The Rapthor parset

Before Rapthor can be run, a parset describing the reduction must be made. The parset is a simple text file defining the parameters of a run in a number of sections. For example, a minimal parset for a basic reduction on a single machine could look like the following (see Tips for running Rapthor for tips on setting up an optimal parset):

[global]
dir_working = /path/to/rapthor/working/dir
input_ms = /path/to/input/dir/input.ms

The available options are described below under their respective sections.

Note

An example parset is available here.

[global]

dir_working

Full path to working dir where rapthor will run (required). All output will be placed in this directory. E.g., dir_working = /data/rapthor.

input_ms

Full path to the input MS files (required). Wildcards can be used (e.g., input_ms = /path/to/data/*.ms). The paths can also be given as a list (e.g., input_ms = [/path/to/data1/*.ms, /path/to/data2/*.ms, /path/to/data3/obs3.ms]). Note that Rapthor works on a copy of these files and does not modify the originals in any way.

Note

The MS files output by the LINC pipeline can be directly used with Rapthor. See Data preparation for details.

data_colname

Data column to be read from the input MS files (default = DATA).

generate_initial_skymodel

Generate an initial target sky model from the input data (default = True). This option is ignored if a file is specified with the input_skymodel option. When this option is activated, an image of the full field is made from the input data (without doing any calibration). The initial sky model is generated from the clean components as part of this imaging and will be located in the dir_working/skymodels/initial_image directory.

generate_initial_skymodel_radius

The radius out to which the sky model will be generated (default = None, which results in coverage out to a width of 2 * FWHM of the primary beam at the mean frequency and mean elevation of the observations).

generate_initial_skymodel_data_fraction

Fraction of data to use during the generation of the initial sky model (default = 0.2). If less than one, the input data are divided by time into chunks that sum to the requested fraction, spaced out evenly over the full time range.

download_initial_skymodel

Download the initial sky model automatically instead of using a user-provided one (default = False). This option is ignored if a file is specified with the input_skymodel option or if generation of the initial model is activated with the generate_initial_skymodel option. The downloaded sky model will be named dir_working/skymodels/initial_skymodel_{catalog}.txt, where {catalog} is the name of the catalog server specified by the download_initial_skymodel_server option.

download_initial_skymodel_radius

The radius in degrees out to which a sky model should be downloaded (default = 5.0).

download_initial_skymodel_server

Place to download the initial sky model from (default = TGSS). This can either be TGSS to use the TFIR GMRT Sky Survey, LOTSS to use the LOFAR Two-metre Sky Survey, or GSM to use the Global Sky Model.

download_overwrite_skymodel

Overwrite any existing sky model with a downloaded one (default = False).

input_skymodel

Full path to the input sky model file, with true-sky fluxes (required if automatic generation or download is disabled). If you also have a sky model with apparent flux densities, specify it with the apparent_skymodel option.

See Data preparation for more info on preparing the sky model.

apparent_skymodel

Full path to the input sky model file, with apparent-sky fluxes (optional). Note that the source names must be identical to those in the input_skymodel.

regroup_input_skymodel

Regroup input skymodel as needed to meet target flux (default = True). If False, the existing patches are used for the calibration.

strategy

Name of processing strategy to use (default = selfcal). A custom strategy can be used by giving instead the full path to the strategy file. See Setting the processing strategy for details on the available predefined strategies and on making a custom strategy file.

selfcal_data_fraction

Fraction of data to use (default = 0.2). If less than one, the input data are divided by time into chunks that sum to the requested fraction, spaced out evenly over the full time range. Using a low value (0.2 or so) is strongly recommended for typical 8-hour, full-bandwidth observations.

final_data_fraction

A final data fraction can be specified (default = 1.0) such that a final processing pass (i.e., after selfcal finishes) is done with a different fraction.

input_h5parm

Full path to an H5parm file with direction-dependent solutions (default = None). This file is used if no calibration is to be done.

Note

The directions in the H5parm file must match the patches in the input sky model, and the time and frequency coverage must be sufficient to cover the duration and bandwidth of the input dataset.

input_fulljones_h5parm

Full path to an H5parm file with full-Jones solutions (default = None). This file is used if no calibration is to be done.

facet_layout

Full path to a text file that defines the facet layout (default = None). This file must use the WSClean facet format, specified in the WSClean documentation. Also note that the facet centroids (the facet point of interest) must be defined in the file as well. If a facet file is supplied, calibration patches and imaging facets will be set to those specified in the file, if possible, and the calibrator selection parameters specified in the strategy (e.g., target_flux) will be ignored (and therefore the patch and facet layout will be held constant between cycles)

Note

In a given cycle, the calibration patches and imaging facets will match the input facet layout unless the layout would result in one or more empty calibration patches, in which case the empty patches are removed and the layout of the remaining patches is set using Voronoi tessellation.

dde_mode

Mode to use to derive and correct for direction-dependent effects: faceting or hybrid (default = faceting). If faceting, Voronoi faceting is used throughout the processing. If hybrid, faceting is used only during the self calibration steps; in the final cycle (done after self calibration has been completed successfully), IDGCal is used during calibration to generate smooth 2-D screens that are then applied by WSClean in the final imaging step.

Note

The hybrid mode is not yet available; it will be enabled in a future update.

[calibration]

llssolver

The linear least-squares solver to use (one of qr, svd, or lsmr; default = qr).

maxiter

Maximum number of iterations to perform during calibration (default = 150).

propagatesolutions

Propagate solutions to next time slot as initial guess (default = True)?

solveralgorithm

The algorithm used for solving (one of directionsolve, directioniterative, lbfgs, or hybrid; default = directioniterative). When using lbfgs, the stepsize should be set to a small value like 0.001.

onebeamperpatch

Calculate the beam correction once per calibration patch (default = False)? If False, the beam correction is calculated separately for each source in the patch. Setting this to True can speed up calibration and prediction, but can also reduce the quality when the patches are large.

parallelbaselines

Parallelize model calculation over baselines, instead of parallelizing over directions (default = False).

sagecalpredict

Use SAGECal for model calculation, both in predict and calibration (default = False).

fast_datause

This parameter sets the visibilities mode used during the fast-phase solves (one of single, dual, or full; default = single). If set to single, the XX and YY visibilities are averaged together to a single (Stokes I) visibility. If set to dual, only the XX and YY visibilities are used (YX and XY are not used). If set to full, all visibilities are used. Activating the single or dual mode improves the speed of the solves and lowers the memory usage during solving.

Note

Currently, only solveralgorithm = directioniterative is supported when using single or dual modes. If one of these modes is activated and a different solver is specified, the solver will be automatically switched to the directioniterative one.

slow_datause

This parameter sets the the visibilities used during the slow-gain solves (one of dual or full; default = dual). If set to dual, only the XX and YY visibilities are used (YX and XY are not used). If set to full, all visibilities are used. Activating the dual mode improves the speed of the solves and lowers the memory usage during solving.

Note

Currently, only solveralgorithm = directioniterative is supported when using the dual mode. If this modes is activated and a different solver is specified, the solver will be automatically switched to the directioniterative one.

stepsize

Size of steps used during calibration (default = 0.02). When using solveralgorithm = lbfgs, the stepsize should be set to a small value like 0.001.

stepsigma

In order to stop solving iterations when no further improvement is seen, the mean of the step reduction is compared to the standard deviation multiplied by stepsigma factor (default = 2.0). If mean of the step reduction is lower than this value (noise dominated), solver iterations are stopped since no possible improvement can be gained.

tolerance

Tolerance used to check convergence during calibration (default = 5e-3).

fast_freqstep_hz

Frequency step used during fast phase calibration, in Hz (default = 1e6).

fast_smoothnessconstraint

Smoothness constraint bandwidth used during fast phase calibration, in Hz (default = 3e6).

fast_smoothnessreffrequency

Smoothness constraint reference frequency used during fast phase calibration, in Hz. If not specified this will automatically be set to 144 MHz for HBA or the midpoint of the frequency coverage for LBA.

fast_smoothnessrefdistance

Smoothness constraint reference distance used during fast phase calibration, in m (default = 0).

fast_bda_timebase

Maximum baseline used in baseline-dependent averaging (BDA) during the fast-phase calibration, in m (default = 0). A value of 0.0 will disable the averaging. Depending on the solution time step used during the fast-phase calibration, activating this option may improve the speed of the solve and lower the memory usage during solving.

slow_freqstep_hz

Frequency step used during slow amplitude calibration, in Hz (default = 1e6).

slow_smoothnessconstraint_joint

Smoothness constraint bandwidth used during the first slow gain calibration, where a joint solution is found for all stations, in Hz (default = 3e6).

slow_smoothnessconstraint_separate

Smoothness constraint bandwidth used during the second slow gain calibration, where separate solutions are found for each station, in Hz (default = 3e6).

slow_bda_timebase_joint

Maximum baseline used in baseline-dependent averaging (BDA) during the first slow gain calibration, in m (default = 20000). A value of 0 will disable the averaging. Depending on the solution time step used during the slow-gain calibration, activating this option may improve the speed of the solve and lower the memory usage during solving.

slow_bda_timebase_separate

Maximum baseline used in baseline-dependent averaging (BDA) during the second slow gain calibration, in m (default = 20000). A value of 0 will disable the averaging. Depending on the solution time step used during the slow-gain calibration, activating this option may improve the speed of the solve and lower the memory usage during solving.

fulljones_timestep_sec

Time step used during the full-Jones gain calibration, in seconds (default = 600).

fulljones_freqstep_hz

Frequency step used during full-Jones amplitude calibration, in Hz (default = 1e6).

fulljones_smoothnessconstraint

Smoothness constraint bandwidth used during the full-Jones gain calibration, in Hz (default = 0).

dd_interval_factor

Maximum factor by which the direction-dependent solution intervals can be increased, so that fainter calibrators get longer intervals (in the fast and slow solves only; default = 3). The value determines the maximum allowed adjustment factor by which the solution intervals are allowed to be increased for faint sources. For a given direction, the adjustment is calculated from the ratio of the apparent flux density of the calibrator to the target flux density of the cycle (set in the strategy) or, if a target flux density is not defined, to that of the faintest calibrator in the sky model. A value of 1 disables the use of direction-dependent solution intervals; a value greater than 1 enables direction-dependent solution intervals.

Note

Currently, only solveralgorithm = directioniterative is supported when using direction-dependent solution intervals. If direction-dependent solution intervals are activated and a different solver is specified, the solver will be automatically switched to the directioniterative one.

dd_smoothness_factor

Maximum factor by which the smoothnessconstraint can be increased, so that fainter calibrators get more smoothing (default = 3). The factors are calculated in the same way as the direction-dependent interval factors, set by dd_interval_factor. A value of 1 disables the use of direction-dependent smoothness factors; a value greater than 1 enables direction-dependent smoothness factors.

solverlbfgs_dof

Degrees of freedom for the LBFGS solver (only used when solveralgorithm = lbfgs; default = 200.0).

solverlbfgs_minibatches

Number of minibatches for the LBFGS solver (only used when solveralgorithm = lbfgs; default = 1).

solverlbfgs_iter

Number of iterations per minibatch in the LBFGS solver (only used when solveralgorithm = lbfgs; default = 4).

[imaging]

cellsize_arcsec

Pixel size in arcsec (default = 1.25).

robust

Briggs robust parameter (default = -0.5).

min_uv_lambda

Minimum uv distance in lambda to use in imaging (default = 0).

max_uv_lambda

Maximum uv distance in lambda to use in imaging (default = 1e6).

mgain

Cleaning gain for major iterations, passed to the imager (default = 0.8). This setting does not affect the first “initial_image” round.

taper_arcsec

Taper to apply when imaging, in arcsec (default = 0).

local_rms_strength

Strength to use for the local RMS thresholding (default = 0.8). The strength is applied by WSClean to the local RMS map using local_rms ^ strength.

local_rms_window

Size of the window (in number of PSFs) to use for the local RMS thresholding (default = 50).

local_rms_method = rms-with-min

Method to use for the local RMS thresholding: rms or rms-with-min (default = rms-with-min).

do_multiscale_clean

Use multiscale cleaning (default = True)?

dde_method

Method to use to correct for direction-dependent effects during imaging: single or full (default = full). If single, a single, direction-independent solution (i.e., constant across the image sector) will be applied for each sector. In this case, the solution applied is the one in the direction closest to each sector center. If full, the full, direction-dependent solutions are applied (using either facets or screens).

save_visibilities

Save visibilities used for imaging (default = False). If True, the imaging MS files will be saved, with the the direction-independent full-Jones solutions, if available, applied. Note, however, that the direction-dependent solutions will not be applied unless dde_method = single, in which case the solutions closest to the image centers are used.

save_supplementary_images

Save dirty images and the clean masks made during each imaging cycle (default = False).

idg_mode

IDG (image domain gridder) mode to use in WSClean (default = cpu). The mode can be cpu or hybrid.

mem_gb

Maximum memory in GB (per node) to use for WSClean jobs (default = 0 = all available memory).

Note

If the mem_per_node_gb parameter is set, then the maximum memory for WSClean jobs will be set to the smaller of mem_gb and mem_per_node_gb.

apply_diagonal_solutions

Apply separate XX and YY corrections during facet-based imaging (default = True). If False, scalar solutions (the average of the XX and YY solutions) are applied instead. (Separate XX and YY corrections are always applied when using non-facet-based imaging methods.)

make_quv_images

Make Stokes QUV images in addition to the Stokes I image (default = False). If True, Stokes QUV images are made during the final imaging step, once self calibration has been completed.

pol_combine_method

The method used to combine the polarizations during deconvolution can also be specified. This method can be “link” to linked polarization cleaning or “join” to use joined polarization cleaning (default = link). When using linked cleaning, the Stokes I image is used for cleaning and its clean components are subtracted from all polarizations.

dd_psf_grid

The number of direction-dependent PSFs which should be fit horizontally and vertically in the image (default = [0, 0] = scale with the image size, with approximately one PSF per square degree of imaged area). Set to [1, 1] to use a direction-independent PSF.

use_mpi

Use MPI to distribute WSClean jobs over multiple nodes (default = False)? If True and more than one node can be allocated to each WSClean job (i.e., max_nodes / num_images >= 2), then distributed imaging will be used (only available if batch_system = slurm).

Note

If MPI is activated, dir_local (under the [cluster] section below) must not be set unless it is on a shared filesystem.

Note

Currently, Toil does not fully support openmpi. Because of this, imaging can only use the worker nodes, and the master node will be idle.

reweight

Reweight the visibility data before imaging (default = False). If True, data with high residuals (compared to the predicted model visibilities) are down-weighted. This feature is experimental and should be used with caution.

grid_width_ra_deg

Size of area to image when using a grid (default = 1.7 * mean FWHM of the primary beam).

grid_width_dec_deg

Size of area to image when using a grid (default = 1.7 * mean FWHM of the primary beam).

grid_center_ra

Center of area to image when using a grid (default = phase center).

grid_center_dec

Center of area to image when using a grid (default = phase center).

grid_nsectors_ra

Number of sectors along the RA axis (default = 0). The number of sectors in Dec will be determined automatically to ensure the whole area specified with grid_center_ra, grid_center_dec, grid_width_ra_deg, and grid_width_dec_deg is imaged. Set to 0 to force a single sector for the full area. A grid of sectors can be useful for computers with limited memory but generally will give inferior results compared to an equivalent single sector.

sector_center_ra_list

List of image centers (default = []). Instead of a grid, imaging sectors can be defined individually by specifying their centers and widths.

sector_center_dec_list

List of image centers (default = []).

sector_width_ra_deg_list

List of image widths, in degrees (default = []).

sector_width_dec_deg_list

List of image widths, in degrees (default = []).

max_peak_smearing

Max desired peak flux density reduction at center of the image edges due to bandwidth smearing (at the mean frequency) and time smearing (default = 0.15 = 15% reduction in peak flux). Higher values result in shorter run times but more smearing away from the image centers.

skip_final_major_iteration

Skip the final WSClean major iteration for all but the last processing cycle (default = True). If True, the final iteration is skipped during imaging, which speeds up imaging but degrades the image slightly; however, the sky model is not affected by this setting. Therefore, it is safe to use this option for self calibration cycles.

Note

The final WSClean major iteration is never skipped in the final processing cycle regardless of this setting.

skip_corner_sectors

Skip corner sectors defined by the imaging grid (default = False)? If True and a grid is used (defined by the grid_* parameters above), the four corner sectors are not processed (if possible for the given grid).

[cluster]

batch_system

Cluster batch system (only used when Toil is the CWL runner; default = single_machine). Use single_machine when running on a single machine and slurm to use multiple nodes of a Slurm-based cluster.

Note

When using the slurm batch system, additional Slurm arguments can be passed to Toil by setting the TOIL_SLURM_ARGS environment variable in your environment before running Rapthor. See the Toil environment variables page for details.

max_nodes

When batch_system = slurm, the maximum number of nodes of the cluster to use at once (default = 12).

cpus_per_task

When batch_system = slurm, the number of processors per task to request (default = 0 = all). By setting this value to the number of processors per node, one can ensure that each task gets the entire node to itself, which is the recommended way of running Rapthor.

mem_per_node_gb

When batch_system = slurm, the amount of memory per node in GB to request (default = 0 = all).

max_cores

Maximum number of cores per task to use on each node (default = 0 = all).

max_threads

Maximum number of threads per task to use on each node (default = 0 = all).

deconvolution_threads

Number of threads to use by WSClean during deconvolution (default = 0 = 2/5 of max_threads, but not more than 14).

parallel_gridding_threads

Number of threads to use by WSClean for parallel gridding (default = 0 = 2/5 of max_threads, but not more than 6).

dir_local

Full path to a local disk on the nodes for IO-intensive processing (default = not used). The path must exist on all nodes (but does not have to be on a shared filesystem). This parameter is useful if you have a fast local disk (e.g., an SSD) that is not the one used for dir_working. If this parameter is not set, IO-intensive processing (e.g., WSClean) will use a default path in dir_working instead.

Note

This parameter should not be set in the following situations:

• when batch_system = single_machine and multiple imaging sectors are used (as each sector will overwrite files from the other sectors).

• when use_mpi = True under the [imaging] section and dir_local is not on a shared filesystem.

Attention

This parameter is deprecated. Use local_scratch_dir instead.

local_scratch_dir

Full path to a local disk on the nodes for IO-intensive processing (default = /tmp). When batch_system = slurm, the path must exist on all the compute nodes, but not necessarily on the head node. This parameter is useful if you have a fast local disk (e.g., an SSD) that is not the one used for dir_working. If this parameter is not set, IO-intensive processing (e.g., WSClean) will use a default path in dir_working instead.

When cwl_runner = toil and batch_system = single_machine, it is recommended to set this parameter, so that Rapthor can clean up any temporary files and directories that Toil left behind.

Warning

If you want to run multiple instances of Rapthor concurrently using Toil, make sure that you specify different directories as local_scratch_dir. Otherwise, one Rapthor instance will potentially clobber files/directories created by another instance.

global_scratch_dir

Full path to a directory on a shared disk that is readable and writable by all the compute nodes and the head node. This directory will be used to store the intermediate outputs that need to be shared between the different steps in the workflow. If this parameter is not set and batch_system = slurm, then Rapthor will create a temporary directory in dir_working.

When cwl_runner = toil, it is recommended to set this parameter, so that Rapthor can clean up any temporary files and directories that Toil left behind.

Warning

If you want to run multiple instances of Rapthor concurrently using Toil, make sure that you specify different directories as global_scratch_dir. Otherwise, one Rapthor instance will potentially clobber files/directories created by another instance.

use_container

Run the workflows inside a container (default = False)? If True, the CWL workflow for each operation (such as calibrate or image) will be run inside a container. The type of container can be specified with the container_type parameter.

Note

This option should not be used when Rapthor itself is being run inside a container. See Using a (u)Docker/Singularity image for details.

container_type

The type of container to use when use_container = True. The supported types are: docker (the default), udocker, or singularity.

cwl_runner

CWL runner to use. Currently supported runners are: cwltool and toil (default). Toil is the recommended runner, since it provides much more fine-grained control over the execution of a workflow. For example, Toil can use Slurm to automatically distribute workflow steps over different compute nodes, whereas CWLTool can only execute workflows on a single node. With CWLTool you also run the risk of overloading your machine when too many jobs are run in parallel. For debugging purposes CWLTool outshines Toil, because its logs are easier to understand.

debug_workflow

Debug workflow related issues. Enabling this will require significantly more disk space. The working directory will never be cleaned up, stdout and stderr will not be redirectied, and log level of the CWL runner will be set to DEBUG. Additionally, when using Toil as the CWL runner, some tasks will run using only a single thread (to make debugging easier). Use this option with care!

Note

If Toil is the CWL runner, this option will only work when batch_system = single_machine (the default).