def main():
parser = getBasicOptionParser("usage: %prog [options]", "%prog 0.1")
parser.add_option("--job", dest="jobFile", help="Job file containing command to run", default="None")
parser.add_option(
"--treePointer", dest="treePointerFile", help="File containing pointer to the tree data", default="None"
)
options, args = parseBasicOptions(parser)
logger.info("Parsed the input arguments")
job = ET.parse(options.jobFile).getroot()
setLogLevel(job.attrib["log_level"])
logger.info("Parsed the job XML")
treePointer = ET.parse(options.treePointerFile).getroot()
logger.info("Parsed the tree pointer XML")
tree = ET.parse(treePointer.attrib["file"]).getroot()
logger.info("Parsed the tree XML")
for child in tree.find("children").findall("child"):
# Make the chuld tree pointer
childTreePointerFile = makeTreePointer(child.attrib["file"], getTempFile(rootDir=job.attrib["global_temp_dir"]))
# Make the child command
unbornChild = ET.SubElement(job.find("children"), "child")
command = "jobTreeTest_CommandFirst.py --treePointer %s --job JOB_FILE" % (childTreePointerFile,)
unbornChild.attrib["command"] = command
if random.random() > 0.2:
unbornChild.attrib["time"] = str(random.random() * 10)
# Make the child tree pointer
ET.SubElement(treePointer.find("children"), "child", {"file": childTreePointerFile})
job.attrib["command"] = "jobTreeTest_CommandSecond.py --treePointer %s --job JOB_FILE" % (options.treePointerFile,)
logger.info("Made new command")
fileHandle = open(options.jobFile, "w")
ET.ElementTree(job).write(fileHandle)
fileHandle.close()
logger.info("Updated the job file")
print >> sys.stderr, "Checking that we can report to std err" # These lines should end up in the logs
print "Checking that we can report to std out"
if random.random() > 0.9:
logger.info("Going to fail the job")
sys.exit(1)
logger.info("Going to pass the job done okay")
sys.exit(0)
def main():
sys.path += [ sys.argv[1] ]
sys.argv.remove(sys.argv[1])
#Now we can import all the stuff..
from workflow.jobTree.lib.bioio import getBasicOptionParser
from workflow.jobTree.lib.bioio import parseBasicOptions
from workflow.jobTree.lib.bioio import logger
from workflow.jobTree.lib.bioio import addLoggingFileHandler
from workflow.jobTree.lib.bioio import setLogLevel
from workflow.jobTree.lib.bioio import getTotalCpuTime
from workflow.jobTree.lib.master import writeJobs
##########################################
#Construct the arguments.
##########################################
parser = getBasicOptionParser("usage: %prog [options]", "%prog 0.1")
parser.add_option("--job", dest="jobFile",
help="Job file containing command to run",
default="None")
options, args = parseBasicOptions(parser)
assert len(args) == 0
##########################################
#Parse the job.
##########################################
job = ET.parse(options.jobFile).getroot()
##########################################
#Setup the logging
##########################################
#Setup the logging
setLogLevel(job.attrib["log_level"])
addLoggingFileHandler(job.attrib["slave_log_file"], rotatingLogging=False)
logger.info("Parsed arguments and set up logging")
##########################################
#Setup the stats, if requested
##########################################
if job.attrib.has_key("stats"):
startTime = time.time()
startClock = time.clock()
stats = ET.Element("slave")
else:
stats = None
##########################################
#Run the script.
##########################################
maxTime = float(job.attrib["job_time"])
assert maxTime > 0.0
assert maxTime < sys.maxint
jobToRun = job.find("followOns").findall("followOn")[-1]
memoryAvailable = int(jobToRun.attrib["memory"])
cpuAvailable = int(jobToRun.attrib["cpu"])
while True:
processJob(job, jobToRun, memoryAvailable, cpuAvailable, stats)
if job.attrib["colour"] != "black":
logger.info("Exiting the slave because of a failed job")
break
totalRuntime = float(job.attrib["total_time"]) #This is the estimate runtime of the jobs on the followon stack
childrenNode = job.find("children")
childrenList = childrenNode.findall("child")
#childRuntime = sum([ float(child.attrib["time"]) for child in childrenList ])
if len(childrenList) >= 2: # or totalRuntime + childRuntime > maxTime: #We are going to have to return to the parent
logger.info("No more jobs can run in series by this slave, its got %i children" % len(childrenList))
break
followOns = job.find("followOns")
while len(childrenList) > 0:
child = childrenList.pop()
childrenNode.remove(child)
totalRuntime += float(child.attrib["time"])
ET.SubElement(followOns, "followOn", child.attrib.copy())
#assert totalRuntime <= maxTime + 1 #The plus one second to avoid unimportant rounding errors
job.attrib["total_time"] = str(totalRuntime)
assert len(childrenNode.findall("child")) == 0
if len(followOns.findall("followOn")) == 0:
logger.info("No more jobs can run by this slave as we have exhausted the follow ons")
break
#Get the next job and see if we have enough cpu and memory to run it..
jobToRun = job.find("followOns").findall("followOn")[-1]
if int(jobToRun.attrib["memory"]) > memoryAvailable:
logger.info("We need more memory for the next job, so finishing")
break
if int(jobToRun.attrib["cpu"]) > cpuAvailable:
logger.info("We need more cpus for the next job, so finishing")
break
##Updated the job so we can start the next loop cycle
job.attrib["colour"] = "grey"
writeJobs([ job ])
logger.info("Updated the status of the job to grey and starting the next job")
#Write back the job file with the updated jobs, using the checkpoint method.
writeJobs([ job ])
logger.info("Written out an updated job file")
logger.info("Finished running the chain of jobs on this node")
##########################################
#Finish up the stats
##########################################
if stats != None:
stats.attrib["time"] = str(time.time() - startTime)
stats.attrib["clock"] = str(getTotalCpuTime() - startClock)
fileHandle = open(job.attrib["stats"], 'w')
ET.ElementTree(stats).write(fileHandle)
fileHandle.close()
def main():
parser = getBasicOptionParser("usage: %prog [options]", "%prog 0.1")
parser.add_option("--job", dest="jobFile",
help="Job file containing command to run",
default="None")
parser.add_option("--treePointer", dest="treePointer",
help="File containing pointer to the tree data",
default="None")
options, args = parseBasicOptions(parser)
logger.info("Parsed the input arguments")
print >>sys.stderr, "Checking that we can report to std err" #These lines should end up in the logs
print "Checking that we can report to std out"
job = ET.parse(options.jobFile).getroot()
setLogLevel(job.attrib["log_level"])
logger.info("Parsed the job XML")
treePointer = ET.parse(options.treePointer).getroot()
logger.info("Parsed the tree pointer XML")
tree = ET.parse(treePointer.attrib["file"]).getroot()
logger.info("Parsed the tree XML")
i = 0
children = tree.find("children").findall("child")
if len(children) > 0:
for child in children:
#Parse the child XML tree
childTree = ET.parse(child.attrib["file"]).getroot()
i += int(childTree.attrib["count"])
else:
i = 1
tree.attrib["count"] = str(i)
logger.info("Calculated the leaf count: %i" % i)
fileHandle = open(treePointer.attrib["file"], 'w')
ET.ElementTree(tree).write(fileHandle)
fileHandle.close()
logger.info("Updated the tree file: %s" % treePointer.attrib["file"])
for childPointer in treePointer.find("children").findall("child"):
if os.path.isfile(childPointer.attrib["file"]):
os.remove(childPointer.attrib["file"])
logger.info("Removed the child pointer files")
logger.info("No need to update the job file, as we didn't make anything new!")
if random.random() > 0.9:
logger.info("Going to fail the job")
sys.exit(1)
logger.info("Going to pass the job done okay")
sys.exit(0)
def execute(self, jobFile):
job = ET.parse(jobFile).getroot()
setLogLevel(job.attrib["log_level"])
logger.info("Setup logging with level: %s" % job.attrib["log_level"])
self.tempDirAccessed = False
self.localTempDir = job.attrib["local_temp_dir"]
self.globalTempDir = job.attrib["global_temp_dir"]
maxTime = float(job.attrib["job_time"])
memory = int(job.attrib["available_memory"])
cpu = int(job.attrib["available_cpu"])
if job.attrib.has_key("stats"):
stats = ET.Element("stack")
startTime = time.time()
startClock = time.clock()
else:
stats = None
newChildren = [] #List to add all the children to before we package them
#off into stacks
newChildCommands = [] #Ditto for the child commands
newFollowOns = [] #Ditto for the follow-ons
while self.hasRemaining():
if stats != None: #Getting the runtime of the stats module
targetStartTime = time.time()
targetStartClock = getTotalCpuTime()
target = self.popTarget()
target.setStack(self)
#Debug check that we have the right amount of CPU and memory for the job in hand
targetMemory = target.getMemory()
if targetMemory != sys.maxint:
assert targetMemory <= memory
targetCpu = target.getCpu()
if targetCpu != sys.maxint:
assert targetCpu <= cpu
#Run the target, first cleanup then run.
target.run()
#Cleanup after the target
if self.tempDirAccessed:
system("rm -rf %s/*" % self.localTempDir)
self.tempDirAccessed = False
#Handle the follow on
followOn = target.getFollowOn()
#if target.__class__ != CleanupGlobalTempDirTarget and followOn == None:
# followOn = CleanupGlobalTempDirTarget()
if followOn != None: #Target to get rid of follow on when done.
if target.isGlobalTempDirSet():
followOn.setGlobalTempDir(target.getGlobalTempDir())
newFollowOns.append(followOn)
#Now add the children to the newChildren stack
newChildren += target.getChildren()
#Now add the child commands to the newChildCommands stack
newChildCommands += target.getChildCommands()
if stats != None:
ET.SubElement(stats, "target", { "time":str(time.time() - targetStartTime),
"clock":str(getTotalCpuTime() - targetStartClock),
"class":".".join((target.__class__.__name__,)),
"e_time":str(target.getRunTime())})
#######
#Now build the new stacks and corresponding jobs
#######
#First add all the follow ons to the existing stack and make it a follow on job for job-tree
assert not self.hasRemaining()
#First sort out the follow on job
if len(newFollowOns) > 0: #If we have follow ons
followOnRuntime = sum([ followOn.getRunTime() for followOn in newFollowOns ])
if followOnRuntime > maxTime: #We create a parallel list of follow ons
followOnStack = Stack(ParallelFollowOnTarget(newFollowOns))
else:
followOnStack = Stack(newFollowOns.pop())
while len(newFollowOns) > 0:
followOnStack.addTarget(newFollowOns.pop())
job.attrib["command"] = followOnStack.makeRunnable(self.globalTempDir)
job.attrib["time"] = str(followOnStack.getRunTime())
followOnMemory = followOnStack.getMemory()
assert not job.attrib.has_key("memory")
if followOnMemory != sys.maxint:
job.attrib["memory"] = str(followOnMemory)
assert not job.attrib.has_key("cpu")
followOnCpu = followOnStack.getCpu()
if followOnCpu != sys.maxint:
job.attrib["cpu"] = str(followOnCpu)
#Now build stacks of children..
childrenTag = job.find("children")
while len(newChildren) > 0:
childStack = Stack(newChildren.pop())
while len(newChildren) > 0 and childStack.getRunTime() <= maxTime:
childStack.addTarget(newChildren.pop())
childJob = ET.SubElement(childrenTag, "child", { "command":childStack.makeRunnable(self.globalTempDir),
"time":str(childStack.getRunTime()) })
childMemory = childStack.getMemory()
assert not childJob.attrib.has_key("memory")
if childMemory != sys.maxint:
childJob.attrib["memory"] = str(childMemory)
assert not childJob.attrib.has_key("cpu")
childCpu = childStack.getCpu()
if childCpu != sys.maxint:
childJob.attrib["cpu"] = str(childCpu)
#Now build jobs for each child command
for childCommand, runTime in newChildCommands:
ET.SubElement(childrenTag, "child", { "command":str(childCommand),
"time":str(runTime) })
#Now write the updated job file
fileHandle = open(jobFile, 'w')
ET.ElementTree(job).write(fileHandle)
fileHandle.close()
#Finish up the stats
if stats != None:
stats.attrib["time"] = str(time.time() - startTime)
stats.attrib["clock"] = str(getTotalCpuTime() - startClock)
fileHandle = open(job.attrib["stats"], 'w')
ET.ElementTree(stats).write(fileHandle)
fileHandle.close()