Exemple #1
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    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
Exemple #2
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    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
Exemple #3
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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()
Exemple #4
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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()
Exemple #5
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    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        
Exemple #6
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    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
Exemple #7
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    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
Exemple #8
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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()
Exemple #9
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'''

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():
Exemple #11
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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)
Exemple #12
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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)
Exemple #13
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# 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(
Exemple #14
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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:
Exemple #16
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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()
Exemple #17
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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()