Bliss Example: Run a BFAST task on a remote cluster via PBS+SSH

pbssh.py

#!/usr/bin/env python

import sys, time
import bliss.saga as saga

def main(jobno, session, jobservice):
   
    bfast_base_dir = saga.Url("sftp://india.futuregrid.org/N/u/oweidner/software/bfast/")
 
    try:
        workdir = "%s/tmp/run/%s" % (bfast_base_dir.path, str(int(time.time())))
        basedir = saga.filesystem.Directory(bfast_base_dir, session=session)
        basedir.make_dir(workdir)

        jd = saga.job.Description()
        jd.wall_time_limit   = 5 # wall-time in minutes
        jd.total_cpu_count   = 1     
        jd.environment       = {'BFAST_DIR':bfast_base_dir.path}
        jd.working_directory = workdir     
        jd.executable        = '$BFAST_DIR/bin/bfast'
        jd.arguments         = ['match', '-A 1',
                                '-r $BFAST_DIR/data/small/reads_5K/reads.10.fastq',
                                '-f $BFAST_DIR/data/small/reference/hg_2122.fa']

        myjob = js.create_job(jd)
        myjob.run()

        print "Job #%s started with ID '%s' and working directory: '%s'"\
          % (jobno, myjob.jobid, workdir)

        myjob.wait()

        print "Job #%s with ID '%s' finished (RC: %s). Output available in: '%s'"\
          % (jobno, myjob.jobid, myjob.exitcode, workdir)

        basedir.close()

    except saga.Exception, ex:
        print "An error occured during job execution: %s" % (str(ex))
        sys.exit(-1)

if __name__ == "__main__":

    execution_host = saga.Url("pbs+ssh://india.futuregrid.org") 
    ctx = saga.Context()
    ctx.type = saga.Context.SSH
    ctx.userid  = 'oweidner' # like 'ssh username@host ...'
    ctx.userkey = '/Users/oweidner/.ssh/rsa_work' # like ssh -i ...'

    session = saga.Session()
    session.contexts.append(ctx)

    js = saga.job.Service(execution_host, session)
    

    for i in range (0, 4):
        main(i, session, js)