Easy
batch_type
default: ‘slurm’
type: string
title: Batch system
choices: [‘slurm’, ‘torque’]
short description: Type of batch system running on your server
long description: Type of batch system running on your server. Only slurm and torque are supported at this time
group: execution
explevel: easy
clean
default: True
type: boolean
title: Clean the module output files.
short description: Clean the module if run succeeds by compressing or removing output files.
long description: When running haddock through the command-line, the ‘clean’ parameter will instruct the workflow to clean the output files of the module if the whole run succeeds. In this process, PDB and PSF files are compressed to gzip, with the extension .gz. While files with extension .seed, .inp, and .out files are archived, and the original files deleted. The time to perform a cleaning operation depends on the number of files in the folders and the size of the files. However, it should not represent a limit step in the workflow. For example, a rigidbody sampling 10,000 structures takes about 4 minutes in our servers. This operation uses as many cores as allowed by the user in the ‘ncores’ parameter. SSD disks will perform faster by definition. See also the ‘haddock3-clean’ and ‘haddock3-unpack’ command-line clients.
group: clean
explevel: easy
cns_exec
default: ‘’
type: file
title: Path to the CNS executable
short description: If not provided, HADDOCK3 will use the cns path configured during the installation.
long description: CNS is a required component to run HADDOCK. Ideally it should have been configured during installation. If not you can specify with the cns_exec parameter its path.
group: execution
explevel: easy
concat
default: 1
type: integer
title: Number of models to produce per job.
min: 1
max: 9999
short description: Multiple models can be calculated within one job
long description: This defines the number of models that will be generated within on job script. This allows to concatenate the generation of models into one script. In that way jobs might run longer in the batch system and reduce the load on the scheduler.
group: execution
explevel: easy
debug
default: False
type: boolean
title: Write intermediate and stdout files.
short description: Write intermediate and stdout files.
long description: When set to true, this option will increase the amount of I/O operations by writing intermediate input, output and error files on disk. Turning it to false can be useful for example when running on a network file system where I/O operations are slow.
group: execution
explevel: easy
mode
default: ‘local’
type: string
title: Mode of execution
choices: [‘local’, ‘batch’]
short description: Mode of execution of the jobs, either local or using a batch system.
long description: Mode of execution of the jobs, either local or using a batch system. Currently slurm and torque are supported. For the batch mode the queue command must be specified in the queue parameter.
group: execution
explevel: easy
ncores
default: 4
type: integer
title: Number of CPU cores
min: 1
max: 500
short description: Number of CPU cores to use for the CNS calculations. It is truncated to max available CPUs minus 1.
long description: Number of CPU cores to use for the CNS calculations. This will define the number of concurrent jobs being executed. Note that is truncated to the total number of available CPUs minus 1.
group: execution
explevel: easy
offline
default: False
type: boolean
title: Isolate haddock3 from internet.
short description: Completely isolate the haddock3 run & results from internet.
long description: For interactive plots, we are using the plotly library. It can be embedded as a link to the plotly.js library and fetched from the web, or directly copied on the html files AT THE COST OF ~3Mb per file. Setting this parameter to true will add the javascript library in generated files, therefore completely isolating haddock3 from any web call.
group: execution
explevel: easy
queue
default: ‘’
type: string
title: Queue name
short description: Name of the batch queue to which jobs will be submitted
long description: Name of the batch queue to which jobs will be submitted. If not defined the batch system default will be used.
group: execution
explevel: easy
queue_limit
default: 100
type: integer
title: Number of jobs to submit to the batch system
min: 1
max: 9999
short description: Number of jobs to submit to the batch system
long description: This parameter controls the number of jobs that will be submitted to the batch system. In combination with the concat parameter this allow to limit the load on the queueing system and also make sure jobs remain in the queue for some time (if concat > 1) to avoid high system loads on the batch system.
group: execution
explevel: easy
Expert
max_cpus
default: True
type: boolean
title: The max number of CPUs allowed.
short description: By default the max number of CPUs allowed is the max available on the system.
long description: If you want to spare a minimum amount of resources for daily tasks, set max_cpus to false; in that case the maximum number of CPUs allowed will be the total available in the machine minus 1. This calculation is done automatically.
group: execution
explevel: expert
Guru
self_contained
default: False
type: boolean
title: Create a self-contained run
short description: This option will copy the CNS scripts and executable to the run folder.
long description: This option will copy the CNS scripts and executable to the run folder to ensure that all scripts are available within the run dir. This can be useful for for example remote execution of a job or for debugging purpose to allow to edit the scripts without touching the main installation.
group: execution
explevel: guru