def statsAggregatorProcess(jobTreePath, tempDirs, stop):
#Overall timing
startTime = time.time()
startClock = getTotalCpuTime()
#Start off the stats file
fileHandle = open(getStatsFileName(jobTreePath), 'w')
fileHandle.write('<?xml version="1.0" ?><stats>')
statsFile = getStatsFileName(jobTreePath)
#The main loop
while True:
def fn():
i = 0
for dir in tempDirs:
for tempFile in os.listdir(dir):
if tempFile[-3:] != "new":
absTempFile = os.path.join(dir, tempFile)
fH = open(absTempFile, 'r')
for line in fH.readlines():
fileHandle.write(line)
fH.close()
os.remove(absTempFile)
i += 1
return i
if not stop.empty():
fn()
break
if not fn():
time.sleep(0.5) #Avoid cycling too fast
#Finish the stats file
fileHandle.write("<total_time time='%s' clock='%s'/></stats>" % (str(time.time() - startTime), str(getTotalCpuTime() - startClock)))
fileHandle.close()
def statsAggregatorProcess(jobTreePath, tempDirs, stop):
#Overall timing
startTime = time.time()
startClock = getTotalCpuTime()
#Start off the stats file
fileHandle = open(getStatsFileName(jobTreePath), 'w')
fileHandle.write('<?xml version="1.0" ?><stats>')
statsFile = getStatsFileName(jobTreePath)
#The main loop
timeSinceOutFileLastFlushed = time.time()
while True:
def scanDirectoriesAndScrapeStats():
numberOfFilesProcessed = 0
for dir in tempDirs:
for tempFile in os.listdir(dir):
if tempFile[-3:] != "new":
absTempFile = os.path.join(dir, tempFile)
fH = open(absTempFile, 'r')
for line in fH.readlines():
fileHandle.write(line)
fH.close()
os.remove(absTempFile)
numberOfFilesProcessed += 1
return numberOfFilesProcessed
if not stop.empty(
): #This is a indirect way of getting a message to the process to exit
scanDirectoriesAndScrapeStats()
break
if scanDirectoriesAndScrapeStats() == 0:
time.sleep(0.5) #Avoid cycling too fast
if time.time(
) - timeSinceOutFileLastFlushed > 60: #Flush the results file every minute
fileHandle.flush()
timeSinceOutFileLastFlushed = time.time()
#Finish the stats file
fileHandle.write(
"<total_time time='%s' clock='%s'/></stats>" %
(str(time.time() - startTime), str(getTotalCpuTime() - startClock)))
fileHandle.close()
def statsAggregatorProcess(jobTreePath, tempDirs, stop):
#Overall timing
startTime = time.time()
startClock = getTotalCpuTime()
#Start off the stats file
fileHandle = open(getStatsFileName(jobTreePath), 'w')
fileHandle.write('<?xml version="1.0" ?><stats>')
statsFile = getStatsFileName(jobTreePath)
#The main loop
timeSinceOutFileLastFlushed = time.time()
while True:
def scanDirectoriesAndScrapeStats():
numberOfFilesProcessed = 0
for dir in tempDirs:
for tempFile in os.listdir(dir):
if tempFile[-3:] != "new":
absTempFile = os.path.join(dir, tempFile)
fH = open(absTempFile, 'r')
for line in fH.readlines():
fileHandle.write(line)
fH.close()
os.remove(absTempFile)
numberOfFilesProcessed += 1
return numberOfFilesProcessed
if not stop.empty(): #This is a indirect way of getting a message to the process to exit
scanDirectoriesAndScrapeStats()
break
if scanDirectoriesAndScrapeStats() == 0:
time.sleep(0.5) #Avoid cycling too fast
if time.time() - timeSinceOutFileLastFlushed > 60: #Flush the results file every minute
fileHandle.flush()
timeSinceOutFileLastFlushed = time.time()
#Finish the stats file
fileHandle.write("<total_time time='%s' clock='%s'/></stats>" % (str(time.time() - startTime), str(getTotalCpuTime() - startClock)))
fileHandle.close()
def processJob(job, jobToRun, memoryAvailable, cpuAvailable, stats, environment,
localSlaveTempDir, localTempDir):
"""Runs a job.
"""
from sonLib.bioio import logger
from sonLib.bioio import system
from sonLib.bioio import getTotalCpuTime
from sonLib.bioio import redirectLoggerStreamHandlers
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"]
#Temp file dirs for job.
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)
#Run the actual command
tempLogFile = os.path.join(localSlaveTempDir, "temp.log")
fileHandle = open(tempLogFile, 'w')
if stats != None:
tempJob.attrib["stats"] = ""
startTime = time.time()
startClock = getTotalCpuTime()
#If you're a script tree python process, we don't need to python
if command[:10] == "scriptTree":
import jobTree.scriptTree.scriptTree
savedStdErr = sys.stderr
savedStdOut = sys.stdout
exitValue = 0
try:
sys.stderr = fileHandle
sys.stdout = fileHandle
redirectLoggerStreamHandlers(savedStdErr, fileHandle)
l = command.split()
jobTree.scriptTree.scriptTree.run(tempJob, l[1], l[2:])
except:
traceback.print_exc(file = fileHandle)
exitValue = 1
sys.stderr = savedStdErr
sys.stdout = savedStdOut
redirectLoggerStreamHandlers(fileHandle, sys.stderr)
if exitValue == 1:
logger.critical("Caught an exception in the target being run")
else:
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
#Now write the temp job file
tempFile = os.path.join(localSlaveTempDir, "tempJob.xml")
fileHandle2 = open(tempFile, 'w')
tree = ET.ElementTree(tempJob)
tree.write(fileHandle2)
fileHandle2.close()
logger.info("Copied the jobs files ready for the job")
process = subprocess.Popen(command.replace("JOB_FILE", tempFile), shell=True, stdout=fileHandle, stderr=subprocess.STDOUT, env=environment)
sts = os.waitpid(process.pid, 0)
exitValue = sts[1]
if exitValue == 0:
tempJob = ET.parse(tempFile).getroot()
fileHandle.close()
truncateFile(tempLogFile, int(job.attrib["max_log_file_size"]))
logger.info("Ran the job command=%s with exit status %i" % (command, exitValue))
if exitValue == 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 tempJob.find("stack") != None:
jobTag.append(tempJob.find("stack"))
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.critical("Failed the job")
job.attrib["colour"] = "red" #Update the colour
#Clean up
system("rm -rf %s/*" % (localTempDir))
logger.info("Cleaned up by removing the contents of the local temporary file directory for the job")
return tempLogFile
def main():
sys.path.append(sys.argv[1])
sys.argv.remove(sys.argv[1])
#Now we can import all the stuff..
from sonLib.bioio import getBasicOptionParser
from sonLib.bioio import parseBasicOptions
from sonLib.bioio import logger
from sonLib.bioio import addLoggingFileHandler
from sonLib.bioio import setLogLevel
from sonLib.bioio import getTotalCpuTime
from sonLib.bioio import getTempDirectory
from jobTree.src.master import writeJobs
from jobTree.src.master import readJob
from sonLib.bioio import system
##########################################
#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 = readJob(options.jobFile)
##########################################
#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 = getTotalCpuTime()
stats = ET.Element("slave")
else:
stats = None
##########################################
#Load the environment for the job
##########################################
#First load the environment for the job.
fileHandle = open(job.attrib["environment_file"], 'r')
environment = cPickle.load(fileHandle)
fileHandle.close()
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)
#os.environ = environment
#os.putenv(key, value)
logger.info("Loaded the environment for the process")
##########################################
#Setup the temporary directories.
##########################################
#Dir to put all the temp files in.
localSlaveTempDir = getTempDirectory()
localTempDir = os.path.join(localSlaveTempDir, "localTempDir")
os.mkdir(localTempDir)
os.chmod(localTempDir, 0777)
##########################################
#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"])
startTime = time.time()
while True:
tempLogFile = processJob(job, jobToRun, memoryAvailable, cpuAvailable, stats, environment, localSlaveTempDir, localTempDir)
if job.attrib["colour"] != "black":
logger.critical("Exiting the slave because of a failed job")
system("mv %s %s" % (tempLogFile, job.attrib["log_file"])) #Copy back the job log file, because we saw failure
break
elif job.attrib.has_key("reportAllJobLogFiles"):
logger.info("Exiting because we've been asked to report all logs, and this involves returning to the master")
#Copy across the log file
system("mv %s %s" % (tempLogFile, job.attrib["log_file"]))
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
if time.time() - startTime > maxTime:
logger.info("We are breaking because the maximum time the job should run for has been exceeded")
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, we ran for a total of %f seconds" % (time.time() - startTime))
##########################################
#Cleanup the temporary directory
##########################################
system("rm -rf %s" % localSlaveTempDir)
##########################################
#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 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 'grey' 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 = readJob(jobFile)
if job.attrib["colour"] not in ("blue"):
updatedJobFiles.add(jobFile)
logger.info("Got the active (non 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
reportAllJobLogFiles = bool(int(config.attrib["reportAllJobLogFiles"]))
stats = config.attrib.has_key("stats")
if stats:
startTime = time.time()
startClock = getTotalCpuTime()
#Stuff do handle the maximum number of issued jobs
queueingJobs = []
maxJobs = int(config.attrib["max_jobs"])
cpusUsed = 0
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)))
for jobFile in list(updatedJobFiles):
job = readJob(jobFile)
assert job.attrib["colour"] is not "blue"
##Check the log files exist, because they must ultimately be cleaned up by their respective file trees.
def checkFileExists(fileName, type):
if not os.path.isfile(fileName): #We need to keep these files in existence.
open(fileName, 'w').close()
logger.critical("The file %s of type %s for job %s had disappeared" % (fileName, type, jobFile))
checkFileExists(job.attrib["log_file"], "log_file")
checkFileExists(job.attrib["slave_log_file"], "slave_log_file")
if stats:
checkFileExists(job.attrib["stats"], "stats")
def reissueJob(job):
#Reset the log files for the job.
updatedJobFiles.remove(jobFile)
open(job.attrib["slave_log_file"], 'w').close()
open(job.attrib["log_file"], 'w').close()
assert job.attrib["colour"] == "grey"
return issueJobs([ job ], jobIDsToJobsHash, batchSystem, queueingJobs, maxJobs, cpusUsed)
def makeGreyAndReissueJob(job):
job.attrib["colour"] = "grey"
writeJobs([ job ])
return reissueJob(job)
if job.attrib["colour"] == "grey": #Get ready to start the job
cpusUsed = reissueJob(job)
elif job.attrib["colour"] == "black": #Job has finished okay
logger.debug("Job: %s has finished okay" % job.attrib["file"])
if reportAllJobLogFiles:
reportJobLogFiles(job)
#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.critical("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 %i children to schedule" % (job.attrib["file"], len(unbornChildren.findall("child"))))
newChildren = []
while unbornChild != None:
newJob = createJob(unbornChild.attrib, job.attrib["file"], config)
totalJobFiles += 1
newChildren.append(newJob)
unbornChildren.remove(unbornChild)
unbornChild = unbornChildren.find("child")
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
cpusUsed = issueJobs(newChildren, jobIDsToJobsHash, batchSystem, queueingJobs, maxJobs, cpusUsed) #Issue the new children directly
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"]
cpusUsed = makeGreyAndReissueJob(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 = readJob(job.attrib["parent"])
assert job.attrib["parent"] != jobFile
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
updatedJobFiles.remove(job.attrib["file"])
totalJobFiles -= 1
deleteJob(job, config)
elif job.attrib["colour"] == "red": #Job failed
logger.critical("Job: %s failed" % job.attrib["file"])
reportJobLogFiles(job)
#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)
logger.critical("Job: %s will be restarted, it has %s goes left" % (job.attrib["file"], job.attrib["remaining_retry_count"]))
cpusUsed = makeGreyAndReissueJob(job)
else:
assert remainingRetyCount == 0
updatedJobFiles.remove(job.attrib["file"]) #We remove the job and neither delete it or reissue it
logger.critical("Job: %s is completely failed" % job.attrib["file"])
else: #This case should only occur after failure
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 command is issued to ensure any queing jobs are issued at the end of the loop
cpusUsed = issueJobs([], jobIDsToJobsHash, batchSystem, queueingJobs, maxJobs, cpusUsed)
if len(jobIDsToJobsHash) == 0 and len(updatedJobFiles) == 0:
logger.info("Only failed jobs and their dependents (%i total) are remaining, so exiting." % totalJobFiles)
assert cpusUsed == 0
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 successfully" % jobIDsToJobsHash[jobID][0])
else:
logger.critical("Batch system is reporting that the job %s failed with exit value %i" % (jobIDsToJobsHash[jobID][0], result))
cpusUsed = processFinishedJob(jobID, result, updatedJobFiles, jobIDsToJobsHash, cpusUsed)
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
cpusUsed = reissueOverLongJobs(updatedJobFiles, jobIDsToJobsHash, config, batchSystem, cpusUsed)
logger.info("Reissued any over long jobs")
hasNoMissingJobs, cpusUsed = reissueMissingJobs(updatedJobFiles, jobIDsToJobsHash, batchSystem, cpusUsed)
if hasNoMissingJobs:
timeSinceJobsLastRescued = time.time()
else:
timeSinceJobsLastRescued += 60 #This means we'll try again in 60 seconds
logger.info("Rescued any (long) missing jobs")
#Going to sleep to let the job system catch up.
time.sleep(waitDuration)
##Check that the total number of cpus
assert sum([ cpus for jobID, cpus in jobIDsToJobsHash.values() ]) == cpusUsed
assert cpusUsed <= maxJobs
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 main():
sys.path.append(sys.argv[1])
sys.argv.remove(sys.argv[1])
#Now we can import all the stuff..
from sonLib.bioio import getBasicOptionParser
from sonLib.bioio import parseBasicOptions
from sonLib.bioio import logger
from sonLib.bioio import addLoggingFileHandler, redirectLoggerStreamHandlers
from sonLib.bioio import setLogLevel
from sonLib.bioio import getTotalCpuTime, getTotalCpuTimeAndMemoryUsage
from sonLib.bioio import getTempDirectory
from sonLib.bioio import makeSubDir
from jobTree.src.job import Job
from jobTree.src.master import getEnvironmentFileName, getConfigFileName, listChildDirs, getTempStatsFile, setupJobAfterFailure
from sonLib.bioio import system
##########################################
#Input args
##########################################
jobTreePath = sys.argv[1]
jobFile = sys.argv[2]
##########################################
#Load the environment for the job
##########################################
#First load the environment for the job.
fileHandle = open(getEnvironmentFileName(jobTreePath), 'r')
environment = cPickle.load(fileHandle)
fileHandle.close()
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)
#os.environ = environment
#os.putenv(key, value)
##########################################
#Setup the temporary directories.
##########################################
#Dir to put all the temp files in.
localSlaveTempDir = getTempDirectory()
localTempDir = makeSubDir(os.path.join(localSlaveTempDir, "localTempDir"))
##########################################
#Setup the logging
##########################################
#Setup the logging
tempSlaveLogFile = os.path.join(localSlaveTempDir, "slave_log.txt")
slaveHandle = open(tempSlaveLogFile, 'w')
for handler in list(logger.handlers): #Remove old handlers
logger.removeHandler(handler)
logger.addHandler(logging.StreamHandler(slaveHandle))
origStdErr = sys.stderr
origStdOut = sys.stdout
sys.stderr = slaveHandle
sys.stdout = slaveHandle
##########################################
#Parse input files
##########################################
config = ET.parse(getConfigFileName(jobTreePath)).getroot()
setLogLevel(config.attrib["log_level"])
job = Job.read(jobFile)
job.messages = [] #This is the only way to stop messages logging twice, as are read only in the master
job.children = []
if os.path.exists(job.getLogFileName()): #This cleans the old log file
os.remove(job.getLogFileName())
logger.info("Parsed arguments and set up logging")
#Try loop for slave logging
##########################################
#Setup the stats, if requested
##########################################
if config.attrib.has_key("stats"):
startTime = time.time()
startClock = getTotalCpuTime()
stats = ET.Element("slave")
else:
stats = None
##########################################
#The max time
##########################################
maxTime = float(config.attrib["job_time"])
assert maxTime > 0.0
assert maxTime < sys.maxint
##########################################
#Slave log file trapped from here on in
##########################################
slaveFailed = False
try:
##########################################
#The next job
##########################################
def globalTempDirName(job, depth):
return job.getGlobalTempDirName() + str(depth)
command, memoryAvailable, cpuAvailable, depth = job.followOnCommands[-1]
defaultMemory = int(config.attrib["default_memory"])
defaultCpu = int(config.attrib["default_cpu"])
assert len(job.children) == 0
startTime = time.time()
while True:
job.followOnCommands.pop()
##########################################
#Global temp dir
##########################################
globalTempDir = makeSubDir(globalTempDirName(job, depth))
i = 1
while os.path.isdir(globalTempDirName(job, depth+i)):
system("rm -rf %s" % globalTempDirName(job, depth+i))
i += 1
##########################################
#Old children, not yet deleted
#
#These may exist because of the lazy cleanup
#we do
##########################################
for childDir in listChildDirs(job.jobDir):
logger.debug("Cleaning up old child %s" % childDir)
system("rm -rf %s" % childDir)
##########################################
#Run the job
##########################################
if command != "": #Not a stub
if command[:11] == "scriptTree ":
##########################################
#Run the target
##########################################
loadStack(command).execute(job=job, stats=stats,
localTempDir=localTempDir, globalTempDir=globalTempDir,
memoryAvailable=memoryAvailable, cpuAvailable=cpuAvailable,
defaultMemory=defaultMemory, defaultCpu=defaultCpu, depth=depth)
else: #Is another command
system(command)
##########################################
#Cleanup/reset a successful job/checkpoint
##########################################
job.remainingRetryCount = int(config.attrib["try_count"])
system("rm -rf %s/*" % (localTempDir))
job.update(depth=depth, tryCount=job.remainingRetryCount)
##########################################
#Establish if we can run another job
##########################################
if time.time() - startTime > maxTime:
logger.info("We are breaking because the maximum time the job should run for has been exceeded")
break
#Deal with children
if len(job.children) >= 1: #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(job.children))
break
if len(job.followOnCommands) == 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..
command, memory, cpu, depth = job.followOnCommands[-1]
if memory > memoryAvailable:
logger.info("We need more memory for the next job, so finishing")
break
if cpu > cpuAvailable:
logger.info("We need more cpus for the next job, so finishing")
break
logger.info("Starting the next job")
##########################################
#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)
tempStatsFile = getTempStatsFile(jobTreePath)
fileHandle = open(tempStatsFile + ".new", "w")
ET.ElementTree(stats).write(fileHandle)
fileHandle.close()
os.rename(tempStatsFile + ".new", tempStatsFile) #This operation is atomic
logger.info("Finished running the chain of jobs on this node, we ran for a total of %f seconds" % (time.time() - startTime))
##########################################
#Where slave goes wrong
##########################################
except: #Case that something goes wrong in slave
traceback.print_exc(file = slaveHandle)
logger.critical("Exiting the slave because of a failed job on host %s", socket.gethostname())
job = Job.read(jobFile)
setupJobAfterFailure(job, config)
job.write()
slaveFailed = True
##########################################
#Cleanup
##########################################
#Close the slave logging
slaveHandle.flush()
sys.stderr = origStdErr
sys.stdout = origStdOut
redirectLoggerStreamHandlers(slaveHandle, sys.stderr)
slaveHandle.close()
#Copy back the log file to the global dir, if needed
if slaveFailed:
truncateFile(tempSlaveLogFile)
system("mv %s %s" % (tempSlaveLogFile, job.getLogFileName()))
#Remove the temp dir
system("rm -rf %s" % localSlaveTempDir)
#This must happen after the log file is done with, else there is no place to put the log
if (not slaveFailed) and len(job.followOnCommands) == 0 and len(job.children) == 0 and len(job.messages) == 0:
##########################################
#Cleanup global files at the end of the chain
##########################################
job.delete()
def execute(self, job):
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.SubElement(job, "stack")
startTime = time.time()
startClock = getTotalCpuTime()
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
baseDir = os.getcwd()
while self.hasRemaining():
if stats is not 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()
#Change dir back to cwd dir, if changed by target (this is a safety issue)
if os.getcwd() != baseDir:
os.chdir(baseDir)
#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 is not 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 is not None:
ET.SubElement(stats, "target", { "time":str(time.time() - targetStartTime),
"clock":str(getTotalCpuTime() - targetStartClock),
"class":".".join((target.__class__.__name__,)),
"e_time":str(target.getRunTime())})
for message in target.getMasterLoggingMessages():
if job.find("messages") is None:
ET.SubElement(job, "messages")
ET.SubElement(job.find("messages"), "message", { "message": message} )
#######
#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) })
#Finish up the stats
if stats is not None:
stats.attrib["time"] = str(time.time() - startTime)
stats.attrib["clock"] = str(getTotalCpuTime() - startClock)
def main():
sys.path.append(sys.argv[1])
sys.argv.remove(sys.argv[1])
#Now we can import all the stuff..
from sonLib.bioio import getBasicOptionParser
from sonLib.bioio import parseBasicOptions
from sonLib.bioio import logger
from sonLib.bioio import addLoggingFileHandler, redirectLoggerStreamHandlers
from sonLib.bioio import setLogLevel
from sonLib.bioio import getTotalCpuTime, getTotalCpuTimeAndMemoryUsage
from sonLib.bioio import getTempDirectory
from sonLib.bioio import makeSubDir
from jobTree.src.job import Job
from jobTree.src.master import getEnvironmentFileName, getConfigFileName, listChildDirs, getTempStatsFile, setupJobAfterFailure
from sonLib.bioio import system
##########################################
#Input args
##########################################
jobTreePath = sys.argv[1]
jobFile = sys.argv[2]
##########################################
#Load the environment for the job
##########################################
#First load the environment for the job.
fileHandle = open(getEnvironmentFileName(jobTreePath), 'r')
environment = cPickle.load(fileHandle)
fileHandle.close()
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)
#os.environ = environment
#os.putenv(key, value)
##########################################
#Setup the temporary directories.
##########################################
#Dir to put all the temp files in.
localSlaveTempDir = getTempDirectory()
localTempDir = makeSubDir(os.path.join(localSlaveTempDir, "localTempDir"))
##########################################
#Setup the logging
##########################################
#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?
tempSlaveLogFile = os.path.join(localSlaveTempDir, "slave_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.
logDescriptor = os.open(tempSlaveLogFile, os.O_WRONLY | os.O_CREAT | os.O_APPEND)
#Replace standard output with a descriptor for the log file
os.dup2(logDescriptor, 1)
#Replace standard error with a descriptor for the log file
os.dup2(logDescriptor, 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(logDescriptor)
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))
#Put a message at the top of the log, just to make sure it's working.
print "---JOBTREE SLAVE 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()))
##########################################
#Parse input files
##########################################
config = ET.parse(getConfigFileName(jobTreePath)).getroot()
setLogLevel(config.attrib["log_level"])
job = Job.read(jobFile)
job.messages = [] #This is the only way to stop messages logging twice, as are read only in the master
job.children = [] #Similarly, this is where old children are flushed out.
job.write() #Update status, to avoid reissuing children after running a follow on below.
if os.path.exists(job.getLogFileName()): #This cleans the old log file
os.remove(job.getLogFileName())
logger.info("Parsed arguments and set up logging")
#Try loop for slave logging
##########################################
#Setup the stats, if requested
##########################################
if config.attrib.has_key("stats"):
startTime = time.time()
startClock = getTotalCpuTime()
stats = ET.Element("slave")
else:
stats = None
##########################################
#The max time
##########################################
maxTime = float(config.attrib["job_time"])
assert maxTime > 0.0
assert maxTime < sys.maxint
##########################################
#Slave log file trapped from here on in
##########################################
slaveFailed = False
try:
##########################################
#The next job
##########################################
def globalTempDirName(job, depth):
return job.getGlobalTempDirName() + str(depth)
command, memoryAvailable, cpuAvailable, depth = job.followOnCommands[-1]
defaultMemory = int(config.attrib["default_memory"])
defaultCpu = int(config.attrib["default_cpu"])
assert len(job.children) == 0
startTime = time.time()
while True:
job.followOnCommands.pop()
##########################################
#Global temp dir
##########################################
globalTempDir = makeSubDir(globalTempDirName(job, depth))
i = 1
while os.path.isdir(globalTempDirName(job, depth+i)):
system("rm -rf %s" % globalTempDirName(job, depth+i))
i += 1
##########################################
#Old children, not yet deleted
#
#These may exist because of the lazy cleanup
#we do
##########################################
for childDir in listChildDirs(job.jobDir):
logger.debug("Cleaning up old child %s" % childDir)
system("rm -rf %s" % childDir)
##########################################
#Run the job
##########################################
if command != "": #Not a stub
if command[:11] == "scriptTree ":
##########################################
#Run the target
##########################################
loadStack(command).execute(job=job, stats=stats,
localTempDir=localTempDir, globalTempDir=globalTempDir,
memoryAvailable=memoryAvailable, cpuAvailable=cpuAvailable,
defaultMemory=defaultMemory, defaultCpu=defaultCpu, depth=depth)
else: #Is another command
system(command)
##########################################
#Cleanup/reset a successful job/checkpoint
##########################################
job.remainingRetryCount = int(config.attrib["try_count"])
system("rm -rf %s/*" % (localTempDir))
job.update(depth=depth, tryCount=job.remainingRetryCount)
##########################################
#Establish if we can run another job
##########################################
if time.time() - startTime > maxTime:
logger.info("We are breaking because the maximum time the job should run for has been exceeded")
break
#Deal with children
if len(job.children) >= 1: #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(job.children))
break
if len(job.followOnCommands) == 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..
command, memory, cpu, depth = job.followOnCommands[-1]
if memory > memoryAvailable:
logger.info("We need more memory for the next job, so finishing")
break
if cpu > cpuAvailable:
logger.info("We need more cpus for the next job, so finishing")
break
logger.info("Starting the next job")
##########################################
#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)
tempStatsFile = getTempStatsFile(jobTreePath)
fileHandle = open(tempStatsFile + ".new", "w")
ET.ElementTree(stats).write(fileHandle)
fileHandle.close()
os.rename(tempStatsFile + ".new", tempStatsFile) #This operation is atomic
logger.info("Finished running the chain of jobs on this node, we ran for a total of %f seconds" % (time.time() - startTime))
##########################################
#Where slave goes wrong
##########################################
except: #Case that something goes wrong in slave
traceback.print_exc()
logger.critical("Exiting the slave because of a failed job on host %s", socket.gethostname())
job = Job.read(jobFile)
setupJobAfterFailure(job, config)
job.write()
slaveFailed = True
##########################################
#Cleanup
##########################################
#Close the slave 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 slaveFailed:
truncateFile(tempSlaveLogFile)
system("mv %s %s" % (tempSlaveLogFile, job.getLogFileName()))
#Remove the temp dir
system("rm -rf %s" % localSlaveTempDir)
#This must happen after the log file is done with, else there is no place to put the log
if (not slaveFailed) and len(job.followOnCommands) == 0 and len(job.children) == 0 and len(job.messages) == 0:
##########################################
#Cleanup global files at the end of the chain
##########################################
job.delete()
def execute(self, job, stats, localTempDir, globalTempDir, memoryAvailable,
cpuAvailable, defaultMemory, defaultCpu, depth):
self.tempDirAccessed = False
self.localTempDir = localTempDir
self.globalTempDir = globalTempDir
if stats != None:
startTime = time.time()
startClock = getTotalCpuTime()
baseDir = os.getcwd()
self.target.setStack(self)
#Debug check that we have the right amount of CPU and memory for the job in hand
targetMemory = self.target.getMemory()
if targetMemory != sys.maxint:
assert targetMemory <= memoryAvailable
targetCpu = self.target.getCpu()
if targetCpu != sys.maxint:
assert targetCpu <= cpuAvailable
#Run the target, first cleanup then run.
self.target.run()
#Change dir back to cwd dir, if changed by target (this is a safety issue)
if os.getcwd() != baseDir:
os.chdir(baseDir)
#Cleanup after the target
if self.tempDirAccessed:
system("rm -rf %s/*" % self.localTempDir)
self.tempDirAccessed = False
#Handle the follow on
followOn = self.target.getFollowOn()
if followOn is not None: #Target to get rid of follow on when done.
if self.target.isGlobalTempDirSet():
followOn.setGlobalTempDir(self.target.getGlobalTempDir())
followOnStack = Stack(followOn)
job.followOnCommands.append(
(followOnStack.makeRunnable(self.globalTempDir),
followOnStack.getMemory(defaultMemory),
followOnStack.getCpu(defaultCpu), depth))
#Now add the children to the newChildren stack
newChildren = self.target.getChildren()
newChildren.reverse()
assert len(job.children) == 0
while len(newChildren) > 0:
childStack = Stack(newChildren.pop())
job.children.append((childStack.makeRunnable(self.globalTempDir),
childStack.getMemory(defaultMemory),
childStack.getCpu(defaultCpu)))
#Now build jobs for each child command
for childCommand, runTime in self.target.getChildCommands():
job.children.append((childCommand, defaultMemory, defaultCpu))
for message in self.target.getMasterLoggingMessages():
job.messages.append(message)
#Finish up the stats
if stats != None:
stats = ET.SubElement(stats, "target")
stats.attrib["time"] = str(time.time() - startTime)
totalCpuTime, totalMemoryUsage = getTotalCpuTimeAndMemoryUsage()
stats.attrib["clock"] = str(totalCpuTime - startClock)
stats.attrib["class"] = ".".join(
(self.target.__class__.__name__, ))
stats.attrib["memory"] = str(totalMemoryUsage)
def execute(self, job, stats, localTempDir, globalTempDir,
memoryAvailable, cpuAvailable,
defaultMemory, defaultCpu, depth):
self.tempDirAccessed = False
self.localTempDir = localTempDir
self.globalTempDir = globalTempDir
if stats != None:
startTime = time.time()
startClock = getTotalCpuTime()
baseDir = os.getcwd()
self.target.setStack(self)
#Debug check that we have the right amount of CPU and memory for the job in hand
targetMemory = self.target.getMemory()
if targetMemory != sys.maxint:
assert targetMemory <= memoryAvailable
targetCpu = self.target.getCpu()
if targetCpu != sys.maxint:
assert targetCpu <= cpuAvailable
#Run the target, first cleanup then run.
self.target.run()
#Change dir back to cwd dir, if changed by target (this is a safety issue)
if os.getcwd() != baseDir:
os.chdir(baseDir)
#Cleanup after the target
if self.tempDirAccessed:
system("rm -rf %s/*" % self.localTempDir)
self.tempDirAccessed = False
#Handle the follow on
followOn = self.target.getFollowOn()
if followOn is not None: #Target to get rid of follow on when done.
if self.target.isGlobalTempDirSet():
followOn.setGlobalTempDir(self.target.getGlobalTempDir())
followOnStack = Stack(followOn)
job.followOnCommands.append((followOnStack.makeRunnable(self.globalTempDir),
followOnStack.getMemory(defaultMemory),
followOnStack.getCpu(defaultCpu),
depth))
#Now add the children to the newChildren stack
newChildren = self.target.getChildren()
newChildren.reverse()
assert len(job.children) == 0
while len(newChildren) > 0:
childStack = Stack(newChildren.pop())
job.children.append((childStack.makeRunnable(self.globalTempDir),
childStack.getMemory(defaultMemory),
childStack.getCpu(defaultCpu)))
#Now build jobs for each child command
for childCommand, runTime in self.target.getChildCommands():
job.children.append((childCommand, defaultMemory, defaultCpu))
for message in self.target.getMasterLoggingMessages():
job.messages.append(message)
#Finish up the stats
if stats != None:
stats = ET.SubElement(stats, "target")
stats.attrib["time"] = str(time.time() - startTime)
totalCpuTime, totalMemoryUsage = getTotalCpuTimeAndMemoryUsage()
stats.attrib["clock"] = str(totalCpuTime - startClock)
stats.attrib["class"] = ".".join((self.target.__class__.__name__,))
stats.attrib["memory"] = str(totalMemoryUsage)