def prepare(self):
job = JobObject(self.si)
job.setUniqueJobname("echo_job1")
job.setCommandline("echo \"Hello World\"")
job.addInputFileUrl("/home/markus/tmp/46mbInput0.bin")
job.setApplication(Constants.GENERIC_APPLICATION_NAME)
job.setSubmissionLocation(self.subLoc)
job.createJob()
self.job = job
def prepare(self):
job = JobObject(self.si)
job.setUniqueJobname("echo_job1")
job.setCommandline('echo "Hello World"')
job.addInputFileUrl("/home/markus/tmp/46mbInput0.bin")
job.setApplication(Constants.GENERIC_APPLICATION_NAME)
job.setSubmissionLocation(self.subLoc)
job.createJob()
self.job = job
class simpleStageJob(action):
def __init__(self, si, subLoc=defaultSubLoc):
super(simpleStageJob, self).__init__(si, subLoc)
self.job = JobObject(self.si)
self.job.setCommandline('echo "hello world"')
self.job.setApplication(Constants.GENERIC_APPLICATION_NAME)
self.job.setSubmissionLocation(self.subLoc)
def prepare(self):
self.job.setUniqueJobname(self.name())
self.job.createJob()
def execute(self):
self.job.submitJob()
class simpleStageJob(action):
def __init__(self, si, subLoc=defaultSubLoc):
super(simpleStageJob, self).__init__(si, subLoc)
self.job = JobObject(self.si)
self.job.setCommandline("echo \"hello world\"")
self.job.setApplication(Constants.GENERIC_APPLICATION_NAME)
self.job.setSubmissionLocation(self.subLoc)
def prepare(self):
self.job.setUniqueJobname(self.name())
self.job.createJob()
def execute(self):
self.job.submitJob()
def prepare(self):
job = JobObject(self.si);
job.setUniqueJobname("echo_job1")
job.setCommandline("echo \"Hello World\"")
job.addInputFileUrl("gsiftp://ng2.canterbury.ac.nz/home/gridcloud061/tmp/text0.txt");
job.addInputFileUrl("gsiftp://ng2.canterbury.ac.nz/home/gridcloud061/tmp/text1.txt");
job.addInputFileUrl("gsiftp://ng2.canterbury.ac.nz/home/gridcloud061/tmp/text2.txt");
job.addInputFileUrl("gsiftp://ng2.canterbury.ac.nz/home/gridcloud061/tmp/text3.txt");
job.addInputFileUrl("gsiftp://ng2.canterbury.ac.nz/home/gridcloud061/tmp/text4.txt");
job.setApplication(Constants.GENERIC_APPLICATION_NAME)
job.setSubmissionLocation(self.subLoc)
job.createJob()
self.job = job
def prepare(self):
job = JobObject(self.si)
job.setUniqueJobname("echo_job1")
job.setCommandline("echo \"Hello World\"")
job.addInputFileUrl(
"gsiftp://ng2.canterbury.ac.nz/home/gridcloud061/tmp/text0.txt")
job.addInputFileUrl(
"gsiftp://ng2.canterbury.ac.nz/home/gridcloud061/tmp/text1.txt")
job.addInputFileUrl(
"gsiftp://ng2.canterbury.ac.nz/home/gridcloud061/tmp/text2.txt")
job.addInputFileUrl(
"gsiftp://ng2.canterbury.ac.nz/home/gridcloud061/tmp/text3.txt")
job.addInputFileUrl(
"gsiftp://ng2.canterbury.ac.nz/home/gridcloud061/tmp/text4.txt")
job.setApplication(Constants.GENERIC_APPLICATION_NAME)
job.setSubmissionLocation(self.subLoc)
job.createJob()
self.job = job
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
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()
'''
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()
print 'Waiting for the job to finish...'
exclude_sites.append("AUT")
batch_jobs.setLocationsToExclude(exclude_sites) # Create a blacklist of sites to exclude
# Currently the AUT location is not behaving, so always exclude it
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():
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)
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()
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)
# Since there may be many jobs submitted in the workshop, lets make them a bit unique to avoid issues.
base_job_name = str(random.randint(10000, 99999)) + '-hello-'
print "INFO: Base job name is " + base_job_name
# 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(
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()
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)
amount_of_jobs_total = 10
amount_of_jobs_concurrent = 4
created_jobs = []
submitted_jobs = []
finished_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 = '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:
from grisu.frontend.control.login import LoginManager
from grisu.frontend.model.job import JobObject
from grisu.model import GrisuRegistryManager
si = LoginManager.loginCommandline("LOCAL")
appInfo = GrisuRegistryManager.getDefault(si).getApplicationInformation(
"ImageJ")
print 'app: ' + appInfo.getApplicationName()
for subloc in appInfo.getAvailableAllSubmissionLocations():
print subloc
job = JobObject(si)
job.setTimestampJobname("imageJ")
job.setApplication("java")
job.setApplication("ImageJ")
job.setCommandline("echo Hello")
job.setSubmissionLocation("normal:ng2.ivec.org")
job.createJob("/ARCS/StartUp")
job.submitJob()
job.waitForJobToFinish(3)
print "Stdout: " + job.getStdOutContent()
print "Stderr: " + job.getStdErrContent()
from grisu.frontend.control.login import LoginManager
from grisu.frontend.model.job import JobObject
from grisu.model import GrisuRegistryManager
si = LoginManager.loginCommandline("LOCAL")
appInfo = GrisuRegistryManager.getDefault(si).getApplicationInformation("ImageJ")
print 'app: '+appInfo.getApplicationName()
for subloc in appInfo.getAvailableAllSubmissionLocations():
print subloc
job = JobObject(si);
job.setTimestampJobname("imageJ");
job.setApplication("java");
job.setApplication("ImageJ");
job.setCommandline("echo Hello");
job.setSubmissionLocation("normal:ng2.ivec.org");
job.createJob("/ARCS/StartUp");
job.submitJob();
job.waitForJobToFinish(3);
print "Stdout: "+job.getStdOutContent()
print "Stderr: "+job.getStdErrContent()