.. _rapthor_parset: 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 :ref:`tips` for tips on setting up an optimal parset): .. code-block:: none [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 in the `settings directory `_. In addition, example parsets for running on the SKAO cluster using either a single node, or multiple nodes, are availble in the `examples directory `_ and an example parset for SKA-low is available in `the settings directory `_. .. _parset_global_options: ``[global]`` ------------ .. glossary:: 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 :doc:`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 :term:`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 :term:`input_skymodel` option or if generation of the initial model is activated with the :term:`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 :term:`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 :term:`apparent_skymodel` option. See :doc:`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 :term:`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 :ref:`rapthor_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., :term:`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. .. _parset_calibration_options: ``[calibration]`` ----------------- .. glossary:: use_image_based_predict Use image-based prediction (default = ``False``)? Image-based prediction can be faster than the normal prediction, especially for large sky models. .. note:: Currently, correction for time and frequency smearing cannot be done when image-based prediction is used. If the averaging of the input data is such that time or frequency smearing is significant within the field of view of interest, then the use of image-based prediction is not recommended. 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 :term:`stepsize` should be set to a small value like 0.001. For IDGCal solves, the ``lbfgs`` algorithm is always used. 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 :term:`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. medium_datause This parameter sets the visibilities mode used during the medium-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 :term:`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 :term:`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 :term:`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 :term:`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 the fast calibration, in Hz (default = 1e6). fast_smoothnessconstraint Smoothness constraint bandwidth used during the fast calibration, in Hz (default = 3e6). fast_smoothnessreffrequency Smoothness constraint reference frequency used during the fast 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 the fast calibration, in m (default = 0). medium_freqstep_hz Frequency step used during the medium-fast calibration, in Hz (default = 1e6). medium_smoothnessconstraint Smoothness constraint bandwidth used during the medium-fast calibration, in Hz (default = 3e6). medium_smoothnessreffrequency Smoothness constraint reference frequency used during the medium-fast 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. medium_smoothnessrefdistance Smoothness constraint reference distance used during the medium-fast calibration, in m (default = 0). slow_freqstep_hz Frequency step used during the slow calibration, in Hz (default = 1e6). slow_smoothnessconstraint Smoothness constraint bandwidth used during the slow calibration, in Hz (default = 3e6). fulljones_freqstep_hz Frequency step used during the full-Jones calibration, in Hz (default = 1e6). fulljones_smoothnessconstraint Smoothness constraint bandwidth used during the full-Jones 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 = 1). 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:: Direction-dependent solution intervals are not currently supported; they will be re-enabled in a future update. .. note:: Currently, only :term:`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 :term:`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 :term:`solveralgorithm` = ``lbfgs``; default = 200.0). solverlbfgs_minibatches Number of minibatches for the LBFGS solver (only used when :term:`solveralgorithm` = ``lbfgs``; default = 1). solverlbfgs_iter Number of iterations per minibatch in the LBFGS solver (only used when :term:`solveralgorithm` = ``lbfgs``; default = 4). bda_timebase Maximum baseline used in baseline-dependent time averaging (BDA) during the calibration, in m (default = 20000). A value of 0 will disable the averaging. Depending on the solution time step used during the calibration, activating this option may improve the speed of the solve and lower the memory usage during solving. bda_frequencybase Maximum baseline used in baseline-dependent frequency averaging (BDA) during the calibration, in m (default = 20000). A value of 0 will disable the averaging. Depending on the solution time step used during the calibration, activating this option may improve the speed of the solve and lower the memory usage during solving. correct_time_frequency_smearing Correct for time and frequency smearing during the prediction part of calibration (default = ``False``). Generally, if enabled and imaging is to be done, the identical parameter in the ``[imaging]`` section should also be enabled. .. _parset_imaging_options: ``[imaging]`` ------------- .. glossary:: cellsize_arcsec Pixel size in arcsec (default = 1.5). robust Briggs robust parameter (default = -0.65). min_uv_lambda Minimum uv distance in lambda to use in imaging (default = 80). 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 Method to use for the local RMS thresholding: ``rms`` or ``rms-with-min`` (default = ``rms``). do_multiscale_clean Use multiscale cleaning (default = ``True``)? bda_timebase Maximum baseline used in baseline-dependent averaging (BDA) during imaging, in m (default = 0). A value of 0 will disable the averaging. Activating this option may improve the speed of imaging. .. note:: Currently, correction for time and frequency smearing cannot be done when BDA is used during imaging. If the averaging of the input data is such that time or frequency smearing is significant within the field of view of interest, then the use of BDA is not recommended. 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). filter_skymodel Filter out sky model components that lie outside of islands detected by PyBDSF (default = ``True``). If ``True``, only clean components from WSClean whose centers lie inside of detected islands are kept in the sky model used for calibration in the next cycle. If ``False``, all clean components generated by WSClean are kept in the sky model. .. note:: It is not recommneded to turn off filtering of the sky model unless the :term:`use_image_based_predict` parameter is set, as the sky model without filtering can be very large (resulting in runtimes becoming very long unless image-based predict is used). 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 :term:`dde_method` = ``single``, in which case the solutions closest to the image centers are used. save_image_cube Save the Stokes I frequency cube (default = ``False``). If ``True``, a cube is constructed from the channel images made during the final imaging step, once self calibration has been completed. The width of the frequency channels in the cube is set by the :term:`channel_width_hz` parameter in the strategy file. save_supplementary_images Save dirty images and the clean masks made during each imaging cycle (default = ``False``). compress_selfcal_images Compress intermediate selfcal images to reduce storage space (default = ``True``). Uses default ``fpack`` compression parameters, see `fpack documentation `_ for details on precision. Some tools may be unable to read compressed fits files and will require decompression to be run first. This can be done with the ``funpack`` tool . compress_final_images Compress the final images to reduce storage space (default = ``False``). See :term:`compress_selfcal_images` option for compression details. 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 :term:`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 :term:`batch_system` = ``slurm``). .. note:: If MPI is activated, :term:`dir_local` (under the :ref:`parset_cluster_options` 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. .. note:: When running on SKAO cluster, be sure to export the ``SALLOC_PARTITION`` to ensure Toil uses a specific partition (see example SLURM script `here `_). 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 :term:`grid_center_ra`, :term:`grid_center_dec`, :term:`grid_width_ra_deg`, and :term:`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. correct_time_frequency_smearing Correct for time and frequency smearing during imaging (default = ``False``). Generally, if enabled and calibration is to be done, the identical parameter in the ``[calibration]`` section should also be enabled. 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). .. _parset_cluster_options: ``[cluster]`` ------------- .. glossary:: batch_system Cluster batch system (only used when either StreamFlow or 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 :term:`batch_system` = ``slurm``, the maximum number of nodes of the cluster to use at once (default = 12). cpus_per_task When :term:`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 :term:`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 :term:`dir_working`. If this parameter is not set, IO-intensive processing (e.g., WSClean) will use a default path in :term:`dir_working` instead. .. note:: This parameter should not be set in the following situations: - when :term:`batch_system` = ``single_machine`` and multiple imaging sectors are used (as each sector will overwrite files from the other sectors). - when :term:`use_mpi` = ``True`` under the :ref:`parset_imaging_options` section and ``dir_local`` is not on a shared filesystem. .. attention:: This parameter is deprecated. Use :term:`local_scratch_dir` instead. local_scratch_dir Full path to a local disk on the nodes for IO-intensive processing (default = ``/tmp``). When :term:`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 :term:`dir_working`. If this parameter is not set, IO-intensive processing (e.g., WSClean) will use a default path in :term:`dir_working` instead. When :term:`cwl_runner` = ``toil`` and :term:`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 :term:`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 :term:`batch_system` = ``slurm``, then Rapthor will create a temporary directory in :term:`dir_working`. When :term:`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 :term:`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 :term:`container_type` parameter. .. note:: This option should not be used when Rapthor itself is being run inside a container. See :ref:`using_containers` for details. container_type The type of container to use when :term:`use_container` = ``True``. The supported types are: ``docker`` (the default), ``udocker``, or ``singularity``. cwl_runner CWL runner to use. Currently supported runners are: ``cwltool``, ``streamflow``, 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 and StreamFlow 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 (default = ``False``). Enabling this option implies that temporary files, produced during the workflow run, will be kept (i.e. the option ``keep_temporary_files`` is implicitly set to ``True``). 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 :term:`batch_system` = ``single_machine`` (the default). keep_temporary_files Keep temporary files created during the workflow execution (default = ``False``). If ``True``, temporary files and directories created during the workflow execution will not be deleted at the end of the run. This will require significantly more disk space. This option is useful for debugging purposes. .. note:: This option will be set to ``True`` automatically when :term:`debug_workflow` = ``True``.