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
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
batch_job_name = "test_batch";
# create the batchjob
batch_job = BatchJobObject(si, batch_job_name, "/nz/nesi", "UnixCommands", Constants.NO_VERSION_INDICATOR_STRING);
# now we can calculate the relative path (from every job directory) to the common input file folder
pathToInputFiles = batch_job.pathToInputFiles()
for i in range(0, numberOfJobs):
# create the single job
job = JobObject(si)
# better to set the application to use explicitely because in that case we don't need to use mds (faster)
job.setCommandline('cat ' + pathToInputFiles+'commonJobFile.txt ' + 'singleJobFile.txt')
# adding a job-specific input file
job.addInputFileUrl("/home/markus/tmp/singleJobFile.txt")
# adding the job to the multijob
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);
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).
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() + " 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!"
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)
batch_job = BatchJobObject(si, batch_job_name, "/nz/nesi", "cat",
Constants.NO_VERSION_INDICATOR_STRING)
# now we can calculate the relative path (from every job directory) to the common input file folder
pathToInputFiles = batchJob.pathToInputFiles()
for i in range(0, numberOfJobs):
# create the single job
job = JobObject(si)
# better to set the application to use explicitely because in that case we don't need to use mds (faster)
job.setCommandline('cat ' + pathToInputFiles + 'commonFile.txt ' +
'singleJobFile.txt')
# adding a job-specific input file
job.addInputFileUrl("/home/markus/tmp/singleJobFile.txt")
# adding the job to the multijob
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:
else:
print 'Not a file: '+line
sys.exit(1)
return files_to_upload
files_to_upload = read_files(files_file)
filemanager = GrisuRegistryManager.getDefault(si).getFileManager()
job = JobObject(si)
job.setSubmissionLocation('pan:pan.nesi.org.nz')
job.setTimestampJobname(jobname_template)
job.setCommandline(commandline)
job.setCpus(cpus)
job.addInputFileUrl('nonmem_wrap.sh')
# 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()
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):
try:
job.addInputFileUrl(arg)
print "Stagin in: " + arg
file.write("stagin in 1" + arg + '\n')
except Exception, e:
print "Cannot stage in: " + arg
print e
job.kill(True)
sys.exit(-3)
elif ((os.path.exists(arg)) or (os.path.isfile(arg)==True)) and (arg not in input_files) and ("_file" in arg):
try:
folder=arg.split('/')[len(arg.split('/'))-2]
fil= arg.split('/')[len(arg.split('/'))-1]
argupdate=os.path.join(working_directory,os.path.join((folder.split('.')[0]), fil))
print "argupdate " + argupdate
if(os.path.isfile(argupdate)):
print "Stagin in: " + argupdate
# 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 '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...'
# 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)
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)
finished = job.waitForJobToFinish(10)
if not finished:
print "not finished yet."
# kill the job on the backend anyway
print 'Not a file: ' + line
sys.exit(1)
return files_to_upload
files_to_upload = read_files(files_file)
filemanager = GrisuRegistryManager.getDefault(si).getFileManager()
job = JobObject(si)
job.setSubmissionLocation('pan:pan.nesi.org.nz')
job.setTimestampJobname(jobname_template)
job.setCommandline(commandline)
job.setCpus(cpus)
job.addInputFileUrl('nonmem_wrap.sh')
# 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 "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)
finished = job.waitForJobToFinish(10)
if not finished:
print "not finished yet."
# kill the job on the backend anyway
si = LoginManager.loginCommandline("Local")
folder = '/home/markus/test/batch/'
original = folder + 'original.txt'
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
# 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():
print "Job: " + job.getJobname() + ", Error: " + error.getFailures().get(job).getLocalizedMessage()
sys.exit(1)
from grisu.frontend.control.login import LoginManager
from grisu.frontend.model.job import JobObject
import sys
si = LoginManager.loginCommandline("Local")
folder = '/home/markus/test/batchWrap/'
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 '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...'
# 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);
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)
files_to_upload = read_files(files_file)
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)
from grisu.frontend.control.login import LoginManager
from grisu.frontend.model.job import JobObject
si = LoginManager.loginCommandline("BeSTGRID")
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)
files_to_upload = read_files(files_file)
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 "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 " +
