# I can't get pymc3 to work

**URL:** <https://discourse.pymc.io/t/i-cant-get-pymc3-to-work/6578>\
**Category:** Questions\
**Tags:** bug\
**Created:** [January 12, 2021, 5:41pm UTC](https://discourse.pymc.io/t/i-cant-get-pymc3-to-work/6578 "2021-01-12T17:41:34Z")\
**Posts on this page:** 5\
**Page:** 1

<div class="post-metadata">

**Author:** ![Yuri\_Stickney](https://yyz2.discourse-cdn.com/flex036/user_avatar/discourse.pymc.io/yuri_stickney/32/3514_2.png) [@Yuri\_Stickney](https://discourse.pymc.io/u/Yuri_Stickney)\
**Post date:** [January 12, 2021, 5:41pm UTC](https://discourse.pymc.io/t/i-cant-get-pymc3-to-work/6578/1 "2021-01-12T17:41:34Z")

</div>

I’ve been spinning my wheels for a bit trying to get pymc3 to work in an anaconda jupyter notebook. I’m trying to create a media mix model as specified in this post:

[A Bayesian Approach to Media Mix Modeling by Michael Johns & Zhenyu Wang - PyMCon / PyMCon2020 - PyMC Discourse](https://discourse.pymc.io/t/a-bayesian-approach-to-media-mix-modeling-by-michael-johns-zhenyu-wang/6024)

I’ve tried installing pymc3 in multiple different ways:

Method 1)

conda install pymc3

Method 2)  
pip install pymc3  
conda install m2w64-toolchain libpython pygpu

Not sure what the best way to put my code is but here it is:

### CODE START

import numpy as np  
import pandas as pd  
import pymc3 as pm  
from pymc3 import \*  
import arviz as az  
import theano  
import theano.tensor as tt

df\_in = pd.read\_csv(‘Modeling Table for Python.csv’)

delay\_channels = ‘’#[‘Display’]  
non\_lin\_channels = [‘Metasearch’, ‘Paid\_Search’, ‘CTC’, ‘Display’]  
control\_vars = [‘ADR’, ‘Compset ADR’]  
index\_vars = ‘’#[‘MonthID’, ‘YearID’, ‘COVID-19\_ID’]  
outcome = ‘Bookings’

def geometric\_adstock\_tt(x\_t, alpha=0, L=84, normalize=True):  
‘’’  
:param alpha: rate of decay (float)  
:param L: Length of time carryover effects can have an impact (int)  
:normalize: Boolean  
:return: transformed spend vector  
‘’’  
w = tt.as\_tensor\_variable([tt.power(alpha, i) for i in range(L)])  
xx = tt.stack([tt.concatenate([tt.zeros(i), x\_t[:x\_t.shape[0] - i]]) for i in range(L)])

```
if not normalize:
    y= tt.dot(w, xx)
    
else:
    y = tt.dot(w / tt.sum(w), xx)
return y

```

def logistic\_function(x\_t, mu=0.1): #Saturation Function  
‘’’  
:param x\_t: marketing spend vector (float)  
:param mu: half-saturation point (float)  
:return: transformed spend vector  
‘’’  
return (1 - np.exp(-mu \* x\_t)) / (1 + np.exp(-mu \* x\_t))

with Model() as model:  
response\_mean = []

```
# channels that can have DECAY and SATURATION effects
for channel_name in delay_channels:
    print(channel_name)
    xx = df_in[channel_name].values
    #print(xx)
    print(xx.shape)
    
    print(f'Adding Delayed Channels: {channel_name}')
    channel_b = HalfNormal(f'beta_{channel_name}', sd=5) # Keep Coefficients Positive
    
    alpha = Beta(f'alpha_{channel_name}', alpha=3, beta=3)
    channel_mu = Gamma(f'mu_{channel_name}', alpha=3, beta=1)
    response_mean.append(logistic_function(geometric_adstock_tt(xx,alpha),channel_mu) * channel_b)

# channels that can have SATURATION effects only
for channel_name in non_lin_channels:
    xx = df_in[channel_name].values
    
    print(f'Adding Non-Linear Logistic Channel: {channel_name}')
    channel_b = HalfNormal(f'beta_{channel_name}', sd=5)
    
    #logistic reach curve
    channel_mu = Gamma(f'mu_{channel_name}', alpha=3, beta=1)
    response_mean.append(logistic_function(xx, channel_mu) * channel_b)
    
# Continuous control variabls
if control_vars:
    for channel_name in control_vars:
        x = df_in[channel_name].values
        
        print(f'Adding Control: {channel_name}')
        
        control_beta = Normal(f'beta_{channel_name}', sd=.25)
        channel_contrib = control_beta * x
        response_mean.append(channel_contrib)
        
# Categorical control variables
if index_vars:
    for var_name in index_vars:
        x = df_in[var_name].values

        shape_v = len(set(x))

        print(f'Adding Index Variable: {var_name}')

        ind_beta = Normal('beta_' + var_name, sd=.5, shape=shape_v)

        channel_contrib = ind_beta[x]
        response_mean.append(channel_contrib)
        
# Noise level
sigma = Exponential('sigma', 10)

# Define likelihood
likelihood = Normal(outcome, mu=sum(response_mean), sd=sigma, observed=df_in[outcome].values)

```

with model:  
# instantiate sampler  
#step = pm.Slice()

```
# draw 5000 posterior samples
trace = pm.sample(target_accept=.8, return_inferencedata=True)#step=step, cores=2)

```

pm.traceplot(trace);

### CODE END

My code fails 95% of the time on the pm.sample() statement and I get many different errors depending on how I’ve installed pymc3.

Here are some of the errors:

Errors Using Install Method 1:

[I 08:18:39.093 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).  
[C 08:18:39.099 NotebookApp]

```
To access the notebook, open this file in a browser:
    file:///C:/Users/yuris/AppData/Roaming/jupyter/runtime/nbserver-26796-open.html
Or copy and paste one of these URLs:
    http://localhost:8888/?token=4d4335a96dec91ed8ce17b62b5caaee32c0189d20979afbe
 or http://127.0.0.1:8888/?token=4d4335a96dec91ed8ce17b62b5caaee32c0189d20979afbe

```

[W 08:18:49.764 NotebookApp] Notebook XXX/PYTHON/MMM V2.ipynb is not trusted  
[W 08:18:49.793 NotebookApp] 404 GET /nbextensions/widgets/notebook/js/extension.js?v=20210112081838 (::1) 8.000000ms referer=http://localhost:8888/notebooks/XXX/PYTHON/MMM%20V2.ipynb  
[I 08:18:50.082 NotebookApp] Kernel started: 7861bade-adb8-4520-a071-86a4f3753b2c, name: python3

You can find the C code in this temporary file: C:\Users\yuris\AppData\Local\Temp\theano\_compilation\_error\_sm\_j33in  
Traceback (most recent call last):  
File “”, line 1, in   
File “C:\Users\yuris\anaconda3\envs\pymc3\lib\multiprocessing\spawn.py”, line 105, in spawn\_main  
exitcode = \_main(fd)  
File “C:\Users\yuris\anaconda3\envs\pymc3\lib\multiprocessing\spawn.py”, line 115, in \_main  
self = reduction.pickle.load(from\_parent)  
File “C:\Users\yuris\anaconda3\envs\pymc3\lib\site-packages\theano\compile\function\_module.py”, line 1082, in \_constructor\_Function  
f = maker.create(input\_storage, trustme=True)  
File “C:\Users\yuris\anaconda3\envs\pymc3\lib\site-packages\theano\compile\function\_module.py”, line 1715, in create  
input\_storage=input\_storage\_lists, storage\_map=storage\_map)  
File “C:\Users\yuris\anaconda3\envs\pymc3\lib\site-packages\theano\gof\link.py”, line 699, in make\_thunk  
storage\_map=storage\_map)[:3]  
File “C:\Users\yuris\anaconda3\envs\pymc3\lib\site-packages\theano\gof\vm.py”, line 1091, in make\_all  
impl=impl))  
File “C:\Users\yuris\anaconda3\envs\pymc3\lib\site-packages\theano\gof\op.py”, line 955, in make\_thunk  
no\_recycling)  
File “C:\Users\yuris\anaconda3\envs\pymc3\lib\site-packages\theano\gof\op.py”, line 858, in make\_c\_thunk  
output\_storage=node\_output\_storage)  
File “C:\Users\yuris\anaconda3\envs\pymc3\lib\site-packages\theano\gof\cc.py”, line 1217, in make\_thunk  
keep\_lock=keep\_lock)  
File “C:\Users\yuris\anaconda3\envs\pymc3\lib\site-packages\theano\gof\cc.py”, line 1157, in **compile**  
keep\_lock=keep\_lock)  
File “C:\Users\yuris\anaconda3\envs\pymc3\lib\site-packages\theano\gof\cc.py”, line 1624, in cthunk\_factory  
key=key, lnk=self, keep\_lock=keep\_lock)  
File “C:\Users\yuris\anaconda3\envs\pymc3\lib\site-packages\theano\gof\cmodule.py”, line 1189, in module\_from\_key  
module = lnk.compile\_cmodule(location)  
File “C:\Users\yuris\anaconda3\envs\pymc3\lib\site-packages\theano\gof\cc.py”, line 1527, in compile\_cmodule  
preargs=preargs)  
File “C:\Users\yuris\anaconda3\envs\pymc3\lib\site-packages\theano\gof\cmodule.py”, line 2399, in compile\_str  
(status, compile\_stderr.replace(’\n’, '. ')))  
Exception: (‘The following error happened while compiling the node’, Alloc(TensorConstant{(1,) of 0.0}, Shape\_i{0}.0), ‘\n’, 'Compilation failed (return status=3): ', ‘[Alloc(TensorConstant{(1,) of 0.0}, \<TensorType(int64, scalar)\>)]’)  
forrtl: error (200): program aborting due to control-C event  
Image PC Routine Line Source  
libifcoremd.dll 00007FF9C9543B58 Unknown Unknown Unknown  
KERNELBASE.dll 00007FFA4AD6B443 Unknown Unknown Unknown  
KERNEL32.DLL 00007FFA4BCC7034 Unknown Unknown Unknown  
ntdll.dll 00007FFA4D3BD0D1 Unknown Unknown Unknown  
forrtl: error (200): program aborting due to control-C event  
Image PC Routine Line Source  
libifcoremd.dll 00007FF9C9543B58 Unknown Unknown Unknown  
KERNELBASE.dll 00007FFA4AD6B443 Unknown Unknown Unknown  
KERNEL32.DLL 00007FFA4BCC7034 Unknown Unknown Unknown  
ntdll.dll 00007FFA4D3BD0D1 Unknown Unknown Unknown  
forrtl: error (200): program aborting due to control-C event  
Image PC Routine Line Source  
libifcoremd.dll 00007FF9C9543B58 Unknown Unknown Unknown  
KERNELBASE.dll 00007FFA4AD6B443 Unknown Unknown Unknown  
KERNEL32.DLL 00007FFA4BCC7034 Unknown Unknown Unknown  
ntdll.dll 00007FFA4D3BD0D1 Unknown Unknown Unknown  
forrtl: error (200): program aborting due to control-C event  
Image PC Routine Line Source  
libifcoremd.dll 00007FF9C9543B58 Unknown Unknown Unknown  
KERNELBASE.dll 00007FFA4AD6B443 Unknown Unknown Unknown  
KERNEL32.DLL 00007FFA4BCC7034 Unknown Unknown Unknown  
ntdll.dll 00007FFA4D3BD0D1 Unknown Unknown Unknown  
forrtl: error (200): program aborting due to control-C event  
Image PC Routine Line Source  
libifcoremd.dll 00007FF9C9543B58 Unknown Unknown Unknown  
KERNELBASE.dll 00007FFA4AD6B443 Unknown Unknown Unknown  
KERNEL32.DLL 00007FFA4BCC7034 Unknown Unknown Unknown  
ntdll.dll 00007FFA4D3BD0D1 Unknown Unknown Unknown  
[I 08:20:36.826 NotebookApp] Interrupted…  
[I 08:20:36.827 NotebookApp] Shutting down 1 kernel  
[I 08:20:36.940 NotebookApp] Kernel shutdown: 7861bade-adb8-4520-a071-86a4f3753b2c  
[I 08:20:36.941 NotebookApp] Shutting down 0 terminals

Errors Using Install Method 2:

[I 09:02:48.605 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).  
[C 09:02:48.653 NotebookApp]

```
To access the notebook, open this file in a browser:
    file:///C:/Users/yuris/AppData/Roaming/jupyter/runtime/nbserver-15460-open.html
Or copy and paste one of these URLs:
    http://localhost:8888/?token=b85e37d0839705bb3119e978b8cc3f8e29d2f987910654ec
 or http://127.0.0.1:8888/?token=b85e37d0839705bb3119e978b8cc3f8e29d2f987910654ec

```

[W 09:02:56.952 NotebookApp] Notebook XXX/PYTHON/MMM V2.ipynb is not trusted  
[W 09:02:56.981 NotebookApp] 404 GET /nbextensions/widgets/notebook/js/extension.js?v=20210112090248 (::1) 8.510000ms referer=http://localhost:8888/notebooks/XXX/PYTHON/MMM%20V2.ipynb  
[I 09:02:57.237 NotebookApp] Kernel started: 39902f59-d6bb-4a94-81fc-ea89a0fd6204, name: python3  
[I 09:04:57.222 NotebookApp] Saving file at /XXX/PYTHON/MMM V2.ipynb  
[W 09:04:57.223 NotebookApp] Notebook XXX/PYTHON/MMM V2.ipynb is not trusted  
[I 09:05:41.708 NotebookApp] Interrupted…  
[I 09:05:41.708 NotebookApp] Shutting down 1 kernel  
[I 09:05:47.160 NotebookApp] Kernel shutdown: 39902f59-d6bb-4a94-81fc-ea89a0fd6204  
[I 09:05:47.161 NotebookApp] Shutting down 0 terminals  
[I 09:05:47.163 NotebookApp] KernelRestarter: restarting kernel (1/5), keep random ports  
WARNING:root:kernel 39902f59-d6bb-4a94-81fc-ea89a0fd6204 restarted

in Python:

BrokenPipeError Traceback (most recent call last)  
~\anaconda3\envs\pymc3\_2\lib\multiprocessing\connection.py in \_recv\_bytes(self, maxsize)  
301 ov, err = \_winapi.ReadFile(self.\_handle, bsize,  
 → 302 overlapped=True)  
303 try:

BrokenPipeError: [WinError 109] The pipe has been ended

During handling of the above exception, another exception occurred:

EOFError Traceback (most recent call last)  
~\anaconda3\envs\pymc3\_2\lib\site-packages\pymc3\sampling.py in \_mp\_sample(draws, tune, step, chains, cores, chain, random\_seed, start, progressbar, trace, model, callback, discard\_tuned\_samples, mp\_ctx, pickle\_backend, \*\*kwargs)  
1475 with sampler:  
-\> 1476 for draw in sampler:  
1477 trace = traces[draw.chain - chain]

~\anaconda3\envs\pymc3\_2\lib\site-packages\pymc3\parallel\_sampling.py in **iter** (self)  
479 while self.\_active:  
 → 480 draw = ProcessAdapter.recv\_draw(self.\_active)  
481 proc, is\_last, draw, tuning, stats, warns = draw

~\anaconda3\envs\pymc3\_2\lib\site-packages\pymc3\parallel\_sampling.py in recv\_draw(processes, timeout)  
351 proc = idxs[id(ready[0])]  
 → 352 msg = ready[0].recv()  
353

~\anaconda3\envs\pymc3\_2\lib\multiprocessing\connection.py in recv(self)  
249 self.\_check\_readable()  
 → 250 buf = self.\_recv\_bytes()  
251 return \_ForkingPickler.loads(buf.getbuffer())

~\anaconda3\envs\pymc3\_2\lib\multiprocessing\connection.py in \_recv\_bytes(self, maxsize)  
320 if e.winerror == \_winapi.ERROR\_BROKEN\_PIPE:  
 → 321 raise EOFError  
322 else:

EOFError:

During handling of the above exception, another exception occurred:

KeyboardInterrupt Traceback (most recent call last)  
~\anaconda3\envs\pymc3\_2\lib\site-packages\pymc3\sampling.py in \_mp\_sample(draws, tune, step, chains, cores, chain, random\_seed, start, progressbar, trace, model, callback, discard\_tuned\_samples, mp\_ctx, pickle\_backend, \*\*kwargs)  
1487 if callback is not None:  
-\> 1488 callback(trace=trace, draw=draw)  
1489

~\anaconda3\envs\pymc3\_2\lib\site-packages\pymc3\parallel\_sampling.py in **exit** (self, \*args)  
512 def **exit** (self, \*args):  
 → 513 ProcessAdapter.terminate\_all(self.\_samplers)  
514

KeyboardInterrupt:

During handling of the above exception, another exception occurred:

ValueError Traceback (most recent call last)  
 in   
4  
5 # draw 5000 posterior samples  
----\> 6 trace = pm.sample(target\_accept=.8)#step=step, cores=2)

~\anaconda3\envs\pymc3\_2\lib\site-packages\pymc3\sampling.py in sample(draws, step, init, n\_init, start, trace, chain\_idx, chains, cores, tune, progressbar, model, random\_seed, discard\_tuned\_samples, compute\_convergence\_checks, callback, jitter\_max\_retries, return\_inferencedata, idata\_kwargs, mp\_ctx, pickle\_backend, \*\*kwargs)  
555 \_print\_step\_hierarchy(step)  
556 try:  
 → 557 trace = \_mp\_sample(\*\*sample\_args, \*\*parallel\_args)  
558 except pickle.PickleError:  
559 \_log.warning(“Could not pickle model, sampling singlethreaded.”)

~\anaconda3\envs\pymc3\_2\lib\site-packages\pymc3\sampling.py in \_mp\_sample(draws, tune, step, chains, cores, chain, random\_seed, start, progressbar, trace, model, callback, discard\_tuned\_samples, mp\_ctx, pickle\_backend, \*\*kwargs)  
1500 except KeyboardInterrupt:  
1501 if discard\_tuned\_samples:  
-\> 1502 traces, length = \_choose\_chains(traces, tune)  
1503 else:  
1504 traces, length = \_choose\_chains(traces, 0)

~\anaconda3\envs\pymc3\_2\lib\site-packages\pymc3\sampling.py in \_choose\_chains(traces, tune)  
1518 lengths = [max(0, len(trace) - tune) for trace in traces]  
1519 if not sum(lengths):  
-\> 1520 raise ValueError(“Not enough samples to build a trace.”)  
1521  
1522 idxs = np.argsort(lengths)[::-1]

ValueError: Not enough samples to build a trace.

Sadly, I can’t provide the data, but there are 201 weekly records. I’m not using the adstock functions in this example and omit the seasonal variables.

I can provide more details and errors I’ve encountered as well.

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 13, 2021, 12:25am UTC](https://discourse.pymc.io/t/i-cant-get-pymc3-to-work/6578/2 "2021-01-13T00:25:22Z")

</div>

Does running this code, or code like it, work when just running it as an executable python script? Also, what version of pymc3 is installed when using each of those methods? I know that there was some difficulty with multi-threading on windows that was recently addressed, though I am not super familiar with the details.

---

<div class="post-metadata">

**Author:** ![Yuri\_Stickney](https://yyz2.discourse-cdn.com/flex036/user_avatar/discourse.pymc.io/yuri_stickney/32/3514_2.png) [@Yuri\_Stickney](https://discourse.pymc.io/u/Yuri_Stickney)\
**Post date:** [January 15, 2021, 1:30am UTC](https://discourse.pymc.io/t/i-cant-get-pymc3-to-work/6578/3 "2021-01-15T01:30:24Z")

</div>

I was able to get pm.sample() to work by using it in this way:

with model:  
trace = pm.sample(2000, tune=1000, chains=2, init=“adapt\_diag”, random\_seed=SEED, return\_inferencedata=True, cores=1)

I’m starting a new threat with my questions about interpreting my results and whether I’m on the right track.

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 15, 2021, 1:41am UTC](https://discourse.pymc.io/t/i-cant-get-pymc3-to-work/6578/4 "2021-01-15T01:41:51Z")

</div>

I suspect that it was the `cores=1` that did it (as I said, the multi-threading has been problematic on windows).

---

<div class="post-metadata">

**Author:** ![Yuri\_Stickney](https://yyz2.discourse-cdn.com/flex036/user_avatar/discourse.pymc.io/yuri_stickney/32/3514_2.png) [@Yuri\_Stickney](https://discourse.pymc.io/u/Yuri_Stickney)\
**Post date:** [January 15, 2021, 2:11am UTC](https://discourse.pymc.io/t/i-cant-get-pymc3-to-work/6578/5 "2021-01-15T02:11:05Z")

</div>

Thanks! It feels nice to be able to run a model without having jupyter crash every time. . .

Now moving onto interpreting my results and seeing what I’m doing wrong (or right)!