job.setCommandline('R --no-readline --no-restore --no-save -f '+path_to_inputfile)
batch_job.addJob(job)
batch_job.addInputFile('/home/markus/Desktop/R/'+inputfilename)
batch_job.setDefaultNoCpus(1)
batch_job.setDefaultWalltimeInSeconds(walltime)
print 'preparing jobs on backend...'
batch_job.prepareAndCreateJobs(redistribute)
if redistribute:
print 'job distribution:'
print batch_job.getOptimizationResult()
print 'submitting jobs to grid...'
batch_job.submit(True)
print 'submission finished...'
try:
print "Creating jobs on the backend and staging files..."
# by specifying "True" we tell the backend to automatically distribute the jobs to all available submission locations
# this can be finetuned by exluding or including sites. another option would be to specifying the submission location
# for every single job and setting "False" below (this would make job submission faster since jobs don't need to be re-distributed/moved on the backend).
batch_job.prepareAndCreateJobs(True)
except (JobsException), error:
for job in error.getFailures().keySet():
print "Job: " + job.getJobname() + ", Error: " + error.getFailures(
).get(job).getLocalizedMessage()
sys.exit()
print "Job distribution:"
print batch_job.getOptimizationResult()
print "Submitting jobs..."
batch_job.submit()
# now we wait for all jobs to be finished, checking for updates every 10 seconds. in real life we would set a much higher check intervall since we don't want to overload
# the backend and also it's not really necessary
batch_job.waitForJobToFinish(10)
print "BatchJob " + batch_job.getJobname() + " finished."
# finally, everything is ready. We could do a lot more here, but you get the idea...
for job in batch_job.getJobs():
print "Job: " + job.getJobname() + ", Status: " + job.getStatusString(
False)
print "Submitted to: " + job.getJobProperty(Constants.SUBMISSION_SITE_KEY)
try:
print "Creating jobs on the backend and staging files..."
# by specifying "True" we tell the backend to automatically distribute the jobs to all available submission locations
# this can be finetuned by exluding or including sites. another option would be to specifying the submission location
# for every single job and setting "False" below (this would make job submission faster since jobs don't need to be re-distributed/moved on the backend).
batch_job.prepareAndCreateJobs(True)
except (JobsException), error:
for job in error.getFailures().keySet():
print "Job: " + job.getJobname() + ", Error: " + error.getFailures(
).get(job).getLocalizedMessage()
sys.exit()
print "Job distribution:"
for subLoc in batch_job.getOptimizationResult().keySet():
print subLoc + " : " + batch_job.getOptimizationResult().get(subLoc)
print "Submitting jobs..."
batch_job.submit()
restarted = False
# now we wait for all jobs to finish. Actually, we probably should test whether the job was successful as well...
while not batch_job.isFinished(True):
# printing some stats
print batch_job.getProgress()
# restart failed jobs everytime
failedpolicy = DefaultResubmitPolicy()
# to only resubmit failed jobs, we have to remove the waiting jobs resubmission that is set by default
try:
print "Creating jobs on the backend and staging files..."
# by specifying "True" we tell the backend to automatically distribute the jobs to all available submission locations
# this can be finetuned by exluding or including sites. another option would be to specifying the submission location
# for every single job and setting "False" below (this would make job submission faster since jobs don't need to be re-distributed/moved on the backend).
batch_job.prepareAndCreateJobs(True)
except (JobsException), error:
for job in error.getFailures().keySet():
print "Job: "+job.getJobname()+", Error: "+error.getFailures().get(job).getLocalizedMessage()
sys.exit()
print "Job distribution:"
for subLoc in batch_job.getOptimizationResult().keySet():
print subLoc + " : " +batch_job.getOptimizationResult().get(subLoc)
print "Submitting jobs..."
batch_job.submit()
restarted = False
# now we wait for all jobs to finish. Actually, we probably should test whether the job was successful as well...
while not batch_job.isFinished(True):
# printing some stats
print batch_job.getProgress()
# restart failed jobs everytime
failedpolicy = DefaultResubmitPolicy()
