def pipelineLoop():
try:
while (1 == 1):
time.sleep( 100 )
jobs = database.getActiveJobs()
if len(jobs) > 0:
print "Checking " + str(len(jobs)) + " job/s"
for job in jobs:
jobid = job['jid']
newstate = checkSlurmJob( job['slurmid'] )
if newstate == database.JOB_RUNNING and job['state'] != database.JOB_RUNNING:
database.setJobRunning( jobid )
if newstate == database.JOB_COMPLETED:
userid = job['uid']
slurmid = job['slurmid']
# stageout
outs = ["jor_"+str(slurmid)+".out", "jor_"+str(slurmid)+".err"]
for fileoutname in outs:
fileout = database.createFile( userid, fileoutname )
database.addJobFile( jobid, fileout, database.FILEOUT )
localfile = database.getFileFullName( fileout )
(localdir, localbase) = os.path.split( localfile )
remotedir = os.path.join( remotehome, localdir )
remotefile = os.path.join( remotehome, localfile )
os.system('scp "%s:%s" "%s"' % (remotehost, remotefile, localfile) )
database.setJobCompleted( jobid )
except KeyboardInterrupt:
print "ending pipeline loop"
def runjob(user, jobid, var1, fileid):
print "RUNNING JOB " + str(jobid)
# stagein
localfile = database.getFileFullName(fileid)
(localdir, localbase) = os.path.split(localfile)
remotedir = os.path.join(remotehome, localdir)
remotefile = os.path.join(remotehome, localfile)
os.system('ssh "%s" "mkdir -p %s"' % (remotehost, remotedir))
os.system('scp "%s" "%s:%s"' % (localfile, remotehost, remotefile))
database.addJobFile(jobid, fileid, database.FILEIN)
# submit
command = [
"ssh", remotehost, "./launch_pipeline.sh", user, var1, remotefile
]
proc = subprocess.Popen(command, stdout=subprocess.PIPE)
output = proc.communicate()[0]
mm = reJOBID.search(output)
if mm:
slurmid = int(mm.group('slurmid'))
print "Slurm ID", str(slurmid)
database.setJobSubmitted(jobid, slurmid)
else:
raise (-1)
def runjob( user, jobid, var1, fileid ):
print "RUNNING JOB " + str(jobid)
# stagein
localfile = database.getFileFullName( fileid )
(localdir, localbase) = os.path.split( localfile )
remotedir = os.path.join( remotehome, localdir )
remotefile = os.path.join( remotehome, localfile )
os.system('ssh "%s" "mkdir -p %s"' % (remotehost, remotedir) )
os.system('scp "%s" "%s:%s"' % (localfile, remotehost, remotefile) )
database.addJobFile( jobid, fileid, database.FILEIN )
# submit
command = ["ssh", remotehost, "./launch_pipeline.sh", user, var1, remotefile ]
proc = subprocess.Popen( command, stdout=subprocess.PIPE )
output = proc.communicate()[0]
mm = reJOBID.search( output )
if mm:
slurmid = int(mm.group('slurmid'))
print "Slurm ID", str(slurmid)
database.setJobSubmitted( jobid, slurmid )
else:
raise (-1)
def pipelineLoop():
try:
while (1 == 1):
time.sleep(100)
jobs = database.getActiveJobs()
if len(jobs) > 0:
print "Checking " + str(len(jobs)) + " job/s"
for job in jobs:
jobid = job['jid']
newstate = checkSlurmJob(job['slurmid'])
if newstate == database.JOB_RUNNING and job[
'state'] != database.JOB_RUNNING:
database.setJobRunning(jobid)
if newstate == database.JOB_COMPLETED:
userid = job['uid']
slurmid = job['slurmid']
# stageout
outs = [
"jor_" + str(slurmid) + ".out",
"jor_" + str(slurmid) + ".err"
]
for fileoutname in outs:
fileout = database.createFile(userid, fileoutname)
database.addJobFile(jobid, fileout, database.FILEOUT)
localfile = database.getFileFullName(fileout)
(localdir, localbase) = os.path.split(localfile)
remotedir = os.path.join(remotehome, localdir)
remotefile = os.path.join(remotehome, localfile)
os.system('scp "%s:%s" "%s"' %
(remotehost, remotefile, localfile))
database.setJobCompleted(jobid)
except KeyboardInterrupt:
print "ending pipeline loop"