Exemple #1
0
def workerScript(jobStore,
                 config,
                 jobName,
                 jobStoreID,
                 redirectOutputToLogFile=True):
    """
    Worker process script, runs a job. 
    
    :param str jobName: The "job name" (a user friendly name) of the job to be run
    :param str jobStoreLocator: Specifies the job store to use
    :param str jobStoreID: The job store ID of the job to be run
    
    :return int: 1 if a job failed, or 0 if all jobs succeeded
    """

    configure_root_logger()
    set_log_level(config.logLevel)

    ##########################################
    #Create the worker killer, if requested
    ##########################################

    logFileByteReportLimit = config.maxLogFileSize

    if config.badWorker > 0 and random.random() < config.badWorker:
        # We need to kill the process we are currently in, to simulate worker
        # failure. We don't want to just send SIGKILL, because we can't tell
        # that from a legitimate OOM on our CI runner. We're going to send
        # SIGUSR1 so our terminations are distinctive, and then SIGKILL if that
        # didn't stick. We definitely don't want to do this from *within* the
        # process we are trying to kill, so we fork off. TODO: We can still
        # leave the killing code running after the main Toil flow is done, but
        # since it's now in a process instead of a thread, the main Python
        # process won't wait around for its timeout to expire. I think this is
        # better than the old thread-based way where all of Toil would wait
        # around to be killed.

        killTarget = os.getpid()
        sleepTime = config.badWorkerFailInterval * random.random()
        if os.fork() == 0:
            # We are the child
            # Let the parent run some amount of time
            time.sleep(sleepTime)
            # Kill it gently
            os.kill(killTarget, signal.SIGUSR1)
            # Wait for that to stick
            time.sleep(0.01)
            try:
                # Kill it harder. Hope the PID hasn't already been reused.
                # If we succeeded the first time, this will OSError
                os.kill(killTarget, signal.SIGKILL)
            except OSError:
                pass
            # Exit without doing any of Toil's cleanup
            os._exit(0)

        # We don't need to reap the child. Either it kills us, or we finish
        # before it does. Either way, init will have to clean it up for us.

    ##########################################
    #Load the environment for the job
    ##########################################

    #First load the environment for the job.
    with jobStore.readSharedFileStream("environment.pickle") as fileHandle:
        environment = safeUnpickleFromStream(fileHandle)
    env_reject = {
        "TMPDIR", "TMP", "HOSTNAME", "HOSTTYPE", "HOME", "LOGNAME", "USER",
        "DISPLAY", "JAVA_HOME"
    }
    for i in environment:
        if i == "PATH":
            # Handle path specially. Sometimes e.g. leader may not include
            # /bin, but the Toil appliance needs it.
            if i in os.environ and os.environ[i] != '':
                # Use the provided PATH and then the local system's PATH
                os.environ[i] = environment[i] + ':' + os.environ[i]
            else:
                # Use the provided PATH only
                os.environ[i] = environment[i]
        elif i not in env_reject:
            os.environ[i] = environment[i]
    # sys.path is used by __import__ to find modules
    if "PYTHONPATH" in environment:
        for e in environment["PYTHONPATH"].split(':'):
            if e != '':
                sys.path.append(e)

    toilWorkflowDir = Toil.getLocalWorkflowDir(config.workflowID,
                                               config.workDir)

    ##########################################
    #Setup the temporary directories.
    ##########################################

    # Dir to put all this worker's temp files in.
    localWorkerTempDir = tempfile.mkdtemp(dir=toilWorkflowDir)
    os.chmod(localWorkerTempDir, 0o755)

    ##########################################
    #Setup the logging
    ##########################################

    #This is mildly tricky because we don't just want to
    #redirect stdout and stderr for this Python process; we want to redirect it
    #for this process and all children. Consequently, we can't just replace
    #sys.stdout and sys.stderr; we need to mess with the underlying OS-level
    #file descriptors. See <http://stackoverflow.com/a/11632982/402891>

    #When we start, standard input is file descriptor 0, standard output is
    #file descriptor 1, and standard error is file descriptor 2.

    # Do we even want to redirect output? Let the config make us not do it.
    redirectOutputToLogFile = redirectOutputToLogFile and not config.disableWorkerOutputCapture

    #What file do we want to point FDs 1 and 2 to?
    tempWorkerLogPath = os.path.join(localWorkerTempDir, "worker_log.txt")

    if redirectOutputToLogFile:
        # Announce that we are redirecting logging, and where it will now go.
        # This is important if we are trying to manually trace a faulty worker invocation.
        logger.info("Redirecting logging to %s", tempWorkerLogPath)
        sys.stdout.flush()
        sys.stderr.flush()

        # Save the original stdout and stderr (by opening new file descriptors
        # to the same files)
        origStdOut = os.dup(1)
        origStdErr = os.dup(2)

        # Open the file to send stdout/stderr to.
        logFh = os.open(tempWorkerLogPath,
                        os.O_WRONLY | os.O_CREAT | os.O_APPEND)

        # Replace standard output with a descriptor for the log file
        os.dup2(logFh, 1)

        # Replace standard error with a descriptor for the log file
        os.dup2(logFh, 2)

        # Since we only opened the file once, all the descriptors duped from
        # the original will share offset information, and won't clobber each
        # others' writes. See <http://stackoverflow.com/a/5284108/402891>. This
        # shouldn't matter, since O_APPEND seeks to the end of the file before
        # every write, but maybe there's something odd going on...

        # Close the descriptor we used to open the file
        os.close(logFh)

    debugging = logging.getLogger().isEnabledFor(logging.DEBUG)
    ##########################################
    #Worker log file trapped from here on in
    ##########################################

    jobAttemptFailed = False
    statsDict = MagicExpando()
    statsDict.jobs = []
    statsDict.workers.logsToMaster = []
    blockFn = lambda: True
    listOfJobs = [jobName]
    job = None
    try:

        #Put a message at the top of the log, just to make sure it's working.
        logger.info("---TOIL WORKER OUTPUT LOG---")
        sys.stdout.flush()

        logProcessContext(config)

        ##########################################
        #Connect to the deferred function system
        ##########################################
        deferredFunctionManager = DeferredFunctionManager(toilWorkflowDir)

        ##########################################
        #Load the JobDescription
        ##########################################

        jobDesc = jobStore.load(jobStoreID)
        listOfJobs[0] = str(jobDesc)
        logger.debug("Parsed job description")

        ##########################################
        #Cleanup from any earlier invocation of the job
        ##########################################

        if jobDesc.command == None:
            logger.debug("Job description has no body to run.")
            # Cleanup jobs already finished
            predicate = lambda jID: jobStore.exists(jID)
            jobDesc.filterSuccessors(predicate)
            jobDesc.filterServiceHosts(predicate)
            logger.debug(
                "Cleaned up any references to completed successor jobs")

        # This cleans the old log file which may
        # have been left if the job is being retried after a job failure.
        oldLogFile = jobDesc.logJobStoreFileID
        if oldLogFile != None:
            jobDesc.logJobStoreFileID = None
            jobStore.update(jobDesc)  #Update first, before deleting any files
            jobStore.deleteFile(oldLogFile)

        ##########################################
        # If a checkpoint exists, restart from the checkpoint
        ##########################################

        if isinstance(
                jobDesc,
                CheckpointJobDescription) and jobDesc.checkpoint is not None:
            # The job is a checkpoint, and is being restarted after previously completing
            logger.debug("Job is a checkpoint")
            # If the checkpoint still has extant successors or services, its
            # subtree didn't complete properly. We handle the restart of the
            # checkpoint here, removing its previous subtree.
            if next(jobDesc.successorsAndServiceHosts(), None) is not None:
                logger.debug("Checkpoint has failed; restoring")
                # Reduce the try count
                assert jobDesc.remainingTryCount >= 0
                jobDesc.remainingTryCount = max(0,
                                                jobDesc.remainingTryCount - 1)
                jobDesc.restartCheckpoint(jobStore)
            # Otherwise, the job and successors are done, and we can cleanup stuff we couldn't clean
            # because of the job being a checkpoint
            else:
                logger.debug(
                    "The checkpoint jobs seems to have completed okay, removing any checkpoint files to delete."
                )
                #Delete any remnant files
                list(
                    map(
                        jobStore.deleteFile,
                        list(
                            filter(jobStore.fileExists,
                                   jobDesc.checkpointFilesToDelete))))

        ##########################################
        #Setup the stats, if requested
        ##########################################

        if config.stats:
            startClock = get_total_cpu_time()

        startTime = time.time()
        while True:
            ##########################################
            #Run the job body, if there is one
            ##########################################

            logger.info("Working on job %s", jobDesc)

            if jobDesc.command is not None:
                assert jobDesc.command.startswith("_toil ")
                logger.debug("Got a command to run: %s" % jobDesc.command)
                # Load the job. It will use the same JobDescription we have been using.
                job = Job.loadJob(jobStore, jobDesc)
                if isinstance(jobDesc, CheckpointJobDescription):
                    # If it is a checkpoint job, save the command
                    jobDesc.checkpoint = jobDesc.command

                logger.info("Loaded body %s from description %s", job, jobDesc)

                # Create a fileStore object for the job
                fileStore = AbstractFileStore.createFileStore(
                    jobStore,
                    jobDesc,
                    localWorkerTempDir,
                    blockFn,
                    caching=not config.disableCaching)
                with job._executor(stats=statsDict if config.stats else None,
                                   fileStore=fileStore):
                    with deferredFunctionManager.open() as defer:
                        with fileStore.open(job):
                            # Get the next block function to wait on committing this job
                            blockFn = fileStore.waitForCommit

                            # Run the job, save new successors, and set up
                            # locally (but don't commit) successor
                            # relationships and job completion.
                            # Pass everything as name=value because Cactus
                            # likes to override _runner when it shouldn't and
                            # it needs some hope of finding the arguments it
                            # wants across multiple Toil versions. We also
                            # still pass a jobGraph argument to placate old
                            # versions of Cactus.
                            job._runner(jobGraph=None,
                                        jobStore=jobStore,
                                        fileStore=fileStore,
                                        defer=defer)

                # Accumulate messages from this job & any subsequent chained jobs
                statsDict.workers.logsToMaster += fileStore.loggingMessages

                logger.info("Completed body for %s", jobDesc)

            else:
                #The command may be none, in which case
                #the JobDescription is either a shell ready to be deleted or has
                #been scheduled after a failure to cleanup
                logger.debug("No user job to run, so finishing")
                break

            if AbstractFileStore._terminateEvent.isSet():
                raise RuntimeError("The termination flag is set")

            ##########################################
            #Establish if we can run another job within the worker
            ##########################################
            successor = nextChainable(jobDesc, jobStore, config)
            if successor is None or config.disableChaining:
                # Can't chain any more jobs. We are going to stop.

                logger.info("Not chaining from job %s", jobDesc)

                # TODO: Somehow the commit happens even if we don't start it here.

                break

            logger.info("Chaining from %s to %s", jobDesc, successor)

            ##########################################
            # We have a single successor job that is not a checkpoint job. We
            # reassign the ID of the current JobDescription to the successor.
            # We can then delete the successor JobDescription (under its old
            # ID) in the jobStore, as it is wholly incorporated into the
            # current one.
            ##########################################

            # Make sure nothing has gone wrong and we can really chain
            assert jobDesc.memory >= successor.memory
            assert jobDesc.cores >= successor.cores

            # Save the successor's original ID, so we can clean it (and its
            # body) up after we finish executing it.
            successorID = successor.jobStoreID

            # add the successor to the list of jobs run
            listOfJobs.append(str(successor))

            # Now we need to become that successor, under the original ID.
            successor.replace(jobDesc)
            jobDesc = successor

            # Problem: successor's job body is a file that will be cleaned up
            # when we delete the successor job by ID. We can't just move it. So
            # we need to roll up the deletion of the successor job by ID with
            # the deletion of the job ID we're currently working on.
            jobDesc.jobsToDelete.append(successorID)

            # Clone the now-current JobDescription (which used to be the successor).
            # TODO: Why??? Can we not?
            jobDesc = copy.deepcopy(jobDesc)

            # Build a fileStore to update the job and commit the replacement.
            # TODO: can we have a commit operation without an entire FileStore???
            fileStore = AbstractFileStore.createFileStore(
                jobStore,
                jobDesc,
                localWorkerTempDir,
                blockFn,
                caching=not config.disableCaching)

            # Update blockFn to wait for that commit operation.
            blockFn = fileStore.waitForCommit

            # This will update the job once the previous job is done updating
            fileStore.startCommit(jobState=True)

            # Clone the current job description again, so that further updates
            # to it (such as new successors being added when it runs) occur
            # after the commit process we just kicked off, and aren't committed
            # early or partially.
            jobDesc = copy.deepcopy(jobDesc)

            logger.debug("Starting the next job")

        ##########################################
        #Finish up the stats
        ##########################################
        if config.stats:
            totalCPUTime, totalMemoryUsage = get_total_cpu_time_and_memory_usage(
            )
            statsDict.workers.time = str(time.time() - startTime)
            statsDict.workers.clock = str(totalCPUTime - startClock)
            statsDict.workers.memory = str(totalMemoryUsage)

        # log the worker log path here so that if the file is truncated the path can still be found
        if redirectOutputToLogFile:
            logger.info(
                "Worker log can be found at %s. Set --cleanWorkDir to retain this log",
                localWorkerTempDir)

        logger.info(
            "Finished running the chain of jobs on this node, we ran for a total of %f seconds",
            time.time() - startTime)

    ##########################################
    #Trapping where worker goes wrong
    ##########################################
    except:  #Case that something goes wrong in worker
        traceback.print_exc()
        logger.error("Exiting the worker because of a failed job on host %s",
                     socket.gethostname())
        AbstractFileStore._terminateEvent.set()

    ##########################################
    #Wait for the asynchronous chain of writes/updates to finish
    ##########################################

    blockFn()

    ##########################################
    #All the asynchronous worker/update threads must be finished now,
    #so safe to test if they completed okay
    ##########################################

    if AbstractFileStore._terminateEvent.isSet():
        # Something has gone wrong.

        # Clobber any garbage state we have for this job from failing with
        # whatever good state is still stored in the JobStore
        jobDesc = jobStore.load(jobStoreID)
        # Remember that we failed
        jobAttemptFailed = True

    ##########################################
    #Cleanup
    ##########################################

    # Close the worker logging
    # Flush at the Python level
    sys.stdout.flush()
    sys.stderr.flush()
    if redirectOutputToLogFile:
        # Flush at the OS level
        os.fsync(1)
        os.fsync(2)

        # Close redirected stdout and replace with the original standard output.
        os.dup2(origStdOut, 1)

        # Close redirected stderr and replace with the original standard error.
        os.dup2(origStdErr, 2)

        # sys.stdout and sys.stderr don't need to be modified at all. We don't
        # need to call redirectLoggerStreamHandlers since they still log to
        # sys.stderr

        # Close our extra handles to the original standard output and standard
        # error streams, so we don't leak file handles.
        os.close(origStdOut)
        os.close(origStdErr)

    # Now our file handles are in exactly the state they were in before.

    # Copy back the log file to the global dir, if needed.
    # Note that we work with bytes instead of characters so we can seek
    # relative to the end (since Python won't decode Unicode backward, or even
    # interpret seek offsets in characters for us). TODO: We may get invalid or
    # just different Unicode by breaking up a character at the boundary!
    if jobAttemptFailed and redirectOutputToLogFile:
        jobDesc.logJobStoreFileID = jobStore.getEmptyFileStoreID(
            jobDesc.jobStoreID, cleanup=True)
        jobDesc.chainedJobs = listOfJobs
        with jobStore.updateFileStream(jobDesc.logJobStoreFileID) as w:
            with open(tempWorkerLogPath, 'rb') as f:
                if os.path.getsize(
                        tempWorkerLogPath) > logFileByteReportLimit != 0:
                    if logFileByteReportLimit > 0:
                        f.seek(-logFileByteReportLimit,
                               2)  # seek to last tooBig bytes of file
                    elif logFileByteReportLimit < 0:
                        f.seek(logFileByteReportLimit,
                               0)  # seek to first tooBig bytes of file
                # Dump the possibly-invalid-Unicode bytes into the log file
                w.write(f.read())  # TODO load file using a buffer
        # Commit log file reference back to JobStore
        jobStore.update(jobDesc)

    elif ((debugging or (config.writeLogsFromAllJobs
                         and not jobName.startswith(CWL_INTERNAL_JOBS)))
          and redirectOutputToLogFile):  # write log messages
        with open(tempWorkerLogPath, 'rb') as logFile:
            if os.path.getsize(
                    tempWorkerLogPath) > logFileByteReportLimit != 0:
                if logFileByteReportLimit > 0:
                    logFile.seek(-logFileByteReportLimit,
                                 2)  # seek to last tooBig bytes of file
                elif logFileByteReportLimit < 0:
                    logFile.seek(logFileByteReportLimit,
                                 0)  # seek to first tooBig bytes of file
            # Make sure lines are Unicode so they can be JSON serialized as part of the dict.
            # We may have damaged the Unicode text by cutting it at an arbitrary byte so we drop bad characters.
            logMessages = [
                line.decode('utf-8', 'skip')
                for line in logFile.read().splitlines()
            ]
        statsDict.logs.names = listOfJobs
        statsDict.logs.messages = logMessages

    if (debugging or config.stats or statsDict.workers.logsToMaster
        ) and not jobAttemptFailed:  # We have stats/logging to report back
        jobStore.writeStatsAndLogging(
            json.dumps(statsDict, ensure_ascii=True).encode())

    #Remove the temp dir
    cleanUp = config.cleanWorkDir
    if cleanUp == 'always' or (cleanUp == 'onSuccess' and
                               not jobAttemptFailed) or (cleanUp == 'onError'
                                                         and jobAttemptFailed):
        shutil.rmtree(localWorkerTempDir)

    #This must happen after the log file is done with, else there is no place to put the log
    if (not jobAttemptFailed) and jobDesc.command == None and next(
            jobDesc.successorsAndServiceHosts(), None) is None:
        # We can now safely get rid of the JobDescription, and all jobs it chained up
        for otherID in jobDesc.jobsToDelete:
            jobStore.delete(otherID)
        jobStore.delete(jobDesc.jobStoreID)

    if jobAttemptFailed:
        return 1
    else:
        return 0
Exemple #2
0
def workerScript(jobStore, config, jobName, jobStoreID, redirectOutputToLogFile=True):
    """
    Worker process script, runs a job. 
    
    :param str jobName: The "job name" (a user friendly name) of the job to be run
    :param str jobStoreLocator: Specifies the job store to use
    :param str jobStoreID: The job store ID of the job to be run
    :param bool redirectOutputToLogFile: Redirect standard out and standard error to a log file
    """
    logging.basicConfig()
    setLogLevel(config.logLevel)

    ##########################################
    #Create the worker killer, if requested
    ##########################################

    logFileByteReportLimit = config.maxLogFileSize

    if config.badWorker > 0 and random.random() < config.badWorker:
        # We need to kill the process we are currently in, to simulate worker
        # failure. We don't want to just send SIGKILL, because we can't tell
        # that from a legitimate OOM on our CI runner. We're going to send
        # SIGUSR1 so our terminations are distinctive, and then SIGKILL if that
        # didn't stick. We definitely don't want to do this from *within* the
        # process we are trying to kill, so we fork off. TODO: We can still
        # leave the killing code running after the main Toil flow is done, but
        # since it's now in a process instead of a thread, the main Python
        # process won't wait around for its timeout to expire. I think this is
        # better than the old thread-based way where all of Toil would wait
        # around to be killed.
        
        killTarget = os.getpid()
        sleepTime = config.badWorkerFailInterval * random.random()
        if os.fork() == 0:
            # We are the child
            # Let the parent run some amount of time
            time.sleep(sleepTime)
            # Kill it gently
            os.kill(killTarget, signal.SIGUSR1)
            # Wait for that to stick
            time.sleep(0.01)
            try:
                # Kill it harder. Hope the PID hasn't already been reused.
                # If we succeeded the first time, this will OSError
                os.kill(killTarget, signal.SIGKILL)
            except OSError:
                pass
            # Exit without doing any of Toil's cleanup
            os._exit()
            
        # We don't need to reap the child. Either it kills us, or we finish
        # before it does. Either way, init will have to clean it up for us.

    ##########################################
    #Load the environment for the jobGraph
    ##########################################
    
    #First load the environment for the jobGraph.
    with jobStore.readSharedFileStream("environment.pickle") as fileHandle:
        environment = safeUnpickleFromStream(fileHandle)
    for i in environment:
        if i not in ("TMPDIR", "TMP", "HOSTNAME", "HOSTTYPE"):
            os.environ[i] = environment[i]
    # sys.path is used by __import__ to find modules
    if "PYTHONPATH" in environment:
        for e in environment["PYTHONPATH"].split(':'):
            if e != '':
                sys.path.append(e)

    toilWorkflowDir = Toil.getWorkflowDir(config.workflowID, config.workDir)
    
    ##########################################
    #Setup the temporary directories.
    ##########################################
        
    # Dir to put all this worker's temp files in.
    localWorkerTempDir = tempfile.mkdtemp(dir=toilWorkflowDir)
    os.chmod(localWorkerTempDir, 0o755)

    ##########################################
    #Setup the logging
    ##########################################

    #This is mildly tricky because we don't just want to
    #redirect stdout and stderr for this Python process; we want to redirect it
    #for this process and all children. Consequently, we can't just replace
    #sys.stdout and sys.stderr; we need to mess with the underlying OS-level
    #file descriptors. See <http://stackoverflow.com/a/11632982/402891>
    
    #When we start, standard input is file descriptor 0, standard output is
    #file descriptor 1, and standard error is file descriptor 2.

    #What file do we want to point FDs 1 and 2 to?
    tempWorkerLogPath = os.path.join(localWorkerTempDir, "worker_log.txt")

    if redirectOutputToLogFile:
        # Announce that we are redirecting logging, and where it will now go.
        # This is important if we are trying to manually trace a faulty worker invocation.
        logger.info("Redirecting logging to %s", tempWorkerLogPath)
        sys.stdout.flush()
        sys.stderr.flush()
        
        # Save the original stdout and stderr (by opening new file descriptors
        # to the same files)
        origStdOut = os.dup(1)
        origStdErr = os.dup(2)

        # Open the file to send stdout/stderr to.
        logFh = os.open(tempWorkerLogPath, os.O_WRONLY | os.O_CREAT | os.O_APPEND)

        # Replace standard output with a descriptor for the log file
        os.dup2(logFh, 1)

        # Replace standard error with a descriptor for the log file
        os.dup2(logFh, 2)

        # Since we only opened the file once, all the descriptors duped from
        # the original will share offset information, and won't clobber each
        # others' writes. See <http://stackoverflow.com/a/5284108/402891>. This
        # shouldn't matter, since O_APPEND seeks to the end of the file before
        # every write, but maybe there's something odd going on...

        # Close the descriptor we used to open the file
        os.close(logFh)

    debugging = logging.getLogger().isEnabledFor(logging.DEBUG)
    ##########################################
    #Worker log file trapped from here on in
    ##########################################

    workerFailed = False
    statsDict = MagicExpando()
    statsDict.jobs = []
    statsDict.workers.logsToMaster = []
    blockFn = lambda : True
    listOfJobs = [jobName]
    job = None
    try:

        #Put a message at the top of the log, just to make sure it's working.
        logger.info("---TOIL WORKER OUTPUT LOG---")
        sys.stdout.flush()
        
        logProcessContext(config)

        ##########################################
        #Load the jobGraph
        ##########################################
        
        jobGraph = jobStore.load(jobStoreID)
        listOfJobs[0] = str(jobGraph)
        logger.debug("Parsed job wrapper")
        
        ##########################################
        #Cleanup from any earlier invocation of the jobGraph
        ##########################################
        
        if jobGraph.command == None:
            logger.debug("Wrapper has no user job to run.")
            # Cleanup jobs already finished
            f = lambda jobs : [z for z in [[y for y in x if jobStore.exists(y.jobStoreID)] for x in jobs] if len(z) > 0]
            jobGraph.stack = f(jobGraph.stack)
            jobGraph.services = f(jobGraph.services)
            logger.debug("Cleaned up any references to completed successor jobs")

        #This cleans the old log file which may 
        #have been left if the job is being retried after a job failure.
        oldLogFile = jobGraph.logJobStoreFileID
        if oldLogFile != None:
            jobGraph.logJobStoreFileID = None
            jobStore.update(jobGraph) #Update first, before deleting any files
            jobStore.deleteFile(oldLogFile)

        ##########################################
        # If a checkpoint exists, restart from the checkpoint
        ##########################################

        # The job is a checkpoint, and is being restarted after previously completing
        if jobGraph.checkpoint != None:
            logger.debug("Job is a checkpoint")
            # If the checkpoint still has extant jobs in its
            # (flattened) stack and services, its subtree didn't
            # complete properly. We handle the restart of the
            # checkpoint here, removing its previous subtree.
            if len([i for l in jobGraph.stack for i in l]) > 0 or len(jobGraph.services) > 0:
                logger.debug("Checkpoint has failed.")
                # Reduce the retry count
                assert jobGraph.remainingRetryCount >= 0
                jobGraph.remainingRetryCount = max(0, jobGraph.remainingRetryCount - 1)
                jobGraph.restartCheckpoint(jobStore)
            # Otherwise, the job and successors are done, and we can cleanup stuff we couldn't clean
            # because of the job being a checkpoint
            else:
                logger.debug("The checkpoint jobs seems to have completed okay, removing any checkpoint files to delete.")
                #Delete any remnant files
                list(map(jobStore.deleteFile, list(filter(jobStore.fileExists, jobGraph.checkpointFilesToDelete))))

        ##########################################
        #Setup the stats, if requested
        ##########################################
        
        if config.stats:
            startClock = getTotalCpuTime()

        startTime = time.time()
        while True:
            ##########################################
            #Run the jobGraph, if there is one
            ##########################################
            
            if jobGraph.command is not None:
                assert jobGraph.command.startswith("_toil ")
                logger.debug("Got a command to run: %s" % jobGraph.command)
                #Load the job
                job = Job._loadJob(jobGraph.command, jobStore)
                # If it is a checkpoint job, save the command
                if job.checkpoint:
                    jobGraph.checkpoint = jobGraph.command

                # Create a fileStore object for the job
                fileStore = FileStore.createFileStore(jobStore, jobGraph, localWorkerTempDir, blockFn,
                                                      caching=not config.disableCaching)
                with job._executor(jobGraph=jobGraph,
                                   stats=statsDict if config.stats else None,
                                   fileStore=fileStore):
                    with fileStore.open(job):
                        # Get the next block function and list that will contain any messages
                        blockFn = fileStore._blockFn

                        job._runner(jobGraph=jobGraph, jobStore=jobStore, fileStore=fileStore)

                # Accumulate messages from this job & any subsequent chained jobs
                statsDict.workers.logsToMaster += fileStore.loggingMessages

            else:
                #The command may be none, in which case
                #the jobGraph is either a shell ready to be deleted or has
                #been scheduled after a failure to cleanup
                logger.debug("No user job to run, so finishing")
                break
            
            if FileStore._terminateEvent.isSet():
                raise RuntimeError("The termination flag is set")

            ##########################################
            #Establish if we can run another jobGraph within the worker
            ##########################################
            successorJobGraph = nextChainableJobGraph(jobGraph, jobStore)
            if successorJobGraph is None or config.disableChaining:
                # Can't chain any more jobs.
                break

            ##########################################
            #We have a single successor job that is not a checkpoint job.
            #We transplant the successor jobGraph command and stack
            #into the current jobGraph object so that it can be run
            #as if it were a command that were part of the current jobGraph.
            #We can then delete the successor jobGraph in the jobStore, as it is
            #wholly incorporated into the current jobGraph.
            ##########################################

            # add the successor to the list of jobs run
            listOfJobs.append(str(successorJobGraph))

            #Clone the jobGraph and its stack
            jobGraph = copy.deepcopy(jobGraph)
            
            #Remove the successor jobGraph
            jobGraph.stack.pop()

            #Transplant the command and stack to the current jobGraph
            jobGraph.command = successorJobGraph.command
            jobGraph.stack += successorJobGraph.stack
            # include some attributes for better identification of chained jobs in
            # logging output
            jobGraph.unitName = successorJobGraph.unitName
            jobGraph.jobName = successorJobGraph.jobName
            assert jobGraph.memory >= successorJobGraph.memory
            assert jobGraph.cores >= successorJobGraph.cores
            
            #Build a fileStore to update the job
            fileStore = FileStore.createFileStore(jobStore, jobGraph, localWorkerTempDir, blockFn,
                                                  caching=not config.disableCaching)

            #Update blockFn
            blockFn = fileStore._blockFn

            #Add successorJobGraph to those to be deleted
            fileStore.jobsToDelete.add(successorJobGraph.jobStoreID)
            
            #This will update the job once the previous job is done
            fileStore._updateJobWhenDone()            
            
            #Clone the jobGraph and its stack again, so that updates to it do
            #not interfere with this update
            jobGraph = copy.deepcopy(jobGraph)
            
            logger.debug("Starting the next job")
        
        ##########################################
        #Finish up the stats
        ##########################################
        if config.stats:
            totalCPUTime, totalMemoryUsage = getTotalCpuTimeAndMemoryUsage()
            statsDict.workers.time = str(time.time() - startTime)
            statsDict.workers.clock = str(totalCPUTime - startClock)
            statsDict.workers.memory = str(totalMemoryUsage)

        # log the worker log path here so that if the file is truncated the path can still be found
        if redirectOutputToLogFile:
            logger.info("Worker log can be found at %s. Set --cleanWorkDir to retain this log", localWorkerTempDir)
        
        logger.info("Finished running the chain of jobs on this node, we ran for a total of %f seconds", time.time() - startTime)
    
    ##########################################
    #Trapping where worker goes wrong
    ##########################################
    except: #Case that something goes wrong in worker
        traceback.print_exc()
        logger.error("Exiting the worker because of a failed job on host %s", socket.gethostname())
        FileStore._terminateEvent.set()
    
    ##########################################
    #Wait for the asynchronous chain of writes/updates to finish
    ########################################## 
       
    blockFn() 
    
    ##########################################
    #All the asynchronous worker/update threads must be finished now, 
    #so safe to test if they completed okay
    ########################################## 
    
    if FileStore._terminateEvent.isSet():
        jobGraph = jobStore.load(jobStoreID)
        jobGraph.setupJobAfterFailure(config)
        workerFailed = True
        if job and jobGraph.remainingRetryCount == 0:
            job._succeeded = False

    ##########################################
    #Cleanup
    ##########################################

    # Close the worker logging
    # Flush at the Python level
    sys.stdout.flush()
    sys.stderr.flush()
    if redirectOutputToLogFile:
        # Flush at the OS level
        os.fsync(1)
        os.fsync(2)

        # Close redirected stdout and replace with the original standard output.
        os.dup2(origStdOut, 1)

        # Close redirected stderr and replace with the original standard error.
        os.dup2(origStdErr, 2)

        # sys.stdout and sys.stderr don't need to be modified at all. We don't
        # need to call redirectLoggerStreamHandlers since they still log to
        # sys.stderr

        # Close our extra handles to the original standard output and standard
        # error streams, so we don't leak file handles.
        os.close(origStdOut)
        os.close(origStdErr)

    # Now our file handles are in exactly the state they were in before.

    #Copy back the log file to the global dir, if needed
    if workerFailed and redirectOutputToLogFile:
        jobGraph.logJobStoreFileID = jobStore.getEmptyFileStoreID(jobGraph.jobStoreID)
        jobGraph.chainedJobs = listOfJobs
        with jobStore.updateFileStream(jobGraph.logJobStoreFileID) as w:
            with open(tempWorkerLogPath, "r") as f:
                if os.path.getsize(tempWorkerLogPath) > logFileByteReportLimit !=0:
                    if logFileByteReportLimit > 0:
                        f.seek(-logFileByteReportLimit, 2)  # seek to last tooBig bytes of file
                    elif logFileByteReportLimit < 0:
                        f.seek(logFileByteReportLimit, 0)  # seek to first tooBig bytes of file
                w.write(f.read().encode('utf-8')) # TODO load file using a buffer
        jobStore.update(jobGraph)

    elif debugging and redirectOutputToLogFile:  # write log messages
        with open(tempWorkerLogPath, 'r') as logFile:
            if os.path.getsize(tempWorkerLogPath) > logFileByteReportLimit != 0:
                if logFileByteReportLimit > 0:
                    logFile.seek(-logFileByteReportLimit, 2)  # seek to last tooBig bytes of file
                elif logFileByteReportLimit < 0:
                    logFile.seek(logFileByteReportLimit, 0)  # seek to first tooBig bytes of file
            logMessages = logFile.read().splitlines()
        statsDict.logs.names = listOfJobs
        statsDict.logs.messages = logMessages

    if (debugging or config.stats or statsDict.workers.logsToMaster) and not workerFailed:  # We have stats/logging to report back
        jobStore.writeStatsAndLogging(json.dumps(statsDict, ensure_ascii=True))

    #Remove the temp dir
    cleanUp = config.cleanWorkDir
    if cleanUp == 'always' or (cleanUp == 'onSuccess' and not workerFailed) or (cleanUp == 'onError' and workerFailed):
        shutil.rmtree(localWorkerTempDir)
    
    #This must happen after the log file is done with, else there is no place to put the log
    if (not workerFailed) and jobGraph.command == None and len(jobGraph.stack) == 0 and len(jobGraph.services) == 0:
        # We can now safely get rid of the jobGraph
        jobStore.delete(jobGraph.jobStoreID)