Setting up a Run

The suggest method of setting up a BayesWave run is to make a config file, and a bash script which calls bayeswave_pipe.

Config files

A config file will be a .ini file, and follows common .ini syntax. Sections are labeled in [square brackets],

`[input]`

General settings for the run

Required:

seglen=float: duration of data (s)
window=float: duration of time window for model characterization runs (i.e the window where wavelets will can be placed)
flow=float: minimum frequency (Hz)
srate=float: sampling rate (Hz). Must be a power of 2.
PSDlength=float: GPS start time for PSD estimation
ifolist=float: List of IFOs to include in the analysis, for example [‘H1’,’L1’]

Optional:

dataseed=integer: Required if using simulated noise. Seed for noise realisation. Integer.

`[engine]`

Information about where BayesWave executable and related scripts are

Required:

bayeswave=str: Path to the BayesWave executabe, for example {path_to_executables}/BayesWave
bayeswave_post=str: Path to BayesWavePost executable, e.g. {path_to_executables}/BayesWavePost
megaplot=str: Path to megaplot executable, e.g. {path_to_executables}/megaplot.py

`[datafind]`

Information about the type of data to be used. If real using real data, sets up gw_data_find call to make cache files.

Required:

frtype-list=dict: List of frame times for each IFO. Takes dictionary in form {'IFO_1':'frame_type','IFO_2':'frame_type'}
channel-list=dict: List of channels for each IFO.
url-type=file – information about how cache is made.

Optional:

veto-categories=list: Data quality vetoes

`[bayeswave_options]`

Command line options for BayesWave. See BayesWave –help for a detailed list. Any flag can by passed to the BayesWave command line by setting exampleFlag=, and a flag with an argument can passed with exampleFlag=arugment.

Optional command line options for BayesWave.:

Run parameters

--segment-start SEGSTART

GPS start time of segment (trigtime + 2 - seglen)

--CBC-trigtime TRIGTIME

window for CBC is set around this time, any other window unchanged

--glitchBuster

Preform deterministic glitch subtraction as initial point in glitch model

--Niter NITER

number of iterations (4000000)

--Nchain NCHAIN

number of parallel chains (20)

--Nthreads NTHREAD

number of openmp threads to use (1). Recommended to have Nchain a multiple of Nthreads

--Ncycle NCYCLE

number of model updates per RJMCMC iteration (100)

--Nburnin NBURNIN

number of burn-in iterations (50000)

--maxLogL MAXLOGL

use maximized likelihood during burnin

--chainseed SEED

random number seed for Markov chain (1234)

--runName NAME

run name for output files

--outputDir DIRECTORY

absolute path of where the output should be written

--waveletStart FILEPATH

path to files containing wavelet starting parameters

--0noise

no noise realization

--prior

sample from prior using logL = constant test

--gnuplot

output files for gnuplot animations

--verbose

output hot chains

--window WINDOW

duration of time window for model characterization runs

--CBCwindow WINDOW

window for CBC is set around trigtime (or CBC-trigtime if given) with this length

--Niter-search NITER

number of iterations used in CBC search phase (5000)

--checkpoint

enable self-checkpointing

--version

print BayesWave version and exit

--help

print BayesWave options and exit

Model parameters

--chirplets

use chirplets as reconstruction basis

--fullOnly

require signal && glitch model

--noClean

skip cleaning phase and go right to reduced window

--noSignal

skip signal phase and quit after glitch model

--noGlitch

skip glitch phase

--cleanOnly

run bayesline & glitch cleaning phase only

--noiseOnly

use noise model only (no signal or glitches or cbc)

--signalOnly

use signal model only (no glitches or cbc)

--glitchOnly

use glitch model only (no signal or cbc)

--cbcOnly

use full CBC model only (incl. extrinsic parameters, no signal or glitches)

--CBCGlitch

use full CBC model and glitch model (incl. extrinsic parameters, no signal)

--noPSDfit

keep PSD parameters fixed

--bayesLine

use BayesLine for PSD model

--bayesCBC-tidal

specify BayesCBC waveform used: NRTidal_V or NoNRT_V (default)) (

--bayesCBC-skip-ext

skip BayesCBC extrinsic burnin (

Priors and Proposals

--Dmin MIN

minimum number of wavelets total (1)

--Dmax MAX

maximum number of wavelets per channel (100)

--fixD D

fix # of wavelets for signal/IFO. Overrides –Dmin,–Dmax

--Qmin MIN

minimum quality factor for wavelets (0.1)

--Qmax MAX

maximum quality factor for wavelets (40)

--waveletFmin MIN

minimum frequency for wavelets

--waveletFmax MAX

maximum frequency for wavelets

--noWaveletPrior

revert to uniform p(D)

--updateGeocenterPSD

geocenter PSD depends on extrinsic parameters

--waveletPrior

use empirical distribution on number of wavelets (O1)

--backgroundPrior FILE

name of 2-column bkg frequency distribution file

--noOrientationProposal

disable MCMC proposal for psi/ecc

--uniformAmplitudePrior

don’t use SNR-dependent amplitude prior

--noSignalAmplitudePrior

use same SNR-dependent prior for signal & glitch model

--noAmplitudeProposal

don’t draw from SNR-dependent amplitude prior

--varyExtrinsicAmplitude

update wavelet amplitudes in extrinsic update (FIXED?)

--noPolarization

do not assume elliptical polarization for signal model

--noClusterProposal

disable clustering & TF density proposal

--clusterWeight WEIGHT

fractional weight for TF to proximity proposal (0.5)

--ampPriorPeak PEAK

SNR where amplitude prior peaks (5)

--signalPriorPeak PEAK

SNR where signal amplitude prior peaks (5)

--dimensionDecayRate RATE

e-folding time for number of wavelets (1000)

--fixIntrinsicParams

hold intrinsic parameters fixed

--fixExtrinsicParams

hold extrinsic parameters fixed

--loudGlitchPrior

set floor of PSD prior to .01*Sn(f=200Hz)

--fixSky

hold sky locaiton fixed

--fixRA RA

right ascension in radians of fixed sky location

--fixDEC

DEC declination in radians of fixed sky location

--TFQ-resize

increases nQ/nf spacing for high srate/Qmax in TFQ proposal

--TFQ-nf-spacing

set custom nf spacing value for TFQ proposal

--TFQ-nQ-spacing

set custom nQ spacing value for TFQ proposal

Parallel Tempering parameters

--tempMin MIN

minimum temperature chain (1)

--noAdaptTemperature

disable adjust PT ladder to maintain acc. rate across chains

--tempSpacing SPACING

set temperature spacing for geometric ladder (1.2)

--noSplineEvidence

disable spline thermodynamic integration

LALInference injection options

--inj INJFILE

Injection XML file to use

--event N

Event number from Injection XML file to use

Burst MDC injection options

--MDC-channel CHANNEL

IFO1-chan, IFO2-chan, etc

--MDC-cache CACHE

IFO1-mdcframe, IFO2-mdcframe, etc

--MDC-prefactor PREFACTOR

Rescale injection amplitude (1.0)

BayesWave internal injection bayeswave_options

--BW-inject MODEL

(signal/glitch)

--BW-injName NAME

runName that produced the chain file

--BW-path PATH

Path to BW chain file for injection (./chains)

--BW-event EVENT

Which sample from BayesWave chain (200000)

`[bayeswave_post_options]`

Required:

0noise=: Always required for technical purposes.

`[injections]`

Optional. Use if doing injections from an xml file.

If using, required:

events=list of events: Flexible syntax. Can set to all, or for a smaller set of events a list like 0:10 or 1,3,5.
inj-fref=float: Reference frequency for injection.

Todo

include MDC section*

`[condor]`

Information for setting up the condor job. More details on running condor jobs can be found at HTCondor.

Required: - universe=vanilla

bayeswave-request-memory=int: Required memory for BayesWave
bayeswave_post-request-memory=int: Required memory for BayesWavePost
bayeswave-request-disk=int: Required disk space for BayesWave
bayeswave_post-request-disk=int: Required disk space for BayesWavePost
datafind=/usr/bin/gw_data_find: Specify the gw_data_find executable
ligolw_print=/usr/bin/ligolw_print: Specify the ligolw_print executable
accounting-group=str LIGO accounting group

Optional: - checkpoint=: Self checkpointing. If running on condor this should be used.

Running `bayeswave_pipe`

Once you have created a config file, you can run bayeswave_pipe to set up your BayesWave run, or your batch of runs.

positional arguments

configfile

options

--help, -h

show this help message and exit

--workdir WORKDIR, -r WORKDIR

name of directory for this batch of jobs

--trigger-time TRIGGER_TIME, -t TRIGGER_TIME

GPS trigger time

--trigger-list TRIGGER_LIST, -l TRIGGER_LIST

List of GPS trigger times

--cwb-trigger-list CWB_TRIGGER_LIST

cWB style trigger list

--CBC-trigger-list CBC_TRIGGER_LIST

Trigger list for CBCs

--bayesline-median-psd

Print out median bayesLine PSD

--server SERVER

LIGO data find server

--copy-frames

Copy .gwf frames (for OSG use (TODO someone check this))

--skip-datafind

Skip gw_data_find

--sim-data

Use simulated data

-I INJFILE, --injfile INJFILE

xml file for injection

-F FOLLOWUP_INJECTIONS, --followup-injections FOLLOWUP_INJECTIONS

TODO; fill this out

--bw-inject

BayesWave internal injections

-G GRACEID, --graceID GRACEID

GraceID of event

--graceID-list GRACEID_LIST

List of GRACEIDs

--gdb-playground

Use GraceDB playground

--submit-to-gracedb

Submit results to GraceDB ONLY USE THIS IF YOU KNOW EXACTLY WHAT YOU’RE DOING

--skip-megapy

Skip megaplot plotting script

--skip-post

Skip BayesWavePost

--separate-post-dag

Make a separate dag for postprocessing

--trigger-time-delta TRIGGER_TIME_DELTA

Offset from trigger time

--bayeswave-clean-frame

Make glitch subtracted .gwf frames

--condor-precommand

Include conodr precommand for smart restart after checkpoint

--condor-submit

Automatically submit dag to condor

--bayeswave-retries BAYESWAVE_RETRIES

Number of times to retry on condor if job fails

--osg-deploy

Deploy job on open science grid

--transfer-files

Transfer files with condor job

--shared-filesystem

Condor shared filesystem

--singularity SINGULARITY

Use singularity

Launching the BayesWave Job

Using Condor

If using condor, you will submit a DAG input file. The DAG will manage the workflow – launching first the BayesWave job, then BayesWavePost job after the BayesWave job completes, and the megaplot job after the postprocessing completes. If running large batches of jobs, the individual jobs will be launched in parallel.

When running bayeswave_pipe, you can include --condor-submit to launch the job automatically. Otherwise, you can submit the dag from via

$ condor_submit_dag WORKDIR.dag

where WORKDIR is the directory name used in the bayeswave_pipe call.

Without Condor

If you are running without condor (for example, running on your own laptop), you can use the bash script to run BayesWave, the postproccessing, and plotting. The bash script can be found in the working directory, names WORKDIR.sh, where WORKDIR is the name of your directory.

Note

Warning! If you are running a batch of jobs, for example a bunch of injections, this will run all of those in sequence. So be mindful of how you use this script!

Setting up a Run

Config files

[input]

[engine]

[datafind]

[bayeswave_options]

Run parameters

Model parameters

Priors and Proposals

Parallel Tempering parameters

LALInference injection options

Burst MDC injection options

BayesWave internal injection bayeswave_options

[bayeswave_post_options]

[injections]

[condor]

Running bayeswave_pipe

positional arguments

options

Launching the BayesWave Job

Using Condor

Without Condor

`[input]`

`[engine]`

`[datafind]`

`[bayeswave_options]`

`[bayeswave_post_options]`

`[injections]`

`[condor]`

Running `bayeswave_pipe`