def iterator(alignedSegment, refSeq, readSeq):
"""Generates aligned pairs from a pysam.AlignedSegment object.
"""
readOffset = getFirstNonClippedPositionInRead(alignedSegment, readSeq)
pPair = None
assert len(alignedSegment.query_sequence) <= len(readSeq)
for readPos, refPos in alignedSegment.aligned_pairs: #Iterate over the block
if readPos != None and refPos != None:
assert refPos >= alignedSegment.reference_start and refPos < alignedSegment.reference_end
if refPos >= len(refSeq): #This is masking an (apparently minor?) one
#off error in the BWA sam files?
logger.critical("Detected an aligned reference position out of \
bounds! Reference length: %s, reference coordinate: %s" % \
(len(refSeq), refPos))
continue
aP = AlignedPair(refPos, refSeq, abs(readOffset + readPos),
alignedSegment.is_reverse, readSeq, pPair)
'''if aP.getReadBase().upper() != alignedSegment.query_alignment_sequence[readPos].upper():
logger.critical("Detected a discrepancy between the absolute read \
sequence and the aligned read sequence. Bases: %s %s, \
read-position: %s, is reversed: %s, absolute read offset: %s, \
length absolute read sequence %s, length aligned read sequence %s, \
length aligned read sequence plus soft clipping %s, read name: %s"
% (aP.getReadBase().upper(), alignedSegment.query_alignment_sequence[readPos].upper(),
readPos, alignedSegment.is_reverse, readOffset, len(readSeq),
len(alignedSegment.query_alignment_sequence), len(alignedSegment.query_sequence),
alignedSegment.query_name))
'''
pPair = aP
yield aP
def fixJobsList(config, jobFiles):
"""Traverses through and finds any .old files, using there saved state to recover a
valid state of the job tree.
"""
updatingFiles = []
for fileName in jobFiles[:]:
if "updating" in fileName:
updatingFiles.append(fileName)
for updatingFileName in updatingFiles: #Things crashed while the state was updating, so we should remove the 'updating' and '.new' files
fileHandle = open(updatingFileName, 'r')
for fileName in fileHandle.readline().split():
if os.path.isfile(fileName):
config.attrib["job_file_dir"].destroyTempFile(fileName)
jobFiles.remove(fileName)
fileHandle.close()
config.attrib["job_file_dir"].destroyTempFile(updatingFileName)
jobFiles.remove(updatingFileName)
for fileName in jobFiles[:]: #Else any '.new' files will be switched in place of the original file.
if fileName[-3:] == 'new':
originalFileName = fileName[:-4]
os.rename(fileName, originalFileName)
jobFiles.remove(fileName)
if originalFileName not in jobFiles:
jobFiles.append(originalFileName)
logger.critical("Fixing the file: %s from %s" % (originalFileName, fileName))
def iterator(alignedRead, refSeq, readSeq):
"""Generates aligned pairs from a pysam.AlignedRead object.
"""
readOffset = getAbsoluteReadOffset(alignedRead, refSeq, readSeq)
pPair = None
assert len(alignedRead.seq) <= len(readSeq)
for readPos, refPos in alignedRead.aligned_pairs: #Iterate over the block
if readPos != None and refPos != None:
assert refPos >= alignedRead.pos and refPos < alignedRead.aend
if refPos >= len(
refSeq
): #This is masking an (apparently minor?) one off error in the BWA sam files?
logger.critical(
"Detected an aligned reference position out of bounds! Reference length: %s, reference coordinate: %s"
% (len(refSeq), refPos))
continue
aP = AlignedPair(refPos, refSeq, abs(readOffset + readPos),
alignedRead.is_reverse, readSeq, pPair)
if aP.getReadBase().upper(
) != alignedRead.query[readPos].upper():
logger.critical(
"Detected a discrepancy between the absolute read sequence and the aligned read sequence. Bases: %s %s, read-position: %s, is reversed: %s, absolute read offset: %s, length absolute read sequence %s, length aligned read sequence %s, length aligned read sequence plus soft clipping %s, read name: %s, cigar string %s"
% (aP.getReadBase().upper(),
alignedRead.query[readPos].upper(), readPos,
alignedRead.is_reverse, readOffset, len(readSeq),
len(alignedRead.query), len(alignedRead.seq),
alignedRead.qname, alignedRead.cigarstring))
assert aP.getReadBase().upper(
) == alignedRead.query[readPos].upper()
pPair = aP
yield aP
def reissueMissingJobs(updatedJobFiles, jobIDsToJobsHash, batchSystem, killAfterNTimesMissing=3):
"""Check all the current job ids are in the list of currently running batch system jobs.
If a job is missing, we mark it as so, if it is missing for a number of runs of
this function (say 10).. then we try deleting the job (though its probably lost), we wait
then we pass the job to processFinishedJob.
"""
runningJobs = set(batchSystem.getIssuedJobIDs())
jobIDsSet = set(jobIDsToJobsHash.keys())
assert runningJobs.issubset(jobIDsSet)
for jobID in set(jobIDsSet.difference(runningJobs)):
jobFile = jobIDsToJobsHash[jobID]
if reissueMissingJobs_missingHash.has_key(jobID):
reissueMissingJobs_missingHash[jobID] = reissueMissingJobs_missingHash[jobID]+1
else:
reissueMissingJobs_missingHash[jobID] = 1
timesMissing = reissueMissingJobs_missingHash[jobID]
logger.critical("Job %s with id %i is missing for the %i time" % (jobFile, jobID, timesMissing))
if timesMissing == killAfterNTimesMissing:
reissueMissingJobs_missingHash.pop(jobID)
batchSystem.killJobs([ jobID ])
processFinishedJob(jobID, 1, updatedJobFiles, jobIDsToJobsHash)
if len(reissueMissingJobs_missingHash) > 0:
logger.critical("Going to sleep before trying again before trying to find missing jobs")
time.sleep(60)
reissueMissingJobs(updatedJobFiles, jobIDsToJobsHash, batchSystem, killAfterNTimesMissing)
def makeFastaSequenceNamesUnique(inputFastaFile, outputFastaFile):
"""Makes a fasta file with unique names
"""
names = set()
fileHandle = open(outputFastaFile, 'w')
for name, seq in fastaRead(open(inputFastaFile, 'r')):
while name in names:
logger.critical("Got a duplicate fasta sequence name: %s" % name)
name += "i"
names.add(name)
fastaWrite(fileHandle, name, seq)
fileHandle.close()
return outputFastaFile
def makeFastaSequenceNamesUnique(inputFastaFile, outputFastaFile):
"""Makes a fasta file with unique names
"""
names = set()
fileHandle = open(outputFastaFile, 'w')
for name, seq in fastaRead(open(inputFastaFile, 'r')):
while name in names:
logger.critical("Got a duplicate fasta sequence name: %s" % name)
name += "i"
names.add(name)
fastaWrite(fileHandle, name, seq)
fileHandle.close()
return outputFastaFile
def reissueOverLongJobs(updatedJobFiles, jobIDsToJobsHash, config, batchSystem):
"""Check each issued job - if it is running for longer than desirable.. issue a kill instruction.
Wait for the job to die then we pass the job to processFinishedJob.
"""
maxJobDuration = float(config.attrib["max_job_duration"])
if maxJobDuration < 10000000: #We won't both doing anything is the rescue time is more than 10 weeks.
runningJobs = batchSystem.getRunningJobIDs()
for jobID in runningJobs.keys():
if runningJobs[jobID] > maxJobDuration:
logger.critical("The job: %s has been running for: %s seconds, more than the max job duration: %s, we'll kill it" % \
(jobIDsToJobsHash[jobID], str(runningJobs[jobID]), str(maxJobDuration)))
batchSystem.killJobs([ jobID ])
processFinishedJob(jobID, 1, updatedJobFiles, jobIDsToJobsHash)
def killJobs(self, jobIDs):
"""Kills the given jobs, represented as Job ids, then checks they are dead by checking
they are not in the list of issued jobs.
"""
while True:
for jobID in jobIDs:
i = popenParasolCommand("parasol remove job %i" % jobID, tmpFileForStdOut=self.scratchFile, runUntilSuccessful=None)
logger.info("Tried to remove jobID: %i, with exit value: %i" % (jobID, i))
runningJobs = self.getIssuedJobIDs()
if set(jobIDs).difference(set(runningJobs)) == set(jobIDs):
return
time.sleep(5)
logger.critical("Tried to kill some jobs, but something happened and they are still going, so I'll try again")
def makeFastqSequenceNamesUnique(inputFastqFile, outputFastqFile):
"""Makes a fastq file with unique names
"""
names = set()
fileHandle = open(outputFastqFile, 'w')
for name, seq, quals in fastqRead(open(inputFastqFile, 'r')):
name = name.split()[0] #Get rid of any white space
while name in names:
logger.critical("Got a duplicate fastq sequence name: %s" % name)
name += "i"
names.add(name)
fastqWrite(fileHandle, name, seq, quals)
fileHandle.close()
return outputFastqFile
def makeFastqSequenceNamesUnique(inputFastqFile, outputFastqFile):
"""Makes a fastq file with unique names
"""
names = set()
fileHandle = open(outputFastqFile, 'w')
for name, seq, quals in fastqRead(open(inputFastqFile, 'r')):
name = name.split()[0] #Get rid of any white space
while name in names:
logger.critical("Got a duplicate fastq sequence name: %s" % name)
name += "i"
names.add(name)
fastqWrite(fileHandle, name, seq, quals)
fileHandle.close()
return outputFastqFile
def iterator(alignedRead, refSeq, readSeq):
"""Generates aligned pairs from a pysam.AlignedRead object.
"""
readOffset = getAbsoluteReadOffset(alignedRead, refSeq, readSeq)
pPair = None
assert len(alignedRead.seq) <= len(readSeq)
for readPos, refPos in alignedRead.aligned_pairs: #Iterate over the block
if readPos != None and refPos != None:
assert refPos >= alignedRead.pos and refPos < alignedRead.aend
if refPos >= len(refSeq): #This is masking an (apparently minor?) one off error in the BWA sam files?
logger.critical("Detected an aligned reference position out of bounds! Reference length: %s, reference coordinate: %s" % (len(refSeq), refPos))
continue
aP = AlignedPair(refPos, refSeq, abs(readOffset + readPos), alignedRead.is_reverse, readSeq, pPair)
if aP.getReadBase().upper() != alignedRead.query[readPos].upper():
logger.critical("Detected a discrepancy between the absolute read sequence and the aligned read sequence. Bases: %s %s, read-position: %s, is reversed: %s, absolute read offset: %s, length absolute read sequence %s, length aligned read sequence %s, length aligned read sequence plus soft clipping %s, read name: %s, cigar string %s" % (aP.getReadBase().upper(), alignedRead.query[readPos].upper(), readPos, alignedRead.is_reverse, readOffset, len(readSeq), len(alignedRead.query), len(alignedRead.seq), alignedRead.qname, alignedRead.cigarstring))
assert aP.getReadBase().upper() == alignedRead.query[readPos].upper()
pPair = aP
yield aP
def popenParasolCommand(command, tmpFileForStdOut, runUntilSuccessful=True):
"""Issues a parasol command using popen to capture the output.
If the command fails then it will try pinging parasol until it gets a response.
When it gets a response it will recursively call the issue parasol command, repeating this pattern
for a maximum of N times.
The final exit value will reflect this.
"""
while True:
fileHandle = open(tmpFileForStdOut, 'w')
process = subprocess.Popen(command, shell=True, stdout=fileHandle)
sts = os.waitpid(process.pid, 0)
fileHandle.close()
i = sts[1]
if i != 0 and runUntilSuccessful:
logger.critical("The following parasol command failed: %s" % command)
time.sleep(10)
logger.critical("Waited for a few seconds, will try again")
else:
return i
def killJobs(self, jobIDs):
"""Kills the given jobs, represented as Job ids, then checks they are dead by checking
they are not in the list of issued jobs.
"""
for jobID in jobIDs:
self.currentjobs.remove(jobID)
process = subprocess.Popen(["qdel", self.getSgeID(jobID)])
del self.jobIDs[self.sgeJobIDs[jobID]]
del self.sgeJobIDs[jobID]
toKill = set(jobIDs)
while len(toKill) > 0:
for jobID in toKill:
(job,task) = self.sgeJobIDs[jobID]
if getjobexitcode(job, task) is None:
toKill.remove(jobID)
if len(toKill) > 0:
logger.critical("Tried to kill some jobs, but something happened and they are still going, so I'll try again")
time.sleep(5)
def mainLoop(config, batchSystem):
"""This is the main loop from which jobs are issued and processed.
"""
waitDuration = float(config.attrib["wait_duration"])
assert waitDuration >= 0
rescueJobsFrequency = float(config.attrib["rescue_jobs_frequency"])
maxJobDuration = float(config.attrib["max_job_duration"])
assert maxJobDuration >= 0
logger.info("Got parameters, wait duration %s, rescue jobs frequency: %s max job duration: %s" % \
(waitDuration, rescueJobsFrequency, maxJobDuration))
#Kill any jobs on the batch system queue from the last time.
assert len(batchSystem.getIssuedJobIDs()) == 0 #Batch system must start with no active jobs!
logger.info("Checked batch system has no running jobs and no updated jobs")
jobFiles = config.attrib["job_file_dir"].listFiles()
logger.info("Got a list of job files")
#Repair the job tree using any .old files
fixJobsList(config, jobFiles)
logger.info("Fixed the job files using any .old files")
#Get jobs that were running, or that had failed reset to 'white' status
restartFailedJobs(config, jobFiles)
logger.info("Reworked failed jobs")
updatedJobFiles = set() #Jobs whose status needs updating, either because they have finished, or because they need to be started.
for jobFile in jobFiles:
job = ET.parse(jobFile).getroot()
if job.attrib["colour"] not in ("grey", "blue"):
updatedJobFiles.add(jobFile)
logger.info("Got the active (non grey/blue) job files")
totalJobFiles = len(jobFiles) #Total number of job files we have.
jobIDsToJobsHash = {} #A hash of the currently running jobs ids, made by the batch system.
idealJobTime = float(config.attrib["job_time"])
assert idealJobTime > 0.0
maxIssuedJobs = int(config.attrib["max_jobs"]) #The maximum number of jobs to issue to the batch system
assert maxIssuedJobs >= 1
stats = config.attrib.has_key("stats")
if stats:
startTime = time.time()
startClock = getTotalCpuTime()
logger.info("Starting the main loop")
timeSinceJobsLastRescued = time.time() - rescueJobsFrequency + 100 #We hack it so that we rescue jobs after the first 100 seconds to get around an apparent parasol bug
while True:
if len(updatedJobFiles) > 0:
logger.debug("Built the jobs list, currently have %i job files, %i jobs to update and %i jobs currently issued" % (totalJobFiles, len(updatedJobFiles), len(jobIDsToJobsHash)))
jobsToIssue = []
for jobFile in list(updatedJobFiles):
job = ET.parse(jobFile).getroot()
assert job.attrib["colour"] not in ("grey", "blue")
if job.attrib["colour"] == "white": #Get ready to start the job
if len(jobIDsToJobsHash) < maxIssuedJobs:
logger.debug("Job: %s is being started" % job.attrib["file"])
updatedJobFiles.remove(job.attrib["file"])
#Reset the log files for the job.
open(job.attrib["slave_log_file"], 'w').close()
open(job.attrib["log_file"], 'w').close()
job.attrib["colour"] = "grey"
#writeJobs([ job ]) #Check point, do this before issuing job, so state is not read until issued
#issueJobs([ job ], jobIDsToJobsHash, batchSystem)
jobsToIssue.append(job)
else:
logger.debug("Job: %s is not being issued yet because we have %i jobs issued" % (job.attrib["file"], len(jobIDsToJobsHash)))
elif job.attrib["colour"] == "black": #Job has finished okay
logger.debug("Job: %s has finished okay" % job.attrib["file"])
#Deal with stats
if stats:
system("cat %s >> %s" % (job.attrib["stats"], config.attrib["stats"]))
open(job.attrib["stats"], 'w').close() #Reset the stats file
if job.find("messages") != None:
for message in job.find("messages").findall("message"):
logger.info("Received the following message from job: %s" % message.attrib["message"])
job.remove(job.find("messages"))
childCount = int(job.attrib["child_count"])
blackChildCount = int(job.attrib["black_child_count"])
assert childCount == blackChildCount #Has no currently running child jobs
#Launch any unborn children
unbornChildren = job.find("children")
unbornChild = unbornChildren.find("child")
if unbornChild != None: #We must give birth to the unborn children
logger.debug("Job: %s has children to schedule" % job.attrib["file"])
newChildren = []
while unbornChild != None:
cummulativeChildTime = float(unbornChild.attrib["time"])
newJob = createJob(unbornChild.attrib.copy(), job.attrib["file"], config)
totalJobFiles += 1
updatedJobFiles.add(newJob.attrib["file"])
newChildren.append(newJob)
unbornChildren.remove(unbornChild)
unbornChild = unbornChildren.find("child")
#This was code to aggregate groups of children into one job, but we don't do this now
#while cummulativeChildTime < idealJobTime and unbornChild != None: #Cummulate a series of children into each job as a stack of jobs (to balance cost of parellelism with cost of running stuff in serially).
# cummulativeChildTime += float(unbornChild.attrib["time"])
# ET.SubElement(newJob.find("followOns"), "followOn", unbornChild.attrib.copy())
# unbornChildren.remove(unbornChild)
# unbornChild = unbornChildren.find("child")
newJob.attrib["total_time"] = str(cummulativeChildTime)
updatedJobFiles.remove(job.attrib["file"])
job.attrib["child_count"] = str(childCount + len(newChildren))
job.attrib["colour"] = "blue" #Blue - has children running.
writeJobs([ job ] + newChildren ) #Check point
elif len(job.find("followOns").findall("followOn")) != 0: #Has another job
logger.debug("Job: %s has a new command that we can now issue" % job.attrib["file"])
##Reset the job run info
job.attrib["remaining_retry_count"] = config.attrib["retry_count"]
job.attrib["colour"] = "white"
##End resetting the job
writeJobs([ job ])
else: #Job has finished, so we can defer to any parent
logger.debug("Job: %s is now dead" % job.attrib["file"])
job.attrib["colour"] = "dead"
if job.attrib.has_key("parent"):
parent = ET.parse(job.attrib["parent"]).getroot()
assert parent.attrib["colour"] == "blue"
assert int(parent.attrib["black_child_count"]) < int(parent.attrib["child_count"])
parent.attrib["black_child_count"] = str(int(parent.attrib["black_child_count"]) + 1)
if int(parent.attrib["child_count"]) == int(parent.attrib["black_child_count"]):
parent.attrib["colour"] = "black"
assert parent.attrib["file"] not in updatedJobFiles
updatedJobFiles.add(parent.attrib["file"])
writeJobs([ job, parent ]) #Check point
else:
writeJobs([ job ])
elif job.attrib["colour"] == "red": #Job failed
logger.critical("Job: %s failed" % job.attrib["file"])
logger.critical("The log file of the failed job")
logFile(job.attrib["log_file"], logger.critical)
logger.critical("The log file of the slave for the failed job")
logFile(job.attrib["slave_log_file"], logger.critical) #We log the job log file in the main loop
#Checks
assert len(job.find("children").findall("child")) == 0
assert int(job.attrib["child_count"]) == int(job.attrib["black_child_count"])
remainingRetyCount = int(job.attrib["remaining_retry_count"])
if remainingRetyCount > 0: #Give it another try, maybe there is a bad node somewhere
job.attrib["remaining_retry_count"] = str(remainingRetyCount-1)
job.attrib["colour"] = "white"
logger.critical("Job: %s will be restarted, it has %s goes left" % (job.attrib["file"], job.attrib["remaining_retry_count"]))
writeJobs([ job ]) #Check point
else:
assert remainingRetyCount == 0
updatedJobFiles.remove(job.attrib["file"])
logger.critical("Job: %s is completely failed" % job.attrib["file"])
else:
logger.debug("Job: %s is already dead, we'll get rid of it" % job.attrib["file"])
assert job.attrib["colour"] == "dead"
updatedJobFiles.remove(job.attrib["file"])
totalJobFiles -= 1
deleteJob(job, config) #This could be done earlier, but I like it this way.
###End of for loop
writeJobs(jobsToIssue) #Check point, do this before issuing job, so state is not read until issued
issueJobs(jobsToIssue, jobIDsToJobsHash, batchSystem)
if len(jobIDsToJobsHash) == 0 and len(updatedJobFiles) == 0:
logger.info("Only failed jobs and their dependents (%i total) are remaining, so exiting." % totalJobFiles)
break
if len(updatedJobFiles) > 0:
updatedJobs = batchSystem.getUpdatedJobs() #Asks the batch system what jobs have been completed.
else:
updatedJobs = pauseForUpdatedJobs(batchSystem.getUpdatedJobs) #Asks the batch system what jobs have been completed.
for jobID in updatedJobs.keys(): #Runs through a map of updated jobs and there status,
result = updatedJobs[jobID]
if jobIDsToJobsHash.has_key(jobID):
if result == 0:
logger.debug("Batch system is reporting that the job %s ended sucessfully" % jobIDsToJobsHash[jobID])
else:
logger.critical("Batch system is reporting that the job %s failed with exit value %i" % (jobIDsToJobsHash[jobID], result))
processFinishedJob(jobID, result, updatedJobFiles, jobIDsToJobsHash)
else:
logger.info("A result seems to already have been processed: %i" % jobID) #T
if time.time() - timeSinceJobsLastRescued >= rescueJobsFrequency: #We only rescue jobs every N seconds
reissueOverLongJobs(updatedJobFiles, jobIDsToJobsHash, config, batchSystem)
logger.info("Reissued any over long jobs")
reissueMissingJobs(updatedJobFiles, jobIDsToJobsHash, batchSystem)
logger.info("Rescued any (long) missing jobs")
timeSinceJobsLastRescued = time.time()
#Going to sleep to let the job system catch up.
time.sleep(waitDuration)
if stats:
fileHandle = open(config.attrib["stats"], 'a')
fileHandle.write("<total_time time='%s' clock='%s'/></stats>" % (str(time.time() - startTime), str(getTotalCpuTime() - startClock)))
fileHandle.close()
logger.info("Finished the main loop")
return totalJobFiles #Returns number of failed jobs
def processFinishedJob(jobID, resultStatus, updatedJobFiles, jobIDsToJobsHash):
"""Function reads a processed job file and updates it state.
"""
assert jobID in jobIDsToJobsHash
jobFile = jobIDsToJobsHash.pop(jobID)
updatingFileIsPresent = os.path.isfile(jobFile + ".updating")
newFileIsPresent = os.path.isfile(jobFile + ".new")
if resultStatus == 0 and updatingFileIsPresent:
logger.critical("Despite the batch system claiming success there is a .updating file present: %s", jobFile + ".updating")
if resultStatus == 0 and newFileIsPresent:
logger.critical("Despite the batch system claiming success there is a .new file present: %s", jobFile + ".new")
if resultStatus != 0 or newFileIsPresent or updatingFileIsPresent: #Job not successful according to batchsystem, or according to the existance of a .new or .updating file
if updatingFileIsPresent: #The job failed while attempting to write the job file.
logger.critical("There was an .updating file for the crashed job: %s" % jobFile)
if os.path.isfile(jobFile + ".new"): #The job failed while writing the updated job file.
logger.critical("There was an .new file for the crashed job: %s" % jobFile)
os.remove(jobFile + ".new") #The existance of the .updating file means it wasn't complete
os.remove(jobFile + ".updating") #Delete second the updating file second to preserve a correct state
assert os.path.isfile(jobFile)
job = ET.parse(jobFile).getroot() #The original must still be there.
assert job.find("children").find("child") == None #The original can not reflect the end state of the job.
assert int(job.attrib["black_child_count"]) == int(job.attrib["child_count"])
job.attrib["colour"] = "red" #It failed, so we mark it so and continue.
writeJobs([ job ])
logger.critical("We've reverted to the original job file and marked it as failed: %s" % jobFile)
else:
if newFileIsPresent: #The job was not properly updated before crashing
logger.critical("There is a valid .new file %s" % jobFile)
if os.path.isfile(jobFile):
os.remove(jobFile)
os.rename(jobFile + ".new", jobFile)
job = ET.parse(jobFile).getroot()
if job.attrib["colour"] == "grey": #The job failed while preparing to run another job on the slave
assert job.find("children").find("child") == None #File
job.attrib["colour"] = "red"
writeJobs([ job ])
assert job.attrib["colour"] in ("black", "red")
else:
logger.critical("There was no valid .new file %s" % jobFile)
assert os.path.isfile(jobFile)
job = ET.parse(jobFile).getroot() #The job may have failed before or after creating this file, we check the state.
if job.attrib["colour"] == "black": #The job completed okay, so we'll keep it
logger.critical("Despite the batch system job failing, the job appears to have completed okay")
else:
assert job.attrib["colour"] in ("grey", "red")
assert job.find("children").find("child") == None #File
assert int(job.attrib["black_child_count"]) == int(job.attrib["child_count"])
if job.attrib["colour"] == "grey":
job.attrib["colour"] = "red"
writeJobs([ job ])
logger.critical("We've reverted to the original job file and marked it as failed: %s" % jobFile)
else:
job = ET.parse(jobFile).getroot()
##Now check the log files exist, because they must ultimately be cleaned up by their respective file trees.
if not os.path.isfile(job.attrib["log_file"]): #We need to keep these files in existence.
open(job.attrib["log_file"], 'w').close()
logger.critical("The log file %s for job %s had disappeared" % (job.attrib["log_file"], jobFile))
if not os.path.isfile(job.attrib["slave_log_file"]):
open(job.attrib["slave_log_file"], 'w').close()
logger.critical("The slave log file %s for job %s had disappeared" % (job.attrib["slave_log_file"], jobFile))
assert jobFile not in updatedJobFiles
updatedJobFiles.add(jobFile) #Now we know the job is done we can add it to the list of updated job files
logger.debug("Added job: %s to active jobs" % jobFile)
def processJob(job, jobToRun, memoryAvailable, cpuAvailable, stats):
"""Runs a job.
"""
from jobTree.src.bioio import getTempFile
from jobTree.src.bioio import getTempDirectory
from jobTree.src.bioio import logger
from jobTree.src.bioio import system
from jobTree.src.bioio import getTotalCpuTime
assert len(job.find("children").findall("child")) == 0
assert int(job.attrib["child_count"]) == int(job.attrib["black_child_count"])
command = jobToRun.attrib["command"]
#Copy the job file to be edited
tempJob = ET.Element("job")
ET.SubElement(tempJob, "children")
#Log for job
tempJob.attrib["log_level"] = job.attrib["log_level"]
#Time length of 'ideal' job before further parallelism is required
tempJob.attrib["job_time"] = job.attrib["job_time"]
#Dir to put all the temp files in.
localSlaveTempDir = getTempDirectory()
#Temp file dirs for job.
localTempDir = getTempDirectory(rootDir=localSlaveTempDir)
tempJob.attrib["local_temp_dir"] = localTempDir
depth = len(job.find("followOns").findall("followOn"))
tempJob.attrib["global_temp_dir"] = os.path.join(job.attrib["global_temp_dir"], str(depth))
if not os.path.isdir(tempJob.attrib["global_temp_dir"]): #Ensures that the global temp dirs of each level are kept separate.
os.mkdir(tempJob.attrib["global_temp_dir"])
os.chmod(tempJob.attrib["global_temp_dir"], 0777)
if os.path.isdir(os.path.join(job.attrib["global_temp_dir"], str(depth+1))):
system("rm -rf %s" % os.path.join(job.attrib["global_temp_dir"], str(depth+1)))
assert not os.path.isdir(os.path.join(job.attrib["global_temp_dir"], str(depth+2)))
#Deal with memory and cpu requirements (this pass tells the running job how much cpu and memory they have,
#according to the batch system
tempJob.attrib["available_memory"] = str(memoryAvailable)
tempJob.attrib["available_cpu"] = str(cpuAvailable)
if stats != None:
tempJob.attrib["stats"] = getTempFile(rootDir=localSlaveTempDir)
os.remove(tempJob.attrib["stats"])
#Now write the temp job file
tempFile = getTempFile(rootDir=localSlaveTempDir)
fileHandle = open(tempFile, 'w')
tree = ET.ElementTree(tempJob)
tree.write(fileHandle)
fileHandle.close()
logger.info("Copied the jobs files ready for the job")
if "JOB_FILE" not in command:
logger.critical("There is no 'JOB_FILE' string in the command to be run to take the job-file argument: %s" % command)
job.attrib["colour"] = "red" #Update the colour
else:
#First load the environment for the job.
fileHandle = open(job.attrib["environment_file"], 'r')
environment = cPickle.load(fileHandle)
fileHandle.close()
logger.info("Loaded the environment for the process")
#Run the actual command
tempLogFile = getTempFile(suffix=".log", rootDir=localSlaveTempDir)
fileHandle = open(tempLogFile, 'w')
finalCommand = command.replace("JOB_FILE", tempFile)
if stats != None:
startTime = time.time()
startClock = getTotalCpuTime()
process = subprocess.Popen(finalCommand, shell=True, stdout=fileHandle, stderr=subprocess.STDOUT, env=environment)
sts = os.waitpid(process.pid, 0)
fileHandle.close()
truncateFile(tempLogFile, int(job.attrib["max_log_file_size"]))
#Copy across the log file
system("mv %s %s" % (tempLogFile, job.attrib["log_file"]))
i = sts[1]
logger.info("Ran the job command=%s with exit status %i" % (finalCommand, i))
if i == 0:
logger.info("Passed the job, okay")
if stats != None:
jobTag = ET.SubElement(stats, "job", { "time":str(time.time() - startTime), "clock":str(getTotalCpuTime() - startClock) })
if os.path.exists(tempJob.attrib["stats"]):
jobTag.append(ET.parse(tempJob.attrib["stats"]).getroot())
tempJob = ET.parse(tempFile).getroot()
job.attrib["colour"] = "black" #Update the colour
#Deal with any logging messages directed at the master
if tempJob.find("messages") != None:
messages = job.find("messages")
if messages == None:
messages = ET.SubElement(job, "messages")
for messageTag in tempJob.find("messages").findall("message"):
messages.append(messageTag)
#Update the runtime of the stack..
totalRuntime = float(job.attrib["total_time"]) #This is the estimate runtime of the jobs on the followon stack
runtime = float(jobToRun.attrib["time"])
totalRuntime -= runtime
if totalRuntime < 0.0:
totalRuntime = 0.0
#The children
children = job.find("children")
assert len(children.findall("child")) == 0 #The children
assert tempJob.find("children") != None
for child in tempJob.find("children").findall("child"):
memory, cpu, compTime = getMemoryCpuAndTimeRequirements(job, child)
ET.SubElement(children, "child", { "command":child.attrib["command"],
"time":str(compTime), "memory":str(memory), "cpu":str(cpu) })
logger.info("Making a child with command: %s" % (child.attrib["command"]))
#The follow on command
followOns = job.find("followOns")
followOns.remove(followOns.findall("followOn")[-1]) #Remove the old job
if tempJob.attrib.has_key("command"):
memory, cpu, compTime = getMemoryCpuAndTimeRequirements(job, tempJob)
ET.SubElement(followOns, "followOn", { "command":tempJob.attrib["command"],
"time":str(compTime), "memory":str(memory), "cpu":str(cpu) })
##Add the runtime to the total runtime..
totalRuntime += compTime
logger.info("Making a follow on job with command: %s" % tempJob.attrib["command"])
elif len(tempJob.find("children").findall("child")) != 0: #This is to keep the stack of follow on jobs consistent.
ET.SubElement(followOns, "followOn", { "command":"echo JOB_FILE", "time":"0", "memory":"1000000", "cpu":"1" })
logger.info("Making a stub follow on job")
#Write back the runtime, after addin the follow on time and subtracting the time of the run job.
job.attrib["total_time"] = str(totalRuntime)
else:
logger.info("Failed the job")
job.attrib["colour"] = "red" #Update the colour
#Clean up
system("rm -rf %s" % (localSlaveTempDir))
logger.info("Cleaned up by removing temp jobfile (the copy), and the temporary file directory for the job")