print "INFO: Adding common files to Batch Job Object " + batch_job_name batch_jobs.addInputFile(os.path.join(current_dir, dictionary_path)) batch_jobs.addInputFile(os.path.join(current_dir, "countbacon.py")) print "INFO: Defining jobs from input directory" job_count = 0 for file_name in os.listdir(input_path): print "INFO: Defining job for " + file_name job_name = base_job_name + "-" + file_name job = JobObject(service_interface) job.setJobname(job_name) job.setApplication("python") # Set the application being run job.setApplicationVersion("2.4") # Set the application version, note this is an exact match job.addInputFileUrl(os.path.join(current_dir, input_path, file_name)) job.setCommandline("python ../countbacon.py ../" + dictionary_path + " " + file_name) print "INFO: " + job.getJobname() + " defined" batch_jobs.addJob(job) print "INFO: " + job.getJobname() + " added to batch " + batch_jobs.getJobname() job_count += 1 print "INFO: " + str(job_count) + " jobs defined" print "INFO: Sending batch " + batch_jobs.getJobname() + " to " + backend + " and staging files..." try: batch_jobs.prepareAndCreateJobs(False) except (JobsException), error: print ("HALT: Exception submitting jobs from BatchJobObject " + batch_jobs.getJobname() + "!") for job in error.getFailures().keySet(): print "Job: " + job.getJobname() + ", Error: " + error.getFailures().get(job).getLocalizedMessage() sys.exit(1) except (BackendException), error: print ("HALT: Exception from grisu backend " + backend + "!")
submitted_jobs = [] # better make that unique for each run, so we can resume workflows easier if necessary (this introduces quite a bit more complexity though) jobname_base = 'staging_test' for total in range(1, amount_of_jobs_total + 1): job = JobObject(si) job.setJobname(jobname_base + '_' + str(total)) # always good to set the application if you know it, processing the job will be faster job.setApplication('UnixCommands') # also good to set queue if you know where you want to submit your job, not necessary, but processing of the job will be faster job.setSubmissionLocation('default:gram5.ceres.auckland.ac.nz') # create a random sized outfile mbsize = 1024 * 1024 random_size = random.randrange(10, 100) size_string = str(mbsize * random_size) job.setCommandline('dd if=/dev/zero of=outfile bs=' + size_string + ' count=1') job.createJob('/nz/nesi') job.submitJob() print 'created and submitted job: ' + job.getJobname() + ' (size: ' + str( random_size) + 'mb)' submitted_jobs.append(job) print 'Submission finished' sys.exit(0)
# better make that unique for each run, so we can resume workflows easier if necessary (this introduces quite a bit more complexity though) jobname_base = 'workflow_test' for total in range(1, amount_of_jobs_total+1): job = JobObject(si) job.setJobname(jobname_base+'_'+str(total)) # always good to set the application if you know it, processing the job will be faster job.setApplication('UnixCommands') # also good to set queue if you know where you want to submit your job, not necessary, but processing of the job will be faster job.setSubmissionLocation('default:gram5.ceres.auckland.ac.nz') # job sleeps for a random time random_sleep = random.randrange(5, 75) job.setCommandline('sleep '+str(random_sleep)) job.createJob('/nz/nesi') print 'created job: '+ job.getJobname()+' (sleeptime: '+str(random_sleep)+')' created_jobs.append(job) finished = False while not finished: # submit another bunch of jobs while there are some if len(created_jobs) > 0: print 'still '+str(len(created_jobs))+' jobs to submit...' while len(submitted_jobs) < amount_of_jobs_concurrent: if len(created_jobs) <= 0: break job = created_jobs[0]
# now we are adding a file that can be used by all of the child jobs. it needs to be referenced via the pathToInputFiles() method shown above batch_job.addInputFile('/home/markus/tmp/commonJobFile.txt') batch_job.setDefaultNoCpus(1); batch_job.setDefaultWalltimeInSeconds(60); batch_job.setLocationsToExclude(["gt5test:ng1.canterbury.ac.nz"]) 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)
from grisu.frontend.control.login import LoginManager from grisu.frontend.model.job import JobObject import sys # create a service interface to the BeSTGRID backend service_interface = LoginManager.loginCommandline("BeSTGRID") print 'Creating job object...' job = JobObject(service_interface) job.setJobname("echo_job-1") # job name must be unique print 'Set jobname to: ' + job.getJobname() # set the name of the application as it is published in MDS. # "generic" means not to use MDS for the lookup. job.setApplication("generic") # "generic" jobs require a submission location to be specified job.setSubmissionLocation("all.q:ng2.scenzgrid.org#SGE") # set the command that needs to be executed job.setCommandline("echo \"Hello World\"") # create the job on the backend and specify the VO to use job.createJob("/ARCS/BeSTGRID") print 'Submitting job...' # submit the job job.submitJob() print 'Waiting for the job to finish...' # this waits until the job is finished. Checks every 10 seconds (which would be too often for a real job) finished = job.waitForJobToFinish(10)
batch_job.addJob(job) # now we are adding a file that can be used by all of the child jobs. it needs to be referenced via the pathToInputFiles() method shown above batch_job.addInputFile('/home/markus/tmp/commonJobFile.txt') batch_job.setDefaultNoCpus(1) batch_job.setDefaultWalltimeInSeconds(60) 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):
batch_jobs.addInputFile(os.path.join(current_dir, "countbacon.py")) print "INFO: Defining jobs from input directory" job_count = 0 for file_name in os.listdir(input_path): print "INFO: Defining job for " + file_name job_name = base_job_name + "-" + file_name job = JobObject(service_interface) job.setJobname(job_name) job.setApplication("python") # Set the application being run job.setApplicationVersion( "2.4") # Set the application version, note this is an exact match job.addInputFileUrl(os.path.join(current_dir, input_path, file_name)) job.setCommandline("python ../countbacon.py ../" + dictionary_path + " " + file_name) print "INFO: " + job.getJobname() + " defined" batch_jobs.addJob(job) print "INFO: " + job.getJobname( ) + " added to batch " + batch_jobs.getJobname() job_count += 1 print "INFO: " + str(job_count) + " jobs defined" print "INFO: Sending batch " + batch_jobs.getJobname( ) + " to " + backend + " and staging files..." try: batch_jobs.prepareAndCreateJobs(False) except (JobsException), error: print("HALT: Exception submitting jobs from BatchJobObject " + batch_jobs.getJobname() + "!") for job in error.getFailures().keySet(): print "Job: " + job.getJobname() + ", Error: " + error.getFailures(
jobnames = [] for i in range(10): file = folder + "test" + str(i) + ".txt" job = JobObject(si) job.setUniqueJobname("diff_" + str(i)) job.setApplication("UnixCommands") job.setCommandline("diff original.txt test" + str(i) + ".txt") job.createJob("/ARCS/BeSTGRID") job.addInputFileUrl(file) job.addInputFileUrl(original) job.submitJob() jobnames.append(job.getJobname()) for jobname in jobnames: finished = job.waitForJobToFinish(10) print "Job: " + jobname print print "Stdout:" print job.getStdOutContent() print print "Stderr:" print job.getStdErrContent() print print
si = LoginManager.loginCommandline() print "Parsing commandline arguments..." file1url = sys.argv[1] file1Name = FileManager.getFilename(file1url) file2url = sys.argv[2] file2Name = FileManager.getFilename(file2url) print "Creating job..." # create the job object job = JobObject(si) # set a unique jobname job.setTimestampJobname("diff_job") print "Set jobname to: " + job.getJobname() # setting the application. this means that grisu can figure out the submission location and # you don't have to do that manually job.setApplication("UnixCommands") # set the commandline that needs to be executed job.setCommandline("diff " + file1Name + " " + file2Name) job.addInputFileUrl(file1url) job.addInputFileUrl(file2url) # create the job on the backend and specify the VO to use job.createJob("/ARCS/StartUp") print "Submitting job..." # submit the job job.submitJob()
# Creating a list of jobs jobs = [] print "INFO: Defining " + str(job_count) + " helloworld jobs" for i in range(1, job_count + 1): print "INFO: Defining job " + str(i) + " of " + str(job_count) #The next lines define the actual job's parameters job = JobObject(service_interface) # Create a job job.setJobname(base_job_name + str(i)) # Give it a (hopefully) unique name job.setApplication("python") # Set the application being run job.setApplicationVersion( "2.4") # Set the application version, note this is an exact match # job.setSubmissionLocation("all.q:ng2.scenzgrid.org#SGE") # Set the location the job will be submitted to job.addInputFileUrl(os.path.join(current_dir, "helloworld.py")) # Add a file job.setCommandline("python helloworld.py") # Set the command to be run print "INFO: job " + job.getJobname() + " defined" jobs.append(job) # Submit the jobs to be run # Note the exception catching to give more information about a job failing for job in jobs: time_start = time.time() try: print "INFO: Creating job " + job.getJobname( ) + " on " + backend + " backend, with " + group + " group" job.createJob(group) print "INFO: Submitting job " + job.getJobname() job.submitJob() except (JobsException), error: print "HALT: Exception submitting job!" print "Job: " + job.getJobname() + ", Error: " + error.getFailures(
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()) njn.close() except: print "Cannot write jobname to file" sys.exit(-2) command_arguments = command.split() print input_files new_commandline = "" file = open("/home/jamesboocock/blah.txt", 'a') for arg in command_arguments: file.write(arg + '\n') arg=arg.replace('"','') print("arg: " + arg) if ((os.path.exists(arg)) or (os.path.isfile(arg)==True)) and (arg not in input_files) and ("_file" not in arg):
# There are three stages, creating the jobs, submitting the jobs, then after they have finished, retrieving the job outputs # Creating a list of jobs jobs = [] print "INFO: Defining " + str(job_count) + " helloworld jobs" for i in range(1, job_count + 1): print "INFO: Defining job " + str(i) + " of " + str(job_count) #The next lines define the actual job's parameters job = JobObject(service_interface) # Create a job job.setJobname(base_job_name + str(i)) # Give it a (hopefully) unique name job.setApplication("python") # Set the application being run job.setApplicationVersion("2.4") # Set the application version, note this is an exact match # job.setSubmissionLocation("all.q:ng2.scenzgrid.org#SGE") # Set the location the job will be submitted to job.addInputFileUrl(os.path.join(current_dir, "helloworld.py")) # Add a file job.setCommandline("python helloworld.py") # Set the command to be run print"INFO: job " + job.getJobname() + " defined" jobs.append(job) # Submit the jobs to be run # Note the exception catching to give more information about a job failing for job in jobs: time_start = time.time() try: print "INFO: Creating job " + job.getJobname() + " on " + backend + " backend, with " + group + " group" job.createJob(group) print "INFO: Submitting job " + job.getJobname() job.submitJob() except (JobsException), error: print "HALT: Exception submitting job!" print "Job: " + job.getJobname() + ", Error: " + error.getFailures().get(job).getLocalizedMessage() print"========================"
submitted_jobs = [] # better make that unique for each run, so we can resume workflows easier if necessary (this introduces quite a bit more complexity though) jobname_base = 'staging_test' for total in range(1, amount_of_jobs_total+1): job = JobObject(si) job.setJobname(jobname_base+'_'+str(total)) # always good to set the application if you know it, processing the job will be faster job.setApplication('UnixCommands') # also good to set queue if you know where you want to submit your job, not necessary, but processing of the job will be faster job.setSubmissionLocation('default:gram5.ceres.auckland.ac.nz') # create a random sized outfile mbsize = 1024*1024 random_size = random.randrange(10, 100) size_string = str(mbsize*random_size) job.setCommandline('dd if=/dev/zero of=outfile bs='+size_string+' count=1') job.createJob('/nz/nesi') job.submitJob() print 'created and submitted job: '+ job.getJobname()+' (size: '+str(random_size)+'mb)' submitted_jobs.append(job) print 'Submission finished' sys.exit(0)
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: print "Creating jobs on the backend and staging files..." batchJob.prepareAndCreateJobs(True) except (JobsException), error: for job in error.getFailures().keySet(): print "Job: "+job.getJobname()+", Error: "+error.getFailures().get(job).getLocalizedMessage() sys.exit() # this is not really needed print "Job distribution:" for subLoc in batchJob.getOptimizationResult().keySet(): print subLoc + " : " +batchJob.getOptimizationResult().get(subLoc) print "Submitting jobs..." batchJob.submit(True) print 'Submission finished.' print 'Name of submitted batchjob: '+batchJobName
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: print "Creating jobs on the backend and staging files..." batchJob.prepareAndCreateJobs(True) except (JobsException), error: for job in error.getFailures().keySet(): print "Job: " + job.getJobname() + ", Error: " + error.getFailures( ).get(job).getLocalizedMessage() sys.exit() # this is not really needed print "Job distribution:" for subLoc in batchJob.getOptimizationResult().keySet(): print subLoc + " : " + batchJob.getOptimizationResult().get(subLoc) print "Submitting jobs..." batchJob.submit(True) print 'Submission finished.' print 'Name of submitted batchjob: ' + batchJobName
jobnames = [] for i in range(10): file = folder+'test'+str(i)+'.txt' job = JobObject(si); job.setUniqueJobname('diff_'+str(i)) job.setApplication('UnixCommands') job.setCommandline('diff original.txt test'+str(i)+'.txt') job.createJob("/ARCS/BeSTGRID") job.addInputFileUrl(file) job.addInputFileUrl(original) job.submitJob() jobnames.append(job.getJobname()) for jobname in jobnames: finished = job.waitForJobToFinish(10) print 'Job: '+jobname print print 'Stdout:' print job.getStdOutContent() print print 'Stderr:' print job.getStdErrContent() print print
@author: markus ''' from grisu.frontend.control.login import LoginManager from grisu.frontend.model.job import JobObject import sys si = LoginManager.loginCommandline() print 'Creating job...' # create the job object job = JobObject(si); # set a unique jobname job.setUniqueJobname("echo_job1") print 'Set jobname to: '+ job.getJobname() # set the name of the application like it is published in mds. "generic" means not to use mds for the lookup. job.setApplication("generic") # since we are using a "generic" job, we need to specify a submission location. I'll make that easier later on... job.setSubmissionLocation("dque@edda-m:ng2.vpac.org") # set the commandline that needs to be executed job.setCommandline("echo \"Hello World\"") job.addInputFileUrl('/home/markus/test/singleJobFile_0.txt'); # create the job on the backend and specify the VO to use job.createJob("/ARCS/NGAdmin") print 'Submitting job...' # submit the job job.submitJob()
script = folder + 'wrap.sh' job = JobObject(si); job.setUniqueJobname('diff_wrap') job.setApplication('UnixCommands') job.setCommandline('sh wrap.sh 0 9') job.addInputFileUrl(original) job.addInputFileUrl(script) for i in range(10): file = folder+'test'+str(i)+'.txt' job.addInputFileUrl(file) job.createJob("/ARCS/BeSTGRID") job.submitJob() finished = job.waitForJobToFinish(10) print 'Job: '+job.getJobname() print print 'Stdout:' print job.getStdOutContent() print print 'Stderr:' print job.getStdErrContent() print print sys.exit()
# better make that unique for each run, so we can resume workflows easier if necessary (this introduces quite a bit more complexity though) jobname_base = 'workflow_test' for total in range(1, amount_of_jobs_total + 1): job = JobObject(si) job.setJobname(jobname_base + '_' + str(total)) # always good to set the application if you know it, processing the job will be faster job.setApplication('UnixCommands') # also good to set queue if you know where you want to submit your job, not necessary, but processing of the job will be faster job.setSubmissionLocation('default:gram5.ceres.auckland.ac.nz') # job sleeps for a random time random_sleep = random.randrange(5, 75) job.setCommandline('sleep ' + str(random_sleep)) job.createJob('/nz/nesi') print 'created job: ' + job.getJobname() + ' (sleeptime: ' + str( random_sleep) + ')' created_jobs.append(job) finished = False while not finished: # submit another bunch of jobs while there are some if len(created_jobs) > 0: print 'still ' + str(len(created_jobs)) + ' jobs to submit...' while len(submitted_jobs) < amount_of_jobs_concurrent: if len(created_jobs) <= 0: break
original = folder + 'original.txt' script = folder + 'wrap.sh' job = JobObject(si) job.setUniqueJobname('diff_wrap') job.setApplication('UnixCommands') job.setCommandline('sh wrap.sh 0 9') job.addInputFileUrl(original) job.addInputFileUrl(script) for i in range(10): file = folder + 'test' + str(i) + '.txt' job.addInputFileUrl(file) job.createJob("/ARCS/BeSTGRID") job.submitJob() finished = job.waitForJobToFinish(10) print 'Job: ' + job.getJobname() print print 'Stdout:' print job.getStdOutContent() print print 'Stderr:' print job.getStdErrContent() print print sys.exit()