Parallelization

(and other common options)

Throughout Captus’ modules we provide common options that allow you limit the computer’s resources available to Captus, change the way of running parallel tasks, and control the amount of text shown during a run:

--ram

With this option you can specify the maximum RAM in GB that Captus is allowed to use. For example, if your system has 64 GB of RAM and you want to limit the use to 32.5 GB you would set the argument --ram 32.5.

This argument is optional, the default is auto (= 99% of available RAM).

--threads

Similarly, you can specify the maximum number of CPU cores that Captus is allowed to use. If your system has 16 CPU cores but you need some cores for other analyses you could reduce it to, for example, 8 cores with --threads 8.

This argument is optional, the default is auto (= all CPU cores).

--concurrent

This option sets the maximum number of tasks to run in parallel at any moment. For example, let’s imagine you set --threads 16 and --concurrent 2, this means that Captus will run only 2 tasks in parallel but each of those tasks can use up to 8 CPU cores.

This argument is optional, the default is auto (the automatic adjustment varies between analysis steps).

--debug

This flag enables the debugging mode, this disables parallelization so errors can be logged to screen. If you are seeing some samples failing steps or some other unexpected behavior you can enable --debug and submit the error shown to the Issues (https://github.com/edgardomortiz/Captus/issues) section in our GitHub repository.

--show_less

This flag produces less verbose screen printout. Essentially, information about each sample will not be shown (but still logged) during the run.

Created by Edgardo M. Ortiz (06.08.2021)
Last modified by Edgardo M. Ortiz (11.11.2022)