bayesbeat 0.1.0b0

Bayesian inference for two decaying beating signals

BayesBeat

Bayesian analysis of ringdowns.

Warning: the following instructions have only been tested on Linux and may be updated after testing on other platforms.

Downloading the code

The recommended way to download the code is by cloning this repository.

Alternatively, you can download the code as a Zip from this URL.

Installation

Before installing nessai you'll need to download and install conda. See the instructions here. If running on computing cluster you will not have to do this step.

Then open a terminal, i.e. PowerShell, Command Line or equivalent.

Creating a conda environment

We start by creating an environment from the environment file, this will install all the necessary packages:

conda env create -f environment.yml

The environment will be called bayes-beat.

Note: this can be very slow and on certain systems.

Activating the environment

We must activate the environment to use the installed packages:

conda activate bayes-beat

You should now see (bayes-beat) in your terminal.

Installing bayesbeat

Once you have activated the environment, install bayesbeat by running the following command in the root directory of the repository

pip install .

All the necessary dependencies should already be installed, so this should be quite quick.

Running the analysis

Before running the analysis, make sure you have activated the environment. See the section above for instructions.

Here is an example of how to the run analysis for a data file called PyTotalAnalysis.mat located in data/. The index determines which of ringdowns in the data file will be analyzed.

Creating an ini file

Create an .ini file with a given name, e.g. example.ini

bayesbeat_create_ini example.ini

Note: if you plan to use a scheduler, e.g. HTCondor or Slurm to run the analyses you should append --scheduler HTCondor or --scheduler Slurm to the above command. This will add the relevant section.

Open the new ini file and set the values for the different fields. You must specify output and datafile, the other settings will all have defaults that should work. The most important are:

• indices: determines which ringdowns in the data file will be analyzed. Only used if running via Condor. If None or 'all' all indices will be analysed. Otherwise, should be a list of integers (starting at 0).
• The parameters in the Model section. This will depend on the model being used.
• n-pool: the number of cores to use. We recommend setting this to at least 4.

The file should look something like this (this example uses HTCondor):

[General]
output = "outdir/"
label = "disk_0"
datafile = "data/PyTotalAnalysis.mat"
indices = [0]
seed = 1234
plot = True

[Data]
rescale-amplitude = False
maximum-amplitude = None

[Model]
name = GenericAnalyticGaussianBeam
equation_name = General_Equation_3_Terms.txt
photodiode-size = 1e-2
photodiode-gap = 0.25e-3
n-terms = 3
include-gap = True
beam_radius = 1e-3
x_offset = 0.0
rin_noise = True
prior_bounds = {"a_ratio": [0, 1], "tau_1": [290, 310], "tau_2": [140, 160], "dphi": [0, 3.141592654], "domega": [0.18, 0.22], "a_scale": [0, 10], "sigma_noise": [0, 10.0]}

[Analysis]
n-pool = 4
resume = True

[Sampler]
nlive = 1000
reset_flow = 8

[HTCondor]
request-disk = "2GB"
request-memory = "2GB"
request-cpus = 4

Running with HTCondor or Slurm

The recommended way to use bayesbeat is on a cluster with HTCondor or Slurm installed. This allows analyses to run in parallel rather than one-by-one on a local machine. To run a local machine, see the section below.

When creating a ini file, add the --scheduler arguments with either htcondor or slurm. This will add the relevant section to the file.

Once you have a create an ini file, the analyses can be prepared (built) and then submitted. To do so run

bayesbeat_build example.ini

this will construct the relevant files which can be submitted using the command that is printed after the command has run. The exact command will depend on which scheduler you are using. Alternatively, if you run

bayesbeat_build example.ini --submit

the analysis will be built and submitted in a single step.

Note: if the output directory already exists, an error will be raised and the analysis will not be built or submitted. The --overwrite flag will ignore this but is not recommended as this can lead to data loss.

Running on a local machine (without HTCondor or Slurm)

To run an analysis locally instead of via scheduler, use the following command

bayesbeat_run example.ini --index 0

where --index specifies which ringdown in the datafile to analyse.

Note: this ignores the value of indices in the ini file.

Note: it is not possible to analyse multiple ringdowns with a single call to bayesbeat_run.