def submit(self): if self.jobs: print 'There is already a run with the name "'+self.jobname+'". Exiting...' sys.exit(1) # uploading input file once, so we don't need to do it for every job again and again fm.cp(self.filepath, 'gsiftp://pan.nesi.org.nz/~/inputfiles/'+self.jobname, True) for i in range(0,self.runs): # create the job object job = JobObject(si); # set a unique jobname number = str(i+1).zfill(4) job.setUniqueJobname(self.jobname+"_run_"+number) # set the commandline that needs to be executed job.setCommandline(megabeast_path+' '+remote_home_dir+'/inputfiles/'+self.jobname+'/'+self.filename) job.setSubmissionLocation('pan:pan.nesi.org.nz') job.setCpus(self.cpus) job.setWalltime(self.walltime) job.setMemory(self.memory) job.setApplication('UltraBEAST') job.setApplicationVersion('0.1') #job.addInputFileUrl(self.filepath) # create the job on the backend and specify the VO to use temp_jobname = job.createJob("/nz/nesi") print "created job: '"+temp_jobname+"', submitting..." # submit the job job.submitJob() print "submission finished: " + temp_jobname
%s """ 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")