmann](https://discourse.pymc.io/u/cluhmann)\
**Post date:** [January 10, 2023, 4:14am UTC](https://discourse.pymc.io/t/pymc-v5-0-1-tutorials-in-docs-page-not-working-from-the-conda-environment-windows-11/11151/4 "2023-01-10T04:14:06Z")

</div>

It looks like you may be running into one of the issues discussed [here](https://github.com/pymc-devs/pymc/issues/3140). I would start by wrapping your script in a function and wrapping a call to that function in an `if __name__ == ' __main__':` statement. If one of the solutions discussed there works for you, great. If not, let us know and/or you can open a new issue (as you can see, that issue was closed because it turned into a combination of several different issues).

---

<div class="post-metadata">

**Author:** ![the\_Hypogliph](https://yyz2.discourse-cdn.com/flex036/user_avatar/discourse.pymc.io/the_hypogliph/32/6005_2.png) [@the\_Hypogliph](https://discourse.pymc.io/u/the_Hypogliph)\
**Post date:** [January 10, 2023, 4:43am UTC](https://discourse.pymc.io/t/pymc-v5-0-1-tutorials-in-docs-page-not-working-from-the-conda-environment-windows-11/11151/5 "2023-01-10T04:43:39Z")

</div>

Hi,

Thanks for the suggestion,  
Just wrapped it on the `if __name__ == ' __main__':` statement, like so:

```auto
import pandas as pd
import numpy as np

print(' ***Start script***')

if __name__ == ' __main__':

    disaster_data = pd.Series(
    [4, 5, 4, 0, 1, 4, 3, 4, 0, 6, 3, 3, 4, 0, 2, 6,
    3, 3, 5, 4, 5, 3, 1, 4, 4, 1, 5, 5, 3, 4, 2, 5,
    2, 2, 3, 4, 2, 1, 3, np.nan, 2, 1, 1, 1, 1, 3, 0, 0,
    1, 0, 1, 1, 0, 0, 3, 1, 0, 3, 2, 2, 0, 1, 1, 1,
    0, 1, 0, 1, 0, 0, 0, 2, 1, 0, 0, 0, 1, 1, 0, 2,
    3, 3, 1, np.nan, 2, 1, 1, 1, 1, 2, 4, 2, 0, 0, 1, 4,
    0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 1])

    years = np.arange(1851, 1962)

    with pm.Model() as disaster_model:

        switchpoint = pm.DiscreteUniform("switchpoint", lower=years.min(), upper=years.max())

        early_rate = pm.Exponential("early_rate", 1.0)
        late_rate = pm.Exponential("late_rate", 1.0)

        # Allocate appropriate Poisson rates to years before and after current
        rate = pm.math.switch(switchpoint >= years, early_rate, late_rate)

        disasters = pm.Poisson("disasters", rate, observed=disaster_data)

    with disaster_model:
        idata = pm.sample(10000)

```

and I get same error as above.  
for chains =1, it is able to sample,  
for chains\>1, get the same error as above.

for any number of cores, and chains=1 it samples.  
for any number of cores, and chains\>1 it does not sample.

Is there anything I could do on Windows to reset any settings that might be causing this, or something along those lines? Thank you

---

<div class="post-metadata">

**Author:** ![the\_Hypogliph](https://yyz2.discourse-cdn.com/flex036/user_avatar/discourse.pymc.io/the_hypogliph/32/6005_2.png) [@the\_Hypogliph](https://discourse.pymc.io/u/the_Hypogliph)\
**Post date:** [January 10, 2023, 5:14am UTC](https://discourse.pymc.io/t/pymc-v5-0-1-tutorials-in-docs-page-not-working-from-the-conda-environment-windows-11/11151/6 "2023-01-10T05:14:05Z")

</div>

Hello again,

Just wanted to leave this here, I stumbled across this post:

> <https://github.com/pymc-devs/pymc/issues/6413>
>
> \### Issue with current documentation:
> 
> I ran into much trouble trying to install… PyMC on my windows 10 machine. I believe the installation instructions should be updated as described below from @sreedat post on Aug 21, 2021, and maybe expanded upon.
> 
> \### Idea or request for content:
> 
> @twiecki After posting this I could make my pymc3 work without installing m2w64-toolchain in the first place any where, either the base Anaconda or one of the envs. Here are the steps I followed.
> 
> Downloaded the latest 64-bit RTools from this page https://cran.r-project.org/bin/windows/Rtools/ and installed it with Admin rights so that the mingw compilers are on the System PATH and also First on the PATH. I installed RTools to the default location installer prefers C:\\rtools40
> 
> Note: RTools on WIndows has to be installed in directory paths without any space in the directory names.
> 
> Restarted the machine.
> 
> All of the next steps are in Anaconda.
> 
> Used the following command to create a basic environment:
> conda create -n pm3env -c conda forge "python=3.8" libpython mkl mkl-service numba scipy python-graphviz
> 
> conda activate pm3env
> 
> pip install pymc3==3.11.2 (I'm running everything with Admin rights)
> 
> (pm3env) C:\\Users\\SreeDatta\> which gcc and then which g++ (to ensure C:\\rtools40\\mingw64\\bin is referenced as the primary C and C++ compiler.
> 
> (pm3env) C:\\Users\\SreeDatta\>conda install -c conda-forge blas libblas (I did this a preemptive install. I got tired of seeing the invalid register theano error.
> 
> For reference these were the versions \`installed:
> blas 1.0 mkl conda-forge
> \`\`\`libblas 3.9.0 1\_h8933c1f\_netlib conda-forge\`\`\`
> 
> After this step, I stalled jupyter using conda install -c conda-forge notebook as that is my preferred way to interact with pymc3
> 
> Then I could run the basic and some advanced hierarchical models without the theano-pymc error.
> 
> I do not know how long this working environment will last. I also verified that on my WSL Ubuntu as well as my dedicated Ubuntu laptop, I've gcc 8.3.0 - compared to Windows 10, Linux / Ubuntu has been a breeze, but all of my team members work on WIndows 10 and I needed to get a decent Windows 10 environment for pymc3.
> 
> I will post more here as I see what happens with different users.

and realized that in my previous environments, I always install jupyter with `pip install jupyter`, after installing Pymc.

However, installing notebook from conda-forge seems to solve the issue that I described above, with:

```auto
conda create -c conda-forge -n pymc5 "pymc>=4" python=3.11
conda activate pymc5
conda install -c conda-forge notebook

```

Now I am able to run the examples smoothly.

---

<div class="post-metadata">

**Author:** ![cluhmann](https://yyz2.discourse-cdn.com/flex036/user_avatar/discourse.pymc.io/cluhmann/32/3083_2.png) [@cluhmann](https://discourse.pymc.io/u/cluhmann)\
**Post date:** [January 10, 2023, 2:43pm UTC](https://discourse.pymc.io/t/pymc-v5-0-1-tutorials-in-docs-page-not-working-from-the-conda-environment-windows-11/11151/7 "2023-01-10T14:43:32Z")

</div>

Great to hear!