def submit_subjob(self,replica_id, jd):
####### submit job via pilot job ######
i=replica_id
if(i < self.RPB):
k=0
sj = subjob()
sj.submit_job(self.bjs[k].pilot_url, jd)
self.job_start_times[sj]=time.time()
self.job_states[sj] = sj.get_state()
return sj
elif((i>=self.RPB) and (i<2*self.RPB)):
k=1
sj = subjob()
sj.submit_job(self.bjs[k].pilot_url, jd)
self.job_start_times[sj]=time.time()
self.job_states[sj] = sj.get_state()
return sj
elif((i>=2*self.RPB) and (i<3*self.RPB)):
k=2
sj = subjob()
sj.submit_job(self.bjs[k].pilot_url, jd)
self.job_start_times[sj]=time.time()
self.job_states[sj] = sj.get_state()
return sj
else:
k=3
sj = subjob()
sj.submit_job(self.bjs[k].pilot_url, jd)
self.job_start_times[sj]=time.time()
self.job_states[sj] = sj.get_state()
return sj
def submit_subjob(self, replica_id, jd):
####### submit job via pilot job ######
i = replica_id
if (i < self.RPB):
k = 0
sj = subjob()
sj.submit_job(self.bjs[k].pilot_url, jd)
self.job_start_times[sj] = time.time()
self.job_states[sj] = sj.get_state()
return sj
elif ((i >= self.RPB) and (i < 2 * self.RPB)):
k = 1
sj = subjob()
sj.submit_job(self.bjs[k].pilot_url, jd)
self.job_start_times[sj] = time.time()
self.job_states[sj] = sj.get_state()
return sj
elif ((i >= 2 * self.RPB) and (i < 3 * self.RPB)):
k = 2
sj = subjob()
sj.submit_job(self.bjs[k].pilot_url, jd)
self.job_start_times[sj] = time.time()
self.job_states[sj] = sj.get_state()
return sj
else:
k = 3
sj = subjob()
sj.submit_job(self.bjs[k].pilot_url, jd)
self.job_start_times[sj] = time.time()
self.job_states[sj] = sj.get_state()
return sj
def main():
# Start BigJob
##########################################################################################
# Edit parameters for BigJob
queue=None # if None default queue is used
project=None # if None default allocation is used
walltime=10
processes_per_node=1
number_of_processes = 1
workingdirectory="." # working directory for agent
userproxy = None # userproxy (not supported yet due to context issue w/ SAGA)
#lrms_url = "ec2+ssh://localhost" # resource url to run on GCE
lrms_url = "gce+ssh://locahost"
##########################################################################################
print "Start Pilot Job/BigJob at: " + lrms_url
bj = bigjob(COORDINATION_URL)
bj.start_pilot_job( lrms_url,
number_of_processes,
queue,
project,
workingdirectory,
userproxy,
walltime,
processes_per_node)
print "Pilot Job/BigJob URL: " + bj.pilot_url + " State: " + str(bj.get_state())
##########################################################################################
# Submit SubJob through BigJob
jd = description()
jd.executable = "/bin/echo"
#jd.executable = "$HOME/hello.sh"
jd.number_of_processes = "1"
jd.arguments = ["$HELLOWORLD"]
jd.environment = ['HELLOWORLD=hello_world']
jd.input_data = ["hi", "ho"]
# specify an optinal working directory if sub-job should be executed outside of bigjob sandbox
#jd.working_directory = "/tmp"
jd.output = "stdout.txt"
jd.error = "stderr.txt"
sj = subjob()
sj.submit_job(bj.pilot_url, jd)
#########################################
# busy wait for completion
while 1:
state = str(sj.get_state())
print "state: " + state
if(state=="Failed" or state=="Done"):
break
time.sleep(2)
##########################################################################################
# Cleanup - stop BigJob
bj.cancel()
def _submit_cu(self, compute_unit):
""" Submits compute unit to Bigjob """
logger.debug("Submit CU to big-job")
sj = subjob()
sj.submit_job(self.__bigjob.pilot_url, compute_unit.subjob_description)
self.__subjobs.append(sj)
compute_unit._update_subjob(sj)
return compute_unit
def _submit_cu(self, compute_unit):
""" Submits compute unit to Bigjob """
logger.debug("Submit CU to big-job")
sj = subjob()
sj.submit_job(self.__bigjob.pilot_url, compute_unit.subjob_description)
self.__subjobs.append(sj)
compute_unit._update_subjob(sj)
return compute_unit
def main():
# Start BigJob
##########################################################################################
# Edit parameters for BigJob
queue = None # if None default queue is used
project = None # if None default allocation is used
walltime = 10
processes_per_node = 8
number_nodes = 24
workingdirectory = os.getcwd() # working directory for agent
userproxy = None # userproxy (not supported yet due to context issue w/ SAGA)
"""
URL of the SAGA Job Service that is used to dispatch the pilot job.
The following URLs are accepted:
lrms_url = "gram://oliver1.loni.org/jobmanager-pbs" # globus resource url used when globus is used. (LONI)
lrms_url = "pbspro://louie1.loni.org" # pbspro resource url used when pbspro scheduling system is used.(Futuregrid or LSU Machines)
lrms_url = "ssh://louie1.loni.org" # ssh resource url which launches jobs on target machine. Jobs not submitted to scheduling system.
lrms_url = "pbs-ssh://louie1.loni.org" # Submit jobs to scheduling system of remote machine.
lrms_url = "xt5torque://localhost" # torque resource url.
Please ensure that the respective SAGA adaptor is installed and working
"""
lrms_url = "pbs://localhost" # resource url to run the jobs on localhost
##########################################################################################
print "Start Pilot Job/BigJob at: " + lrms_url
bj = bigjob(COORDINATION_URL)
bj.start_pilot_job(lrms_url, number_nodes, queue, project,
workingdirectory, userproxy, walltime,
processes_per_node)
print "Pilot Job/BigJob URL: " + bj.pilot_url + " State: " + str(
bj.get_state())
##########################################################################################
# Submit SubJob through BigJob
jd = description()
jd.executable = "/bin/hostname"
jd.number_of_processes = "2"
jd.spmd_variation = "single"
jd.arguments = [""]
#jd.working_directory = "/tmp"
jd.output = "stdout.txt"
jd.error = "stderr.txt"
for i in range(0, 12):
sj = subjob()
sj.submit_job(bj.pilot_url, jd)
##########################################################################################
# Cleanup - stop BigJob
bj.wait()
bj.cancel()
def main():
# Start BigJob
##########################################################################################
# Edit parameters for BigJob
queue = None # if None default queue is used
project = None # if None default allocation is used
walltime = 10
processes_per_node = 1
number_of_processes = 1
workingdirectory = "." # working directory for agent
userproxy = None # userproxy (not supported yet due to context issue w/ SAGA)
#lrms_url = "ec2+ssh://localhost" # resource url to run on GCE
lrms_url = "gce+ssh://locahost"
##########################################################################################
print "Start Pilot Job/BigJob at: " + lrms_url
bj = bigjob(COORDINATION_URL)
bj.start_pilot_job(lrms_url, number_of_processes, queue, project,
workingdirectory, userproxy, walltime,
processes_per_node)
print "Pilot Job/BigJob URL: " + bj.pilot_url + " State: " + str(
bj.get_state())
##########################################################################################
# Submit SubJob through BigJob
jd = description()
jd.executable = "/bin/echo"
#jd.executable = "$HOME/hello.sh"
jd.number_of_processes = "1"
jd.arguments = ["$HELLOWORLD"]
jd.environment = ['HELLOWORLD=hello_world']
jd.input_data = ["hi", "ho"]
# specify an optinal working directory if sub-job should be executed outside of bigjob sandbox
#jd.working_directory = "/tmp"
jd.output = "stdout.txt"
jd.error = "stderr.txt"
sj = subjob()
sj.submit_job(bj.pilot_url, jd)
#########################################
# busy wait for completion
while 1:
state = str(sj.get_state())
print "state: " + state
if (state == "Failed" or state == "Done"):
break
time.sleep(2)
##########################################################################################
# Cleanup - stop BigJob
bj.cancel()
def __submit_cu(self, compute_unit):
""" Submits compute unit to Bigjob """
if len(self.pilot_job_services)!=1:
raise PilotError("No PilotComputeService found. Please start a PCS before submitting ComputeUnits.")
sj = subjob()
self.pcs_coordination_namespace=self.pilot_job_services[0].coordination_queue
logger.debug("Submit CU to big-job via external queue: %s"%self.pcs_coordination_namespace)
sj.submit_job(self.pcs_coordination_namespace, compute_unit.subjob_description)
compute_unit._update_subjob(sj)
return compute_unit
def __init__(self, compute_unit_description=None, compute_data_service=None, cu_url=None):
if cu_url==None:
self.id = self.CU_ID_PREFIX + str(uuid.uuid1())
if compute_data_service!=None:
self.url = compute_data_service.url + "/" + self.id
logger.debug("Created CU: %s"%self.url)
self.state = State.New
self.__subjob = None # reference to BigJob Subjob
self.compute_unit_description = compute_unit_description # CU Description
self.subjob_description = self.__translate_cu_sj_description(compute_unit_description)
else:
self.__subjob = subjob(subjob_url=cu_url)
def __init__(self,
compute_unit_description=None,
compute_data_service=None,
cu_url=None):
if cu_url == None:
self.id = self.CU_ID_PREFIX + str(uuid.uuid1())
if compute_data_service != None:
self.url = compute_data_service.url + "/" + self.id
logger.debug("Created CU: %s" % self.url)
self.state = State.New
self.__subjob = None # reference to BigJob Subjob
self.compute_unit_description = compute_unit_description # CU Description
self.subjob_description = self.__translate_cu_sj_description(
compute_unit_description)
else:
self.__subjob = subjob(subjob_url=cu_url)
project,
workingdirectory,
userproxy,
walltime,
processes_per_node)
print "Pilot Job/BigJob URL: " + bj.get_url() + " State: " + str(bj.get_state())
##########################################################################################
# Submit SubJob through BigJob
jobs = []
job_start_times = {}
job_states = {}
for i in range(0, NUMBER_JOBS):
jd = description()
jd.executable = "/bin/date"
jd.number_of_processes = "1"
jd.spmd_variation = "single"
jd.arguments = [""]
jd.output = "sj-stdout-"+str(i)+".txt"
jd.error = "sj-stderr-"+str(i)+".txt"
sj = subjob()
sj.submit_job(bj.pilot_url, jd)
jobs.append(sj)
job_start_times[sj]=time.time()
job_states[sj] = sj.get_state()
print "Terminating application. You can reconnect to BJ via the following URL: %s"%bj.get_url()
##########################################################################################
# Submit SubJob through BigJob
jobs = []
job_start_times = {}
job_states = {}
for i in range(0, NUMBER_JOBS):
jd = saga.job.description()
jd.executable = "/bin/date"
jd.number_of_processes = "1"
jd.spmd_variation = "single"
jd.arguments = [""]
jd.working_directory = os.getcwd()
jd.output = "sj-stdout-" + str(i) + ".txt"
jd.error = "sj-stderr" + str(i) + ".txt"
sj = subjob(advert_host)
sj.submit_job(bj.pilot_url, jd)
jobs.append(sj)
job_start_times[sj] = time.time()
job_states[sj] = sj.get_state()
# busy wait for completion
while 1:
finish_counter = 0
result_map = {}
for i in range(0, NUMBER_JOBS):
old_state = job_states[jobs[i]]
state = jobs[i].get_state()
if result_map.has_key(state) == False:
result_map[state] = 1
else:
def main():
# Start BigJob
##########################################################################################
# Edit parameters for BigJob
queue=None # if None default queue is used
project=None # if None default allocation is used
walltime=10
processes_per_node=4
number_of_processes = 8
workingdirectory= os.path.join(os.getcwd(), "agent")
userproxy = None # userproxy (not supported yet due to context issue w/ SAGA)
"""
URL of the SAGA Job Service that is used to dispatch the pilot job.
The following URLs are accepted:
lrms_url = "gram://oliver1.loni.org/jobmanager-pbs" # globus resource url used when globus is used. (LONI)
lrms_url = "pbspro://louie1.loni.org" # pbspro resource url used when pbspro scheduling system is used.(Futuregrid or LSU Machines)
lrms_url = "ssh://louie1.loni.org" # ssh resource url which launches jobs on target machine. Jobs not submitted to scheduling system.
lrms_url = "pbs-ssh://louie1.loni.org" # Submit jobs to scheduling system of remote machine.
lrms_url = "xt5torque://localhost" # torque resource url.
Please ensure that the respective SAGA adaptor is installed and working
"""
lrms_url = "condor://localhost"
##########################################################################################
input_file = os.path.join(os.path.dirname(os.path.abspath(__file__)), "..", "test.txt")
bj_filetransfers = [input_file +" > test.txt"]
print "Start Pilot Job/BigJob at: " + lrms_url
bj = bigjob(COORDINATION_URL)
bj.start_pilot_job( lrms_url,
None,
number_of_processes,
queue,
project,
workingdirectory,
userproxy,
walltime,
processes_per_node,
bj_filetransfers)
print "Pilot Job/BigJob URL: " + bj.pilot_url + " State: " + str(bj.get_state())
##########################################################################################
# Submit SubJob through BigJob
jd = description()
jd.executable = "/bin/cat"
jd.number_of_processes = "1"
jd.spmd_variation = "single"
jd.arguments = ["test.txt"]
#jd.working_directory = ""
jd.output = "sj-stdout.txt"
jd.error = "sj-stderr.txt"
sj = subjob()
sj.submit_job(bj.pilot_url, jd)
#########################################
# busy wait for completion
while 1:
state = str(sj.get_state())
bj_state = bj.get_state()
print "bj state: " + str(bj_state) + " state: " + state
if(state=="Failed" or state=="Done"):
break
time.sleep(2)
##########################################################################################
# Cleanup - stop BigJob
bj.cancel()
def main():
# Start BigJob
##########################################################################################
# Edit parameters for BigJob
queue = "normal" # if None default queue is used
project = None # if None default allocation is used
walltime = 10
processes_per_node = 4
number_of_processes = 8
#workingdirectory=os.path.join(os.getcwd(), "agent") # working directory for agent
workingdirectory = "agent"
userproxy = None # userproxy (not supported yet due to context issue w/ SAGA)
"""
URL of the SAGA Job Service that is used to dispatch the pilot job.
The following URLs are accepted:
lrms_url = "gram://oliver1.loni.org/jobmanager-pbs" # globus resource url used when globus is used. (LONI)
lrms_url = "pbspro://louie1.loni.org" # pbspro resource url used when pbspro scheduling system is used.(Futuregrid or LSU Machines)
lrms_url = "ssh://louie1.loni.org" # ssh resource url which launches jobs on target machine. Jobs not submitted to scheduling system.
lrms_url = "pbs-ssh://louie1.loni.org" # Submit jobs to scheduling system of remote machine.
lrms_url = "xt5torque://localhost" # torque resource url.
Please ensure that the respective SAGA adaptor is installed and working
"""
lrms_url = "ssh://boskop"
#lrms_url = "sge://localhost"
#lrms_url = "fork://localhost"
##########################################################################################
# for i in range(99999):
# js = saga.job.Service (lrms_url)
# j = js.run_job ("/bin/sleep 1000")
# print "%4d: %s" % (i, j.state)
for i in range(99999):
print i
print "Start Pilot Job/BigJob at: " + lrms_url
bj = bigjob(COORDINATION_URL)
bj.start_pilot_job(lrms_url, number_of_processes, queue, project,
workingdirectory, userproxy, walltime,
processes_per_node)
print "Pilot Job/BigJob URL: " + bj.pilot_url + " State: " + str(
bj.get_state())
##########################################################################################
# Submit SubJob through BigJob
jd = description()
jd.executable = "/bin/echo"
#jd.executable = "$HOME/hello.sh"
jd.number_of_processes = "1"
jd.arguments = ["$HELLOWORLD"]
jd.environment = ['HELLOWORLD=hello_world']
#jd.spmd_variation = "mpi"
# specify an optinal working directory if sub-job should be executed outside of bigjob sandbox
#jd.working_directory = "/tmp"
jd.output = "stdout.txt"
jd.error = "stderr.txt"
sj = subjob()
sj.submit_job(bj.pilot_url, jd)
#########################################
# busy wait for completion
while 1:
state = str(sj.get_state())
print "state: " + state
if (state == "Failed" or state == "Done"):
break
time.sleep(2)
##########################################################################################
# Cleanup - stop BigJob
bj.cancel()
sjs = []
cpr = CPR
for i in range(0, NUMBER_REPLICAS):
stage_files(i)
jd = saga.job.description()
# jd.executable = "namd2"
jd.number_of_processes = cpr
jd.spmd_variation = "mpi"
# jd.arguments = ["NPT.conf"]
jd.working_directory = WORK_DIR + "agent/" + str(i) + "/"
# os.system("cp NPT.conf NPT.conf")
jd.arguments = ["NPT.conf"]
jd.output = str(i) + "/stdout-" + str(i) + ".txt"
jd.error = str(i) + "/stderr-" + str(i) + ".txt"
jds.append(jd)
sj = bigjob.subjob(advert_host)
sjs.append(sj)
# prepare config and scp other files to remote machine
NAMD_config(i)
if i < RPB:
j = 0
jd.executable = EXE
copy_with_saga(i)
sjs[i].submit_job(bjs[j].pilot_url, jds[i], str(i))
elif i >= RPB and i < (2 * RPB):
j = 1
jd.executable = EXE1
copy_with_saga(i)
sjs[i].submit_job(bjs[j].pilot_url, jds[i], str(i))
elif i >= (2 * RPB) and i < (3 * RPB):
j = 2
job_states = {}
# Submit Jobs through BigJob
# Here you can add any arguments to each SubJob, change the ouput and error filenames and so on
# change this to your heart's content, but be careful
for i in range(0, NUMBER_JOBS):
jd = description()
jd.executable = "/bin/echo"
jd.number_of_processes = "4"
jd.spmd_variation = "mpi" # for serial codes jd.spmd_variation="single"
jd.arguments = ["$INFRASTRUCTURE"]
jd.environment = ["INFRASTRUCTURE=FutureGrid"]
jd.output = "sj-stdout-"+str(i)+".txt"
jd.error = "sj-stderr-"+str(i)+".txt"
sj = subjob()
jobs.append(sj)
sj.submit_job(bj.pilot_url, jd)
job_start_times[sj]=time.time()
job_states[sj] = sj.get_state()
# busy wait for completion
while 1:
finish_counter=0
result_map = {}
for i in range(0, NUMBER_JOBS):
old_state = job_states[jobs[i]]
state = jobs[i].get_state()
if result_map.has_key(state)==False:
result_map[state]=1
def main():
# Start BigJob
##########################################################################################
# Edit parameters for BigJob
queue=None # if None default queue is used
project=None # if None default allocation is used
walltime=10
processes_per_node=4
number_of_processes = 8
userproxy = None # userproxy (not supported yet due to context issue w/ SAGA)
"""
URL of the SAGA Job Service that is used to dispatch the pilot job.
The following URLs are accepted:
lrms_url = "gram://oliver1.loni.org/jobmanager-pbs" # globus resource url used when globus is used. (LONI)
lrms_url = "pbspro://louie1.loni.org" # pbspro resource url used when pbspro scheduling system is used.(Futuregrid or LSU Machines)
lrms_url = "ssh://louie1.loni.org" # ssh resource url which launches jobs on target machine. Jobs not submitted to scheduling system.
lrms_url = "pbs-ssh://louie1.loni.org" # Submit jobs to scheduling system of remote machine.
lrms_url = "xt5torque://localhost" # torque resource url.
Please ensure that the respective SAGA adaptor is installed and working
"""
lrms_url = "sge-ssh://lonestar.tacc.teragrid.org"
"""
To use Globus Online the working directory must be specified using the following conventions
"""
workingdirectory="go://"+GLOBUS_ONLINE_USER+":"+GLOBUS_ONLINE_PASSWORD+"@globusonline.org?ep=xsede#lonestar4&path=~/bigjob/"
##########################################################################################
print "Start Pilot Job/BigJob at: " + lrms_url
bj = bigjob(COORDINATION_URL)
bj_filetransfers = ["go://"+GLOBUS_ONLINE_USER+":"+GLOBUS_ONLINE_PASSWORD+"@globusonline.org?ep=drelu#MacBook&path=" + os.path.dirname(os.path.abspath(__file__))
+ "/test.txt > BIGJOB_WORK_DIR"]
bj.start_pilot_job( lrms_url,
None,
number_of_processes,
queue,
project,
workingdirectory,
userproxy,
walltime,
processes_per_node,
bj_filetransfers)
print "Pilot Job/BigJob URL: " + bj.pilot_url + " State: " + str(bj.get_state())
##########################################################################################
# Submit SubJob through BigJob
jd = description()
jd.executable = "/bin/cat"
jd.number_of_processes = "1"
jd.spmd_variation = "single"
jd.arguments = ["test.txt"]
jd.output = "stdout.txt"
jd.error = "stderr.txt"
jd.file_transfer = ["go://"+GLOBUS_ONLINE_USER+":"+GLOBUS_ONLINE_PASSWORD+"@globusonline.org?ep=drelu#MacBook&path=" + os.path.dirname(os.path.abspath(__file__))
+ "/test.txt > SUBJOB_WORK_DIR"]
sj = subjob()
sj.submit_job(bj.pilot_url, jd)
#########################################
# busy wait for completion
while 1:
state = str(sj.get_state())
print "state: " + state
if(state=="Failed" or state=="Done"):
break
time.sleep(2)
##########################################################################################
# Cleanup - stop BigJob
bj.cancel()
def main():
# Start BigJob
##########################################################################################
# Edit parameters for BigJob
queue = None # if None default queue is used
project = None # if None default allocation is used
walltime = 10
processes_per_node = 4
number_of_processes = 8
workingdirectory = os.path.join(os.getcwd(),
"agent") # working directory for agent
userproxy = None # userproxy (not supported yet due to context issue w/ SAGA)
"""
URL of the SAGA Job Service that is used to dispatch the pilot job.
The following URLs are accepted:
lrms_url = "gram://oliver1.loni.org/jobmanager-pbs" # globus resource url used when globus is used. (LONI)
lrms_url = "pbspro://louie1.loni.org" # pbspro resource url used when pbspro scheduling system is used.(Futuregrid or LSU Machines)
lrms_url = "ssh://louie1.loni.org" # ssh resource url which launches jobs on target machine. Jobs not submitted to scheduling system.
lrms_url = "pbs-ssh://louie1.loni.org" # Submit jobs to scheduling system of remote machine.
lrms_url = "xt5torque://localhost" # torque resource url.
Please ensure that the respective SAGA adaptor is installed and working
"""
#lrms_url = "fork://localhost" # resource url to run the jobs on localhost
lrms_url = "condorg://brgw1.renci.org:2119/jobmanager-pbs"
#lrms_url = "ssh://[email protected]"
##########################################################################################
print "Start Pilot Job/BigJob at: " + lrms_url
bj = bigjob(COORDINATION_URL)
bj.start_pilot_job(lrms_url, None, number_of_processes, queue, project,
workingdirectory, userproxy, walltime,
processes_per_node)
print "Pilot Job/BigJob URL: " + bj.pilot_url + " State: " + str(
bj.get_state())
##########################################################################################
# Submit SubJob through BigJob
jd = description()
jd.executable = "/bin/date"
jd.number_of_processes = "1"
jd.spmd_variation = "single"
#jd.arguments = ["match -f bgr1.fa -A 0 -r reads_1.fastq -n 4 -T /tmp/ > bfast.matches.file.bgr.1.bmf"]
jd.arguments = [""]
#jd.working_directory = ""
jd.output = "bfast-stdout.txt"
jd.error = "bfast-stderr.txt"
sj = subjob()
sj.submit_job(bj.pilot_url, jd)
#########################################
# busy wait for completion
while 1:
state = str(sj.get_state())
print "state: " + state
if (state == "Failed" or state == "Done"):
break
time.sleep(2)
##########################################################################################
# Cleanup - stop BigJob
bj.cancel()
def main():
# Start BigJob
##########################################################################################
# Edit parameters for BigJob
queue="normal" # if None default queue is used
project=None # if None default allocation is used
walltime=10
processes_per_node=4
number_of_processes = 8
#workingdirectory=os.path.join(os.getcwd(), "agent") # working directory for agent
workingdirectory="agent"
userproxy = None # userproxy (not supported yet due to context issue w/ SAGA)
"""
URL of the SAGA Job Service that is used to dispatch the pilot job.
The following URLs are accepted:
lrms_url = "gram://oliver1.loni.org/jobmanager-pbs" # globus resource url used when globus is used. (LONI)
lrms_url = "pbspro://louie1.loni.org" # pbspro resource url used when pbspro scheduling system is used.(Futuregrid or LSU Machines)
lrms_url = "ssh://louie1.loni.org" # ssh resource url which launches jobs on target machine. Jobs not submitted to scheduling system.
lrms_url = "pbs-ssh://louie1.loni.org" # Submit jobs to scheduling system of remote machine.
lrms_url = "xt5torque://localhost" # torque resource url.
Please ensure that the respective SAGA adaptor is installed and working
"""
lrms_url = "fork://localhost" # resource url to run the jobs on localhost
#lrms_url = "sge://localhost" # resource url to run the jobs on localhost
#lrms_url = "ssh://localhost" # resource url to run the jobs on localhost
##########################################################################################
print "Start Pilot Job/BigJob at: " + lrms_url
bj = bigjob(COORDINATION_URL)
bj.start_pilot_job( lrms_url,
number_of_processes,
queue,
project,
workingdirectory,
userproxy,
walltime,
processes_per_node)
print "Pilot Job/BigJob URL: " + bj.pilot_url + " State: " + str(bj.get_state())
##########################################################################################
# Submit SubJob through BigJob
jd = description()
jd.executable = "/bin/echo"
#jd.executable = "$HOME/hello.sh"
jd.number_of_processes = "1"
jd.arguments = ["$HELLOWORLD"]
jd.environment = ['HELLOWORLD=hello_world']
#jd.spmd_variation = "mpi"
# specify an optinal working directory if sub-job should be executed outside of bigjob sandbox
#jd.working_directory = "/tmp"
jd.output = "stdout.txt"
jd.error = "stderr.txt"
sj = subjob()
sj.submit_job(bj.pilot_url, jd)
#########################################
# busy wait for completion
while 1:
state = str(sj.get_state())
print "state: " + state
if(state=="Failed" or state=="Done"):
break
time.sleep(2)
##########################################################################################
# Cleanup - stop BigJob
bj.cancel()
jds = []
sjs = []
for i in range(0, NUMBER_REPLICAS):
stage_files(i)
jd = saga.job.description()
jd.executable = "namd2"
jd.number_of_processes = "16"
jd.spmd_variation = "mpi"
# jd.arguments = ["NPT.conf"]
jd.working_directory = WORK_DIR + "agent/" + str(i) + "/"
#os.system("cp NPT.conf NPT.conf")
jd.arguments = ["NPT.conf"]
jd.output = str(i) + "/stdout-" + str(i) + ".txt"
jd.error = str(i) + "/stderr-" + str(i) + ".txt"
jds.append(jd)
sj = bigjob.subjob(advert_host)
sjs.append(sj)
#prepare config and scp other files to remote machine
NAMD_config(i)
if i < RPB:
j = 0
copy_with_saga(i)
sjs[i].submit_job(bjs[j].pilot_url, jds[i], str(i))
elif (i >= RPB and i < (2 * RPB)):
j = 1
copy_with_saga(i)
sjs[i].submit_job(bjs[j].pilot_url, jds[i], str(i))
elif (i >= (2 * RPB) and i < (3 * RPB)):
j = 2
copy_with_saga(i)
sjs[i].submit_job(bjs[j].pilot_url, jds[i], str(i))
def main():
# Start BigJob
##########################################################################################
# Edit parameters for BigJob
queue = None # if None default queue is used
project = None # if None default allocation is used
walltime = 10
processes_per_node = 4
number_of_processes = 8
workingdirectory = os.path.join(os.getcwd(), "agent")
userproxy = None # userproxy (not supported yet due to context issue w/ SAGA)
"""
URL of the SAGA Job Service that is used to dispatch the pilot job.
The following URLs are accepted:
lrms_url = "gram://oliver1.loni.org/jobmanager-pbs" # globus resource url used when globus is used. (LONI)
lrms_url = "pbspro://louie1.loni.org" # pbspro resource url used when pbspro scheduling system is used.(Futuregrid or LSU Machines)
lrms_url = "ssh://louie1.loni.org" # ssh resource url which launches jobs on target machine. Jobs not submitted to scheduling system.
lrms_url = "pbs-ssh://louie1.loni.org" # Submit jobs to scheduling system of remote machine.
lrms_url = "xt5torque://localhost" # torque resource url.
Please ensure that the respective SAGA adaptor is installed and working
"""
lrms_url = "condor://localhost"
##########################################################################################
input_file = os.path.join(os.path.dirname(os.path.abspath(__file__)), "..",
"test.txt")
bj_filetransfers = [input_file + " > test.txt"]
print "Start Pilot Job/BigJob at: " + lrms_url
bj = bigjob(COORDINATION_URL)
bj.start_pilot_job(lrms_url, None, number_of_processes, queue, project,
workingdirectory, userproxy, walltime,
processes_per_node, bj_filetransfers)
print "Pilot Job/BigJob URL: " + bj.pilot_url + " State: " + str(
bj.get_state())
##########################################################################################
# Submit SubJob through BigJob
jd = description()
jd.executable = "/bin/cat"
jd.number_of_processes = "1"
jd.spmd_variation = "single"
jd.arguments = ["test.txt"]
#jd.working_directory = ""
jd.output = "sj-stdout.txt"
jd.error = "sj-stderr.txt"
sj = subjob()
sj.submit_job(bj.pilot_url, jd)
#########################################
# busy wait for completion
while 1:
state = str(sj.get_state())
bj_state = bj.get_state()
print "bj state: " + str(bj_state) + " state: " + state
if (state == "Failed" or state == "Done"):
break
time.sleep(2)
##########################################################################################
# Cleanup - stop BigJob
bj.cancel()
sj_nimbus.submit_job(jd_nimbus)
jobs_nimbus.append(sj_nimbus)
number_started_jobs = number_started_jobs + 1
for i in range(0, NUMBER_JOBS_EC2):
print "Start job no.: " +str(number_started_jobs + 1) + " on EC2"
sj_ec2 = bigjob_cloud.subjob(bigjob=bj_ec2)
jd_ec2.output = "stdout_ec2.txt."+str(number_started_jobs+1)
jd_ec2.error = "stderr_ec2.txt."+str(number_started_jobs+1)
sj_ec2.submit_job(jd_ec2)
jobs_ec2.append(sj_ec2)
number_started_jobs = number_started_jobs + 1
for i in range(0, NUMBER_JOBS_GRID):
print "Start job no.: " +str(number_started_jobs + 1) + " on Grid"
sj_tg = bigjob.subjob(advert_host)
jd.output = "stdout_tg.txt."+str(number_started_jobs+1)
jd.error = "stderr_tg.txt."+str(number_started_jobs+1)
sj_tg.submit_job(bj_tg.pilot_url, jd)
jobs_tg.append(sj_tg)
number_started_jobs = number_started_jobs + 1
for i in range(0, NUMBER_JOBS_CONDOR):
print "Start job no.: " +str(number_started_jobs + 1) + " on Condor"
sj_condor = bigjob_condor.subjob(bigjob=bj_condor)
jd_condor.output = "stdout_condor.txt."+str(number_started_jobs+1)
jd_condor.error = "stderr_condor.txt."+str(number_started_jobs+1)
sj_condor.submit_job(jd_condor)
jobs_condor.append(sj_condor)
number_started_jobs = number_started_jobs + 1
