コード例 #1
0
ファイル: kubernetes.py プロジェクト: vincenzopennone/galaxy
 def finish_job(self, job_state):
     super().finish_job(job_state)
     jobs = find_job_object_by_name(self._pykube_api, job_state.job_id,
                                    self.runner_params['k8s_namespace'])
     if len(jobs.response['items']) != 1:
         log.warning(
             "More than one job matches selector. Possible configuration error"
             " in job id '%s'", job_state.job_id)
     job = Job(self._pykube_api, jobs.response['items'][0])
     self.__cleanup_k8s_job(job)
コード例 #2
0
ファイル: kubernetes.py プロジェクト: mvdbeek/galaxy
 def finish_job(self, job_state):
     self._handle_metadata_externally(job_state.job_wrapper, resolve_requirements=True)
     super().finish_job(job_state)
     jobs = find_job_object_by_name(self._pykube_api, job_state.job_id, self.runner_params['k8s_namespace'])
     if len(jobs.response['items']) > 1:
         log.warning("More than one job matches selector: %s. Possible configuration error"
                     " in job id '%s'" % (jobs.response['items'], job_state.job_id))
     elif len(jobs.response['items']) == 0:
         log.warning("No k8s job found which matches job id '%s'. Ignoring...", job_state.job_id)
     else:
         job = Job(self._pykube_api, jobs.response['items'][0])
         if self.__has_guest_ports(job_state.job_wrapper):
             self.__cleanup_k8s_guest_ports(job_state.job_wrapper, job)
         self.__cleanup_k8s_job(job)
コード例 #3
0
ファイル: kubernetes.py プロジェクト: usegalaxy-au/galaxy
 def stop_job(self, job_wrapper):
     """Attempts to delete a dispatched job to the k8s cluster"""
     job = job_wrapper.get_job()
     try:
         name = self.__produce_unique_k8s_job_name(job.get_id_tag())
         namespace = self.runner_params['k8s_namespace']
         job_to_delete = find_job_object_by_name(self._pykube_api, name, namespace)
         if job_to_delete:
             self.__cleanup_k8s_job(job_to_delete)
         # TODO assert whether job parallelism == 0
         # assert not job_to_delete.exists(), "Could not delete job,"+job.job_runner_external_id+" it still exists"
         log.debug("(%s/%s) Terminated at user's request" % (job.id, job.job_runner_external_id))
     except Exception as e:
         log.exception("(%s/%s) User killed running job, but error encountered during termination: %s" % (
             job.id, job.job_runner_external_id, e))
コード例 #4
0
ファイル: kubernetes.py プロジェクト: mvdbeek/galaxy
    def stop_job(self, job_wrapper):
        """Attempts to delete a dispatched job to the k8s cluster"""
        job = job_wrapper.get_job()
        try:
            job_to_delete = find_job_object_by_name(self._pykube_api, job.get_job_runner_external_id(), self.runner_params['k8s_namespace'])
            if job_to_delete and len(job_to_delete.response['items']) > 0:
                k8s_job = Job(self._pykube_api, job_to_delete.response['items'][0])
                if self.__has_guest_ports(job_wrapper):
                    self.__cleanup_k8s_guest_ports(job_wrapper, k8s_job)
                self.__cleanup_k8s_job(k8s_job)
            # TODO assert whether job parallelism == 0
            # assert not job_to_delete.exists(), "Could not delete job,"+job.job_runner_external_id+" it still exists"
            log.debug(f"({job.id}/{job.job_runner_external_id}) Terminated at user's request")

        except Exception as e:
            log.exception("({}/{}) User killed running job, but error encountered during termination: {}".format(
                job.id, job.get_job_runner_external_id(), e))
コード例 #5
0
    def check_watched_item(self, job_state):
        """Checks the state of a job already submitted on k8s. Job state is an AsynchronousJobState"""
        jobs = find_job_object_by_name(self._pykube_api, job_state.job_id,
                                       self.runner_params['k8s_namespace'])

        if len(jobs.response['items']) == 1:
            job = Job(self._pykube_api, jobs.response['items'][0])
            job_destination = job_state.job_wrapper.job_destination
            succeeded = 0
            active = 0
            failed = 0

            if 'max_pod_retries' in job_destination.params:
                max_pod_retries = int(
                    job_destination.params['max_pod_retries'])
            elif 'k8s_pod_retries' in self.runner_params:
                max_pod_retries = int(self.runner_params['k8s_pod_retries'])
            else:
                max_pod_retries = 1

            # Check if job.obj['status'] is empty,
            # return job_state unchanged if this is the case
            # as probably this means that the k8s API server hasn't
            # had time to fill in the object status since the
            # job was created only too recently.
            if len(job.obj['status']) == 0:
                return job_state
            if 'succeeded' in job.obj['status']:
                succeeded = job.obj['status']['succeeded']
            if 'active' in job.obj['status']:
                active = job.obj['status']['active']
            if 'failed' in job.obj['status']:
                failed = job.obj['status']['failed']

            job_persisted_state = job_state.job_wrapper.get_state()

            # This assumes jobs dependent on a single pod, single container
            if succeeded > 0 or job_state == model.Job.states.STOPPED:
                job_state.running = False
                self.mark_as_finished(job_state)
                return None
            elif active > 0 and failed <= max_pod_retries:
                if not job_state.running:
                    if self.__job_pending_due_to_unschedulable_pod(job_state):
                        if self.runner_params.get(
                                'k8s_unschedulable_walltime_limit'):
                            creation_time_str = job.obj['metadata'].get(
                                'creationTimestamp')
                            creation_time = datetime.strptime(
                                creation_time_str, '%Y-%m-%dT%H:%M:%SZ')
                            elapsed_seconds = (datetime.utcnow() -
                                               creation_time).total_seconds()
                            if elapsed_seconds > self.runner_params[
                                    'k8s_unschedulable_walltime_limit']:
                                return self._handle_unschedulable_job(
                                    job, job_state)
                            else:
                                pass
                        else:
                            pass
                    else:
                        job_state.running = True
                        job_state.job_wrapper.change_state(
                            model.Job.states.RUNNING)
                return job_state
            elif job_persisted_state == model.Job.states.DELETED:
                # Job has been deleted via stop_job and job has not been deleted,
                # remove from watched_jobs by returning `None`
                if job_state.job_wrapper.cleanup_job in ("always",
                                                         "onsuccess"):
                    job_state.job_wrapper.cleanup()
                return None
            else:
                return self._handle_job_failure(job, job_state)

        elif len(jobs.response['items']) == 0:
            if job_state.job_wrapper.get_job(
            ).state == model.Job.states.DELETED:
                # Job has been deleted via stop_job and job has been deleted,
                # cleanup and remove from watched_jobs by returning `None`
                if job_state.job_wrapper.cleanup_job in ("always",
                                                         "onsuccess"):
                    job_state.job_wrapper.cleanup()
                return None
            # there is no job responding to this job_id, it is either lost or something happened.
            log.error("No Jobs are available under expected selector app=%s",
                      job_state.job_id)
            self.mark_as_failed(job_state)
            # job is no longer viable - remove from watched jobs
            return None
        else:
            # there is more than one job associated to the expected unique job id used as selector.
            log.error("More than one Kubernetes Job associated to job id '%s'",
                      job_state.job_id)
            self.mark_as_failed(job_state)
            # job is no longer viable - remove from watched jobs
            return None