def issueJobs(self, jobCommands):
"""Issues parasol with job commands.
"""
issuedJobs = {}
for jobCommand, memory, cpu, logFile in jobCommands:
assert memory != None
assert cpu != None
assert logFile != None
pattern = re.compile("your job ([0-9]+).*")
command = "parasol -verbose -ram=%i -cpu=%i -results=%s add job '%s'" % (memory, cpu, self.parasolResultsFile, jobCommand)
while True:
#time.sleep(0.1) #Sleep to let parasol catch up #Apparently unnecessary
popenParasolCommand(command, self.scratchFile)
fileHandle = open(self.scratchFile, 'r')
line = fileHandle.readline()
fileHandle.close()
match = pattern.match(line)
if match != None: #This is because parasol add job will return success, even if the job was not properly issued!
break
else:
logger.info("We failed to properly add the job, we will try again after a sleep")
time.sleep(5)
jobID = int(match.group(1))
logger.debug("Got the job id: %s from line: %s" % (jobID, line))
assert jobID not in issuedJobs.keys()
issuedJobs[jobID] = jobCommand
logger.debug("Issued the job command: %s with job id: %i " % (command, jobID))
return issuedJobs
def getUpdatedJobs(self):
"""We use the parasol results to update the status of jobs, adding them
to the list of updated jobs.
Results have the following structure.. (thanks Mark D!)
int status; /* Job status - wait() return format. 0 is good. */
char *host; /* Machine job ran on. */
char *jobId; /* Job queuing system job ID */
char *exe; /* Job executable file (no path) */
int usrTicks; /* 'User' CPU time in ticks. */
int sysTicks; /* 'System' CPU time in ticks. */
unsigned submitTime; /* Job submission time in seconds since 1/1/1970 */
unsigned startTime; /* Job start time in seconds since 1/1/1970 */
unsigned endTime; /* Job end time in seconds since 1/1/1970 */
char *user; /* User who ran job */
char *errFile; /* Location of stderr file on host */
plus you finally have the command name..
"""
line = self.parasolResultsFileHandle.readline()
updatedJobs = {}
while line != '':
results = line.split()
if line[-1] == '\n':
line = line[:-1]
logger.debug("Parasol completed a job, this is what we got: %s" % line)
result = int(results[0])
jobID = int(results[2])
updatedJobs[jobID] = result
line = self.parasolResultsFileHandle.readline()
return updatedJobs
def addJob(self, command, sgeJobID, issuedJobs, index=None):
jobID = self.nextJobID
self.nextJobID += 1
self.jobIDs[(sgeJobID, index)] = jobID
self.sgeJobIDs[jobID] = (sgeJobID, index)
assert jobID not in issuedJobs.keys()
issuedJobs[jobID] = command
logger.debug("Issued the job command: %s with job id: %s " % (command, str(jobID)))
self.currentjobs.add(jobID)
self.newJobsQueue.put((sgeJobID, index))
def prepareQsub(cpu, mem):
qsubline = list(["qsub","-b","y","-terse","-j" ,"y", "-cwd","-v",
"LD_LIBRARY_PATH=%s" % os.environ["LD_LIBRARY_PATH"]])
reqline = list()
if cpu is not None:
reqline.append("p="+str(cpu))
if mem is not None:
reqline.append("vf="+str(mem/ 1024)+"K")
if len(reqline) > 0:
qsubline.extend(["-hard","-l", ",".join(reqline)])
logger.debug("**"+" ".join(qsubline))
return qsubline
def issueJobs(self, commands):
"""Runs the jobs right away.
"""
issuedJobs = {}
for command, memory, cpu, logFile in commands: #Add the commands to the queue
assert memory != None
assert cpu != None
assert logFile != None
logger.debug("Issuing the command: %s with memory: %i, cpu: %i" % (command, memory, cpu))
self.jobs[self.jobIndex] = command
issuedJobs[self.jobIndex] = command
self.inputQueue.put((command, logFile, self.jobIndex))
self.jobIndex += 1
return issuedJobs
def getUpdatedJobs(self):
"""Returns a map of the run jobs and the return value of their processes.
"""
runJobs = {}
try:
while True:
command, exitValue, jobID = self.outputQueue.get_nowait()
runJobs[jobID] = exitValue
self.jobs.pop(jobID)
logger.debug("Ran the command: %s with exit value: %i" % (command, exitValue))
self.outputQueue.task_done()
except Empty:
pass
return runJobs
def issueJobs(jobs, jobIDsToJobsHash, batchSystem):
"""Issues jobs to the batch system.
"""
jobCommands = {}
for job in jobs:
jobCommand = os.path.join(workflowRootPath(), "bin", "jobTreeSlave")
followOnJob = job.find("followOns").findall("followOn")[-1]
jobCommands["%s -E %s %s --job %s" % (sys.executable, jobCommand, os.path.split(workflowRootPath())[0], job.attrib["file"])] = (job.attrib["file"], int(followOnJob.attrib["memory"]), int(followOnJob.attrib["cpu"]), job.attrib["slave_log_file"])
issuedJobs = batchSystem.issueJobs([ (key, jobCommands[key][1], jobCommands[key][2], jobCommands[key][3]) for key in jobCommands.keys() ])
assert len(issuedJobs.keys()) == len(jobCommands.keys())
for jobID in issuedJobs.keys():
command = issuedJobs[jobID]
jobFile = jobCommands[command][0]
assert jobID not in jobIDsToJobsHash
jobIDsToJobsHash[jobID] = jobFile
logger.debug("Issued the job: %s with job id: %i " % (jobFile, jobID))
def extract_fastq(target, genome, institute, tissue, bam, reference, out_dir):
out_path = build_out_dirs(out_dir, genome, institute, tissue, bam)
if is_paired_sequencing(bam) is True:
logger.debug("Extracting paired sequencing for bam {} with out_path {}".format(bam, out_path))
name_sorted_sam_path = os.path.join(out_path, "name_sorted.sam")
system("samtools sort -n -O sam -T {} {} > {}".format(target.getLocalTempDir(), bam, name_sorted_sam_path))
fwd_fastq_path = os.path.join(out_path, os.path.basename(bam).split(".")[0] + ".fwd.fastq")
rev_fastq_path = os.path.join(out_path, os.path.basename(bam).split(".")[0] + ".rev.fastq")
target.setFollowOnTargetFn(get_paired_fastqs, args=(genome, institute, tissue, bam, reference, out_dir,
name_sorted_sam_path, fwd_fastq_path, rev_fastq_path))
else:
logger.debug("Extracting UNPAIRED sequencing for bam {} with out_path {}".format(bam, out_path))
fastq_path = os.path.join(out_path, os.path.basename(bam).split(".")[0] + ".fastq")
system(r"""samtools view {} | grep -v ^@ | awk '{{print "@"$1"\n"$10"\n+\n"$11}}' > {}""".format(bam,
fastq_path))
read_size = fastq_read_size(fastq_path)
target.setFollowOnTargetFn(kallisto_single, args=(genome, institute, tissue, bam, reference, out_dir,
fastq_path, read_size))
def run(self):
self.options.tracks = os.path.join(self.options.dir, "tracks")
if not os.path.exists(self.options.tracks):
os.mkdir(self.options.tracks)
self.addChildTarget(PrepareBAMBAMGraph(self.options))
self.addChildTarget(PrepareCBSGraph(self.options))
self.addChildTarget(PrepareBreakendGraph(self.options))
self.addChildTarget(PrepareCycleGraph(self.options))
self.addChildTarget(PrepareCactusCoverageGraphs(self.options))
if self.options.bam is not None:
os.chdir(self.options.tracks)
logger.debug(os.path.basename(self.options.bam))
if os.path.lexists(os.path.basename(self.options.bam) + ".bai"):
os.remove(os.path.basename(self.options.bam) + ".bai")
if os.path.lexists(os.path.basename(self.options.bam)):
os.remove(os.path.basename(self.options.bam))
do("ln -s %s" % self.options.bam)
do("ln -s %s.bai" % self.options.bam)
self.setFollowOnTarget(PrepareIndex(self.options))
def run(self):
self.options.tracks = os.path.join(self.options.dir, "tracks")
if not os.path.exists(self.options.tracks):
os.mkdir(self.options.tracks)
self.addChildTarget(PrepareBAMBAMGraph(self.options))
self.addChildTarget(PrepareCBSGraph(self.options))
self.addChildTarget(PrepareBreakendGraph(self.options))
self.addChildTarget(PrepareCycleGraph(self.options))
self.addChildTarget(PrepareCactusCoverageGraphs(self.options))
if self.options.bam is not None:
os.chdir(self.options.tracks)
logger.debug(os.path.basename(self.options.bam))
if os.path.lexists(os.path.basename(self.options.bam) + ".bai"):
os.remove(os.path.basename(self.options.bam) + ".bai")
if os.path.lexists(os.path.basename(self.options.bam)):
os.remove(os.path.basename(self.options.bam))
do("ln -s %s" % self.options.bam)
do("ln -s %s.bai" % self.options.bam)
self.setFollowOnTarget(PrepareIndex(self.options))
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 qsub(qsubline):
logger.debug("**"+" ".join(qsubline))
process = subprocess.Popen(qsubline, stdout=subprocess.PIPE)
result = int(process.stdout.readline().strip().split('.')[0])
logger.debug("Got the job id: %s" % (str(result)))
return result