babs submit: Submit jobs

Command-Line Arguments

Submit jobs to cluster compute nodes.

usage: babs submit [-h] [--count COUNT | --all | --job JOB [JOB ...]] [PATH]

Positional Arguments

PATH

Absolute path to the root of BABS project. For example, '/path/to/my_BABS_project/' (default is current working directory).

Named Arguments

--count

Number of jobs to submit. It should be a positive integer.

--all

Request to run all jobs that haven't been submitted.

--job

The subject ID (and session ID) whose job to be submitted. Can repeat to submit more than one job. Format would be --job sub-xx for single-session dataset, and --job sub-xx ses-yy for multiple-session dataset.

Warning

Do NOT kill babs submit while it's running! Otherwise, new job IDs may not be captured or saved into the job_status.csv!

Example commands

Basic use

If users only provide the required argument project_root, babs submit will only submit one job:

babs submit /path/to/my_BABS_project

Submitting a certain amount of jobs

babs submit \
    /path/to/my_BABS_project \
    --count N

Change N to the number of jobs to be submitted.

Submit all remaining jobs

To submit jobs for remaining subjects (and sessions) whose jobs haven't been submitted yet:

babs submit \
    /path/to/my_BABS_project \
    --all

Submit jobs for specific subjects (and sessions)

For single-session dataset, say you'd like to submit jobs for sub-01 and sub-02:

babs submit \
    /path/to/my_BABS_project \
    --job sub-01 \
    --job sub-02

For multi-session dataset, say you'd like to submit jobs for sub-01, ses-A and sub-02, ses-B:

babs submit \
    /path/to/my_BABS_project \
    --job sub-01 ses-A \
    --job sub-02 ses-B