def submitJob(self, jobs, config):
if len(jobs)>1:
indexArray = []
for j in jobs:
indexArray.append(j.jobSeq)
jobName = config.name + formatArray(indexArray)
else:
jobName = config.name
config.generateScripts(jobs)
#Create the bsub command
cmd = ["bsub -q " + config.queue]
cmd[0] = cmd[0] + " -J \"" + jobName + "\""
if config.requirement:
cmd[0] = cmd[0] + " -R \"" + config.requirement + "\""
#Run the command with timeout
#print jobs[0].script
subOutput = subCommand(cmd, jobs[0].script, 10).Run()
#If failed, return
if subOutput==None:
return
#Gather information about the job that was created (id + queue)
m = re.search("Job <([0-9]+)> .*? <(.+?)>.*", subOutput)
jobID = "";
queue = "";
if m:
jobID = int(m.group(1))
queue = m.group(2)
if len(jobs)>1:
for j in jobs:
j.jobID = jobID
j.queue = queue
j.attempts += 1
#Update the job with the information
config.updateCorrespondance((j.jobID, j.jobSeq+1), j.jobSeq)
jobIndex = -1
else:
jobs[0].jobID = jobID
jobs[0].queue = queue
jobs[0].attempts += 1
#Update the job with the information
config.updateCorrespondance(jobs[0].jobID, jobs[0].jobSeq)
jobIndex = jobs[0].index
return jobID,jobIndex
def refreshInfo(self):
cmd = ["bjobs -wa"]
monOutput = subCommand(cmd, None, 10).Run()
for line in monOutput.splitlines():
elements = line.split()
if elements[0]=="JOBID":
continue
job = LSFMonitor.LSFJob()
job.lsfStatus = elements[2]
job.lsfID = int(elements[0])
m = re.search("(.*)\[([0-9]+)\]", elements[6])
if m:
job.lsfName = m.group(1)
job.arrayIndex = int(m.group(2))
self.jobsList[job.lsfID,job.arrayIndex] = job
else:
job.lsfName = elements[6]
self.jobsList[job.lsfID] = job
def deleteJobs(self, name):
cmd = ["bkill -J " + name]
_ = subCommand(cmd, None, 30).Run()
