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Source code for galaxy.jobs.runners.condor

Job control via the Condor DRM.
import logging
import os

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.
        super(CondorJobState, self).__init__(**kwargs)
        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(CondorJobRunner, self).__init__(app, nworkers) self._init_monitor_thread() self._init_worker_threads()
[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_CONFIGURED="1"' % galaxy_slots else: galaxy_slots_statement = 'GALAXY_SLOTS="1"' # define job attributes cjs = CondorJobState( files_dir=self.app.config.cluster_files_directory, job_wrapper=job_wrapper ) cluster_directory = self.app.config.cluster_files_directory cjs.user_log = os.path.join(cluster_directory, 'galaxy_%s.condor.log' % galaxy_id_tag) cjs.register_cleanup_file_attribute('user_log') submit_file = os.path.join(cluster_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, ) 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("(%s) submitting file %s" % (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 %s: %s" % (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("(%s) queued as %s" % (galaxy_id_tag, external_job_id)) # store runner information for tracking if Galaxy restarts job_wrapper.set_job_destination(job_destination, 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() try: if 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("(%s/%s) Unable to check job status" % (galaxy_id_tag, job_id)) log.warning("(%s/%s) job will now be errored" % (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 and not cjs.running: log.debug("(%s/%s) job is now running" % (galaxy_id_tag, job_id)) cjs.job_wrapper.change_state(model.Job.states.RUNNING) if not job_running and cjs.running: log.debug("(%s/%s) job has stopped running" % (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("(%s/%s) job has completed" % (galaxy_id_tag, job_id)) self.work_queue.put((self.finish_job, cjs)) continue if job_failed: log.debug("(%s/%s) job failed" % (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): """Attempts to delete a job from the DRM queue""" external_id = job.job_runner_external_id failure_message = condor_stop(external_id) if failure_message: log.debug("(%s). Failed to stop condor %s" % (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=self.app.config.cluster_files_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(self.app.config.cluster_files_directory, 'galaxy_%s.condor.log' % galaxy_id_tag) cjs.register_cleanup_file_attribute('user_log') if job.state == model.Job.states.RUNNING: log.debug("(%s/%s) is still in running state, adding to the DRM queue" % (job.id, job.job_runner_external_id)) cjs.running = True self.monitor_queue.put(cjs) elif job.state == model.Job.states.QUEUED: log.debug("(%s/%s) is still in DRM queued state, adding to the DRM queue" % (job.id, job.job_runner_external_id)) cjs.running = False self.monitor_queue.put(cjs)