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Slurm

Command-line interface for preparing SLURM submission scripts for simulations.

add_slurm_subparser(subparsers)

Adds the 'slurm' subcommand to the Simlify CLI for rendering and writing SLURM files.

This function configures an argparse subparser named 'slurm' which allows users to specify the directory where the SLURM script should be written, the path for the SLURM submission script relative to that directory, and optional YAML configuration files to customize the SLURM settings.

PARAMETER DESCRIPTION
subparsers

An argparse._SubParsersAction object where the 'slurm' subparser will be added. This is typically obtained by calling add_subparsers() on an ArgumentParser object.
RETURNS DESCRIPTION

The configured argparse parser object for the 'slurm' subcommand.

The 'slurm' subcommand accepts the following arguments:

  • dir_write: Directory to write the SLURM submission script and potentially other input files.
  • path_slurm_write: Local path to write the SLURM submission script, relative to the dir_write. For example, if dir_write is /home/user/simulations and path_slurm_write is submit.sh, the script will be written to /home/user/simulations/submit.sh.
  • --yaml: One or more paths to YAML configuration files. These files will be loaded in the order provided, with later files overriding settings from earlier ones. This allows users to specify default SLURM settings in a base YAML file and then override specific parameters for a particular simulation using another YAML file.

The function sets the default action for this subparser to be the cli_slurm_prep function, which will be called when the user invokes the 'slurm' subcommand.

cli_extract_atoms(args, parser)

Command-line interface function to prepare SLURM submission scripts.

This function serves as the entry point when the user executes the 'slurm' subcommand of the Simlify CLI. It receives the parsed command-line arguments and the argument parser object. It initializes a SimlifyConfig object and loads configuration settings from any YAML files provided via the --yaml argument, with later files taking precedence. It then sets the SLURM job name from the args.name_job attribute (which should be added by a higher-level parser or configuration). Finally, it calls the run_slurm_prep function from the simlify.simulation.slurm module to create the SLURM submission script.

PARAMETER DESCRIPTION
args

An argparse.Namespace object containing the parsed command-line arguments for the 'slurm' subcommand.

TYPE: Namespace

parser

The argument parser object for the 'slurm' subcommand, used to display help messages if necessary (though not explicitly used in this function).

TYPE: ArgumentParser

The function retrieves the following arguments from the args object:

  • dir_write: The directory where the SLURM script will be written.
  • path_slurm_write: The path to the SLURM script relative to dir_write.
  • yaml: A list of paths to YAML configuration files.
  • name_job: The name of the SLURM job (expected to be set elsewhere).

It initializes a SimlifyConfig, loads YAML configurations in reverse order of precedence, sets the SLURM job name, and then calls run_slurm_prep to perform the SLURM script preparation.