Source code for toil.batchSystems.abstractBatchSystem

# Copyright (C) 2015-2016 Regents of the University of California
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# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
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#     http://www.apache.org/licenses/LICENSE-2.0
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# Unless required by applicable law or agreed to in writing, software
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from __future__ import absolute_import

from future import standard_library
standard_library.install_aliases()
from builtins import object
import os
import shutil
import logging
import time
from abc import ABCMeta, abstractmethod
from collections import namedtuple
from queue import Queue, Empty
from contextlib import contextmanager

from bd2k.util.objects import abstractclassmethod

from toil.common import Toil, cacheDirName
from toil.fileStore import shutdownFileStore
from future.utils import with_metaclass

logger = logging.getLogger(__name__)


# A class containing the information required for worker cleanup on shutdown of the batch system.
WorkerCleanupInfo = namedtuple('WorkerCleanupInfo', (
    # A path to the value of config.workDir (where the cache would go)
    'workDir',
    # The value of config.workflowID (used to identify files specific to this workflow)
    'workflowID',
    # The value of the cleanWorkDir flag
    'cleanWorkDir'))

[docs]class AbstractBatchSystem(with_metaclass(ABCMeta, object)): """ An abstract (as far as Python currently allows) base class to represent the interface the batch system must provide to Toil. """ # noinspection PyMethodParameters @abstractclassmethod
[docs] def supportsHotDeployment(cls): """ Whether this batch system supports hot deployment of the user script itself. If it does, the :meth:`.setUserScript` can be invoked to set the resource object representing the user script. Note to implementors: If your implementation returns True here, it should also override :rtype: bool """ raise NotImplementedError()
# noinspection PyMethodParameters @abstractclassmethod
[docs] def supportsWorkerCleanup(cls): """ Indicates whether this batch system invokes :meth:`workerCleanup` after the last job for a particular workflow invocation finishes. Note that the term *worker* refers to an entire node, not just a worker process. A worker process may run more than one job sequentially, and more than one concurrent worker process may exist on a worker node, for the same workflow. The batch system is said to *shut down* after the last worker process terminates. :rtype: bool """ raise NotImplementedError()
[docs] def setUserScript(self, userScript): """ Set the user script for this workflow. This method must be called before the first job is issued to this batch system, and only if :meth:`.supportsHotDeployment` returns True, otherwise it will raise an exception. :param toil.resource.Resource userScript: the resource object representing the user script or module and the modules it depends on. """ raise NotImplementedError()
@abstractmethod
[docs] def issueBatchJob(self, jobNode): """ Issues a job with the specified command to the batch system and returns a unique jobID. :param jobNode a toil.job.JobNode :return: a unique jobID that can be used to reference the newly issued job :rtype: int """ raise NotImplementedError()
@abstractmethod
[docs] def killBatchJobs(self, jobIDs): """ Kills the given job IDs. :param jobIDs: list of IDs of jobs to kill :type jobIDs: list[int] """ raise NotImplementedError()
# FIXME: Return value should be a set (then also fix the tests) @abstractmethod
[docs] def getIssuedBatchJobIDs(self): """ Gets all currently issued jobs :return: A list of jobs (as jobIDs) currently issued (may be running, or may be waiting to be run). Despite the result being a list, the ordering should not be depended upon. :rtype: list[str] """ raise NotImplementedError()
@abstractmethod
[docs] def getRunningBatchJobIDs(self): """ Gets a map of jobs as jobIDs that are currently running (not just waiting) and how long they have been running, in seconds. :return: dictionary with currently running jobID keys and how many seconds they have been running as the value :rtype: dict[str,float] """ raise NotImplementedError()
@abstractmethod
[docs] def getUpdatedBatchJob(self, maxWait): """ Returns a job that has updated its status. :param float maxWait: the number of seconds to block, waiting for a result :rtype: tuple(str, int) or None :return: If a result is available, returns a tuple (jobID, exitValue, wallTime). Otherwise it returns None. wallTime is the number of seconds (a float) in wall-clock time the job ran for or None if this batch system does not support tracking wall time. Returns None for jobs that were killed. """ raise NotImplementedError()
@abstractmethod
[docs] def shutdown(self): """ Called at the completion of a toil invocation. Should cleanly terminate all worker threads. """ raise NotImplementedError()
[docs] def setEnv(self, name, value=None): """ Set an environment variable for the worker process before it is launched. The worker process will typically inherit the environment of the machine it is running on but this method makes it possible to override specific variables in that inherited environment before the worker is launched. Note that this mechanism is different to the one used by the worker internally to set up the environment of a job. A call to this method affects all jobs issued after this method returns. Note to implementors: This means that you would typically need to copy the variables before enqueuing a job. If no value is provided it will be looked up from the current environment. """ raise NotImplementedError()
@classmethod
[docs] def getRescueBatchJobFrequency(cls): """ Gets the period of time to wait (floating point, in seconds) between checking for missing/overlong jobs. """ raise NotImplementedError()
@classmethod
[docs] def setOptions(cls, setOption): """ Process command line or configuration options relevant to this batch system. The :param setOption: A function with signature setOption(varName, parsingFn=None, checkFn=None, default=None) used to update run configuration """ pass
class BatchSystemSupport(AbstractBatchSystem): """ Partial implementation of AbstractBatchSystem, support methods. """ def __init__(self, config, maxCores, maxMemory, maxDisk): """ Initializes initial state of the object :param toil.common.Config config: object is setup by the toilSetup script and has configuration parameters for the jobtree. You can add code to that script to get parameters for your batch system. :param float maxCores: the maximum number of cores the batch system can request for any one job :param int maxMemory: the maximum amount of memory the batch system can request for any one job, in bytes :param int maxDisk: the maximum amount of disk space the batch system can request for any one job, in bytes """ super(BatchSystemSupport, self).__init__() self.config = config self.maxCores = maxCores self.maxMemory = maxMemory self.maxDisk = maxDisk self.environment = {} """ :type: dict[str,str] """ self.workerCleanupInfo = WorkerCleanupInfo(workDir=self.config.workDir, workflowID=self.config.workflowID, cleanWorkDir=self.config.cleanWorkDir) def checkResourceRequest(self, memory, cores, disk): """ Check resource request is not greater than that available or allowed. :param int memory: amount of memory being requested, in bytes :param float cores: number of cores being requested :param int disk: amount of disk space being requested, in bytes :raise InsufficientSystemResources: raised when a resource is requested in an amount greater than allowed """ assert memory is not None assert disk is not None assert cores is not None if cores > self.maxCores: raise InsufficientSystemResources('cores', cores, self.maxCores) if memory > self.maxMemory: raise InsufficientSystemResources('memory', memory, self.maxMemory) if disk > self.maxDisk: raise InsufficientSystemResources('disk', disk, self.maxDisk) def setEnv(self, name, value=None): """ Set an environment variable for the worker process before it is launched. The worker process will typically inherit the environment of the machine it is running on but this method makes it possible to override specific variables in that inherited environment before the worker is launched. Note that this mechanism is different to the one used by the worker internally to set up the environment of a job. A call to this method affects all jobs issued after this method returns. Note to implementors: This means that you would typically need to copy the variables before enqueuing a job. If no value is provided it will be looked up from the current environment. NB: Only the Mesos and single-machine batch systems support passing environment variables. On other batch systems, this method has no effect. See https://github.com/BD2KGenomics/toil/issues/547. :param str name: the environment variable to be set on the worker. :param str value: if given, the environment variable given by name will be set to this value. if None, the variable's current value will be used as the value on the worker :raise RuntimeError: if value is None and the name cannot be found in the environment """ if value is None: try: value = os.environ[name] except KeyError: raise RuntimeError("%s does not exist in current environment", name) self.environment[name] = value @classmethod def getRescueBatchJobFrequency(cls): """ Gets the period of time to wait (floating point, in seconds) between checking for missing/overlong jobs. :return: time in seconds to wait in between checking for lost jobs :rtype: float """ raise NotImplementedError() def _getResultsFileName(self, toilPath): """ Get a path for the batch systems to store results. GridEngine, slurm, and LSF currently use this and only work if locator is file. """ # Use parser to extract the path and type locator, filePath = Toil.parseLocator(toilPath) assert locator == "file" return os.path.join(filePath, "results.txt") @staticmethod def workerCleanup(info): """ Cleans up the worker node on batch system shutdown. Also see :meth:`supportsWorkerCleanup`. :param WorkerCleanupInfo info: A named tuple consisting of all the relevant information for cleaning up the worker. """ assert isinstance(info, WorkerCleanupInfo) workflowDir = Toil.getWorkflowDir(info.workflowID, info.workDir) workflowDirContents = os.listdir(workflowDir) shutdownFileStore(workflowDir, info.workflowID) if (info.cleanWorkDir == 'always' or info.cleanWorkDir in ('onSuccess', 'onError') and workflowDirContents in ([], [cacheDirName(info.workflowID)])): shutil.rmtree(workflowDir) class NodeInfo(object): """ The coresUsed attribute is a floating point value between 0 (all cores idle) and 1 (all cores busy), reflecting the CPU load of the node. The memoryUsed attribute is a floating point value between 0 (no memory used) and 1 (all memory used), reflecting the memory pressure on the node. The coresTotal and memoryTotal attributes are the node's resources, not just the used resources The requestedCores and requestedMemory attributes are all the resources that Toil Jobs have reserved on the node, regardless of whether the resources are actually being used by the Jobs. The workers attribute is an integer reflecting the number of workers currently active workers on the node. """ def __init__(self, coresUsed, memoryUsed, coresTotal, memoryTotal, requestedCores, requestedMemory, workers): self.coresUsed = coresUsed self.memoryUsed = memoryUsed self.coresTotal = coresTotal self.memoryTotal = memoryTotal self.requestedCores = requestedCores self.requestedMemory = requestedMemory self.workers = workers class AbstractScalableBatchSystem(AbstractBatchSystem): """ A batch system that supports a variable number of worker nodes. Used by :class:`toil. provisioners.clusterScaler.ClusterScaler` to scale the number of worker nodes in the cluster up or down depending on overall load. """ @abstractmethod def getNodes(self, preemptable=None): """ Returns a dictionary mapping node identifiers of preemptable or non-preemptable nodes to NodeInfo objects, one for each node. :param bool preemptable: If True (False) only (non-)preemptable nodes will be returned. If None, all nodes will be returned. :rtype: dict[str,NodeInfo] """ raise NotImplementedError() @abstractmethod def nodeInUse(self, nodeIP): """ Can be used to determine if a worker node is running any tasks. If the node is doesn't exist, this function should simply return False. :param str nodeIP: The worker nodes private IP address :return: True if the worker node has been issued any tasks, else False :rtype: bool """ raise NotImplementedError() @abstractmethod @contextmanager def nodeFiltering(self, filter): """ Used to prevent races in autoscaling where 1) nodes have reported to the autoscaler as having no jobs 2) scaler decides to terminate these nodes. In parallel the batch system assigns jobs to the same nodes 3) scaler terminates nodes, resulting in job failures for all jobs on that node. Call this method prior to node termination to ensure that nodes being considered for termination are not assigned new jobs. Call the method again passing None as the filter to disable the filtering after node termination is done. :param method: This will be used as a filter on nodes considered when assigning new jobs. After this context manager exits the filter should be removed :rtype: None """ raise NotImplementedError() @abstractmethod def ignoreNode(self, nodeAddress): """ Stop sending jobs to this node. Used in autoscaling when the autoscaler is ready to terminate a node, but jobs are still running. This allows the node to be terminated after the current jobs have finished. :param str: IP address of node to ignore. :rtype: None """ raise NotImplementedError() @abstractmethod def unignoreNode(self, nodeAddress): """ Stop ignoring this address, presumably after a node with this address has been terminated. This allows for the possibility of a new node having the same address as a terminated one. """ raise NotImplementedError() class InsufficientSystemResources(Exception): """ To be raised when a job requests more of a particular resource than is either currently allowed or avaliable """ def __init__(self, resource, requested, available): """ Creates an instance of this exception that indicates which resource is insufficient for current demands, as well as the amount requested and amount actually available. :param str resource: string representing the resource type :param int|float requested: the amount of the particular resource requested that resulted in this exception :param int|float available: amount of the particular resource actually available """ self.requested = requested self.available = available self.resource = resource def __str__(self): return 'Requesting more {} than either physically available, or enforced by --max{}. ' \ 'Requested: {}, Available: {}'.format(self.resource, self.resource.capitalize(), self.requested, self.available)