LocalThreadJob.run script


def run_script(self, script, files=[], trial_run=False)

Run a script on the server in the LocalThreadJob.conda_env, and wait for it to complete.

This is useful for short installation/setup scripts that do not belong in the scheduled job.

The resulting script and files are copied to LocalThreadJob.remote_directory in the server directory and then script is executed.

See LocalThreadJob.submit_script to submit a script via the slurm scheduler and leave running in the background on the server.

Arguments

script (string or list): shell script to run in the server directory, including any necessary installation steps. Note that the script can call any other scripts in files. If a string, must be the path of a valid file which will be copied to the server. If a list, must be a list of commands (i.e. a newline will be placed between each item in the list and sent as a single script to the server).
files (list, optional, default=[]): list of paths to additional files to copy to the server required in order to successfully execute script.
trial_run (bool, optional, default=False): if True, the commands that would be sent to the server are returned but not executed.