A Working Example of a bin_overrides Script

sbatch is the Slurm scheduler’s submission client. In this example we will show how cluster configuration’s bin_overrides may be used to change default behavior.

This example demonstrates a few uses of wrapping the default scheduler clients:

• Using SSH from the web host to launch sbatch on the submit host

• Altering arguments passed to the scheduler

• Altering the script passed to sbatch (which is almost certainly a terrible idea)

• Logging values passed to the scheduler in a custom location (note that the values passed to sbatch are also logged to the PUN log file at /var/log/ondemand-nginx/$USER/error.log by the Dashboard and Job Composer when submitting jobs)

Warning

This wrapper when used with the OOD Job Composer will place any stdout or stderr files in $HOME instead of the usual location of $HOME/ondemand/data/sys/myjobs/projects/default/$JOBID.

#!/usr/bin/env python36
from getpass import getuser
from select import select
from sh import ssh, ErrorReturnCode  # pip3 install sh
import logging
import os
import re
import sys

'''
An example of a `bin_overrides` replacing Slurm `sbatch` for use with Open OnDemand.

Requirements:

- $USER must be able to SSH from web node to submit node without using a password

Examples:

- SSH's from a web node to a submit node
- Logging values passed to sbatch
- Altering arguments passed to sbatch
- Altering the script passed to sbatch (which is almost certainly a bad idea)

Thoughts for further development:

- Add out of script configuration (SUBMISSION_NODE, logging preferences)
- Improve logging permission handling (right now it needs to be done manually)
- Solve problem of CWD being set to the $HOME

Note that as of v1.4.9 OOD's job adapters parse stdout but may not validate;
changing the format of sbatch's stdout can break applications. For exit codes
OOD's job adapters require that the wrapper exit 0 on success and non 0 on
failure.
'''

logging.basicConfig(filename='/tmp/sbatch.log', level=logging.INFO)

SUBMISSION_NODE = 'head'
USER = os.environ['USER']


def run_remote_sbatch(script, *argv):
  """
  @brief      SSH and submit the job from the submission node

  @param      script (str)  The script
  @param      argv (list<str>)    The argument vector for sbatch

  @return     output (str) The merged stdout/stderr of the remote sbatch call
  """

  output = None

  try:
    result = ssh(
      '@'.join([USER, SUBMISSION_NODE]),
      '-oBatchMode=yes',  # ensure that SSH does not hang waiting for a password that will never be sent
      '/opt/slurm/bin/sbatch',  # the real sbatch on the remote
      *argv,  # any arguments that sbatch should get
      _in=script,  # redirect the script's contents into stdin
      _err_to_out=True  # merge stdout and stderr
    )

    output = result.stdout.decode('utf-8')
    logging.info(output)
  except ErrorReturnCode as e:
    output = e.stdout.decode('utf-8')
    logging.info(output)
    print(output)
    sys.exit(e.exit_code)

  return output


def filter_argv(argv):
  """
  @brief      Filter the argument vector to add or remove arguments

  @param      argv (list<str>) The original argument vector passed to sbatch

  @return     argv (list<str>) The altered argument vector to pass to the real sbatch
  """

  logging.info('ARGV:')
  for arg in argv:
    logging.info(argv)

  argv += ['--export=THE_ANSWER=42']

  return argv


def filter_script(script):
  """
  @brief      Alter the script that the user is sending to sbatch

  This is a terrible fragile idea, but it is possible, so let's try it! We will set
  an environment variable and cleanup /tmp after the user.

  @param      script (str)  The script

  @return     script (str) The altered script
  """

  shebang = '#!/bin/bash\n'
  match = re.match('^(#!.+)\n', script)
  if match:
    shebang = match.group()
    script  = script.replace(shebang, '')

  return shebang + '''
  export THE_QUESTION='6*9=?'
  ''' + script + '''
  rm -rf /tmp 2>/dev/null
  '''


def load_script():
  """
  @brief      Loads a script from stdin.

  With OOD and Slurm the user's script is read from disk and passed to sbatch via stdin
  https://github.com/OSC/ood_core/blob/5b4d93636e0968be920cf409252292d674cc951d/lib/ood_core/job/adapters/slurm.rb#L138-L148

  @return     script (str) The script content
  """
  # Do not hang waiting for stdin that is not coming
  if not select([sys.stdin], [], [], 0.0)[0]:
    print('No script available on stdin!')
    sys.exit(1)

  return sys.stdin.read()


def main():
  """
  @brief      SSHs from web node to submit node and executes the remote sbatch.
  """
  output = run_remote_sbatch(
    filter_script(load_script()),
    filter_argv(sys.argv[1:])
  )

  print(output)

if __name__ == '__main__':
  main()