Problem with multiple job service instances

[oweidner]

Multiple instances of a job service during a session fail more or less randomly:

#!/usr/bin/env python

# vim: tabstop=8 expandtab shiftwidth=4 softtabstop=4

'''This examples shows how to copy a file to a remote 
   host via ssh using a custom security context.

   If something doesn't work as expected, try to set 
   SAGA_VERBOSE=3 in your environment before you run the
   script in order to get some debug output.

   If you think you have encountered a defect, please 
   report it at: https://github.com/oweidner/bliss/issues
'''

__author__    = "Ole Christian Weidner"
__email__     = "ole.weidner@me.com"
__copyright__ = "Copyright 2011, Ole Christian Weidner"
__license__   = "MIT"

import time
import bliss.saga as saga

def main():

    execution_host = saga.Url("pbs+ssh://queenbee.loni.org") 
    bfast_base_dir = saga.Url("sftp://queenbee.loni.org/work/oweidner/bfast")

    try:
        ctx = saga.Context()
        ctx.type = saga.Context.SSH
        ctx.userid  = 'oweidner' # like 'ssh username@host ...'
        ctx.usercert = '/Users/s1063117/.ssh/id_rsa' # like ssh -i ...'

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

        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)

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

        jd = saga.job.Description()
        jd.wall_time_limit   = "0:05:00"
        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()
        time.sleep(1)
        print "Job started with ID '%s' and working directory: '%s'"\
          % (myjob.jobid, workdir)

        myjob.wait()

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

    except saga.Exception, ex:
        print "Oh, snap! An error occured: %s" % (str(ex))

if __name__ == "__main__":
    for i in range (0,8):
        main()

[pradeepmantha]

Below script fails...

import sys, time
import bliss.saga as saga

def main():

try:
# set up a security context (optional)
# if no security context is defined, the PBS
# plugin will pick up the default set of ssh
# credentials of the user, i.e., ~/.ssh/id_rsa

   # create a job service for Futuregrid's 'india' PBS cluster
   # and attach the SSH security context to it
   js = saga.job.Service("pbs+ssh://alamo.futuregrid.org")
   js1 = saga.job.Service("pbs+ssh://alamo.futuregrid.org")

   # describe our job
   jd = saga.job.Description()
   # resource requirements
   jd.wall_time_limit = 5 #minutes
   jd.total_cpu_count = 1
   # environment, executable & arguments
   jd.environment = {'SLEEP_TIME':"hello_saga"}
   jd.executable  = '/bin/cat'
   jd.arguments   = ['$SLEEP_TIME']
   # output options
   jd.output = "bliss_pbssh_job.stdout"
   jd.error  = "bliss_pbssh_job.stderr"

   # create the job (state: New)
   myjob = js.create_job(jd)
   myjob1 = js1.create_job(jd)

   print "Job ID    : %s" % (myjob.jobid)
   print "Job State : %s" % (myjob.get_state())

   print "\n...starting job...\n"
   # run the job (submit the job to PBS)
   myjob.run()
   myjob1.run()

   print "Job ID    : %s" % (myjob.jobid)
   print "Job State : %s" % (myjob.get_state())

   print "\n...waiting for job...\n"
   # wait for the job to either finish or fail
   myjob.wait()
   myjob1.wait()

   print "Job State : %s" % (myjob.get_state())
   print "Exitcode  : %s" % (myjob.exitcode)

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

if name == "main":
main()