Example of how to run this code
usage: lalinference_mcmc_submit_new.py [-h] [--alloc ALLOC] [--queue QUEUE] [--jobName JOBNAME] [--dir DIR] [--dep DEP] [--name NAME] [--walltime WALLTIME] [--cores-per-node CORES_PER_NODE] [--multiple-nodes] [--nPar NPAR] [--branch BRANCH] [--rc RC] [--sim-quest] [--quest-iwd QUEST_IWD] [--era ERA] [--psd PSD [PSD ...]] [--ifo IFO [IFO ...]] [--inj INJ] [--event EVENT] [--trigtime TRIGTIME] [--approx APPROX] [--amporder AMPORDER] [--flow FLOW] [--lowM1 LOWM1] [--lowM2 LOWM2] [--fhigh FHIGH] [--srate SRATE] [--seglen SEGLEN] [--psdlength PSDLENGTH] [--psdstart PSDSTART] [--temp-ladder-top-down] [--noisy] [--distance-max DISTANCE_MAX] [--no-malmquist] [--no-margtimephi] [--trigSNR TRIGSNR] [--tempMin TEMPMIN] [--tempMax TEMPMAX] [--Neff NEFF] [--Niter NITER] [--fix-rightascension] [--fix-declination] [--fix-distance] [--fix-costheta_jn]
Generate a submit file for lalinference_mcmc on grail.
optional arguments: -h, --help show this help message and exit
MSUB: --alloc ALLOC Allocation to charge SUs to (default=b1011). --queue QUEUE Queue for job (default=ligo). --jobName JOBNAME Name of job, used for output file names and queue listing. --dir DIR Directory where submit script is written and executed from (default=current directory). --dep DEP Wait for dependent job ID to complete (default=None). --name NAME Name of submit file (default=submit). --walltime WALLTIME Walltime for job (default=2:00:00:00). --cores-per-node CORES_PER_NODE Number of cores per node (default=16). --multiple-nodes If nChains > 16 then use more than one node. --nPar NPAR Number of dimensions for MCMC. Defaults for common templates are set, assuming no PSD fitting.
env: --branch BRANCH Branchname to use, assuming /projects/p20251/USER/lsc/BRANCHNAME/etc/lscsoftrc exists (default=master). --rc RC Specify direct path to rc files to be sourced (e.g. lscsoftrc). /projects/b1011/non-lsc/lscsoft-user- env.sh added by default. --sim-quest Act as if on Quest. Useful for setting up submit files on local computer for uploading to Quest --quest-iwd QUEST_IWD Working directory for Quest submit script. lalinference_mcmc: --era ERA Era ("initial" or "advanced") of detector PSD for SNR calculation. If no cache arguments given, this will add the appropriate analytical PSD arguments to the submit file. --psd PSD [PSD ...] Pre-computed PSD(s), either as a single xml, or list of ascii files, one for each IFO in the order the IFOs were specified. XMLs are converted using lalinference_pipe_utils. --ifo IFO [IFO ...] IFOs for the analysis. --inj INJ Injection XML file. --event EVENT Event number in XML to inject. --trigtime TRIGTIME Trigger time of event. Automatically set when injecting. --approx APPROX Specify a template approximant (default SpinTaylorT4). --amporder AMPORDER Specify amplitude order of template. --flow FLOW Lower frequency bound for all detectors (default=40). --lowM1 LOWM1 Lowest reasonable M1 of the binary your are searching for. Used to determine appropraite seglength. --lowM2 LOWM2 Lowest reasonable M2 of the binary your are searching for. Used to determine appropraite seglength. --fhigh FHIGH Upper frequency bound for all detectors, given as a fraction of the injection's ISCO frequency. --srate SRATE Sampling rate of the waveform. If not provided and an injection is peformed, it is set to be sufficient for the signal being injected. If no injection, it defaults to a sufficient value for a 1.4-1.4 binary coalescence (expensive!). --seglen SEGLEN Length of data segment used for likelihood compuatation. Same default behavior as "--srate". --psdlength PSDLENGTH Length of data segment to use for PSD estimation. Defaults to 32*seglen. --psdstart PSDSTART GPS time to start PSD calculation. Defaults to trigtime - psdlength - seglen --temp-ladder-top-down Build the temperature ladder from the bottom up, using an analytic prescription for the spacing that should ensure communication between chains. Sets the number of cores so that the hottest temperature should be sampling the prior. --noisy Use a non-zero noise realization. --distance-max DISTANCE_MAX Hard outer prior boundary on distance (default=1 Gpc iLIGO, 2 Gpc aLIGO). --no-malmquist Do not use the Malmquist prior, which by default approximates the selection effects imposed by the detection processes as a cut in the SNR in the second loudest detector. --no-margtimephi Do not use the time and phase marginalized likelihood function. --trigSNR TRIGSNR SNR of the trigger (calculated automatically if injecting). --tempMin TEMPMIN Temperature of coldest chain (default=1.0). --tempMax TEMPMAX Temperature of hotest chain. Determined automatically if injecting, or trigSNR is given. --Neff NEFF Requested number of independent samples. --Niter NITER Maximum number of MCMC iterations to allow. --fix-rightascension Fix RA --fix-declination Fix DEC --fix-distance Fix Distance --fix-costheta_jn Fix costheta_jn
Help from LAL_MCMC
========== LALInference_MCMC ========== ---------------------------------------------- --- Data Parameters -------------------------- ---------------------------------------------- --ifo IFO1 [--ifo IFO2 ...] IFOs can be H1,L1,V1 --IFO1-cache cache1 Cache files [--IFO2-cache2 cache2 ...] lal PSDs: LAL{Ad}LIGO, LALVirgo lalsimuation PSDs: LALSim{Ad}LIGO, LALSim{Ad}Virgo --psdstart GPStime GPS start time of PSD estimation data --psdlength length Length of PSD estimation data in seconds --seglen length Length of segments for PSD estimation and analysis in seconds (--dont-dump-extras) If given, won't save PSD and SNR files (--trigtime GPStime) GPS time of the trigger to analyse (optional when using --margtime or --margtimephi) (--segment-start) GPS time of the start of the segment (optional with --trigtime, default: seglen-2 s before --trigtime) (--srate rate) Downsample data to rate in Hz (4096.0,) (--padding PAD [sec] Override default 0.4 seconds padding (--injectionsrate rate) Downsample injection signal to rate in Hz (--srate) (--IFO1-flow freq1 Specify lower frequency cutoff for overlap integral (40.0) [--IFO2-flow freq2 ...]) (--IFO1-fhigh freq1 Specify higher frequency cutoff for overlap integral (Nyquist [--IFO2-fhigh freq2 ...]) freq 0.5*srate) (--IFO1-channel chan1 Specify channel names when reading cache files [--IFO2-channel chan2 ...]) (--IFO1-psd psd1-ascii.txt Read in PSD from ascii file. This is not equivalent [--IFO2-psd psd2-ascii.txt ...]) to using --IFO1-cache interp:file.txt since the former won't use the ascii psd to generate fake noise. (--dataseed number) Specify random seed to use when generating data (--lalinspiralinjection) Enables injections via the LALInspiral package (--inj-fref) Reference frequency of parameters in injection XML (default 100Hz) (--inj-lambda1) value of lambda1 to be injected, LALSimulation only (0) (--inj-lambda2) value of lambda2 to be injected, LALSimulation only (0) (--inj-lambdaT value of lambdaT to be injected (0) (--inj-dlambdaT value of dlambdaT to be injected (0) (--inj-spinOrder PNorder) Specify twice the injection PN order (e.g. 5 <==> 2.5PN) of spin effects effects to use, only for LALSimulation (default: -1 <==> Use all spin effects). (--inj-tidalOrder PNorder) Specify twice the injection PN order (e.g. 10 <==> 5PN) of tidal effects to use, only for LALSimulation (default: -1 <==> Use all tidal effects). (--inj-spin-frame FRAME Specify injection spin frame: choice of total-j, orbital-l, view. (Default = OrbitalL). (--0noise) Sets the noise realisation to be identically zero (for the fake caches above only)
--- Calibration Errors Handling Arguments ------------------------------------------------------------------------
(--AddCalibrationErrors) Adds calibration errors into the f domain datastream (that includes both noise and signal) (--RandomCE) Add a random realization of phase and amplitude CE, using the S6/VSR2-3 error budget as an indication of the 1-sigma errors (--ConstantCE) Assumes calibration errors are constant over the bandwidth (requires --IFO-constant_calamp and --IFO-constant_calpha for each ifo) (--IFO-constant_calamp Constant amplitude CE for instrument IFO. 0.0 means no error, 0.1 means 10 percent (--IFO-constant_calpha Constant phase CE for instrument IFO. 0.0 means no error, 5 means a 5 degree shift (--RandomLinearCE ) Assumes CE are given by a contant plateau plus a random jittering of a few percent. After a given frequency f CE increase linearly with a given slope (requires --IFO-calamp_plateau, --IFO-calamp_knee, --IFO-calamp_slope AND similar with calamp<->calpha. Phase Errors in degree, Amp errors are relative (0.05=5%) (--IFO-calamp_plateau, --IFO-calamp_knee, --IFO-calamp_slope) Add on the i-th IFO's stream amplitude errors on the form (IFOi_c + jitter) for f<IFOi_f and (IFOi_c-f)*IFOi_slope for f>IFOi_f (--IFO-calpha_plateau, --IFO-calpha_knee, --IFO-calpha_slope) Add on the i-th IFO's stream phase errors on the form (IFOi_c + jitter) for f<IFOi_f and (IFOi_c-f)*IFOi_slope for f>IFOi_f
-
Constant Calibration Model (--MarginalizeConstantCalAmp ) If given, will add a constant value of Amplitude CE per each IFO on the top of the CBC parameters. (--MarginalizeConstantCalPha ) If given, will add a constant value of Phase CE per each IFO on the top of the CBC parameters. (--constcal_ampsigma ) If given, will use gaussian prior on the constant amplitude error with this sigma (e.g. 0.05=5%) . (--constcal_phasigma ) If given, will use gaussian prior on the constant phase error with this sigma (e.g. 5=5degs).
-
Spline Calibration Model (--enable-spline-calibration) Enable cubic-spline calibration error model. (--spcal-nodes N) Set the number of spline nodes per detector (default 5) (--spcal-amp-uncertainty X) Set the prior on relative amplitude uncertainty (default 0.1) (--spcal-phase-uncertainty X) Set the prior on phase uncertanity in degrees (default 5)
(--nsteps n) Maximum number of steps to take (1e7) (--neff N) Number of independent samples to collect (nsteps) (--skip n) Number of steps between writing samples to file (100) (--adapt-tau) Adaptation decay power, results in adapt length of 10^tau (5) (--no-adapt) Do not adapt run (--randomseed seed) Random seed of sampling distribution (random)
(--temp-skip N) Number of steps between temperature swap proposals (100) (--tempKill N) Iteration number to stop temperature swapping (Niter) (--ntemps N) Number of temperature chains in ladder (as many as needed) (--temp-min T) Lowest temperature for parallel tempering (1.0) (--temp-max T) Highest temperature for parallel tempering (50.0) (--anneal) Anneal hot temperature linearly to T=1.0 (--annealStart N) Iteration number to start annealing (510^5) (--annealLength N) Number of iterations to anneal all chains to T=1.0 (110^5)
(--psd-fit) Run with PSD fitting (--psdNblock) Number of noise parameters per IFO channel (8) (--psdFlatPrior) Use flat prior on psd parameters (Gaussian) (--glitch-fit) Run with glitch fitting (--glitchNmax) Maximum number of glitch basis functions per IFO (20)
(--data-dump) Output waveforms to file (--adapt-verbose) Output parameter jump sizes and acceptance rate stats to file (--temp-verbose) Output temperature swapping stats to file (--prop-verbose) Output proposal stats to file (--prop-track) Output proposal parameters (--outfile file) Write output files .<chain_number> (PTMCMC.output.<random_seed>.<mpi_thread>)
(--inj injections.xml) Injection XML file to use (--event N) Event number from Injection XML file to use
(--use-eta) Jump in symmetric mass ratio eta, instead of q=m1/m2 (m1>m2) (--approx) Specify a template approximant and phase order to use (default TaylorF2threePointFivePN). Available approximants: default modeldomain="time": GeneratePPN, TaylorT1, TaylorT2, TaylorT3, TaylorT4, EOB, EOBNR, EOBNRv2, EOBNRv2HM, SEOBNRv1, SpinTaylor, SpinQuadTaylor, SpinTaylorFrameless, SpinTaylorT4, PhenSpinTaylorRD, NumRel. default modeldomain="frequency": TaylorF1, TaylorF2, TaylorF2RedSpin, TaylorF2RedSpinTidal, IMRPhenomA, IMRPhenomB, IMRPhenomP. (--amporder PNorder) Specify a PN order in amplitude to use (defaults: LALSimulation: max available; LALInspiral: newtownian). (--fref f_ref) Specify a reference frequency at which parameters are defined (default 100). (--use-tidal) Enables tidal corrections, only with LALSimulation. (--use-tidalT) Enables reparmeterized tidal corrections, only with LALSimulation. (--spinOrder PNorder) Specify twice the PN order (e.g. 5 <==> 2.5PN) of spin effects to use, only for LALSimulation (default: -1 <==> Use all spin effects). (--tidalOrder PNorder) Specify twice the PN order (e.g. 10 <==> 5PN) of tidal effects to use, only for LALSimulation (default: -1 <==> Use all tidal effects). (--modeldomain) domain the waveform template will be computed in ("time" or "frequency"). If not given will use LALSim to decide (--spinAligned or --aligned-spin) template will assume spins aligned with the orbital angular momentum. (--singleSpin) template will assume only the spin of the most massive binary component exists. (--noSpin, --disable-spin) template will assume no spins (giving this will void spinOrder!=0) (--no-detector-frame) model will NOT use detector-centred coordinates and instead RA,dec
You can generally have MCMC chains to start from a given parameter value by using --parname VALUE. Names currently known to the code are: time Waveform time (overrides random about trigtime). chirpmass Chirpmass eta Symmetric massratio (needs --use-eta) q Asymmetric massratio (a.k.a. q=m2/m1 with m1>m2) phase Coalescence phase. costheta_jn Cosine of angle between J and line of sight [rads] logdistance Log Distance (requires --use-logdistance) rightascension Rightascensions declination Declination. polarisation Polarisation angle.
- Spin Parameters: a_spin1 Spin1 magnitude a_spin2 Spin2 magnitude tilt_spin1 Angle between spin1 and orbital angular momentum tilt_spin2 Angle between spin2 and orbital angular momentum phi_12 Difference between spins' azimuthal angles phi_jl Difference between total and orbital angular momentum azimuthal angles
- Equation of State parameters (requires --use-tidal or --use-tidalT): lambda1 lambda1. lambda2 lambda2. lambdaT lambdaT. dLambdaT dLambdaT.
You can generally use --paramname-min MIN --paramname-max MAX to set the prior range for the parameter paramname The names known to the code are listed below. Component masses, total mass and time have dedicated options listed here:
(--trigtime time) Center of the prior for the time variable. (--comp-min min) Minimum component mass (1.0). (--comp-max max) Maximum component mass (30.0). (--mass1-min min, --mass1-max max) Min and max for mass1 (default: same as comp-min,comp-max, will over-ride these. (--mass2-min min, --mass2-max max) Min and max for mass2 (default: same as comp-min,comp-max, will over-ride these. (--mtotal-min min) Minimum total mass (2.0). (--mtotal-max max) Maximum total mass (35.0). (--dt time) Width of time prior, centred around trigger (0.2s).
(--varyFlow, --flowMin, --flowMax) Allow the lower frequency bound of integration to vary in given range. (--pinparams) List of parameters to set to injected values [mchirp,asym_massratio,etc].
You can generally fix a parameter to be fixed to a given values by using --fix-paramname VALUE where the known names have been listed above.
(--malmquistprior) Impose selection effects on the prior (False) (--malmquist-loudest-snr) Threshold SNR in the loudest detector (0.0) (--malmquist-second-loudest-snr) Threshold SNR in the second loudest detector (5.0) (--malmquist-network-snr) Threshold network SNR (0.0) (--analyticnullprior) Use analytic null prior (--nullprior) Use null prior in the sampled parameters
(--zeroLogLike) Use flat, null likelihood (--studentTLikelihood) Use the Student-T Likelihood that marginalizes over noise (--correlatedGaussianLikelihood) Use analytic, correlated Gaussian for Likelihood (--bimodalGaussianLikelihood) Use analytic, bimodal correlated Gaussian for Likelihood (--rosenbrockLikelihood) Use analytic, Rosenbrock banana for Likelihood (--noiseonly) Using noise-only likelihood (--margphi) Using marginalised phase likelihood (--margtime) Using marginalised time likelihood (--margtimephi) Using marginalised in time and phase likelihood