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Source code for galaxy.jobs.runners.condor

"""Job control via the Condor DRM via CLI.

This plugin has been used in production and isn't unstable but shouldn't be taken as an
example of how to write Galaxy job runners that interface with a DRM using command-line
invocations. When writing new job runners that leverage command-line calls for submitting
and checking the status of jobs please check out the CLI runner (cli.py in this directory)
start by writing a new job plugin in for that (see examples in
/galaxy/jobs/runners/util/cli/job). That approach will result in less boilerplate and allow
greater reuse of the DRM specific hooks you'll need to write. Ideally this plugin would
have been written to target that framework, but we don't have the bandwidth to rewrite
it at this time.
import logging
import os
import subprocess

from galaxy import model
from galaxy.jobs.runners import (
from galaxy.jobs.runners.util.condor import (
from galaxy.util import asbool

log = logging.getLogger(__name__)

__all__ = ('CondorJobRunner', )

class CondorJobState(AsynchronousJobState):
    def __init__(self, **kwargs):
        Encapsulates state related to a job that is being run via the DRM and
        that we need to monitor.
        self.failed = False
        self.user_log = None
        self.user_log_size = 0

[docs]class CondorJobRunner(AsynchronousJobRunner): """ Job runner backed by a finite pool of worker threads. FIFO scheduling """ runner_name = "CondorRunner"
[docs] def __init__(self, app, nworkers): """Initialize this job runner and start the monitor thread""" super().__init__(app, nworkers) self._init_monitor_thread() self._init_worker_threads()
def __old_state_paths(self, cjs): """For recovery of jobs started prior to standardizing the naming of files in the AsychronousJobState object Remove this function in 21.01 """ if cjs.job_wrapper is not None: job_file = "{}/galaxy_{}.sh".format(self.app.config.cluster_files_directory, cjs.job_wrapper.job_id) if not os.path.exists(cjs.job_file) and os.path.exists(job_file): cluster_files_dir_and_id = (self.app.config.cluster_files_directory, cjs.job_wrapper.get_id_tag()) cjs.output_file = "%s/galaxy_%s.o" % cluster_files_dir_and_id cjs.error_file = "%s/galaxy_%s.e" % cluster_files_dir_and_id cjs.exit_code_file = "%s/galaxy_%s.ec" % cluster_files_dir_and_id cjs.user_log = "%s/galaxy_%s.condor.log" % cluster_files_dir_and_id cjs.job_file = job_file
[docs] def queue_job(self, job_wrapper): """Create job script and submit it to the DRM""" # prepare the job include_metadata = asbool(job_wrapper.job_destination.params.get("embed_metadata_in_job", True)) if not self.prepare_job(job_wrapper, include_metadata=include_metadata): return # get configured job destination job_destination = job_wrapper.job_destination # wrapper.get_id_tag() instead of job_id for compatibility with TaskWrappers. galaxy_id_tag = job_wrapper.get_id_tag() # get destination params query_params = submission_params(prefix="", **job_destination.params) container = None universe = query_params.get('universe', None) if universe and universe.strip().lower() == 'docker': container = self._find_container(job_wrapper) if container: # HTCondor needs the image as 'docker_image' query_params.update({'docker_image': container.container_id}) galaxy_slots = query_params.get('request_cpus', None) if galaxy_slots: galaxy_slots_statement = 'GALAXY_SLOTS="%s"; export GALAXY_SLOTS; GALAXY_SLOTS_CONFIGURED="1"; export GALAXY_SLOTS_CONFIGURED;' % galaxy_slots else: galaxy_slots_statement = 'GALAXY_SLOTS="1"; export GALAXY_SLOTS;' # define job attributes cjs = CondorJobState( files_dir=job_wrapper.working_directory, job_wrapper=job_wrapper ) cjs.user_log = os.path.join(job_wrapper.working_directory, 'galaxy_%s.condor.log' % galaxy_id_tag) cjs.register_cleanup_file_attribute('user_log') submit_file = os.path.join(job_wrapper.working_directory, 'galaxy_%s.condor.desc' % galaxy_id_tag) executable = cjs.job_file build_submit_params = dict( executable=executable, output=cjs.output_file, error=cjs.error_file, user_log=cjs.user_log, query_params=query_params, ) submit_file_contents = build_submit_description(**build_submit_params) script = self.get_job_file( job_wrapper, exit_code_path=cjs.exit_code_file, slots_statement=galaxy_slots_statement, shell=job_wrapper.shell, ) try: self.write_executable_script(executable, script) except Exception: job_wrapper.fail("failure preparing job script", exception=True) log.exception("(%s) failure preparing job script" % galaxy_id_tag) return cleanup_job = job_wrapper.cleanup_job try: open(submit_file, "w").write(submit_file_contents) except Exception: if cleanup_job == "always": cjs.cleanup() # job_wrapper.fail() calls job_wrapper.cleanup() job_wrapper.fail("failure preparing submit file", exception=True) log.exception("(%s) failure preparing submit file" % galaxy_id_tag) return # job was deleted while we were preparing it if job_wrapper.get_state() == model.Job.states.DELETED: log.debug("Job %s deleted by user before it entered the queue" % galaxy_id_tag) if cleanup_job in ("always", "onsuccess"): os.unlink(submit_file) cjs.cleanup() job_wrapper.cleanup() return log.debug("({}) submitting file {}".format(galaxy_id_tag, executable)) external_job_id, message = condor_submit(submit_file) if external_job_id is None: log.debug("condor_submit failed for job {}: {}".format(job_wrapper.get_id_tag(), message)) if self.app.config.cleanup_job == "always": os.unlink(submit_file) cjs.cleanup() job_wrapper.fail("condor_submit failed", exception=True) return os.unlink(submit_file) log.info("({}) queued as {}".format(galaxy_id_tag, external_job_id)) # store runner information for tracking if Galaxy restarts job_wrapper.set_external_id(external_job_id) # Store DRM related state information for job cjs.job_id = external_job_id cjs.job_destination = job_destination # Add to our 'queue' of jobs to monitor self.monitor_queue.put(cjs)
[docs] def check_watched_items(self): """ Called by the monitor thread to look at each watched job and deal with state changes. """ new_watched = [] for cjs in self.watched: job_id = cjs.job_id galaxy_id_tag = cjs.job_wrapper.get_id_tag() self.__old_state_paths(cjs) # remove in 21.01 try: if cjs.job_wrapper.tool.tool_type != 'interactive' and os.stat(cjs.user_log).st_size == cjs.user_log_size: new_watched.append(cjs) continue s1, s4, s7, s5, s9, log_size = summarize_condor_log(cjs.user_log, job_id) job_running = s1 and not (s4 or s7) job_complete = s5 job_failed = s9 cjs.user_log_size = log_size except Exception: # so we don't kill the monitor thread log.exception("({}/{}) Unable to check job status".format(galaxy_id_tag, job_id)) log.warning("({}/{}) job will now be errored".format(galaxy_id_tag, job_id)) cjs.fail_message = "Cluster could not complete job" self.work_queue.put((self.fail_job, cjs)) continue if job_running: # If running, check for entry points... cjs.job_wrapper.check_for_entry_points() if job_running and not cjs.running: log.debug("({}/{}) job is now running".format(galaxy_id_tag, job_id)) cjs.job_wrapper.change_state(model.Job.states.RUNNING) if not job_running and cjs.running: log.debug("({}/{}) job has stopped running".format(galaxy_id_tag, job_id)) # Will switching from RUNNING to QUEUED confuse Galaxy? # cjs.job_wrapper.change_state( model.Job.states.QUEUED ) if job_complete: if cjs.job_wrapper.get_state() != model.Job.states.DELETED: external_metadata = not asbool(cjs.job_wrapper.job_destination.params.get("embed_metadata_in_job", True)) if external_metadata: self._handle_metadata_externally(cjs.job_wrapper, resolve_requirements=True) log.debug("({}/{}) job has completed".format(galaxy_id_tag, job_id)) self.work_queue.put((self.finish_job, cjs)) continue if job_failed: log.debug("({}/{}) job failed".format(galaxy_id_tag, job_id)) cjs.failed = True self.work_queue.put((self.finish_job, cjs)) continue cjs.runnning = job_running new_watched.append(cjs) # Replace the watch list with the updated version self.watched = new_watched
[docs] def stop_job(self, job_wrapper): """Attempts to delete a job from the DRM queue""" job = job_wrapper.get_job() external_id = job.job_runner_external_id galaxy_id_tag = job_wrapper.get_id_tag() if job.container: try: log.info("stop_job(): {}: trying to stop container .... ({})".format(job.id, external_id)) # self.watched = [cjs for cjs in self.watched if cjs.job_id != external_id] new_watch_list = list() cjs = None for tcjs in self.watched: if tcjs.job_id != external_id: new_watch_list.append(tcjs) else: cjs = tcjs break self.watched = new_watch_list self._stop_container(job_wrapper) # self.watched.append(cjs) if cjs.job_wrapper.get_state() != model.Job.states.DELETED: external_metadata = not asbool(cjs.job_wrapper.job_destination.params.get("embed_metadata_in_job", True)) if external_metadata: self._handle_metadata_externally(cjs.job_wrapper, resolve_requirements=True) log.debug("({}/{}) job has completed".format(galaxy_id_tag, external_id)) self.work_queue.put((self.finish_job, cjs)) except Exception as e: log.warning("stop_job(): {}: trying to stop container failed. ({})".format(job.id, e)) try: self._kill_container(job_wrapper) except Exception as e: log.warning("stop_job(): {}: trying to kill container failed. ({})".format(job.id, e)) failure_message = condor_stop(external_id) if failure_message: log.debug("({}). Failed to stop condor {}".format(external_id, failure_message)) else: failure_message = condor_stop(external_id) if failure_message: log.debug("({}). Failed to stop condor {}".format(external_id, failure_message))
[docs] def recover(self, job, job_wrapper): """Recovers jobs stuck in the queued/running state when Galaxy started""" # TODO Check if we need any changes here job_id = job.get_job_runner_external_id() galaxy_id_tag = job_wrapper.get_id_tag() if job_id is None: self.put(job_wrapper) return cjs = CondorJobState(job_wrapper=job_wrapper, files_dir=job_wrapper.working_directory) cjs.job_id = str(job_id) cjs.command_line = job.get_command_line() cjs.job_wrapper = job_wrapper cjs.job_destination = job_wrapper.job_destination cjs.user_log = os.path.join(job_wrapper.working_directory, 'galaxy_%s.condor.log' % galaxy_id_tag) cjs.register_cleanup_file_attribute('user_log') self.__old_state_paths(cjs) # remove in 21.01 if job.state == model.Job.states.RUNNING: log.debug("({}/{}) is still in running state, adding to the DRM queue".format(job.id, job.job_runner_external_id)) cjs.running = True self.monitor_queue.put(cjs) elif job.state == model.Job.states.QUEUED: log.debug("({}/{}) is still in DRM queued state, adding to the DRM queue".format(job.id, job.job_runner_external_id)) cjs.running = False self.monitor_queue.put(cjs)
def _stop_container(self, job_wrapper): return self._run_container_command(job_wrapper, 'stop') def _kill_container(self, job_wrapper): return self._run_container_command(job_wrapper, 'kill') def _run_container_command(self, job_wrapper, command): job = job_wrapper.get_job() external_id = job.job_runner_external_id if job: cont = job.container if cont: if cont.container_type == 'docker': return self._run_command(cont.container_info['commands'][command], external_id)[0] def _run_command(self, command, external_job_id): command = 'condor_ssh_to_job {} {}'.format(external_job_id, command) p = subprocess.Popen(command, stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=True, close_fds=True, preexec_fn=os.setpgrp) stdout, stderr = p.communicate() exit_code = p.returncode ret = None if exit_code == 0: ret = stdout.strip() else: log.debug(stderr) # exit_code = subprocess.call(command, # shell=True, # preexec_fn=os.setpgrp) log.debug('_run_command(%s) exit code (%s) and failure: %s', command, exit_code, stderr) return (exit_code, ret)