remote_submit.py

from argparse import ArgumentParser
from os.path import dirname, realpath, join as opj
from spurplus import connect_with_retries
from .upload_scripts import upload_scripts
from .cluster_scripts.config import job_config
from ._helpers import (
                        attempt_load_config,
                        fmt_remote_commands,
                        parse_config,
                        write_remote_submitter
                    )


def remote_submit(sync_changes=False, config_path=None):
    """
    main function that handles submitting jobs on the cluster from your local
    machine

    :param sync_changes: (bool, default: False) if True, upload any local
    changes to cluster scripts before submitting jobs
    :param config_path: (str, optional, default: None) path to your config file.
    If you created your config following the instructions in
    configs/template_config.ini, you can simply leave this empty
    :return: None (other than some hopefully some results, eventually!)
    """
    if config_path is None:
        config = attempt_load_config()
    else:
        config = parse_config(config_path)

    hostname = config['hostname']
    username = config['username']
    password = config['password']
    confirm_overwrite = config['confirm_overwrite_on_upload']

    if username.startswith('f00'):
        job_cmd = 'mksub'
    else:
        job_cmd = 'qsub'

    # set commands
    if job_config['env_type'] == 'conda':
        activate_cmd = 'source activate'
        deactivate_cmd = 'conda deactivate'
    else:
        # TODO: add commands for venv & virtualenv activation
        raise ValueError("Only conda environments are currently supported")

    with connect_with_retries(
                            hostname=hostname,
                            username=username,
                            password=password
                            ) as cluster:
        if sync_changes:
            # upload cluster scripts to remote
            script_dir = opj(dirname(realpath(__file__)), 'cluster_scripts')
            upload_scripts(cluster, script_dir, job_config, confirm_overwrite)

        # create bash script to submit and run submit.py from compute node
        submitter_filepath = write_remote_submitter(
                                                    cluster,
                                                    job_config,
                                                    activate_cmd,
                                                    deactivate_cmd
                                                    )

        # format commands for remote shell
        submitter_cmds = [job_cmd, submitter_filepath]
        remote_command = fmt_remote_commands(submitter_cmds)
        # run the submitter script
        cluster.run(remote_command)



if __name__ == '__main__':
    description = "Submit jobs to run on Dartmouth's high-performance computing\
     cluster from your local machine"
    arg_parser = ArgumentParser(description=description)
    arg_parser.add_argument(
        "--sync-changes",
        action='store_true',
        help="Update remote files with local changes before submitting"
    )
    arg_parser.add_argument(
        "--config-path",
        default=None,
        type=str,
        help="Path to your config file (optional unless you've moved your \
        config file)"
    )

    args = arg_parser.parse_args()
    remote_submit(args.sync_changes, args.config_path)