fast_progress with macOS Safari and Jupyter and can break MCMC sampling

[essandess]

I believe that this fast_progress issue AnswerDotAI/fastprogress#46 causes PyMC3’s .sample method to break on Safari and a Jupyter notebook. Possibly related issues:

• ipython notebook kernel dies with njobs=4 #707
• Hi when ever I tried running NUTS sampling my notebook gets disconnected from kernel.  #3078

This MWE causes high CPU and energy usage when run in Safari. There is an intermittent Safari error message in the Jupyter Notebook tab that says:

This web page has been reloaded because it was using significant energy

Reloading the web page during MCMC sampling causes the Python processes to stall.

This MWE code works fine in Chrome because Chrome doesn’t have this issue.

MWE modified from https://github.com/CamDavidsonPilon/Probabilistic-Programming-and-Bayesian-Methods-for-Hackers/blob/master/Chapter3_MCMC/Ch3_IntroMCMC_PyMC3.ipynb

import numpy as np, pymc3 as pm, theano.tensor as tt

data = np.loadtxt("Chapter3_MCMC/data/mixture_data.csv", delimiter=",")

with pm.Model() as model:
    p1 = pm.Uniform('p', 0, 1)
    p2 = 1 - p1
    p = tt.stack([p1, p2])
    assignment = pm.Categorical("assignment", p, 
                                shape=data.shape[0],
                                testval=np.random.randint(0, 2, data.shape[0]))
with model:
    sds = pm.Uniform("sds", 0, 100, shape=2)
    centers = pm.Normal("centers", 
                        mu=np.array([120, 190]), 
                        sd=np.array([10, 10]), 
                        shape=2)
    
    center_i = pm.Deterministic('center_i', centers[assignment])
    sd_i = pm.Deterministic('sd_i', sds[assignment])
    
    # and to combine it with the observations:
    observations = pm.Normal("obs", mu=center_i, sd=sd_i, observed=data)

with model:
    step1 = pm.Metropolis(vars=[p, sds, centers])
    step2 = pm.CategoricalGibbsMetropolis(vars=[assignment])
    trace = pm.sample(25000, step=[step1, step2])
    
with model:
    trace = pm.sample(50000, step=[step1, step2], trace=trace)

[ricardoV94]

Closing this as it seems unrelated to PyMC, and it refers to the last version