def parasolStop():
"""Function stops the parasol hub and node.
"""
machineList = os.path.join(workflowRootPath(), "workflow", "jobTree", "machineList")
i = os.system("paraNodeStop %s" % machineList)
j = os.system("paraHubStop now")
return i, j
def parasolRestart():
"""Function starts the parasol hub and node.
"""
parasolStop()
while True:
machineList = os.path.join(workflowRootPath(), "workflow", "jobTree", "machineList")
#pathEnvVar = os.environ["PATH"]
os.system("paraNode start -hub=localhost")
#-umask=002 -userPath=%s -sysPath=%s" % (pathEnvVar, pathEnvVar))
os.system("paraHub %s subnet=127.0.0 &" % (machineList,))
tempFile = getTempFile()
dead = True
try:
popen("parasol status", tempFile)
fileHandle = open(tempFile, 'r')
line = fileHandle.readline()
while line != '':
if "Nodes dead" in line:
print line
if int(line.split()[-1]) == 0:
dead = False
line = fileHandle.readline()
fileHandle.close()
except RuntimeError:
pass
os.remove(tempFile)
if not dead:
break
else:
logger.info("Tried to restart the parasol process, but failed, will try again")
parasolStop()
time.sleep(5)
logger.info("Restarted the parasol process")
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))