print 'Creating job: ' + jobname
# create the single job
job = JobObject(si)
job.setJobname(jobname)
# better to set the application to use explicitely because in that case we don't need to use mds (faster)
job.setApplication('UnixCommands')
if i == 3 or i == 13:
# this is just to demonstrate how to restart a failed job later on
job.setCommandline('cat ' + inputFile3relPath)
else:
job.setCommandline('cat ' + inputFile1relPath + ' ' +
inputFile2relPath)
job.setWalltimeInSeconds(60)
# adding the job to the multijob
batchJob.addJob(job)
# this should be set because it's used for the matchmaking/metascheduling
batchJob.setDefaultNoCpus(1)
batchJob.setDefaultWalltimeInSeconds(60)
# now we add an input file that is common to all jobs
batchJob.addInputFile(inputFile1Url)
batchJob.addInputFile(inputFile2Url)
batchJob.addInputFile(inputFile3Url)
# we don't want to submit to tpac because it doesn't work
#multiPartJob.setSitesToExclude(["uq", "hpsc", "auckland", "canterbury"]);
try:
start = 30
end = 40
pathToInputFiles = batchJob.pathToInputFiles()
inputFile1relPath = pathToInputFiles+'inputFile1.txt '
inputFile2relPath = pathToInputFiles+'inputFile2.txt'
for i in range(start, end):
# create a unique jobname for every job
jobname = batchJobName+"_"+ str(i)
print 'Creating job: '+jobname
# create the single job
job = JobObject(si)
job.setJobname(jobname)
# better to set the application to use explicitely because in that case we don't need to use mds (faster)
job.setApplication('UnixCommands')
job.setCommandline('cat '+ inputFile1relPath + ' ' + inputFile2relPath)
job.setWalltimeInSeconds(60)
# adding the job to the multijob
batchJob.addJob(job)
# only start the newly added jobs and wait for the restart to finish
batchJob.restart(False, False, True, True)
# don't forget to exit properly. this cleans up possible existing threads/executors
sys.exit()
"""
if group == '':
group = DEFAULT_GROUP
if queue == '':
queue = DEFAULT_QUEUE
for f in sys.argv[8:]:
input_files.append(f)
try:
job = JobObject(si)
job.setSubmissionLocation(queue)
job.setTimestampJobname("galaxy_" + galaxy_job_id)
job.setMemory(DEFAULT_MEMORY)
job.setWalltimeInSeconds(DEFAULT_WALLTIME)
# stop annoying stats from being written to stderr
job.addEnvironmentVariable("SUPPRESS_STATS", "true")
#create the job script#
except:
print "Cannot setup the job environment"
sys.exit(-4)
#create nesi job_script
try:
# save jobname for job
njn = open(jobname_file, "w")
njn.write(job.getJobname())
