Source code for toil.utils.toilKill

# Copyright (C) 2015-2022 Regents of the University of California
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# See the License for the specific language governing permissions and
# limitations under the License.
"""Kills rogue toil processes."""
import logging
import os
import signal
import sys

from toil.common import Config, Toil, getNodeID, parser_with_common_options
from toil.jobStores.abstractJobStore import NoSuchJobStoreException
from toil.statsAndLogging import set_logging_from_options

logger = logging.getLogger(__name__)

[docs] def main() -> None: parser = parser_with_common_options() parser.add_argument('--force', action='store_true', help="Send SIGKILL to the leader process if local.") options = parser.parse_args() set_logging_from_options(options) config = Config() config.setOptions(options) # Get the job store try: job_store = Toil.resumeJobStore(config.jobStore) except NoSuchJobStoreException: logger.error("The job store %s does not exist.", config.jobStore) return # NOTE: the kill will not work if the leader is still initializing at this # point. Changes to the kill flag will be ignored until the leader sets the # kill flag. # Get the leader PID pid_to_kill = job_store.read_leader_pid() # Check if the leader is on the same machine leader_node_id = job_store.read_leader_node_id() local_leader = leader_node_id == getNodeID() if local_leader: # Check if we can send signals to the leader. If not, process might be # in another container so we fall back to using the kill flag through # the job store. try: os.kill(pid_to_kill, 0) except OSError: local_leader = False if local_leader: try: os.kill(pid_to_kill, signal.SIGKILL if options.force else signal.SIGTERM)"Toil process %i successfully terminated.", pid_to_kill) except OSError: logger.error("Could not signal process %i. Is it still running?", pid_to_kill) sys.exit(1) else: # Flip the flag inside the job store to signal kill job_store.write_kill_flag(kill=True)"Asked the leader to terminate.")