Zero Likelihood run stucks with Dynesty >= 1.1
Hi, recently I try to use bilby.core.likelihood.ZeroLikelihood
in a new installed environment to calculate the prior distribution. But it got stuck after
bilby INFO : Generating initial points from the prior
I have checked the code and it seems that it stuck in an infinite loop in dynesty.sampler._new_point
which should break after logl > loglstar
, but the values of both variables are 0.
The problem only exist for Dynesty >= 1.1. When changing to Dynesty = 1.0.1, it works fine. I haven't checked which changes caused this issue. But this simple test code can reproduce it
Install bilby directly
conda create --name bilby_test
conda activate bilby_test
conda install -c conda-forge bilby
Install with old dynesty
conda create --name bilby_test2
conda activate bilby_test2
conda install -c conda-forge dynesty=1.0.1
conda install -c conda-forge bilby
Then run the simple test python script in two environments
#!/usr/bin/env python
import bilby
import numpy as np
# A few simple setup steps
label = 'gaussian_example'
outdir = 'outdir'
# Here is minimum requirement for a Likelihood class to run with bilby. In this
# case, we setup a GaussianLikelihood, which needs to have a log_likelihood
# method. Note, in this case we will NOT make use of the `bilby`
# waveform_generator to make the signal.
# Making simulated data: in this case, we consider just a Gaussian
data = np.random.normal(3, 4, 100)
class SimpleGaussianLikelihood(bilby.Likelihood):
def __init__(self, data):
"""
A very simple Gaussian likelihood
Parameters
----------
data: array_like
The data to analyse
"""
super().__init__(parameters={'mu': None, 'sigma': None})
self.data = data
self.N = len(data)
def log_likelihood(self):
mu = self.parameters['mu']
sigma = self.parameters['sigma']
res = self.data - mu
return -0.5 * (np.sum((res / sigma)**2) +
self.N * np.log(2 * np.pi * sigma**2))
likelihood = bilby.core.likelihood.ZeroLikelihood(SimpleGaussianLikelihood(data))
priors = dict(mu=bilby.core.prior.Uniform(0, 5, 'mu'),
sigma=bilby.core.prior.Uniform(0, 10, 'sigma'))
# And run sampler
result = bilby.run_sampler(
likelihood=likelihood, priors=priors, sampler='dynesty', npoints=500,
walks=10, outdir=outdir, label=label)
result.plot_corner()
The bilby_test
environment will stuck while the old version works fine.