Slurm scheduler

[sverhoeven]

Adds Slurm scheduler support.

Also adds

• sftp file system to copy input/output to/from a remote Slurm server.
• Testing against slurm is done using a Docker container. using https://github.com/testcontainers/testcontainers-python (fixes Use testcontainers #12)
• Disable more flake8 rules which are false positives or not valid in tests.

To test spin up a Slurm container with

docker run --detach --publish 10022:22 xenonmiddleware/slurm:20

To submit a job in a Python REPL (python -m asyncio or ipython)

from pathlib import Path
from bartender.filesystems.sftp import SftpFileSystem
from bartender.schedulers.abstract import JobDescription
from bartender.schedulers.slurm import SlurmScheduler
from bartender.schedulers.runner import SshCommandRunner

job_dir = Path('/tmp/jobs/myjob')
job_dir.mkdir(parents=True, exist_ok=True)
config = {
            "hostname": 'localhost',
            "port": 10022,
            "username": 'xenon',
            "password": 'javagat',
        }
scheduler = SlurmScheduler(runner=SshCommandRunner(config))
description = JobDescription(command="echo -n hello", job_dir=str(job_dir))
fs = SftpFileSystem(entry='/home/xenon', config=config)
localized_description = fs.localize_description(description, job_dir.parent)

await fs.upload(description, localized_description)

job_id = await scheduler.submit(localized_description)

print(await scheduler.state(job_id))
# Repeat fetching state until it is 'ok' or 'error'

await fs.download(localized_description, description)

After download should have stderr.txt, stdout.txt, returncode files in /tmp/jobs/myjob.

As similar job submission is done at https://github.com/i-VRESSE/bartender/blob/slurm-scheduler/bartender/tests/schedulers/test_slurm.py#L60

Don't forget to docker rm -f <slurm container name or id> when you are done.

[Peter9192]

Just a heads up that I successfully managed to execute the instructions in the top post. I'm still trying to grasp more fully how this works, but that also requires looking at #15.

[Peter9192]

Tested and pair-reviewed!

[Peter9192]

Now, once open it stays open. Would it make sense to close the connection after each transfer?

[sverhoeven]

Postponed to #35