def start_pilot_job(self,
lrms_url,
bigjob_agent_executable=None,
number_nodes=1,
queue=None,
project=None,
working_directory=None,
userproxy=None,
walltime=None,
processes_per_node=1,
filetransfers=None):
""" Start a batch job (using SAGA Job API) at resource manager. Currently, the following resource manager are supported:
fork://localhost/ (Default Job Adaptor
gram://qb1.loni.org/jobmanager-pbs (Globus Adaptor)
pbspro://localhost (PBS Prop Adaptor)
"""
if self.job != None:
raise BigJobError("One BigJob already active. Please stop BigJob first.")
return
##############################################################################
# initialization of coordination and communication subsystem
# Communication & Coordination initialization
lrms_saga_url = saga.url(lrms_url)
self.pilot_url = self.app_url + ":" + lrms_saga_url.host
pilot_url_dict[self.pilot_url]=self
logger.debug("create pilot job entry on backend server: " + self.pilot_url)
self.coordination.set_pilot_state(self.pilot_url, str(Unknown), False)
logger.debug("set pilot state to: " + str(Unknown))
##############################################################################
self.number_nodes=int(number_nodes)
# create job description
jd = saga.job.description()
logger.debug("Adaptor specific modifications: " + str(lrms_saga_url.scheme))
if lrms_saga_url.scheme == "condorg":
jd.arguments = [ "-a", self.coordination.get_address(), "-b",self.pilot_url]
logger.debug("\n\n-a", self.coordination.get_address(),"-b", self.pilot_url)
agent_exe = os.path.abspath(os.path.join(os.getcwd(),"..","bootstrap","bigjob-condor-bootstrap.py"))
logger.debug(agent_exe)
jd.executable = agent_exe
else:
bootstrap_script = self.generate_bootstrap_script(self.coordination.get_address(), self.pilot_url)
if lrms_saga_url.scheme == "gram":
bootstrap_script = self.escape_rsl(bootstrap_script)
elif lrms_saga_url.scheme == "pbspro":
bootstrap_script = self.escape_pbs(bootstrap_script)
elif lrms_saga_url.scheme == "ssh":
bootstrap_script = self.escape_ssh(bootstrap_script)
############ submit pbs script which launches bigjob agent using ssh adaptors##########
elif lrms_saga_url.scheme == "pbs-ssh":
# change the url scheme ssh to use ssh adaptors to launch job
bootstrap_script = self.escape_ssh(bootstrap_script)
### convert walltime in minutes to PBS representation of time ###
hrs=walltime/60
minu=walltime%60
walltimepbs=""+str(hrs)+":"+str(minu)+":00"
if number_nodes%processes_per_node == 0:
number_nodes = number_nodes/processes_per_node
else:
number_nodes = ( number_nodes/processes_per_node) + 1
pbssshj = pbsssh(bootstrap_script,lrms_saga_url, walltimepbs,number_nodes,processes_per_node,userproxy,working_directory)
self.job = pbssshj
self.job.run()
return
elif is_bliss:
bootstrap_script = self.escape_bliss(bootstrap_script)
#logger.debug(bootstrap_script)
if is_bliss==False:
jd.number_of_processes = str(number_nodes)
jd.processes_per_host=str(processes_per_node)
else:
jd.TotalCPUCount=str(int(number_nodes)*int(processes_per_node))
jd.spmd_variation = "single"
#jd.arguments = [bigjob_agent_executable, self.coordination.get_address(), self.pilot_url]
jd.arguments = ["-c", bootstrap_script]
jd.executable = "python"
if queue != None:
jd.queue = queue
if project !=None:
jd.job_project = [project]
if walltime!=None:
jd.wall_time_limit=str(walltime)
# XXX Isn't the working directory about the remote site?
if working_directory != None:
if not os.path.isdir(working_directory) and lrms_saga_url.scheme=="fork":
os.mkdir(working_directory)
self.working_directory = working_directory
else:
self.working_directory = os.path.expanduser("~")
jd.working_directory = self.working_directory
logger.debug("Working directory: " + jd.working_directory)
jd.output = os.path.join(self.__get_bigjob_working_dir(), "stdout-bigjob_agent.txt")
jd.error = os.path.join(self.__get_bigjob_working_dir(),"stderr-bigjob_agent.txt")
# Stage BJ Input files
# build target url
bigjob_working_directory_url = "ssh://" + lrms_saga_url.host + self.__get_bigjob_working_dir()
self.__stage_files(filetransfers, bigjob_working_directory_url)
# Submit job
js = None
if userproxy != None and userproxy != '':
s = saga.session()
os.environ["X509_USER_PROXY"]=userproxy
ctx = saga.context("x509")
ctx.set_attribute ("UserProxy", userproxy)
s.add_context(ctx)
logger.debug("use proxy: " + userproxy)
js = saga.job.service(s, lrms_saga_url)
else:
logger.debug("use standard proxy")
js = saga.job.service(lrms_saga_url)
self.job = js.create_job(jd)
logger.debug("Submit pilot job to: " + str(lrms_saga_url))
self.job.run()
def start_pilot_job(self,
lrms_url,
bigjob_agent_executable=None,
number_nodes=1,
queue=None,
project=None,
working_directory=None,
userproxy=None,
walltime=None,
processes_per_node=1,
filetransfers=None):
""" Start a batch job (using SAGA Job API) at resource manager. Currently, the following resource manager are supported:
fork://localhost/ (Default Job Adaptor
gram://qb1.loni.org/jobmanager-pbs (Globus Adaptor)
pbspro://localhost (PBS Prop Adaptor)
"""
if self.job != None:
raise BigJobError("One BigJob already active. Please stop BigJob first.")
return
##############################################################################
# initialization of coordination and communication subsystem
# Communication & Coordination initialization
lrms_saga_url = saga.url(lrms_url)
self.pilot_url = self.app_url + ":" + lrms_saga_url.host
pilot_url_dict[self.pilot_url]=self
logger.debug("create pilot job entry on backend server: " + self.pilot_url)
self.coordination.set_pilot_state(self.pilot_url, str(Unknown), False)
logger.debug("set pilot state to: " + str(Unknown))
##############################################################################
self.number_nodes=int(number_nodes)
# create job description
jd = saga.job.description()
# XXX Isn't the working directory about the remote site?
# Yes, it is: This is to make sure that if fork
if working_directory != None:
if not os.path.isdir(working_directory) and lrms_saga_url.scheme=="fork":
os.mkdir(working_directory)
self.working_directory = working_directory
else:
# if no working dir is set assume use home directory
# will fail if home directory is not the same on remote machine
# but this is just a guess to avoid failing
self.working_directory = os.path.expanduser("~")
# Stage BJ Input files
# build target url
# this will also create the remote directory for the BJ
if lrms_saga_url.username!=None and lrms_saga_url.username!="":
bigjob_working_directory_url = "ssh://" + lrms_saga_url.username + "@" + lrms_saga_url.host + self.__get_bigjob_working_dir()
else:
bigjob_working_directory_url = "ssh://" + lrms_saga_url.host + self.__get_bigjob_working_dir()
# determine working directory of bigjob
# if a remote sandbox can be created via ssh => create a own dir for each bj job id
# otherwise use specified working directory
if self.__create_remote_directory(bigjob_working_directory_url)==True:
self.working_directory = self.__get_bigjob_working_dir()
self.__stage_files(filetransfers, bigjob_working_directory_url)
else:
logger.warn("For file staging. SSH (incl. password-less authentication is required.")
logger.debug("BJ Working Directory: %s", self.working_directory)
logger.debug("Adaptor specific modifications: " + str(lrms_saga_url.scheme))
if lrms_saga_url.scheme == "condorg":
jd.arguments = [ self.coordination.get_address(), self.pilot_url]
agent_exe = os.path.abspath(os.path.join(os.path.dirname(__file__),"..","bootstrap","bigjob-condor-bootstrap.py"))
logger.debug("agent_exe",agent_exe)
jd.executable = agent_exe
else:
bootstrap_script = self.generate_bootstrap_script(self.coordination.get_address(), self.pilot_url)
if lrms_saga_url.scheme == "gram":
bootstrap_script = self.escape_rsl(bootstrap_script)
elif lrms_saga_url.scheme == "pbspro" or lrms_saga_url.scheme=="xt5torque" or lrms_saga_url.scheme=="torque":
bootstrap_script = self.escape_pbs(bootstrap_script)
elif lrms_saga_url.scheme == "ssh":
bootstrap_script = self.escape_ssh(bootstrap_script)
############ submit pbs script which launches bigjob agent using ssh adaptors##########
elif lrms_saga_url.scheme == "pbs-ssh":
bootstrap_script = self.escape_ssh(bootstrap_script)
# PBS specific BJ plugin
pbssshj = pbsssh(bootstrap_script, lrms_saga_url, walltime, number_nodes,
processes_per_node, userproxy, self.working_directory, self.working_directory)
self.job = pbssshj
self.job.run()
return
############ submit sge script which launches bigjob agent using ssh adaptors##########
elif lrms_saga_url.scheme == "sge-ssh":
bootstrap_script = self.escape_ssh(bootstrap_script)
# PBS specific BJ plugin
sgesshj = sgessh(bootstrap_script, lrms_saga_url, walltime, number_nodes,
processes_per_node, userproxy, project, queue, self.working_directory, self.working_directory)
self.job = sgesshj
self.job.run()
return
elif is_bliss:
bootstrap_script = self.escape_bliss(bootstrap_script)
#logger.debug(bootstrap_script)
if is_bliss==False:
jd.number_of_processes = str(number_nodes)
jd.processes_per_host=str(processes_per_node)
else:
jd.TotalCPUCount=str(int(number_nodes)*int(processes_per_node))
jd.spmd_variation = "single"
#jd.arguments = [bigjob_agent_executable, self.coordination.get_address(), self.pilot_url]
jd.arguments = ["python", "-c", bootstrap_script]
jd.executable = "/usr/bin/env"
if queue != None:
jd.queue = queue
if project !=None:
jd.job_project = [project]
if walltime!=None:
jd.wall_time_limit=str(walltime)
jd.working_directory = self.working_directory
logger.debug("Working directory: " + jd.working_directory)
jd.output = os.path.join(self.working_directory, "stdout-bigjob_agent.txt")
jd.error = os.path.join(self.working_directory,"stderr-bigjob_agent.txt")
# Submit job
js = None
if userproxy != None and userproxy != '':
s = saga.session()
os.environ["X509_USER_PROXY"]=userproxy
ctx = saga.context("x509")
ctx.set_attribute ("UserProxy", userproxy)
s.add_context(ctx)
logger.debug("use proxy: " + userproxy)
js = saga.job.service(s, lrms_saga_url)
else:
logger.debug("use standard proxy")
js = saga.job.service(lrms_saga_url)
logger.debug("Creating pilot job with description: %s" % str(jd))
self.job = js.create_job(jd)
logger.debug("Submit pilot job to: " + str(lrms_saga_url))
self.job.run()
return self.pilot_url