cogwheel.utils.submit_slurm

cogwheel.utils.submit_slurm(job_name, n_hours_limit, stdout_path, stderr_path, args='', sbatch_cmds=(), batch_path=None, multithreading=False)

Generic function to submit a job using slurm.

This function is intended to be called from other modules rather than used interactively. The job will run the calling module as script.

Parameters:

job_namestr

Name of slurm job.

n_hours_limitint

Number of hours to allocate for the job.

stdout_pathstr, os.PathLike

File name, where to direct stdout.

stderr_pathstr, os.PathLike

File name, where to direct stderr.

argsstr

Command line arguments for the calling module’s main() to parse.

sbatch_cmdssequence of str

SBATCH commands, e.g. ('--mem-per-cpu=8G',).

batch_pathstr, os.PathLike, optional

File name where to save the batch script. If not provided, a temporary file will be used.

multithreadingbool

Whether to enable automatic OMP multithreading. Defaults to False because multithreading is found to be slower despite using more resources.