def _execute(self, jobWrapper, stats, localTempDir, jobStore):
"""This is the core method for running the job within a worker.
"""
if stats != None:
startTime = time.time()
startClock = getTotalCpuTime()
baseDir = os.getcwd()
#Run the job, first cleanup then run.
fileStore = Job.FileStore(jobStore, jobWrapper, localTempDir)
returnValues = self.run(fileStore)
#Serialize the new jobs defined by the run method to the jobStore
self._serialiseJobGraph(jobWrapper, jobStore, returnValues, False)
#Change dir back to cwd dir, if changed by job (this is a safety issue)
if os.getcwd() != baseDir:
os.chdir(baseDir)
#Finish up the stats
if stats != None:
stats = ET.SubElement(stats, "job")
stats.attrib["time"] = str(time.time() - startTime)
totalCpuTime, totalMemoryUsage = getTotalCpuTimeAndMemoryUsage()
stats.attrib["clock"] = str(totalCpuTime - startClock)
stats.attrib["class"] = self._jobName()
stats.attrib["memory"] = str(totalMemoryUsage)
#Return any logToMaster logging messages + the files that should be deleted
#from the job store once the job has been registered as complete
return fileStore.loggingMessages, fileStore.deletedJobStoreFileIDs.union(promiseFilesToDelete)
def _execute(self, jobWrapper, stats, localTempDir, jobStore):
"""This is the core method for running the job within a worker.
"""
if stats != None:
startTime = time.time()
startClock = getTotalCpuTime()
baseDir = os.getcwd()
#Run the job, first cleanup then run.
fileStore = Job.FileStore(jobStore, jobWrapper, localTempDir)
returnValues = self.run(fileStore)
#Modify job graph to run any services correctly
self._modifyJobGraphForServices(fileStore)
#Check if the job graph has created
#any cycles of dependencies or has multiple roots
self.checkJobGraphForDeadlocks()
#Set the promised value jobStoreFileIDs
self._setFileIDsForPromisedValues(jobStore, jobWrapper.jobStoreID, set())
#Store the return values for any promised return value
self._setReturnValuesForPromises(self, returnValues, jobStore)
#Turn the graph into a graph of jobs in the jobStore
self._serialiseJobGraph(jobWrapper, jobStore)
#Change dir back to cwd dir, if changed by job (this is a safety issue)
if os.getcwd() != baseDir:
os.chdir(baseDir)
#Finish up the stats
if stats != None:
stats = ET.SubElement(stats, "job")
stats.attrib["time"] = str(time.time() - startTime)
totalCpuTime, totalMemoryUsage = getTotalCpuTimeAndMemoryUsage()
stats.attrib["clock"] = str(totalCpuTime - startClock)
stats.attrib["class"] = self._jobName()
stats.attrib["memory"] = str(totalMemoryUsage)
#Return any logToMaster logging messages
return fileStore.loggingMessages
def main():
logging.basicConfig()
##########################################
#Import necessary modules
##########################################
# This is assuming that worker.py is at a path ending in "/toil/worker.py".
sourcePath = os.path.dirname(os.path.dirname(__file__))
if sourcePath not in sys.path:
sys.path.append(sourcePath)
#Now we can import all the necessary functions
from toil.lib.bioio import setLogLevel
from toil.lib.bioio import getTotalCpuTime
from toil.lib.bioio import getTotalCpuTimeAndMemoryUsage
from toil.lib.bioio import makePublicDir
from toil.lib.bioio import system
from toil.common import loadJobStore
from toil.job import Job
##########################################
#Input args
##########################################
jobStoreString = sys.argv[1]
jobStoreID = sys.argv[2]
##########################################
#Load the jobStore/config file
##########################################
jobStore = loadJobStore(jobStoreString)
config = jobStore.config
##########################################
#Create the worker killer, if requested
##########################################
if config.badWorker > 0 and random.random() < config.badWorker:
def badWorker():
#This will randomly kill the worker process at a random time
time.sleep(config.badWorkerFailInterval * random.random())
os.kill(os.getpid(), signal.SIGKILL) #signal.SIGINT)
#TODO: FIX OCCASIONAL DEADLOCK WITH SIGINT (tested on single machine)
t = Thread(target=badWorker)
t.daemon = True
t.start()
##########################################
#Load the environment for the jobWrapper
##########################################
#First load the environment for the jobWrapper.
with jobStore.readSharedFileStream("environment.pickle") as fileHandle:
environment = cPickle.load(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)
setLogLevel(config.logLevel)
tempRootDir = config.workDir
if tempRootDir is not None and not os.path.exists(tempRootDir):
raise RuntimeError("The temporary directory specified by workDir: %s does not exist" % tempRootDir)
##########################################
#Setup the temporary directories.
##########################################
#Dir to put all the temp files in. If tempRootDir is None, tempdir looks at environment variables to determine
# where to put the tempDir.
localWorkerTempDir = tempfile.mkdtemp(dir=tempRootDir)
os.chmod(localWorkerTempDir, 0755)
##########################################
#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")
#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)
for handler in list(logger.handlers): #Remove old handlers
logger.removeHandler(handler)
#Add the new handler. The sys.stderr stream has been redirected by swapping
#the file descriptor out from under it.
logger.addHandler(logging.StreamHandler(sys.stderr))
debugging = logging.getLogger().isEnabledFor(logging.DEBUG)
##########################################
#Worker log file trapped from here on in
##########################################
workerFailed = False
statsDict = MagicExpando()
messages = []
blockFn = lambda : True
cleanCacheFn = lambda x : True
try:
#Put a message at the top of the log, just to make sure it's working.
print "---TOIL WORKER OUTPUT LOG---"
sys.stdout.flush()
#Log the number of open file descriptors so we can tell if we're leaking
#them.
logger.debug("Next available file descriptor: {}".format(
nextOpenDescriptor()))
##########################################
#Load the jobWrapper
##########################################
jobWrapper = jobStore.load(jobStoreID)
logger.debug("Parsed jobWrapper")
##########################################
#Cleanup from any earlier invocation of the jobWrapper
##########################################
if jobWrapper.command == None:
while len(jobWrapper.stack) > 0:
jobs = jobWrapper.stack[-1]
#If the jobs still exist they have not been run, so break
if jobStore.exists(jobs[0][0]):
break
#However, if they are gone then we can remove them from the stack.
#This is the only way to flush successors that have previously been run
#, as jobs are, as far as possible, read only in the leader.
jobWrapper.stack.pop()
#This cleans the old log file which may
#have been left if the jobWrapper is being retried after a jobWrapper failure.
oldLogFile = jobWrapper.logJobStoreFileID
jobWrapper.logJobStoreFileID = None
jobStore.update(jobWrapper) #Update first, before deleting the file
if oldLogFile != None:
jobStore.delete(oldLogFile)
#Make a temporary file directory for the jobWrapper
localTempDir = makePublicDir(os.path.join(localWorkerTempDir, "localTempDir"))
##########################################
#Setup the stats, if requested
##########################################
if config.stats:
startTime = time.time()
startClock = getTotalCpuTime()
startTime = time.time()
while True:
##########################################
#Run the jobWrapper, if there is one
##########################################
if jobWrapper.command != None:
if jobWrapper.command.startswith( "_toil " ):
#Load the job
job = Job._loadJob(jobWrapper.command, jobStore)
#Cleanup the cache from the previous job
cleanCacheFn(job.effectiveRequirements(jobStore.config).cache)
#Create a fileStore object for the job
fileStore = Job.FileStore(jobStore, jobWrapper, localTempDir,
blockFn)
#Get the next block function and list that will contain any messages
blockFn = fileStore._blockFn
messages = fileStore.loggingMessages
job._execute(jobWrapper=jobWrapper,
stats=statsDict if config.stats else None,
localTempDir=localTempDir,
jobStore=jobStore,
fileStore=fileStore)
#Set the clean cache function
cleanCacheFn = fileStore._cleanLocalTempDir
else: #Is another command (running outside of jobs may be deprecated)
#Cleanup the cache from the previous job
cleanCacheFn(0)
system(jobWrapper.command)
#Set a dummy clean cache fn
cleanCacheFn = lambda x : None
else:
#The command may be none, in which case
#the jobWrapper is either a shell ready to be deleted or has
#been scheduled after a failure to cleanup
break
if Job.FileStore._terminateEvent.isSet():
raise RuntimeError("The termination flag is set")
##########################################
#Establish if we can run another jobWrapper within the worker
##########################################
#No more jobs to run so quit
if len(jobWrapper.stack) == 0:
break
#Get the next set of jobs to run
jobs = jobWrapper.stack[-1]
assert len(jobs) > 0
#If there are 2 or more jobs to run in parallel we quit
if len(jobs) >= 2:
logger.debug("No more jobs can run in series by this worker,"
" it's got %i children", len(jobs)-1)
break
#We check the requirements of the jobWrapper to see if we can run it
#within the current worker
successorJobStoreID, successorMemory, successorCores, successorsDisk, successorPredecessorID = jobs[0]
if successorMemory > jobWrapper.memory:
logger.debug("We need more memory for the next jobWrapper, so finishing")
break
if successorCores > jobWrapper.cores:
logger.debug("We need more cores for the next jobWrapper, so finishing")
break
if successorsDisk > jobWrapper.disk:
logger.debug("We need more disk for the next jobWrapper, so finishing")
break
if successorPredecessorID != None:
logger.debug("The jobWrapper has multiple predecessors, we must return to the leader.")
break
##########################################
#We have a single successor jobWrapper.
#We load the successor jobWrapper and transplant its command and stack
#into the current jobWrapper so that it can be run
#as if it were a command that were part of the current jobWrapper.
#We can then delete the successor jobWrapper in the jobStore, as it is
#wholly incorporated into the current jobWrapper.
##########################################
#Clone the jobWrapper and its stack
jobWrapper = copy.deepcopy(jobWrapper)
#Remove the successor jobWrapper
jobWrapper.stack.pop()
#Load the successor jobWrapper
successorJob = jobStore.load(successorJobStoreID)
#These should all match up
assert successorJob.memory == successorMemory
assert successorJob.cores == successorCores
assert successorJob.predecessorsFinished == set()
assert successorJob.predecessorNumber == 1
assert successorJob.command != None
assert successorJobStoreID == successorJob.jobStoreID
#Transplant the command and stack to the current jobWrapper
jobWrapper.command = successorJob.command
jobWrapper.stack += successorJob.stack
assert jobWrapper.memory >= successorJob.memory
assert jobWrapper.cores >= successorJob.cores
#Build a fileStore to update the job
fileStore = Job.FileStore(jobStore, jobWrapper, localTempDir, blockFn)
#Update blockFn
blockFn = fileStore._blockFn
#Add successorJob to those to be deleted
fileStore.jobsToDelete.add(successorJob.jobStoreID)
#This will update the job once the previous job is done
fileStore._updateJobWhenDone()
#Clone the jobWrapper and its stack again, so that updates to it do
#not interfere with this update
jobWrapper = copy.deepcopy(jobWrapper)
logger.debug("Starting the next jobWrapper")
##########################################
#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)
statsDict.workers.log = messages
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 jobWrapper on host %s", socket.gethostname())
Job.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 Job.FileStore._terminateEvent.isSet():
jobWrapper = jobStore.load(jobStoreID)
jobWrapper.setupJobAfterFailure(config)
workerFailed = True
##########################################
#Cleanup
##########################################
#Close the worker logging
#Flush at the Python level
sys.stdout.flush()
sys.stderr.flush()
#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(origStdOut, 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:
truncateFile(tempWorkerLogPath)
jobWrapper.logJobStoreFileID = jobStore.writeFile( tempWorkerLogPath, jobWrapper.jobStoreID )
os.remove(tempWorkerLogPath)
jobStore.update(jobWrapper)
elif debugging: # write log messages
truncateFile(tempWorkerLogPath)
with open(tempWorkerLogPath, 'r') as logFile:
logMessages = logFile.read().splitlines()
statsDict.logs = [Expando(jobStoreID=jobStoreID,text=logMessage) for logMessage in logMessages]
if (debugging or config.stats or messages) and not workerFailed: # We have stats/logging to report back
jobStore.writeStatsAndLogging(json.dumps(statsDict))
#Remove the temp dir
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 jobWrapper.command == None and len(jobWrapper.stack) == 0:
#We can now safely get rid of the jobWrapper
jobStore.delete(jobWrapper.jobStoreID)
def main():
logging.basicConfig()
##########################################
#Import necessary modules
##########################################
# This is assuming that worker.py is at a path ending in "/toil/worker.py".
sourcePath = os.path.dirname(os.path.dirname(__file__))
if sourcePath not in sys.path:
sys.path.append(sourcePath)
#Now we can import all the necessary functions
from toil.lib.bioio import setLogLevel
from toil.lib.bioio import getTotalCpuTime
from toil.lib.bioio import getTotalCpuTimeAndMemoryUsage
from toil.lib.bioio import makePublicDir
from toil.lib.bioio import system
from toil.job import Job
##########################################
#Input args
##########################################
jobStoreString = sys.argv[1]
jobStoreID = sys.argv[2]
##########################################
#Load the jobStore/config file
##########################################
jobStore = Toil.loadOrCreateJobStore(jobStoreString)
config = jobStore.config
##########################################
#Create the worker killer, if requested
##########################################
if config.badWorker > 0 and random.random() < config.badWorker:
def badWorker():
#This will randomly kill the worker process at a random time
time.sleep(config.badWorkerFailInterval * random.random())
os.kill(os.getpid(), signal.SIGKILL) #signal.SIGINT)
#TODO: FIX OCCASIONAL DEADLOCK WITH SIGINT (tested on single machine)
t = Thread(target=badWorker)
# Ideally this would be a daemon thread but that causes an intermittent (but benign)
# exception similar to the one described here:
# http://stackoverflow.com/questions/20596918/python-exception-in-thread-thread-1-most-likely-raised-during-interpreter-shutd
# Our exception is:
# Exception in thread Thread-1 (most likely raised during interpreter shutdown):
# <type 'exceptions.AttributeError'>: 'NoneType' object has no attribute 'kill'
# This attribute error is caused by the call os.kill() and apparently unavoidable with a
# daemon
t.start()
##########################################
#Load the environment for the jobWrapper
##########################################
#First load the environment for the jobWrapper.
with jobStore.readSharedFileStream("environment.pickle") as fileHandle:
environment = cPickle.load(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)
setLogLevel(config.logLevel)
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, 0755)
##########################################
#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")
#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)
for handler in list(logger.handlers): #Remove old handlers
logger.removeHandler(handler)
#Add the new handler. The sys.stderr stream has been redirected by swapping
#the file descriptor out from under it.
logger.addHandler(logging.StreamHandler(sys.stderr))
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
cleanCacheFn = lambda x : True
try:
#Put a message at the top of the log, just to make sure it's working.
print "---TOIL WORKER OUTPUT LOG---"
sys.stdout.flush()
#Log the number of open file descriptors so we can tell if we're leaking
#them.
logger.debug("Next available file descriptor: {}".format(
nextOpenDescriptor()))
# Setup the caching variable now in case of an exception during loading of jobwrapper, etc
# Flag to identify if the run is cached or not.
FileStore = Job.FileStore if config.disableSharedCache else Job.CachedFileStore
##########################################
#Load the jobWrapper
##########################################
jobWrapper = jobStore.load(jobStoreID)
logger.debug("Parsed jobWrapper")
##########################################
#Cleanup from any earlier invocation of the jobWrapper
##########################################
if jobWrapper.command == None:
# Cleanup jobs already finished
f = lambda jobs : filter(lambda x : len(x) > 0, map(lambda x :
filter(lambda y : jobStore.exists(y[0]), x), jobs))
jobWrapper.stack = f(jobWrapper.stack)
jobWrapper.services = f(jobWrapper.services)
logger.debug("Cleaned up any references to completed successor jobs")
#This cleans the old log file which may
#have been left if the jobWrapper is being retried after a jobWrapper failure.
oldLogFile = jobWrapper.logJobStoreFileID
if oldLogFile != None:
jobWrapper.logJobStoreFileID = None
jobStore.update(jobWrapper) #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 jobWrapper.checkpoint != None:
logger.debug("Job is a checkpoint")
if len(jobWrapper.stack) > 0 or len(jobWrapper.services) > 0 or jobWrapper.command != None:
if jobWrapper.command != None:
assert jobWrapper.command == jobWrapper.checkpoint
logger.debug("Checkpoint job already has command set to run")
else:
jobWrapper.command = jobWrapper.checkpoint
# Reduce the retry count
assert jobWrapper.remainingRetryCount >= 0
jobWrapper.remainingRetryCount = max(0, jobWrapper.remainingRetryCount - 1)
jobStore.update(jobWrapper) # Update immediately to ensure that checkpoint
# is made before deleting any remaining successors
if len(jobWrapper.stack) > 0 or len(jobWrapper.services) > 0:
# If the subtree of successors is not complete restart everything
logger.debug("Checkpoint job has unfinished successor jobs, deleting the jobs on the stack: %s, services: %s " %
(jobWrapper.stack, jobWrapper.services))
# Delete everything on the stack, as these represent successors to clean
# up as we restart the queue
def recursiveDelete(jobWrapper2):
# Recursive walk the stack to delete all remaining jobs
for jobs in jobWrapper2.stack + jobWrapper2.services:
for jobTuple in jobs:
if jobStore.exists(jobTuple[0]):
recursiveDelete(jobStore.load(jobTuple[0]))
else:
logger.debug("Job %s has already been deleted", jobTuple[0])
if jobWrapper2 != jobWrapper:
logger.debug("Checkpoint is deleting old successor job: %s", jobWrapper2.jobStoreID)
jobStore.delete(jobWrapper2.jobStoreID)
recursiveDelete(jobWrapper)
jobWrapper.stack = [ [], [] ] # Initialise the job to mimic the state of a job
# that has been previously serialised but which as yet has no successors
jobWrapper.services = [] # Empty the services
# Update the jobStore to avoid doing this twice on failure and make this clean.
jobStore.update(jobWrapper)
# 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
map(jobStore.deleteFile, filter(jobStore.fileExists, jobWrapper.checkpointFilesToDelete))
##########################################
#Setup the stats, if requested
##########################################
if config.stats:
startTime = time.time()
startClock = getTotalCpuTime()
#Make a temporary file directory for the jobWrapper
#localTempDir = makePublicDir(os.path.join(localWorkerTempDir, "localTempDir"))
startTime = time.time()
while True:
##########################################
#Run the jobWrapper, if there is one
##########################################
if jobWrapper.command is not None:
assert jobWrapper.command.startswith( "_toil " )
logger.debug("Got a command to run: %s" % jobWrapper.command)
#Load the job
job = Job._loadJob(jobWrapper.command, jobStore)
# If it is a checkpoint job, save the command
if job.checkpoint:
jobWrapper.checkpoint = jobWrapper.command
# Need to fix all this for non shared cache runs
if config.disableSharedCache:
#Cleanup the cache from the previous job
cleanCacheFn(job.effectiveRequirements(jobStore.config).cache)
# Create a fileStore object for the job
fileStore = FileStore(jobStore, jobWrapper, localWorkerTempDir, blockFn)
with job._executor(jobWrapper=jobWrapper,
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(jobWrapper=jobWrapper, jobStore=jobStore, fileStore=fileStore)
# Accumulate messages from this job & any subsequent chained jobs
statsDict.workers.logsToMaster += fileStore.loggingMessages
if config.disableSharedCache:
#Set the clean cache function
cleanCacheFn = fileStore._cleanLocalTempDir
else:
#The command may be none, in which case
#the jobWrapper is either a shell ready to be deleted or has
#been scheduled after a failure to cleanup
break
if FileStore._terminateEvent.isSet():
raise RuntimeError("The termination flag is set")
##########################################
#Establish if we can run another jobWrapper within the worker
##########################################
#If no more jobs to run or services not finished, quit
if len(jobWrapper.stack) == 0 or len(jobWrapper.services) > 0 or jobWrapper.checkpoint != None:
logger.debug("Stopping running chain of jobs: length of stack: %s, services: %s, checkpoint: %s",
len(jobWrapper.stack), len(jobWrapper.services), jobWrapper.checkpoint != None)
break
#Get the next set of jobs to run
jobs = jobWrapper.stack[-1]
assert len(jobs) > 0
#If there are 2 or more jobs to run in parallel we quit
if len(jobs) >= 2:
logger.debug("No more jobs can run in series by this worker,"
" it's got %i children", len(jobs)-1)
break
#We check the requirements of the jobWrapper to see if we can run it
#within the current worker
successorJobStoreID, successorMemory, successorCores, successorsDisk, successorsPreemptable, successorPredecessorID = jobs[0]
if successorMemory > jobWrapper.memory:
logger.debug("We need more memory for the next jobWrapper, so finishing")
break
if successorCores > jobWrapper.cores:
logger.debug("We need more cores for the next jobWrapper, so finishing")
break
if successorsDisk > jobWrapper.disk:
logger.debug("We need more disk for the next jobWrapper, so finishing")
break
if successorPredecessorID != None:
logger.debug("The jobWrapper has multiple predecessors, we must return to the leader.")
break
# Load the successor jobWrapper
successorJobWrapper = jobStore.load(successorJobStoreID)
# Somewhat ugly, but check if job is a checkpoint job and quit if
# so
if successorJobWrapper.command.startswith( "_toil " ):
#Load the job
successorJob = Job._loadJob(successorJobWrapper.command, jobStore)
# Check it is not a checkpoint
if successorJob.checkpoint:
logger.debug("Next job is checkpoint, so finishing")
break
##########################################
#We have a single successor job that is not a checkpoint job.
#We transplant the successor jobWrappers command and stack
#into the current jobWrapper so that it can be run
#as if it were a command that were part of the current jobWrapper.
#We can then delete the successor jobWrapper in the jobStore, as it is
#wholly incorporated into the current jobWrapper.
##########################################
#Clone the jobWrapper and its stack
jobWrapper = copy.deepcopy(jobWrapper)
#Remove the successor jobWrapper
jobWrapper.stack.pop()
#These should all match up
assert successorJobWrapper.memory == successorMemory
assert successorJobWrapper.cores == successorCores
assert successorJobWrapper.predecessorsFinished == set()
assert successorJobWrapper.predecessorNumber == 1
assert successorJobWrapper.command != None
assert successorJobStoreID == successorJobWrapper.jobStoreID
#Transplant the command and stack to the current jobWrapper
jobWrapper.command = successorJobWrapper.command
jobWrapper.stack += successorJobWrapper.stack
assert jobWrapper.memory >= successorJobWrapper.memory
assert jobWrapper.cores >= successorJobWrapper.cores
#Build a fileStore to update the job
fileStore = Job.FileStore(jobStore, jobWrapper, localWorkerTempDir, blockFn)
#Update blockFn
blockFn = fileStore._blockFn
#Add successorJobWrapper to those to be deleted
fileStore.jobsToDelete.add(successorJobWrapper.jobStoreID)
#This will update the job once the previous job is done
fileStore._updateJobWhenDone()
#Clone the jobWrapper and its stack again, so that updates to it do
#not interfere with this update
jobWrapper = copy.deepcopy(jobWrapper)
logger.debug("Starting the next jobWrapper")
##########################################
#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
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 jobWrapper 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():
jobWrapper = jobStore.load(jobStoreID)
jobWrapper.setupJobAfterFailure(config)
workerFailed = True
##########################################
#Cleanup
##########################################
#Close the worker logging
#Flush at the Python level
sys.stdout.flush()
sys.stderr.flush()
#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(origStdOut, 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:
jobWrapper.logJobStoreFileID = jobStore.getEmptyFileStoreID(jobWrapper.jobStoreID)
with jobStore.updateFileStream(jobWrapper.logJobStoreFileID) as w:
with open(tempWorkerLogPath, "r") as f:
if os.path.getsize(tempWorkerLogPath) > logFileByteReportLimit:
f.seek(-logFileByteReportLimit, 2) # seek to last tooBig bytes of file
w.write(f.read())
jobStore.update(jobWrapper)
elif debugging: # write log messages
with open(tempWorkerLogPath, 'r') as logFile:
if os.path.getsize(tempWorkerLogPath) > logFileByteReportLimit:
logFile.seek(-logFileByteReportLimit, 2) # seek to last tooBig bytes of file
logMessages = logFile.read().splitlines()
statsDict.logs = [Expando(jobStoreID=jobStoreID, text=logMessage) for logMessage in 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))
#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 jobWrapper.command == None and len(jobWrapper.stack) == 0 and len(jobWrapper.services) == 0:
# We can now safely get rid of the jobWrapper
jobStore.delete(jobWrapper.jobStoreID)
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)
def main():
##########################################
#Import necessary modules
##########################################
# This is assuming that worker.py is at a path ending in "/toil/worker.py".
sourcePath = os.path.dirname(os.path.dirname(__file__))
if sourcePath not in sys.path:
# FIXME: prepending to sys.path should fix #103
sys.path.append(sourcePath)
#Now we can import all the necessary functions
from toil.lib.bioio import setLogLevel
from toil.lib.bioio import getTotalCpuTime
from toil.lib.bioio import getTotalCpuTimeAndMemoryUsage
from toil.lib.bioio import getTempDirectory
from toil.lib.bioio import makeSubDir
from toil.lib.bioio import system
from toil.common import loadJobStore
##########################################
#Input args
##########################################
jobStoreString = sys.argv[1]
jobStoreID = sys.argv[2]
##########################################
#Load the jobStore/config file
##########################################
jobStore = loadJobStore(jobStoreString)
config = jobStore.config
##########################################
#Load the environment for the batchjob
##########################################
#First load the environment for the batchjob.
with jobStore.readSharedFileStream("environment.pickle") as fileHandle:
environment = cPickle.load(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)
setLogLevel(config.attrib["log_level"])
##########################################
#Setup the temporary directories.
##########################################
#Dir to put all the temp files in.
localWorkerTempDir = getTempDirectory()
##########################################
#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")
#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)
for handler in list(logger.handlers): #Remove old handlers
logger.removeHandler(handler)
#Add the new handler. The sys.stderr stream has been redirected by swapping
#the file descriptor out from under it.
logger.addHandler(logging.StreamHandler(sys.stderr))
##########################################
#Worker log file trapped from here on in
##########################################
workerFailed = False
try:
#Put a message at the top of the log, just to make sure it's working.
print "---TOIL WORKER OUTPUT LOG---"
sys.stdout.flush()
#Log the number of open file descriptors so we can tell if we're leaking
#them.
logger.debug("Next available file descriptor: {}".format(
nextOpenDescriptor()))
##########################################
#Load the batchjob
##########################################
batchjob = jobStore.load(jobStoreID)
logger.debug("Parsed batchjob")
##########################################
#Cleanup from any earlier invocation of the batchjob
##########################################
if batchjob.command == None:
while len(batchjob.stack) > 0:
jobs = batchjob.stack[-1]
#If the jobs still exist they have not been run, so break
if jobStore.exists(jobs[0][0]):
break
#However, if they are gone then we can remove them from the stack.
#This is the only way to flush successors that have previously been run
#, as jobs are, as far as possible, read only in the leader.
batchjob.stack.pop()
#This cleans the old log file which may
#have been left if the batchjob is being retried after a batchjob failure.
if batchjob.logJobStoreFileID != None:
batchjob.clearLogFile(jobStore)
##########################################
#Setup the stats, if requested
##########################################
if config.attrib.has_key("stats"):
startTime = time.time()
startClock = getTotalCpuTime()
stats = ET.Element("worker")
else:
stats = None
startTime = time.time()
while True:
##########################################
#Run the batchjob, if there is one
##########################################
if batchjob.command != None:
if batchjob.command[:11] == "scriptTree ":
#Make a temporary file directory for the job
localTempDir = makeSubDir(
os.path.join(localWorkerTempDir, "localTempDir"))
#Is a job command
messages = loadJob(batchjob.command, jobStore)._execute(
batchjob=batchjob,
stats=stats,
localTempDir=localTempDir,
jobStore=jobStore)
#Remove the temporary file directory
shutil.rmtree(localTempDir)
else: #Is another command (running outside of jobs may be deprecated)
system(batchjob.command)
messages = []
else:
#The command may be none, in which case
#the batchjob is just a shell ready to be deleted
assert len(batchjob.stack) == 0
messages = []
break
##########################################
#Establish if we can run another batchjob within the worker
##########################################
#Exceeded the amount of time the worker is allowed to run for so quit
if time.time() - startTime > float(config.attrib["job_time"]):
logger.debug(
"We are breaking because the maximum time the batchjob should run for has been exceeded"
)
break
#No more jobs to run so quit
if len(batchjob.stack) == 0:
break
#Get the next set of jobs to run
jobs = batchjob.stack[-1]
assert len(jobs) > 0
#If there are 2 or more jobs to run in parallel we quit
if len(jobs) >= 2:
logger.debug(
"No more jobs can run in series by this worker,"
" it's got %i children",
len(jobs) - 1)
break
#We check the requirements of the batchjob to see if we can run it
#within the current worker
successorJobStoreID, successorMemory, successorCpu, successorsDisk, successorPredecessorID = jobs[
0]
if successorMemory > batchjob.memory:
logger.debug(
"We need more memory for the next batchjob, so finishing")
break
if successorCpu > batchjob.cpu:
logger.debug(
"We need more cpus for the next batchjob, so finishing")
break
if successorsDisk > batchjob.disk:
logger.debug(
"We need more disk for the next batchjob, so finishing")
break
if successorPredecessorID != None:
logger.debug(
"The batchjob has multiple predecessors, we must return to the leader."
)
break
##########################################
#We have a single successor batchjob.
#We load the successor batchjob and transplant its command and stack
#into the current batchjob so that it can be run
#as if it were a command that were part of the current batchjob.
#We can then delete the successor batchjob in the jobStore, as it is
#wholly incorporated into the current batchjob.
##########################################
#Remove the successor batchjob
batchjob.stack.pop()
#Load the successor batchjob
successorJob = jobStore.load(successorJobStoreID)
#These should all match up
assert successorJob.memory == successorMemory
assert successorJob.cpu == successorCpu
assert successorJob.predecessorsFinished == set()
assert successorJob.predecessorNumber == 1
assert successorJob.command != None
assert successorJobStoreID == successorJob.jobStoreID
#Transplant the command and stack to the current batchjob
batchjob.command = successorJob.command
batchjob.stack += successorJob.stack
assert batchjob.memory >= successorJob.memory
assert batchjob.cpu >= successorJob.cpu
#Checkpoint the batchjob and delete the successorJob
batchjob.jobsToDelete = [successorJob.jobStoreID]
jobStore.update(batchjob)
jobStore.delete(successorJob.jobStoreID)
logger.debug("Starting the next batchjob")
##########################################
#Finish up the stats
##########################################
if stats != None:
totalCpuTime, totalMemoryUsage = getTotalCpuTimeAndMemoryUsage()
stats.attrib["time"] = str(time.time() - startTime)
stats.attrib["clock"] = str(totalCpuTime - startClock)
stats.attrib["memory"] = str(totalMemoryUsage)
m = ET.SubElement(stats, "messages")
for message in messages:
ET.SubElement(m, "message").text = message
jobStore.writeStatsAndLogging(ET.tostring(stats))
elif len(messages
) > 0: #No stats, but still need to report log messages
l = ET.Element("worker")
m = ET.SubElement(l, "messages")
for message in messages:
ET.SubElement(m, "message").text = message
jobStore.writeStatsAndLogging(ET.tostring(l))
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 batchjob on host %s",
socket.gethostname())
batchjob = jobStore.load(jobStoreID)
batchjob.setupJobAfterFailure(config)
workerFailed = True
##########################################
#Cleanup
##########################################
#Close the worker logging
#Flush at the Python level
sys.stdout.flush()
sys.stderr.flush()
#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(origStdOut, 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:
truncateFile(tempWorkerLogPath)
batchjob.setLogFile(tempWorkerLogPath, jobStore)
os.remove(tempWorkerLogPath)
jobStore.update(batchjob)
#Remove the temp dir
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 batchjob.command == None and len(
batchjob.stack) == 0:
#We can now safely get rid of the batchjob
jobStore.delete(batchjob.jobStoreID)
def main():
##########################################
#Import necessary modules
##########################################
# This is assuming that worker.py is at a path ending in "/toil/worker.py".
sourcePath = os.path.dirname(os.path.dirname(__file__))
if sourcePath not in sys.path:
# FIXME: prepending to sys.path should fix #103
sys.path.append(sourcePath)
#Now we can import all the necessary functions
from toil.lib.bioio import setLogLevel
from toil.lib.bioio import getTotalCpuTime
from toil.lib.bioio import getTotalCpuTimeAndMemoryUsage
from toil.lib.bioio import getTempDirectory
from toil.lib.bioio import makeSubDir
from toil.lib.bioio import system
from toil.common import loadJobStore
##########################################
#Input args
##########################################
jobStoreString = sys.argv[1]
jobStoreID = sys.argv[2]
##########################################
#Load the jobStore/config file
##########################################
jobStore = loadJobStore(jobStoreString)
config = jobStore.config
##########################################
#Load the environment for the batchjob
##########################################
#First load the environment for the batchjob.
with jobStore.readSharedFileStream("environment.pickle") as fileHandle:
environment = cPickle.load(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)
setLogLevel(config.attrib["log_level"])
##########################################
#Setup the temporary directories.
##########################################
#Dir to put all the temp files in.
localWorkerTempDir = getTempDirectory()
##########################################
#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")
#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)
for handler in list(logger.handlers): #Remove old handlers
logger.removeHandler(handler)
#Add the new handler. The sys.stderr stream has been redirected by swapping
#the file descriptor out from under it.
logger.addHandler(logging.StreamHandler(sys.stderr))
##########################################
#Worker log file trapped from here on in
##########################################
workerFailed = False
try:
#Put a message at the top of the log, just to make sure it's working.
print "---TOIL WORKER OUTPUT LOG---"
sys.stdout.flush()
#Log the number of open file descriptors so we can tell if we're leaking
#them.
logger.debug("Next available file descriptor: {}".format(
nextOpenDescriptor()))
##########################################
#Load the batchjob
##########################################
batchjob = jobStore.load(jobStoreID)
logger.debug("Parsed batchjob")
##########################################
#Cleanup from any earlier invocation of the batchjob
##########################################
if batchjob.command == None:
while len(batchjob.stack) > 0:
jobs = batchjob.stack[-1]
#If the jobs still exist they have not been run, so break
if jobStore.exists(jobs[0][0]):
break
#However, if they are gone then we can remove them from the stack.
#This is the only way to flush successors that have previously been run
#, as jobs are, as far as possible, read only in the leader.
batchjob.stack.pop()
#This cleans the old log file which may
#have been left if the batchjob is being retried after a batchjob failure.
if batchjob.logJobStoreFileID != None:
batchjob.clearLogFile(jobStore)
##########################################
#Setup the stats, if requested
##########################################
if config.attrib.has_key("stats"):
startTime = time.time()
startClock = getTotalCpuTime()
stats = ET.Element("worker")
else:
stats = None
startTime = time.time()
while True:
##########################################
#Run the batchjob, if there is one
##########################################
if batchjob.command != None:
if batchjob.command[:11] == "scriptTree ":
#Make a temporary file directory for the job
localTempDir = makeSubDir(os.path.join(localWorkerTempDir, "localTempDir"))
#Is a job command
messages = loadJob(batchjob.command, jobStore)._execute(batchjob=batchjob,
stats=stats, localTempDir=localTempDir,
jobStore=jobStore)
#Remove the temporary file directory
shutil.rmtree(localTempDir)
else: #Is another command (running outside of jobs may be deprecated)
system(batchjob.command)
messages = []
else:
#The command may be none, in which case
#the batchjob is just a shell ready to be deleted
assert len(batchjob.stack) == 0
messages = []
break
##########################################
#Establish if we can run another batchjob within the worker
##########################################
#Exceeded the amount of time the worker is allowed to run for so quit
if time.time() - startTime > float(config.attrib["job_time"]):
logger.debug("We are breaking because the maximum time the batchjob should run for has been exceeded")
break
#No more jobs to run so quit
if len(batchjob.stack) == 0:
break
#Get the next set of jobs to run
jobs = batchjob.stack[-1]
assert len(jobs) > 0
#If there are 2 or more jobs to run in parallel we quit
if len(jobs) >= 2:
logger.debug("No more jobs can run in series by this worker,"
" it's got %i children", len(jobs)-1)
break
#We check the requirements of the batchjob to see if we can run it
#within the current worker
successorJobStoreID, successorMemory, successorCpu, successorsDisk, successorPredecessorID = jobs[0]
if successorMemory > batchjob.memory:
logger.debug("We need more memory for the next batchjob, so finishing")
break
if successorCpu > batchjob.cpu:
logger.debug("We need more cpus for the next batchjob, so finishing")
break
if successorsDisk > batchjob.disk:
logger.debug("We need more disk for the next batchjob, so finishing")
break
if successorPredecessorID != None:
logger.debug("The batchjob has multiple predecessors, we must return to the leader.")
break
##########################################
#We have a single successor batchjob.
#We load the successor batchjob and transplant its command and stack
#into the current batchjob so that it can be run
#as if it were a command that were part of the current batchjob.
#We can then delete the successor batchjob in the jobStore, as it is
#wholly incorporated into the current batchjob.
##########################################
#Remove the successor batchjob
batchjob.stack.pop()
#Load the successor batchjob
successorJob = jobStore.load(successorJobStoreID)
#These should all match up
assert successorJob.memory == successorMemory
assert successorJob.cpu == successorCpu
assert successorJob.predecessorsFinished == set()
assert successorJob.predecessorNumber == 1
assert successorJob.command != None
assert successorJobStoreID == successorJob.jobStoreID
#Transplant the command and stack to the current batchjob
batchjob.command = successorJob.command
batchjob.stack += successorJob.stack
assert batchjob.memory >= successorJob.memory
assert batchjob.cpu >= successorJob.cpu
#Checkpoint the batchjob and delete the successorJob
batchjob.jobsToDelete = [ successorJob.jobStoreID ]
jobStore.update(batchjob)
jobStore.delete(successorJob.jobStoreID)
logger.debug("Starting the next batchjob")
##########################################
#Finish up the stats
##########################################
if stats != None:
totalCpuTime, totalMemoryUsage = getTotalCpuTimeAndMemoryUsage()
stats.attrib["time"] = str(time.time() - startTime)
stats.attrib["clock"] = str(totalCpuTime - startClock)
stats.attrib["memory"] = str(totalMemoryUsage)
m = ET.SubElement(stats, "messages")
for message in messages:
ET.SubElement(m, "message").text = message
jobStore.writeStatsAndLogging(ET.tostring(stats))
elif len(messages) > 0: #No stats, but still need to report log messages
l = ET.Element("worker")
m = ET.SubElement(l, "messages")
for message in messages:
ET.SubElement(m, "message").text = message
jobStore.writeStatsAndLogging(ET.tostring(l))
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 batchjob on host %s", socket.gethostname())
batchjob = jobStore.load(jobStoreID)
batchjob.setupJobAfterFailure(config)
workerFailed = True
##########################################
#Cleanup
##########################################
#Close the worker logging
#Flush at the Python level
sys.stdout.flush()
sys.stderr.flush()
#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(origStdOut, 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:
truncateFile(tempWorkerLogPath)
batchjob.setLogFile(tempWorkerLogPath, jobStore)
os.remove(tempWorkerLogPath)
jobStore.update(batchjob)
#Remove the temp dir
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 batchjob.command == None and len(batchjob.stack) == 0:
#We can now safely get rid of the batchjob
jobStore.delete(batchjob.jobStoreID)
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
"""
configureRootLogger()
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(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 = getTotalCpuTime()
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 = 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())
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
def main():
logging.basicConfig()
##########################################
#Import necessary modules
##########################################
# This is assuming that worker.py is at a path ending in "/toil/worker.py".
sourcePath = os.path.dirname(os.path.dirname(__file__))
if sourcePath not in sys.path:
sys.path.append(sourcePath)
#Now we can import all the necessary functions
from toil.lib.bioio import setLogLevel
from toil.lib.bioio import getTotalCpuTime
from toil.lib.bioio import getTotalCpuTimeAndMemoryUsage
from toil.lib.bioio import makePublicDir
from toil.lib.bioio import system
from toil.common import loadJobStore
from toil.job import Job
##########################################
#Input args
##########################################
jobStoreString = sys.argv[1]
jobStoreID = sys.argv[2]
##########################################
#Load the jobStore/config file
##########################################
jobStore = loadJobStore(jobStoreString)
config = jobStore.config
##########################################
#Create the worker killer, if requested
##########################################
if config.badWorker > 0 and random.random() < config.badWorker:
def badWorker():
#This will randomly kill the worker process at a random time
time.sleep(config.badWorkerFailInterval * random.random())
os.kill(os.getpid(), signal.SIGKILL) #signal.SIGINT)
#TODO: FIX OCCASIONAL DEADLOCK WITH SIGINT (tested on single machine)
t = Thread(target=badWorker)
t.daemon = True
t.start()
##########################################
#Load the environment for the jobWrapper
##########################################
#First load the environment for the jobWrapper.
with jobStore.readSharedFileStream("environment.pickle") as fileHandle:
environment = cPickle.load(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)
setLogLevel(config.logLevel)
tempRootDir = config.workDir
if tempRootDir is not None and not os.path.exists(tempRootDir):
raise RuntimeError("The temporary directory specified by workDir: %s does not exist" % tempRootDir)
##########################################
#Setup the temporary directories.
##########################################
#Dir to put all the temp files in. If tempRootDir is None, tempdir looks at environment variables to determine
# where to put the tempDir.
localWorkerTempDir = tempfile.mkdtemp(dir=tempRootDir)
os.chmod(localWorkerTempDir, 0755)
##########################################
#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")
#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)
for handler in list(logger.handlers): #Remove old handlers
logger.removeHandler(handler)
#Add the new handler. The sys.stderr stream has been redirected by swapping
#the file descriptor out from under it.
logger.addHandler(logging.StreamHandler(sys.stderr))
debugging = logging.getLogger().isEnabledFor(logging.DEBUG)
##########################################
#Worker log file trapped from here on in
##########################################
workerFailed = False
statsDict = MagicExpando()
statsDict.jobs = []
messages = []
blockFn = lambda : True
cleanCacheFn = lambda x : True
try:
#Put a message at the top of the log, just to make sure it's working.
print "---TOIL WORKER OUTPUT LOG---"
sys.stdout.flush()
#Log the number of open file descriptors so we can tell if we're leaking
#them.
logger.debug("Next available file descriptor: {}".format(
nextOpenDescriptor()))
##########################################
#Load the jobWrapper
##########################################
jobWrapper = jobStore.load(jobStoreID)
logger.debug("Parsed jobWrapper")
##########################################
#Cleanup from any earlier invocation of the jobWrapper
##########################################
if jobWrapper.command == None:
while len(jobWrapper.stack) > 0:
jobs = jobWrapper.stack[-1]
#If the jobs still exist they have not been run, so break
if jobStore.exists(jobs[0][0]):
break
#However, if they are gone then we can remove them from the stack.
#This is the only way to flush successors that have previously been run
#, as jobs are, as far as possible, read only in the leader.
jobWrapper.stack.pop()
#This cleans the old log file which may
#have been left if the jobWrapper is being retried after a jobWrapper failure.
oldLogFile = jobWrapper.logJobStoreFileID
jobWrapper.logJobStoreFileID = None
jobStore.update(jobWrapper) #Update first, before deleting the file
if oldLogFile != None:
jobStore.delete(oldLogFile)
#Make a temporary file directory for the jobWrapper
localTempDir = makePublicDir(os.path.join(localWorkerTempDir, "localTempDir"))
##########################################
#Setup the stats, if requested
##########################################
if config.stats:
startTime = time.time()
startClock = getTotalCpuTime()
startTime = time.time()
while True:
##########################################
#Run the jobWrapper, if there is one
##########################################
if jobWrapper.command != None:
if jobWrapper.command.startswith( "_toil " ):
#Load the job
job = Job._loadJob(jobWrapper.command, jobStore)
#Cleanup the cache from the previous job
cleanCacheFn(job.effectiveRequirements(jobStore.config).cache)
#Create a fileStore object for the job
fileStore = Job.FileStore(jobStore, jobWrapper, localTempDir,
blockFn)
#Get the next block function and list that will contain any messages
blockFn = fileStore._blockFn
messages = fileStore.loggingMessages
job._execute(jobWrapper=jobWrapper,
stats=statsDict if config.stats else None,
localTempDir=localTempDir,
jobStore=jobStore,
fileStore=fileStore)
#Set the clean cache function
cleanCacheFn = fileStore._cleanLocalTempDir
else: #Is another command (running outside of jobs may be deprecated)
#Cleanup the cache from the previous job
cleanCacheFn(0)
system(jobWrapper.command)
#Set a dummy clean cache fn
cleanCacheFn = lambda x : None
else:
#The command may be none, in which case
#the jobWrapper is either a shell ready to be deleted or has
#been scheduled after a failure to cleanup
break
if Job.FileStore._terminateEvent.isSet():
raise RuntimeError("The termination flag is set")
##########################################
#Establish if we can run another jobWrapper within the worker
##########################################
#No more jobs to run so quit
if len(jobWrapper.stack) == 0:
break
#Get the next set of jobs to run
jobs = jobWrapper.stack[-1]
assert len(jobs) > 0
#If there are 2 or more jobs to run in parallel we quit
if len(jobs) >= 2:
logger.debug("No more jobs can run in series by this worker,"
" it's got %i children", len(jobs)-1)
break
#We check the requirements of the jobWrapper to see if we can run it
#within the current worker
successorJobStoreID, successorMemory, successorCores, successorsDisk, successorPredecessorID = jobs[0]
if successorMemory > jobWrapper.memory:
logger.debug("We need more memory for the next jobWrapper, so finishing")
break
if successorCores > jobWrapper.cores:
logger.debug("We need more cores for the next jobWrapper, so finishing")
break
if successorsDisk > jobWrapper.disk:
logger.debug("We need more disk for the next jobWrapper, so finishing")
break
if successorPredecessorID != None:
logger.debug("The jobWrapper has multiple predecessors, we must return to the leader.")
break
##########################################
#We have a single successor jobWrapper.
#We load the successor jobWrapper and transplant its command and stack
#into the current jobWrapper so that it can be run
#as if it were a command that were part of the current jobWrapper.
#We can then delete the successor jobWrapper in the jobStore, as it is
#wholly incorporated into the current jobWrapper.
##########################################
#Clone the jobWrapper and its stack
jobWrapper = copy.deepcopy(jobWrapper)
#Remove the successor jobWrapper
jobWrapper.stack.pop()
#Load the successor jobWrapper
successorJob = jobStore.load(successorJobStoreID)
#These should all match up
assert successorJob.memory == successorMemory
assert successorJob.cores == successorCores
assert successorJob.predecessorsFinished == set()
assert successorJob.predecessorNumber == 1
assert successorJob.command != None
assert successorJobStoreID == successorJob.jobStoreID
#Transplant the command and stack to the current jobWrapper
jobWrapper.command = successorJob.command
jobWrapper.stack += successorJob.stack
assert jobWrapper.memory >= successorJob.memory
assert jobWrapper.cores >= successorJob.cores
#Build a fileStore to update the job
fileStore = Job.FileStore(jobStore, jobWrapper, localTempDir, blockFn)
#Update blockFn
blockFn = fileStore._blockFn
#Add successorJob to those to be deleted
fileStore.jobsToDelete.add(successorJob.jobStoreID)
#This will update the job once the previous job is done
fileStore._updateJobWhenDone()
#Clone the jobWrapper and its stack again, so that updates to it do
#not interfere with this update
jobWrapper = copy.deepcopy(jobWrapper)
logger.debug("Starting the next jobWrapper")
##########################################
#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)
statsDict.workers.log = messages
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 jobWrapper on host %s", socket.gethostname())
Job.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 Job.FileStore._terminateEvent.isSet():
jobWrapper = jobStore.load(jobStoreID)
jobWrapper.setupJobAfterFailure(config)
workerFailed = True
##########################################
#Cleanup
##########################################
#Close the worker logging
#Flush at the Python level
sys.stdout.flush()
sys.stderr.flush()
#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(origStdOut, 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:
truncateFile(tempWorkerLogPath)
jobWrapper.logJobStoreFileID = jobStore.writeFile( tempWorkerLogPath, jobWrapper.jobStoreID )
os.remove(tempWorkerLogPath)
jobStore.update(jobWrapper)
elif debugging: # write log messages
truncateFile(tempWorkerLogPath)
with open(tempWorkerLogPath, 'r') as logFile:
logMessages = logFile.read().splitlines()
statsDict.logs = [Expando(jobStoreID=jobStoreID,text=logMessage) for logMessage in logMessages]
if (debugging or config.stats or messages) and not workerFailed: # We have stats/logging to report back
jobStore.writeStatsAndLogging(json.dumps(statsDict))
#Remove the temp dir
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 jobWrapper.command == None and len(jobWrapper.stack) == 0:
#We can now safely get rid of the jobWrapper
jobStore.delete(jobWrapper.jobStoreID)
