Exemplo n.º 1
0
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"
Exemplo n.º 2
0
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)
Exemplo n.º 3
0
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)
Exemplo n.º 4
0
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"