def prepare(self):
job = JobObject(self.si)
job.setUniqueJobname("echo_job1")
job.setCommandline('echo "Hello World"')
job.createJob()
self.job = job
def prepare(self):
job = JobObject(self.si)
job.setUniqueJobname("echo_job1")
job.setCommandline("echo \"Hello World\"")
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/text0.txt")
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/text0.txt")
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
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()
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
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 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
if not si:
LoginManager.initEnvironment()
si = LoginManager.login('bestgrid', True)
filemanager = GrisuRegistryManager.getDefault(si).getFileManager()
job = JobObject(si)
job.setSubmissionLocation('pan:pan.nesi.org.nz')
job.setTimestampJobname(jobname_template)
job.setCommandline(commandline)
# add input files
for file in files_to_upload:
job.addInputFileUrl(file)
jobname = job.createJob('/nz/nesi')
print 'Submitting job...'
job.submitJob()
print 'Jobname: ' + jobname
print 'Waiting for job to finish...'
job.waitForJobToFinish(jobstate_check_intervall)
job_directory = job.getJobDirectoryUrl()
print 'Job finished, jobdirectory: ' + job_directory
print 'Downloading results'
target = filemanager.downloadUrl(job_directory, File(target_dir), False)
print 'Download finished, download folder: ' + target.getPath()
from grisu.frontend.control.login import LoginManager
from grisu.frontend.model.job import JobObject
si = LoginManager.loginCommandline("BeSTGRID-DEV")
print "Logged in."
job = JobObject(si)
job.setUniqueJobname("cat_job", si)
job.setCommandline("cat text0.txt")
job.addInputFileUrl("/home/markus/tmp/text0.txt")
job.createJob("/nz/nesi")
# job.setSubmissionLocation('[email protected]:ng2.auckland.ac.nz')
job.submitJob()
print "Job submitted."
job.waitForJobToFinish(10)
print "Job finished. Status: " + job.getStatusString(False)
print "Stdout: " + job.getStdOutContent()
print "Stderr: " + job.getStdErrContent()
job.kill(True)
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()
LoginManager.initEnvironment()
si = LoginManager.login('bestgrid', True)
filemanager = GrisuRegistryManager.getDefault(si).getFileManager()
job = JobObject(si)
job.setSubmissionLocation('pan:pan.nesi.org.nz')
job.setTimestampJobname(jobname_template)
job.setCommandline(commandline)
# add input files
for file in files_to_upload:
job.addInputFileUrl(file)
jobname = job.createJob('/nz/nesi')
print 'Submitting job...'
job.submitJob()
print 'Jobname: '+jobname
print 'Waiting for job to finish...'
job.waitForJobToFinish(jobstate_check_intervall)
job_directory = job.getJobDirectoryUrl()
print 'Job finished, jobdirectory: '+job_directory
print 'Downloading results'
target = filemanager.downloadUrl(job_directory, File(target_dir), False)
print 'Download finished, download folder: '+target.getPath()
# 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 = 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...'
# this waits until the job is finished. Checks every 10 seconds (which would be too often for a real job)
finished = job.waitForJobToFinish(10)
if not finished:
print "not finished yet."
# kill the job on the backend anyway
job.kill(True);
else:
print 'Job finished. Status: '+job.getStatusString(False)
# download and cache the jobs' stdout and display it's content
"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 "========================"
time.sleep(3)
error.printStackTrace()
sys.exit(1)
except (BackendException), error:
print "HALT: Exception from grisu backend!"
print "Job: " + job.getJobname() + ", Error: " + error.getFailures(
).get(job).getLocalizedMessage()
print "========================"
print 'Creating job...'
# create the job object
job = JobObject(si);
# set a unique jobname
job.setTimestampJobname("diff_job")
print 'Set jobname to: '+ job.getJobname()
# 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
job.createJob()
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)
job.waitForJobToFinish(10)
print 'Job finished. Status: '+job.getStatusString(False)
# download and cache the jobs' stdout and display it's content
print "Stdout: " + job.getStdOutContent()
# download and cache the jobs' stderr and display it's content
print "Stderr: " + job.getStdErrContent()
# kill and clean the job on the backend
job.kill(True)
# 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
except:
print "Cannot stage nesi job script"
sys.exit(-5)
#open job file
#stage in the job file
for inputs in input_files:
try:
job.addInputFileUrl(inputs)
print "input: " + inputs
except Exception, e:
print "Cannot stage in: " + arg
print e
job.kill(True)
sys.exit(-3)
job.createJob(group)
print "Submitting job..."
try:
job.submitJob()
except Exception, e:
# Just catch all exceptions for time being. TODO
print "Cannot submit job currently."
print e
job.kill(True)
sys.exit(1)
# That's all folks!
sys.exit(0)
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)
finished = job.waitForJobToFinish(10)
if not finished:
print "not finished yet."
# kill the job on the backend anyway
job.kill(True)
else:
print "Job finished. Status: " + job.getStatusString(False)
# download and cache the jobs' stdout and display it's content
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...'
# this waits until the job is finished. Checks every 10 seconds (which would be too often for a real job)
finished = job.waitForJobToFinish(10)
if not finished:
print "not finished yet."
# kill the job on the backend anyway
job.kill(True)
else:
print 'Job finished. Status: ' + job.getStatusString(False)
# download and cache the jobs' stdout and display it's content
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
from grisu.frontend.control.login import LoginManager
from grisu.frontend.model.job import JobObject
si = LoginManager.loginCommandline("BeSTGRID-DEV")
print 'Logged in.'
job = JobObject(si)
job.setUniqueJobname("cat_job", si)
job.setCommandline("cat text0.txt")
job.addInputFileUrl('/home/markus/tmp/text0.txt')
job.createJob("/nz/nesi")
#job.setSubmissionLocation('[email protected]:ng2.auckland.ac.nz')
job.submitJob()
print 'Job submitted.'
job.waitForJobToFinish(10)
print 'Job finished. Status: ' + job.getStatusString(False)
print "Stdout: " + job.getStdOutContent()
print "Stderr: " + job.getStdErrContent()
job.kill(True)
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 'Job finished. Status: ' + job.getStatusString(False)
# download and cache the jobs' stdout and display it's content
print "Stdout: " + job.getStdOutContent()
# download and cache the jobs' stderr and display it's content
print "Stderr: " + job.getStdErrContent()
# kill and clean the job on the backend
job.kill(True)
