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Source code for galaxy.jobs.runners.drmaa

Job control via the DRMAA API.
from __future__ import absolute_import

import json
import logging
import os
import shlex
import string
import subprocess
import time

from galaxy import model
from galaxy.jobs import JobDestination
from galaxy.jobs.handler import DEFAULT_JOB_PUT_FAILURE_MESSAGE
from galaxy.jobs.runners import (
from galaxy.util import asbool

drmaa = None

log = logging.getLogger(__name__)

__all__ = ('DRMAAJobRunner',)

RETRY_EXCEPTIONS_LOWER = frozenset(['invalidjobexception', 'internalexception'])

[docs]class DRMAAJobRunner(AsynchronousJobRunner): """ Job runner backed by a finite pool of worker threads. FIFO scheduling """ runner_name = "DRMAARunner" restrict_job_name_length = 15
[docs] def __init__(self, app, nworkers, **kwargs): """Start the job runner""" global drmaa runner_param_specs = { 'drmaa_library_path': dict(map=str, default=os.environ.get('DRMAA_LIBRARY_PATH', None))} for retry_exception in RETRY_EXCEPTIONS_LOWER: runner_param_specs[retry_exception + '_state'] = dict(map=str, valid=lambda x: x in (model.Job.states.OK, model.Job.states.ERROR), default=model.Job.states.OK) runner_param_specs[retry_exception + '_retries'] = dict(map=int, valid=lambda x: int(x) >= 0, default=0) if 'runner_param_specs' not in kwargs: kwargs['runner_param_specs'] = dict() kwargs['runner_param_specs'].update(runner_param_specs) super(DRMAAJobRunner, self).__init__(app, nworkers, **kwargs) # This allows multiple drmaa runners (although only one per handler) in the same job config file if 'drmaa_library_path' in kwargs: log.info('Overriding DRMAA_LIBRARY_PATH due to runner plugin parameter: %s', self.runner_params.drmaa_library_path) os.environ['DRMAA_LIBRARY_PATH'] = self.runner_params.drmaa_library_path # Import is delayed until runner initialization to allow for the # drmaa_library_path plugin param to override $DRMAA_LIBRARY_PATH try: drmaa = __import__("drmaa") except (ImportError, RuntimeError) as exc: raise exc.__class__('The Python drmaa package is required to use this ' 'feature, please install it or correct the ' 'following error:\n%s: %s' % (exc.__class__.__name__, str(exc))) from pulsar.managers.util.drmaa import DrmaaSessionFactory # make the drmaa library also available to subclasses self.drmaa = drmaa # Subclasses may need access to state constants self.drmaa_job_states = drmaa.JobState # Descriptive state strings pulled from the drmaa lib itself self.drmaa_job_state_strings = { drmaa.JobState.UNDETERMINED: 'process status cannot be determined', drmaa.JobState.QUEUED_ACTIVE: 'job is queued and active', drmaa.JobState.SYSTEM_ON_HOLD: 'job is queued and in system hold', drmaa.JobState.USER_ON_HOLD: 'job is queued and in user hold', drmaa.JobState.USER_SYSTEM_ON_HOLD: 'job is queued and in user and system hold', drmaa.JobState.RUNNING: 'job is running', drmaa.JobState.SYSTEM_SUSPENDED: 'job is system suspended', drmaa.JobState.USER_SUSPENDED: 'job is user suspended', drmaa.JobState.DONE: 'job finished normally', drmaa.JobState.FAILED: 'job finished, but failed', } # Ensure a DRMAA session exists and is initialized self.ds = DrmaaSessionFactory().get() self.userid = None self._init_monitor_thread() self._init_worker_threads() self.redact_email_in_job_name = self.app.config.redact_email_in_job_name
[docs] def url_to_destination(self, url): """Convert a legacy URL to a job destination""" if not url: return native_spec = url.split('/')[2] if native_spec: params = dict(nativeSpecification=native_spec) log.debug("Converted URL '%s' to destination runner=drmaa, params=%s" % (url, params)) return JobDestination(runner='drmaa', params=params) else: log.debug("Converted URL '%s' to destination runner=drmaa" % url) return JobDestination(runner='drmaa')
[docs] def get_native_spec(self, url): """Get any native DRM arguments specified by the site configuration""" try: return url.split('/')[2] or None except Exception: return None
[docs] def queue_job(self, job_wrapper): """Create job script and submit it to the DRM""" # prepare the job # external_runJob_script can be None, in which case it's not used. external_runjob_script = job_wrapper.get_destination_configuration("drmaa_external_runjob_script", None) 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() job_name = self._job_name(job_wrapper) ajs = AsynchronousJobState(files_dir=job_wrapper.working_directory, job_wrapper=job_wrapper, job_name=job_name) # set up the drmaa job template jt = dict( remoteCommand=ajs.job_file, jobName=ajs.job_name, workingDirectory=job_wrapper.working_directory, outputPath=":%s" % ajs.output_file, errorPath=":%s" % ajs.error_file ) # Avoid a jt.exitCodePath for now - it's only used when finishing. native_spec = job_destination.params.get('nativeSpecification', None) if native_spec is not None: jt['nativeSpecification'] = native_spec # fill in the DRM's job run template script = self.get_job_file(job_wrapper, exit_code_path=ajs.exit_code_file, shell=job_wrapper.shell) try: self.write_executable_script(ajs.job_file, script) except Exception: job_wrapper.fail("failure preparing job script", exception=True) log.exception("(%s) failure writing job script" % galaxy_id_tag) return # job was deleted while we were preparing it if job_wrapper.get_state() == model.Job.states.DELETED: log.debug("(%s) Job deleted by user before it entered the queue" % galaxy_id_tag) if job_wrapper.cleanup_job in ("always", "onsuccess"): job_wrapper.cleanup() return log.debug("(%s) submitting file %s", galaxy_id_tag, ajs.job_file) if native_spec: log.debug("(%s) native specification is: %s", galaxy_id_tag, native_spec) # runJob will raise if there's a submit problem if external_runjob_script is None: # TODO: create a queue for retrying submission indefinitely # TODO: configurable max tries and sleep trynum = 0 external_job_id = None fail_msg = None while external_job_id is None and trynum < 5: try: external_job_id = self.ds.run_job(**jt) break except (drmaa.InternalException, drmaa.DeniedByDrmException) as e: trynum += 1 log.warning('(%s) drmaa.Session.runJob() failed, will retry: %s', galaxy_id_tag, e) fail_msg = "Unable to run this job due to a cluster error, please retry it later" time.sleep(5) except Exception: log.exception('(%s) drmaa.Session.runJob() failed unconditionally', galaxy_id_tag) trynum = 5 else: log.error("(%s) All attempts to submit job failed" % galaxy_id_tag) if not fail_msg: fail_msg = DEFAULT_JOB_PUT_FAILURE_MESSAGE job_wrapper.fail(fail_msg) return else: job_wrapper.change_ownership_for_run() # if user credentials are not available, use galaxy credentials (if permitted) allow_guests = asbool(job_wrapper.job_destination.params.get("allow_guests", False)) pwent = job_wrapper.user_system_pwent if pwent is None: if not allow_guests: fail_msg = "User %s is not mapped to any real user, and not permitted to start jobs." % job_wrapper.user job_wrapper.fail(fail_msg) return pwent = job_wrapper.galaxy_system_pwent log.debug('(%s) submitting with credentials: %s [uid: %s]' % (galaxy_id_tag, pwent[0], pwent[2])) filename = self.store_jobtemplate(job_wrapper, jt) self.userid = pwent[2] external_job_id = self.external_runjob(external_runjob_script, filename, pwent[2]) if external_job_id is None: job_wrapper.fail("(%s) could not queue job" % galaxy_id_tag) return 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 ajs.job_id = external_job_id ajs.old_state = 'new' ajs.job_destination = job_destination # Add to our 'queue' of jobs to monitor self.monitor_queue.put(ajs)
def _complete_terminal_job(self, ajs, drmaa_state, **kwargs): """ Handle a job upon its termination in the DRM. This method is meant to be overridden by subclasses to improve post-mortem and reporting of failures. Returns True if job was not actually terminal, None otherwise. (Note: This function always returns None. Hence this function actually does not determine if a job was terminal, but the implementation in the subclasses is supposed to do this.) """ if drmaa_state == drmaa.JobState.FAILED: if ajs.job_wrapper.get_state() != model.Job.states.DELETED: ajs.stop_job = False ajs.fail_message = "The cluster DRM system terminated this job" self.work_queue.put((self.fail_job, ajs)) elif drmaa_state == drmaa.JobState.DONE: # External metadata processing for external runjobs external_metadata = not asbool(ajs.job_wrapper.job_destination.params.get("embed_metadata_in_job", True)) if external_metadata: self._handle_metadata_externally(ajs.job_wrapper, resolve_requirements=True) if ajs.job_wrapper.get_state() != model.Job.states.DELETED: self.work_queue.put((self.finish_job, ajs))
[docs] def check_watched_item(self, ajs, new_watched): """ look at a single watched job, determine its state, and deal with errors that could happen in this process. to be called from check_watched_items() returns the state or None if exceptions occurred in the latter case the job is appended to new_watched if a 1 drmaa.InternalException, 2 drmaa.InvalidJobExceptionnot, or 3 drmaa.DrmCommunicationException occurred (which causes the job to be tested again in the next iteration of check_watched_items) - the job is finished as errored if any other exception occurs - the job is finished OK or errored after the maximum number of retries depending on the exception Note that None is returned in all cases where the loop in check_watched_items is to be continued """ external_job_id = ajs.job_id galaxy_id_tag = ajs.job_wrapper.get_id_tag() state = None try: assert external_job_id not in (None, 'None'), '(%s/%s) Invalid job id' % (galaxy_id_tag, external_job_id) state = self.ds.job_status(external_job_id) # Reset exception retries for retry_exception in RETRY_EXCEPTIONS_LOWER: setattr(ajs, retry_exception + '_retries', 0) except (drmaa.InternalException, drmaa.InvalidJobException) as e: ecn = type(e).__name__ retry_param = ecn.lower() + '_retries' state_param = ecn.lower() + '_state' retries = getattr(ajs, retry_param, 0) log.warning("(%s/%s) unable to check job status because of %s exception for %d consecutive tries: %s", galaxy_id_tag, external_job_id, ecn, retries + 1, e) if self.runner_params[retry_param] > 0: if retries < self.runner_params[retry_param]: # will retry check on next iteration setattr(ajs, retry_param, retries + 1) new_watched.append(ajs) return None if self.runner_params[state_param] == model.Job.states.OK: log.warning("(%s/%s) job will now be finished OK", galaxy_id_tag, external_job_id) self.work_queue.put((self.finish_job, ajs)) elif self.runner_params[state_param] == model.Job.states.ERROR: log.warning("(%s/%s) job will now be errored", galaxy_id_tag, external_job_id) self.work_queue.put((self.fail_job, ajs)) else: raise Exception("%s is set to an invalid value (%s), this should not be possible. See galaxy.jobs.drmaa.__init__()", state_param, self.runner_params[state_param]) return None except drmaa.DrmCommunicationException as e: log.warning("(%s/%s) unable to communicate with DRM: %s", galaxy_id_tag, external_job_id, e) new_watched.append(ajs) return None except Exception: # so we don't kill the monitor thread log.exception("(%s/%s) unable to check job status: %s" % (galaxy_id_tag, external_job_id)) log.warning("(%s/%s) job will now be errored" % (galaxy_id_tag, external_job_id)) ajs.fail_message = "Cluster could not complete job" self.work_queue.put((self.fail_job, ajs)) return None return state
[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 ajs in self.watched: external_job_id = ajs.job_id galaxy_id_tag = ajs.job_wrapper.get_id_tag() old_state = ajs.old_state state = self.check_watched_item(ajs, new_watched) if state is None: continue if state != old_state: log.debug("(%s/%s) state change: %s" % (galaxy_id_tag, external_job_id, self.drmaa_job_state_strings[state])) if state == drmaa.JobState.RUNNING and not ajs.running: ajs.running = True ajs.job_wrapper.change_state(model.Job.states.RUNNING) if state in (drmaa.JobState.FAILED, drmaa.JobState.DONE): if self._complete_terminal_job(ajs, drmaa_state=state) is not None: # job was not actually terminal state = ajs.old_state else: continue if ajs.check_limits(): self.work_queue.put((self.fail_job, ajs)) continue ajs.old_state = state new_watched.append(ajs) # 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() try: ext_id = job.get_job_runner_external_id() assert ext_id not in (None, 'None'), 'External job id is None' kill_script = job_wrapper.get_destination_configuration("drmaa_external_killjob_script") if kill_script is None: self.ds.kill(ext_id) else: command = shlex.split(kill_script) command.extend([str(ext_id), str(self.userid)]) subprocess.Popen(command, shell=False) log.info("(%s/%s) Removed from DRM queue at user's request" % (job.id, ext_id)) except drmaa.InvalidJobException: log.exception("(%s/%s) User killed running job, but it was already dead" % (job.id, ext_id)) except Exception: log.exception("(%s/%s) User killed running job, but error encountered removing from DRM queue" % (job.id, ext_id))
[docs] def recover(self, job, job_wrapper): """Recovers jobs stuck in the queued/running state when Galaxy started""" job_id = job.get_job_runner_external_id() if job_id is None: self.put(job_wrapper) return ajs = AsynchronousJobState(files_dir=job_wrapper.working_directory, job_wrapper=job_wrapper) ajs.job_id = str(job_id) ajs.command_line = job.get_command_line() ajs.job_wrapper = job_wrapper ajs.job_destination = job_wrapper.job_destination if job.state == model.Job.states.RUNNING: log.debug("(%s/%s) is still in running state, adding to the DRM queue" % (job.id, job.get_job_runner_external_id())) ajs.old_state = drmaa.JobState.RUNNING ajs.running = True self.monitor_queue.put(ajs) elif job.get_state() == model.Job.states.QUEUED: log.debug("(%s/%s) is still in DRM queued state, adding to the DRM queue" % (job.id, job.get_job_runner_external_id())) ajs.old_state = drmaa.JobState.QUEUED_ACTIVE ajs.running = False self.monitor_queue.put(ajs)
[docs] def store_jobtemplate(self, job_wrapper, jt): """ Stores the content of a DRMAA JobTemplate object in a file as a JSON string. Path is hard-coded, but it's no worse than other path in this module. Uses Galaxy's JobID, so file is expected to be unique.""" filename = "%s/%s.jt_json" % (self.app.config.cluster_files_directory, job_wrapper.get_id_tag()) with open(filename, 'w+') as fp: json.dump(jt, fp) log.debug('(%s) Job script for external submission is: %s' % (job_wrapper.job_id, filename)) return filename
[docs] def external_runjob(self, external_runjob_script, jobtemplate_filename, username): """ runs an external script that will QSUB a new job. The external script needs to be run with sudo, and will setuid() to the specified user. Effectively, will QSUB as a different user (than the one used by Galaxy). """ command = shlex.split(external_runjob_script) command.extend([str(username), jobtemplate_filename]) log.info("Running command %s" % command) p = subprocess.Popen(command, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE) (stdoutdata, stderrdata) = p.communicate() exitcode = p.returncode # os.unlink(jobtemplate_filename) if exitcode != 0: # There was an error in the child process log.exception("External_runjob failed (exit code %s). Child process reported error: %s" % (str(exitcode), stderrdata)) return None # The expected output is a single line containing a single numeric value: # the DRMAA job-ID. If not the case, will throw an error. stdoutdata = stdoutdata.strip() if not stdoutdata: log.exception("External_runjob did not returned nothing instead of the job id") return None return stdoutdata
def _job_name(self, job_wrapper): external_runjob_script = job_wrapper.get_destination_configuration("drmaa_external_runjob_script", None) galaxy_id_tag = job_wrapper.get_id_tag() # define job attributes job_name = 'g%s' % galaxy_id_tag if job_wrapper.tool.old_id: job_name += '_%s' % job_wrapper.tool.old_id if not self.redact_email_in_job_name and external_runjob_script is None: job_name += '_%s' % job_wrapper.user job_name = ''.join(x if x in (string.ascii_letters + string.digits + '_') else '_' for x in job_name) if self.restrict_job_name_length: job_name = job_name[:self.restrict_job_name_length] return job_name