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Source code for galaxy.jobs.runners.drmaa
"""
Job control via the DRMAA API.
"""
import json
import logging
import os
import shlex
import string
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 (
AsynchronousJobRunner,
AsynchronousJobState
)
from galaxy.util import (
asbool,
commands,
unicodify
)
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[f"{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[f"{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().__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.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(f"Converted URL '{url}' to destination runner=drmaa, params={params}")
return JobDestination(runner='drmaa', params=params)
else:
log.debug(f"Converted URL '{url}' to destination runner=drmaa")
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=f":{ajs.output_file}",
errorPath=f":{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 None:
native_spec = job_destination.params.get('native_specification', 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(f"({galaxy_id_tag}) failure writing job script")
return
# job was deleted while we were preparing it
if job_wrapper.get_state() in (model.Job.states.DELETED, model.Job.states.STOPPED):
log.debug("(%s) Job deleted/stopped 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(f"({galaxy_id_tag}) All attempts to submit job failed")
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 = f"User {job_wrapper.user} is not mapped to any real user, and not permitted to start jobs."
job_wrapper.fail(fail_msg)
return
pwent = job_wrapper.galaxy_system_pwent
log.debug(f'({galaxy_id_tag}) submitting with credentials: {pwent[0]} [uid: {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(f"({galaxy_id_tag}) could not queue job")
return
log.info(f"({galaxy_id_tag}) queued as {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
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.)
"""
job_state = ajs.job_wrapper.get_state()
if drmaa_state == drmaa.JobState.FAILED and job_state != model.Job.states.STOPPED:
if job_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 or job_state == model.Job.states.STOPPED:
# 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 job_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'), f'({galaxy_id_tag}/{external_job_id}) Invalid job id'
state = self.ds.job_status(external_job_id)
# Reset exception retries
for retry_exception in RETRY_EXCEPTIONS_LOWER:
setattr(ajs, f"{retry_exception}_retries", 0)
except (drmaa.InternalException, drmaa.InvalidJobException) as e:
ecn = type(e).__name__
retry_param = f"{ecn.lower()}_retries"
state_param = f"{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(f"({galaxy_id_tag}/{external_job_id}) unable to check job status")
log.warning(f"({galaxy_id_tag}/{external_job_id}) job will now be errored")
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(f"({galaxy_id_tag}/{external_job_id}) state change: {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.running:
# TODO: stop checking at some point
ajs.job_wrapper.check_for_entry_points()
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:
cmd = shlex.split(kill_script)
cmd.extend([str(ext_id), str(self.userid)])
commands.execute(cmd)
log.info(f"({job.id}/{ext_id}) Removed from DRM queue at user's request")
except drmaa.InvalidJobException:
log.exception(f"({job.id}/{ext_id}) User killed running job, but it was already dead")
except commands.CommandLineException as e:
log.error(f"({job.id}/{ext_id}) User killed running job, but command execution failed: {unicodify(e)}")
except Exception:
log.exception(f"({job.id}/{ext_id}) User killed running job, but error encountered removing from DRM queue")
[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 in (model.Job.states.RUNNING, model.Job.states.STOPPED):
log.debug(f"({job.id}/{job.get_job_runner_external_id()}) is still in {job.state} state, adding to the DRM queue")
ajs.old_state = drmaa.JobState.RUNNING
ajs.running = True
self.monitor_queue.put(ajs)
elif job.get_state() == model.Job.states.QUEUED:
log.debug(f"({job.id}/{job.get_job_runner_external_id()}) is still in DRM queued state, adding to the DRM queue")
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 = f"{self.app.config.cluster_files_directory}/{job_wrapper.get_id_tag()}.jt_json"
with open(filename, 'w+') as fp:
json.dump(jt, fp)
log.debug(f'({job_wrapper.job_id}) Job script for external submission is: {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).
"""
cmd = shlex.split(external_runjob_script)
cmd.extend([str(username), jobtemplate_filename])
log.info(f"Running command: {' '.join(cmd)}")
try:
stdoutdata = commands.execute(cmd).strip()
except commands.CommandLineException:
log.exception("External_runjob failed")
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.
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 = f'g{galaxy_id_tag}'
if job_wrapper.tool.old_id:
job_name += f'_{job_wrapper.tool.old_id}'
if not self.redact_email_in_job_name and external_runjob_script is None:
job_name += f'_{job_wrapper.user}'
job_name = ''.join(x if x in (f"{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