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Source code for galaxy.jobs.runners.kubernetes

Offload jobs to a Kubernetes cluster.

import logging
import re
from os import environ as os_environ
from time import sleep

from six import text_type

from galaxy import model
from galaxy.jobs.runners import (

# pykube imports:
    from pykube.config import KubeConfig
    from pykube.http import HTTPClient
    from pykube.objects import (
except ImportError as exc:
    KubeConfig = None
    K8S_IMPORT_MESSAGE = ('The Python pykube package is required to use '
                          'this feature, please install it or correct the '
                          'following error:\nImportError %s' % str(exc))

log = logging.getLogger(__name__)

__all__ = ('KubernetesJobRunner', )

[docs]class KubernetesJobRunner(AsynchronousJobRunner): """ Job runner backed by a finite pool of worker threads. FIFO scheduling """ runner_name = "KubernetesRunner"
[docs] def __init__(self, app, nworkers, **kwargs): # Check if pykube was importable, fail if not assert KubeConfig is not None, K8S_IMPORT_MESSAGE runner_param_specs = dict( k8s_config_path=dict(map=str, default=os_environ.get('KUBECONFIG', None)), k8s_use_service_account=dict(map=bool, default=False), k8s_persistent_volume_claim_name=dict(map=str), k8s_persistent_volume_claim_mount_path=dict(map=str), k8s_namespace=dict(map=str, default="default"), k8s_galaxy_instance_id=dict(map=str), k8s_timeout_seconds_job_deletion=dict(map=int, valid=lambda x: int > 0, default=30), k8s_job_api_version=dict(map=str, default="batch/v1"), k8s_supplemental_group_id=dict(map=str), k8s_pull_policy=dict(map=str, default="Default"), k8s_fs_group_id=dict(map=int), k8s_default_requests_cpu=dict(map=str, default=None), k8s_default_requests_memory=dict(map=str, default=None), k8s_default_limits_cpu=dict(map=str, default=None), k8s_default_limits_memory=dict(map=str, default=None), k8s_pod_retrials=dict(map=int, valid=lambda x: int > 0, default=3)) if 'runner_param_specs' not in kwargs: kwargs['runner_param_specs'] = dict() kwargs['runner_param_specs'].update(runner_param_specs) """Start the job runner parent object """ super(KubernetesJobRunner, self).__init__(app, nworkers, **kwargs) # self.cli_interface = CliInterface() if "k8s_use_service_account" in self.runner_params and self.runner_params["k8s_use_service_account"]: self._pykube_api = HTTPClient(KubeConfig.from_service_account()) else: self._pykube_api = HTTPClient(KubeConfig.from_file(self.runner_params["k8s_config_path"])) self._galaxy_vol_name = "pvc-galaxy" # TODO this needs to be read from params!! self._galaxy_instance_id = self.__get_galaxy_instance_id() self._supplemental_group = self.__get_supplemental_group() self._fs_group = self.__get_fs_group() self._default_pull_policy = self.__get_pull_policy() self._init_monitor_thread() self._init_worker_threads()
[docs] def queue_job(self, job_wrapper): """Create job script and submit it to Kubernetes cluster""" # prepare the job # We currently don't need to include_metadata or include_work_dir_outputs, as working directory is the same # were galaxy will expect results. log.debug("Starting queue_job for job " + job_wrapper.get_id_tag()) if not self.prepare_job(job_wrapper, include_metadata=False, modify_command_for_container=False): return job_destination = job_wrapper.job_destination # Construction of the Kubernetes Job object follows: http://kubernetes.io/docs/user-guide/persistent-volumes/ k8s_job_name = self.__produce_unique_k8s_job_name(job_wrapper.get_id_tag()) k8s_job_obj = { "apiVersion": self.runner_params['k8s_job_api_version'], "kind": "Job", "metadata": { # metadata.name is the name of the pod resource created, and must be unique # http://kubernetes.io/docs/user-guide/configuring-containers/ "name": k8s_job_name, "namespace": self.runner_params['k8s_namespace'], "labels": {"app": k8s_job_name} }, "spec": self.__get_k8s_job_spec(job_wrapper) } # Checks if job exists and is trusted, or if it needs re-creation. job = Job(self._pykube_api, k8s_job_obj) if job.exists() and not self._galaxy_instance_id: # if galaxy instance id is not set, then we don't trust matching jobs and we simply delete and # re-create the job log.debug("Matching job exists, but Job is not trusted, so it will be deleted and a new one created.") job.delete() elapsed_seconds = 0 while job.exists(): sleep(3) elapsed_seconds += 3 if elapsed_seconds > self.runner_params['k8s_timeout_seconds_job_deletion']: log.debug("Timed out before k8s could delete existing untrusted job " + k8s_job_name + ", not queuing associated Galaxy job.") return log.debug("Waiting for job to be deleted " + k8s_job_name) Job(self._pykube_api, k8s_job_obj).create() elif job.exists() and self._galaxy_instance_id: # The job exists and we trust the identifier. log.debug("Matching job exists, but Job is trusted, so we simply use the existing one for " + k8s_job_name) # We simply leave the k8s job to be handled later on by the check watched-items. else: # Creates the Kubernetes Job if it doesn't exist. job.create() # define job attributes in the AsyncronousJobState for follow-up ajs = AsynchronousJobState(files_dir=job_wrapper.working_directory, job_wrapper=job_wrapper, job_id=k8s_job_name, job_destination=job_destination) self.monitor_queue.put(ajs) # external_runJob_script can be None, in which case it's not used. external_runjob_script = None return external_runjob_script
def __get_pull_policy(self): if "k8s_pull_policy" in self.runner_params: if self.runner_params['k8s_pull_policy'] in ["Always", "IfNotPresent", "Never"]: return self.runner_params['k8s_pull_policy'] return None def __get_supplemental_group(self): if "k8s_supplemental_group_id" in self.runner_params: try: return int(self.runner_params["k8s_supplemental_group_id"]) except Exception: log.warning("Supplemental group passed for Kubernetes runner needs to be an integer, value " + self.runner_params["k8s_supplemental_group_id"] + " passed is invalid") return None return None def __get_fs_group(self): if "k8s_fs_group_id" in self.runner_params: try: return int(self.runner_params["k8s_fs_group_id"]) except Exception: log.warning("FS group passed for Kubernetes runner needs to be an integer, value " + self.runner_params["k8s_fs_group_id"] + " passed is invalid") return None return None def __get_galaxy_instance_id(self): """ Gets the id of the Galaxy instance. This will be added to Jobs and Pods names, so it needs to be DNS friendly, this means: `The Internet standards (Requests for Comments) for protocols mandate that component hostname labels may contain only the ASCII letters 'a' through 'z' (in a case-insensitive manner), the digits '0' through '9', and the minus sign ('-').` It looks for the value set on self.runner_params['k8s_galaxy_instance_id'], which might or not be set. The idea behind this is to allow the Galaxy instance to trust (or not) existing k8s Jobs and Pods that match the setup of a Job that is being recovered or restarted after a downtime/reboot. :return: :rtype: """ if "k8s_galaxy_instance_id" in self.runner_params: if re.match("(?!-)[a-z\d-]{1,20}(?<!-)$", self.runner_params['k8s_galaxy_instance_id']): return self.runner_params['k8s_galaxy_instance_id'] else: log.error("Galaxy instance '" + self.runner_params['k8s_galaxy_instance_id'] + "' is either too long " + '(>20 characters) or it includes non DNS acceptable characters, ignoring it.') return None def __produce_unique_k8s_job_name(self, galaxy_internal_job_id): # wrapper.get_id_tag() instead of job_id for compatibility with TaskWrappers. instance_id = "" if self._galaxy_instance_id and len(self._galaxy_instance_id) > 0: instance_id = self._galaxy_instance_id + "-" return "galaxy-" + instance_id + galaxy_internal_job_id def __get_k8s_job_spec(self, job_wrapper): """Creates the k8s Job spec. For a Job spec, the only requirement is to have a .spec.template.""" k8s_job_spec = {"template": self.__get_k8s_job_spec_template(job_wrapper)} return k8s_job_spec def __get_k8s_job_spec_template(self, job_wrapper): """The k8s spec template is nothing but a Pod spec, except that it is nested and does not have an apiversion nor kind. In addition to required fields for a Pod, a pod template in a job must specify appropriate labels (see pod selector) and an appropriate restart policy.""" k8s_spec_template = { "metadata": { "labels": {"app": self.__produce_unique_k8s_job_name(job_wrapper.get_id_tag())} }, "spec": { "volumes": self.__get_k8s_mountable_volumes(job_wrapper), "restartPolicy": self.__get_k8s_restart_policy(job_wrapper), "containers": self.__get_k8s_containers(job_wrapper) } } # TODO include other relevant elements that people might want to use from # TODO http://kubernetes.io/docs/api-reference/v1/definitions/#_v1_podspec if self._supplemental_group and self._supplemental_group > 0: k8s_spec_template["spec"]["securityContext"] = dict(supplementalGroups=[self._supplemental_group]) if self._fs_group and self._fs_group > 0: if "securityContext" in k8s_spec_template["spec"]: k8s_spec_template["spec"]["securityContext"]["fsGroup"] = self._fs_group else: k8s_spec_template["spec"]["securityContext"] = dict(fsGroup=self._fs_group) return k8s_spec_template def __get_k8s_restart_policy(self, job_wrapper): """The default Kubernetes restart policy for Jobs""" return "Never" def __get_k8s_mountable_volumes(self, job_wrapper): """Provides the required volumes that the containers in the pod should be able to mount. This should be using the new persistent volumes and persistent volumes claim objects. This requires that both a PersistentVolume and a PersistentVolumeClaim are created before starting galaxy (starting a k8s job). """ # TODO on this initial version we only support a single volume to be mounted. k8s_mountable_volume = { "name": self._galaxy_vol_name, "persistentVolumeClaim": { "claimName": self.runner_params['k8s_persistent_volume_claim_name'] } } return [k8s_mountable_volume] def __get_k8s_containers(self, job_wrapper): """Fills in all required for setting up the docker containers to be used, including setting a pull policy if this has been set. """ k8s_container = { "name": self.__get_k8s_container_name(job_wrapper), "image": self._find_container(job_wrapper).container_id, # this form of command overrides the entrypoint and allows multi command # command line execution, separated by ;, which is what Galaxy does # to assemble the command. # TODO possibly shell needs to be set by job_wrapper "command": ["/bin/bash", "-c", job_wrapper.runner_command_line], "workingDir": job_wrapper.working_directory, "volumeMounts": [{ "mountPath": self.runner_params['k8s_persistent_volume_claim_mount_path'], "name": self._galaxy_vol_name }] } resources = self.__get_resources(job_wrapper) if resources: k8s_container['resources'] = resources if self._default_pull_policy: k8s_container["imagePullPolicy"] = self._default_pull_policy # if self.__requires_ports(job_wrapper): # k8s_container['ports'] = self.__get_k8s_containers_ports(job_wrapper) return [k8s_container] # def __get_k8s_containers_ports(self, job_wrapper): # for k,v self.runner_params: # if k.startswith("container_port_"): def __get_resources(self, job_wrapper): mem_request = self.__get_memory_request(job_wrapper) cpu_request = self.__get_cpu_request(job_wrapper) mem_limit = self.__get_memory_limit(job_wrapper) cpu_limit = self.__get_cpu_limit(job_wrapper) requests = {} limits = {} if mem_request: requests['memory'] = mem_request if cpu_request: requests['cpu'] = cpu_request if mem_limit: limits['memory'] = mem_limit if cpu_limit: limits['cpu'] = cpu_limit resources = {} if requests: resources['requests'] = requests if limits: resources['limits'] = limits return resources def __get_memory_request(self, job_wrapper): """Obtains memory requests for job, checking if available on the destination, otherwise using the default""" job_destinantion = job_wrapper.job_destination if 'requests_memory' in job_destinantion.params: return self.__transform_memory_value(job_destinantion.params['requests_memory']) return None def __get_memory_limit(self, job_wrapper): """Obtains memory limits for job, checking if available on the destination, otherwise using the default""" job_destinantion = job_wrapper.job_destination if 'limits_memory' in job_destinantion.params: return self.__transform_memory_value(job_destinantion.params['limits_memory']) return None def __get_cpu_request(self, job_wrapper): """Obtains cpu requests for job, checking if available on the destination, otherwise using the default""" job_destinantion = job_wrapper.job_destination if 'requests_cpu' in job_destinantion.params: return self.__transform_cpu_value(job_destinantion.params['requests_cpu']) return None def __get_cpu_limit(self, job_wrapper): """Obtains cpu requests for job, checking if available on the destination, otherwise using the default""" job_destinantion = job_wrapper.job_destination if 'limits_cpu' in job_destinantion.params: return self.__transform_cpu_value(job_destinantion.params['limits_cpu']) return None def __transform_cpu_value(self, cpu_value): """Transforms cpu value If the value is 0 and not a string, then None is returned. If the value is a float, then it is multiplied by 1000 and expressed as mili cpus. If the value is an integer, then it is and expressed as CPUs (no unit). If it is an already formatted string, it is returned as it was. """ if not isinstance(cpu_value, str) and float(cpu_value) == 0: return None if isinstance(cpu_value, float): return str(int(cpu_value * 1000)) + "m" elif isinstance(cpu_value, int): return str(cpu_value) return cpu_value def __transform_memory_value(self, mem_value): """Transforms memory value If the value is 0 and not a string, then None is returned. If the value has a decimal part, then it is multiplied by 1000 and expressed as Megabytes. If the value is an integer, then it is truncated and expressed as Gigabytes. If it is an already formatted string, it is returned as it was. """ if not isinstance(mem_value, str) and float(mem_value) == 0: return None if isinstance(mem_value, float): return str(int(mem_value * 1000)) + "M" elif isinstance(mem_value, int): return str(mem_value) + "G" return mem_value def __assemble_k8s_container_image_name(self, job_wrapper): """Assembles the container image name as repo/owner/image:tag, where repo, owner and tag are optional""" job_destination = job_wrapper.job_destination # Determine the job's Kubernetes destination (context, namespace) and options from the job destination # definition repo = "" owner = "" if 'repo' in job_destination.params: repo = job_destination.params['repo'] + "/" if 'owner' in job_destination.params: owner = job_destination.params['owner'] + "/" k8s_cont_image = repo + owner + job_destination.params['image'] if 'tag' in job_destination.params: k8s_cont_image += ":" + job_destination.params['tag'] return k8s_cont_image def __get_k8s_container_name(self, job_wrapper): # These must follow a specific regex for Kubernetes. raw_id = job_wrapper.job_destination.id if isinstance(raw_id, str): cleaned_id = re.sub("[^-a-z0-9]", "-", raw_id) if cleaned_id.startswith("-") or cleaned_id.endswith("-"): cleaned_id = "x%sx" % cleaned_id return cleaned_id return "job-container"
[docs] def check_watched_item(self, job_state): """Checks the state of a job already submitted on k8s. Job state is a AsynchronousJobState""" jobs = Job.objects(self._pykube_api).filter(selector="app=" + job_state.job_id, namespace=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 max_pod_retrials = 1 if 'k8s_pod_retrials' in self.runner_params: max_pod_retrials = int(self.runner_params['k8s_pod_retrials']) if 'max_pod_retrials' in job_destination.params: max_pod_retrials = int(job_destination.params['max_pod_retrials']) 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'] # This assumes jobs dependent on a single pod, single container if succeeded > 0: self.__produce_log_file(job_state) with open(job_state.error_file, 'w'): pass job_state.running = False self.mark_as_finished(job_state) return None elif failed > 0 and self.__job_failed_due_to_low_memory(job_state): return self._handle_job_failure(job, job_state, reason="OOM") elif active > 0 and failed <= max_pod_retrials: job_state.running = True return job_state elif failed > max_pod_retrials: return self._handle_job_failure(job, job_state) # We should not get here log.debug( "Reaching unexpected point for Kubernetes job name %s where it is not classified as succ., active nor failed.", job.name) log.debug("k8s full job object:\n%s", job.obj) return job_state elif len(jobs.response['items']) == 0: # 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=" + job_state.job_id) with open(job_state.error_file, 'w') as error_file: error_file.write("No Kubernetes Jobs are available under expected selector app=" + job_state.job_id + "\n") self.mark_as_failed(job_state) return job_state else: # there is more than one job associated to the expected unique job id used as selector. log.error("There is more than one Kubernetes Job associated to job id " + job_state.job_id) self.__produce_log_file(job_state) with open(job_state.error_file, 'w') as error_file: error_file.write("There is more than one Kubernetes Job associated to job id " + job_state.job_id + "\n") self.mark_as_failed(job_state) return job_state
def _handle_job_failure(self, job, job_state, reason=None): self.__produce_log_file(job_state) with open(job_state.error_file, 'w') as error_file: if reason == "OOM": error_file.write("Job killed after running out of memory. Try with more memory.\n") job_state.fail_message = "Tool failed due to insufficient memory. Try with more memory." job_state.runner_state = JobState.runner_states.MEMORY_LIMIT_REACHED else: error_file.write("Exceeded max number of Kubernetes pod retrials allowed for job\n") job_state.fail_message = "More pods failed than allowed. See stdout for pods details." job_state.running = False self.mark_as_failed(job_state) job.scale(replicas=0) return None def __job_failed_due_to_low_memory(self, job_state): """ checks the state of the pod to see if it was killed for being out of memory (pod status OOMKilled). If that is the case marks the job for resubmission (resubmit logic is part of destinations). """ pods = Pod.objects(self._pykube_api).filter(selector="app=" + job_state.job_id) pod = Pod(self._pykube_api, pods.response['items'][0]) if pod.obj['status']['phase'] == "Failed" and \ pod.obj['status']['containerStatuses'][0]['state']['terminated']['reason'] == "OOMKilled": return True return False
[docs] def fail_job(self, job_state): """ Kubernetes runner overrides fail_job (called by mark_as_failed) to rescue the pod's log files which are left as stdout (pods logs are the natural stdout and stderr of the running processes inside the pods) and are deleted in the parent implementation as part of the failing the job process. :param job_state: :return: """ # First we rescue the pods logs try: with open(job_state.output_file, 'r') as outfile: stdout_content = outfile.read() except IOError as e: stdout_content = "<Failed to recuperate log for job {} >".format(job_state.job_id) log.error("Failed to get stdout for job %s", job_state.job_id) log.exception(e) if getattr(job_state, 'stop_job', True): self.stop_job(self.sa_session.query(self.app.model.Job).get(job_state.job_wrapper.job_id)) self._handle_runner_state('failure', job_state) # Not convinced this is the best way to indicate this state, but # something necessary if not job_state.runner_state_handled: job_state.job_wrapper.fail( message=getattr(job_state, 'fail_message', 'Job failed'), stdout=stdout_content, stderr='See stdout for pod\'s stderr.' ) if job_state.job_wrapper.cleanup_job == "always": job_state.cleanup()
def __produce_log_file(self, job_state): pod_r = Pod.objects(self._pykube_api).filter(selector="app=" + job_state.job_id) log_string = "" for pod_obj in pod_r.response['items']: try: pod = Pod(self._pykube_api, pod_obj) log_string += "\n\n==== Pod " + pod.name + " log start ====\n\n" log_string += pod.logs(timestamps=True) log_string += "\n\n==== Pod " + pod.name + " log end ====" except Exception as detail: log.info("Could not write log file for pod %s due to HTTPError %s", pod_obj['metadata']['name'], detail) if isinstance(log_string, text_type): log_string = log_string.encode('utf8') logs_file_path = job_state.output_file try: with open(logs_file_path, mode="w") as logs_file: logs_file.write(log_string) except IOError as e: log.error("Couldn't produce log files for %s", job_state.job_id) log.exception(e) return logs_file_path
[docs] def stop_job(self, job): """Attempts to delete a dispatched job to the k8s cluster""" try: jobs = Job.objects(self._pykube_api).filter(selector="app=" + self.__produce_unique_k8s_job_name(job.get_id_tag())) if len(jobs.response['items']) >= 0: job_to_delete = Job(self._pykube_api, jobs.response['items'][0]) job_to_delete.scale(replicas=0) # 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.debug("(%s/%s) User killed running job, but error encountered during termination: %s" % ( job.id, job.job_runner_external_id, e))
[docs] def recover(self, job, job_wrapper): """Recovers jobs stuck in the queued/running state when Galaxy started""" # TODO this needs to be implemented to override unimplemented base method job_id = job.get_job_runner_external_id() log.debug("k8s trying to recover job: " + job_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.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 runner monitor queue" % ( job.id, job.job_runner_external_id)) ajs.old_state = model.Job.states.RUNNING ajs.running = True self.monitor_queue.put(ajs) elif job.state == model.Job.states.QUEUED: log.debug("(%s/%s) is still in queued state, adding to the runner monitor queue" % ( job.id, job.job_runner_external_id)) ajs.old_state = model.Job.states.QUEUED ajs.running = False self.monitor_queue.put(ajs)