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Source code for galaxy.jobs.runners.kubernetes

Offload jobs to a Kubernetes cluster.

import logging
import math
import os
import re

import yaml

from galaxy import model
from galaxy.jobs.runners import (
from galaxy.jobs.runners.util.pykube_util import (
from galaxy.util.bytesize import ByteSize

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" LABEL_START = re.compile("^[A-Za-z0-9]") LABEL_END = re.compile("[A-Za-z0-9]$") LABEL_REGEX = re.compile("[^-A-Za-z0-9_.]")
[docs] def __init__(self, app, nworkers, **kwargs): # Check if pykube was importable, fail if not ensure_pykube() runner_param_specs = dict( k8s_config_path=dict(map=str, default=None), k8s_use_service_account=dict(map=bool, default=False), k8s_persistent_volume_claims=dict(map=str), k8s_namespace=dict(map=str, default="default"), k8s_pod_priority_class=dict(map=str, default=None), k8s_affinity=dict(map=str, default=None), k8s_node_selector=dict(map=str, default=None), k8s_tolerations=dict(map=str, default=None), k8s_galaxy_instance_id=dict(map=str), k8s_timeout_seconds_job_deletion=dict(map=int, valid=lambda x: int > 0, default=30), k8s_job_api_version=dict(map=str, default=DEFAULT_JOB_API_VERSION), k8s_job_ttl_secs_after_finished=dict(map=int, valid=lambda x: x is None or int(x) >= 0, default=None), k8s_job_metadata=dict(map=str, default=None), k8s_supplemental_group_id=dict(map=str), k8s_pull_policy=dict(map=str, default="Default"), k8s_run_as_user_id=dict(map=str, valid=lambda s: s == "$uid" or s.isdigit()), k8s_run_as_group_id=dict(map=str, valid=lambda s: s == "$gid" or s.isdigit()), k8s_fs_group_id=dict(map=int), k8s_cleanup_job=dict(map=str, valid=lambda s: s in {"onsuccess", "always", "never"}, default="always"), k8s_pod_retries=dict(map=int, valid=lambda x: int(x) >= 0, default=3), k8s_walltime_limit=dict(map=int, valid=lambda x: int(x) >= 0, default=172800)) 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().__init__(app, nworkers, **kwargs) self._pykube_api = pykube_client_from_dict(self.runner_params) self._galaxy_instance_id = self.__get_galaxy_instance_id() self._run_as_user_id = self.__get_run_as_user_id() self._run_as_group_id = self.__get_run_as_group_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() self.setup_volumes()
[docs] def setup_volumes(self): if self.runner_params.get('k8s_persistent_volume_claims'): volume_claims = dict(volume.split(":") for volume in self.runner_params['k8s_persistent_volume_claims'].split(',')) else: volume_claims = {} mountable_volumes = [{'name': claim_name, 'persistentVolumeClaim': {'claimName': claim_name}} for claim_name in volume_claims] self.runner_params['k8s_mountable_volumes'] = mountable_volumes volume_mounts = [{'name': claim_name, 'mountPath': mount_path} for claim_name, mount_path in volume_claims.items()] self.runner_params['k8s_volume_mounts'] = volume_mounts
[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 # where galaxy will expect results. log.debug("Starting queue_job for job " + job_wrapper.get_id_tag()) ajs = AsynchronousJobState(files_dir=job_wrapper.working_directory, job_wrapper=job_wrapper, job_destination=job_wrapper.job_destination) if not self.prepare_job(job_wrapper, include_metadata=False, modify_command_for_container=False, stdout_file=ajs.output_file, stderr_file=ajs.error_file): return script = self.get_job_file(job_wrapper, exit_code_path=ajs.exit_code_file, shell=job_wrapper.shell, galaxy_virtual_env=None) 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" % job_wrapper.get_id_tag()) return # Construction of the Kubernetes Job object follows: http://kubernetes.io/docs/user-guide/persistent-volumes/ k8s_job_prefix = self.__produce_k8s_job_prefix() k8s_job_obj = job_object_dict( self.runner_params, k8s_job_prefix, self.__get_k8s_job_spec(ajs) ) job = Job(self._pykube_api, k8s_job_obj) job.create() job_id = job.metadata['name'] # define job attributes in the AsyncronousJobState for follow-up ajs.job_id = job_id # store runner information for tracking if Galaxy restarts job_wrapper.set_external_id(job_id) self.monitor_queue.put(ajs)
def __get_overridable_params(self, job_wrapper, param_key): dest_params = self.__get_destination_params(job_wrapper) return dest_params.get(param_key, self.runner_params[param_key]) def __get_pull_policy(self): return pull_policy(self.runner_params) def __get_run_as_user_id(self): if "k8s_run_as_user_id" in self.runner_params: run_as_user = self.runner_params["k8s_run_as_user_id"] if run_as_user == "$uid": return os.getuid() else: return int(self.runner_params["k8s_run_as_user_id"]) return None def __get_run_as_group_id(self): if "k8s_run_as_group_id" in self.runner_params: run_as_group = self.runner_params["k8s_run_as_group_id"] if run_as_group == "$gid": return self.app.config.gid else: return int(self.runner_params["k8s_run_as_group_id"]) 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): """Parse the ID of the Galaxy instance from runner params.""" return galaxy_instance_id(self.runner_params) def __produce_k8s_job_prefix(self): instance_id = self._galaxy_instance_id or '' return produce_k8s_job_prefix(app_prefix='gxy', instance_id=instance_id) def __get_k8s_job_spec(self, ajs): """Creates the k8s Job spec. For a Job spec, the only requirement is to have a .spec.template. If the job hangs around unlimited it will be ended after k8s wall time limit, which sets activeDeadlineSeconds""" k8s_job_spec = {"template": self.__get_k8s_job_spec_template(ajs), "activeDeadlineSeconds": int(self.runner_params['k8s_walltime_limit'])} job_ttl = self.runner_params["k8s_job_ttl_secs_after_finished"] if self.runner_params["k8s_cleanup_job"] != "never" and job_ttl is not None: k8s_job_spec["ttlSecondsAfterFinished"] = job_ttl return k8s_job_spec def __force_label_conformity(self, value): """ Make sure that a label conforms to k8s requirements. A valid label must be an empty string or consist of alphanumeric characters, '-', '_' or '.', and must start and end with an alphanumeric character (e.g. 'MyValue', or 'my_value', or '12345', regex used for validation is '(([A-Za-z0-9][-A-Za-z0-9_.]*)?[A-Za-z0-9])?') """ label_val = self.LABEL_REGEX.sub("_", value) if not self.LABEL_START.search(label_val): label_val = 'x' + label_val if not self.LABEL_END.search(label_val): label_val += 'x' return label_val def __get_k8s_job_spec_template(self, ajs): """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.kubernetes.io/name": self.__force_label_conformity(ajs.job_wrapper.tool.old_id), "app.kubernetes.io/instance": self.__produce_k8s_job_prefix(), "app.kubernetes.io/version": self.__force_label_conformity(str(ajs.job_wrapper.tool.version)), "app.kubernetes.io/component": "tool", "app.kubernetes.io/part-of": "galaxy", "app.kubernetes.io/managed-by": "galaxy", "app.galaxyproject.org/job_id": self.__force_label_conformity(ajs.job_wrapper.get_id_tag()), "app.galaxyproject.org/handler": self.__force_label_conformity(self.app.config.server_name), "app.galaxyproject.org/destination": self.__force_label_conformity( str(ajs.job_wrapper.job_destination.id)) }, "annotations": { "app.galaxyproject.org/tool_id": ajs.job_wrapper.tool.id } }, "spec": { "volumes": self.runner_params['k8s_mountable_volumes'], "restartPolicy": self.__get_k8s_restart_policy(ajs.job_wrapper), "containers": self.__get_k8s_containers(ajs), "priorityClassName": self.runner_params['k8s_pod_priority_class'], "tolerations": yaml.safe_load(self.runner_params['k8s_tolerations'] or "[]"), "affinity": yaml.safe_load(self.__get_overridable_params(ajs.job_wrapper, 'k8s_affinity') or "{}"), "nodeSelector": yaml.safe_load(self.__get_overridable_params(ajs.job_wrapper, 'k8s_node_selector') or "{}") } } # TODO include other relevant elements that people might want to use from # TODO http://kubernetes.io/docs/api-reference/v1/definitions/#_v1_podspec k8s_spec_template["spec"]["securityContext"] = self.__get_k8s_security_context() extra_metadata = self.runner_params['k8s_job_metadata'] or '{}' if isinstance(extra_metadata, str): extra_metadata = yaml.safe_load(extra_metadata) k8s_spec_template["metadata"]["labels"].update(extra_metadata.get('labels', {})) k8s_spec_template["metadata"]["annotations"].update(extra_metadata.get('annotations', {})) return k8s_spec_template def __get_k8s_security_context(self): security_context = {} if self._run_as_user_id: security_context["runAsUser"] = self._run_as_user_id if self._run_as_group_id: security_context["runAsGroup"] = self._run_as_group_id if self._supplemental_group and self._supplemental_group > 0: security_context["supplementalGroups"] = [self._supplemental_group] if self._fs_group and self._fs_group > 0: security_context["fsGroup"] = self._fs_group return security_context def __get_k8s_restart_policy(self, job_wrapper): """The default Kubernetes restart policy for Jobs""" return "Never" def __get_k8s_containers(self, ajs): """Fills in all required for setting up the docker containers to be used, including setting a pull policy if this has been set. $GALAXY_VIRTUAL_ENV is set to None to avoid the galaxy virtualenv inside the tool container. $GALAXY_LIB is set to None to avoid changing the python path inside the container. Setting these variables changes the described behaviour in the job file shell script used to execute the tool inside the container. """ k8s_container = { "name": self.__get_k8s_container_name(ajs.job_wrapper), "image": self._find_container(ajs.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. "command": [ajs.job_wrapper.shell], "args": ["-c", ajs.job_file], "workingDir": ajs.job_wrapper.working_directory, "volumeMounts": self.runner_params['k8s_volume_mounts'] } resources = self.__get_resources(ajs.job_wrapper) if resources: envs = [] if 'requests' in resources: requests = resources['requests'] if 'memory' in requests: envs.append({'name': 'GALAXY_MEMORY_MB', 'value': str(ByteSize(requests['memory']).to_unit('M', as_string=False))}) if 'cpu' in requests: envs.append({'name': 'GALAXY_SLOTS', 'value': str(int(math.ceil(float(requests['cpu']))))}) elif 'limits' in resources: limits = resources['limits'] if 'memory' in limits: envs.append({'name': 'GALAXY_MEMORY_MB', 'value': str(ByteSize(limits['memory']).to_unit('M', as_string=False))}) if 'cpu' in limits: envs.append({'name': 'GALAXY_SLOTS', 'value': str(int(math.ceil(float(limits['cpu']))))}) k8s_container['resources'] = resources k8s_container['env'] = envs if self._default_pull_policy: k8s_container["imagePullPolicy"] = self._default_pull_policy return [k8s_container] 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_destination = job_wrapper.job_destination if 'requests_memory' in job_destination.params: return self.__transform_memory_value(job_destination.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_destination = job_wrapper.job_destination if 'limits_memory' in job_destination.params: return self.__transform_memory_value(job_destination.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_destination = job_wrapper.job_destination if 'requests_cpu' in job_destination.params: return job_destination.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_destination = job_wrapper.job_destination if 'limits_cpu' in job_destination.params: return job_destination.params['limits_cpu'] return None def __transform_memory_value(self, mem_value): """ Transforms valid kubernetes memory value to bytes """ return ByteSize(mem_value).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" def __get_destination_params(self, job_wrapper): """Obtains allowable runner param overrides from the destination""" job_destination = job_wrapper.job_destination OVERRIDABLE_PARAMS = ["k8s_node_selector", "k8s_affinity"] new_params = {} for each_param in OVERRIDABLE_PARAMS: if each_param in job_destination.params: new_params[each_param] = job_destination.params[each_param] return new_params
[docs] 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: 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
def _handle_job_failure(self, job, job_state): # Figure out why job has failed with open(job_state.error_file, 'a') as error_file: if self.__job_failed_due_to_low_memory(job_state): 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 elif self.__job_failed_due_to_walltime_limit(job): error_file.write("DeadlineExceeded") job_state.fail_message = "Job was active longer than specified deadline" job_state.runner_state = JobState.runner_states.WALLTIME_REACHED else: error_file.write("Exceeded max number of Kubernetes pod retries 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) try: self.__cleanup_k8s_job(job) except Exception: log.exception("Could not clean up k8s batch job. Ignoring...") return None def __cleanup_k8s_job(self, job): k8s_cleanup_job = self.runner_params['k8s_cleanup_job'] stop_job(job, k8s_cleanup_job) def __job_failed_due_to_walltime_limit(self, job): conditions = job.obj['status'].get('conditions') or [] return any(True for c in conditions if c['type'] == 'Failed' and c['reason'] == 'DeadlineExceeded') 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 = find_pod_object_by_name(self._pykube_api, job_state.job_id, self.runner_params['k8s_namespace']) if not pods.response['items']: return False 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 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]) 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))
[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() 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 in (model.Job.states.RUNNING, model.Job.states.STOPPED): log.debug("({}/{}) is still in {} state, adding to the runner monitor queue".format( job.id, job.job_runner_external_id, job.state)) ajs.old_state = model.Job.states.RUNNING ajs.running = True self.monitor_queue.put(ajs) elif job.state == model.Job.states.QUEUED: log.debug("({}/{}) is still in queued state, adding to the runner monitor queue".format( job.id, job.job_runner_external_id)) ajs.old_state = model.Job.states.QUEUED ajs.running = False self.monitor_queue.put(ajs)
[docs] 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)