def run_job(self, job_details=None):
JobDeploymentBase.run_job(self)
# This function uses the SAGA-Python library to run the job. Separate
# functionality in the library is used for monitoring the job process.
# TODO: Add modules to PBS job confiuguration
# Here we extract the job details from the previously stored job details
# object into a SAGA Python job description object so that we can run
# the job.
job_arguments = getattr(self.job_config, 'args', [])
input_files = getattr(self, 'transferred_input_files', [])
job_arguments += input_files
jd = saga.job.Description()
jd.environment = getattr(self.job_config, 'environment', {})
jd.executable = getattr(self.job_config, 'executable', None)
jd.arguments = job_arguments
jd.working_directory = getattr(self.job_config, 'working_dir', None)
jd.output = getattr(self.job_config, 'stdout', None)
jd.error = getattr(self.job_config, 'stderr', None)
jd.wall_time_limit = getattr(self.job_config, 'time_limit_mins', 0)
jd.total_cpu_count = getattr(self.job_config, 'num_processes', 1)
#jd.processes_per_host = 1
#jd.total_physical_memory = "2400"
self.job = self.svc.create_job(jd)
self.job.run()
def run_job(self):
JobDeploymentBase.run_job(self)
# This function uses the libhpc resource daemon client to talk to the
# resource daemon that is installed on cloud resources. It uses this
# interface to run jobs and monitor their state to see when they are
# complete.
# TODO: Should this be running/managing the job remotely via a SAGA
# SSH session or should we be expecting to communicate with a remote
# resource management service to handle this?
LOG.debug('Run job...')
job_arguments = getattr(self.job_config, 'args', [])
input_files = getattr(self, 'transferred_input_files', [])
job_arguments += input_files
# Check if we have a JOB_ID variable in the arguments or input files.
# If so, replace this variable with the actual job ID.
job_arguments_tmp = job_arguments
job_arguments = []
for item in job_arguments_tmp:
# Can't do a replace on items that are not string types!
if isinstance(item, basestring):
job_arguments.append(
item.replace('$JOB_ID', self.job_config.job_id))
else:
job_arguments.append(item)
LOG.debug('Modified job arguments: %s' % job_arguments)
jd = saga.job.Description()
jd.environment = getattr(self.job_config, 'environment', {})
if self.job_config.num_processes > 1:
jd.executable = ('mpirun -np %s -machinefile /tmp/machinefile' %
(self.job_config.num_processes))
executable = getattr(self.job_config, 'executable', None)
if executable:
job_arguments.insert(0, executable)
else:
jd.executable = getattr(self.job_config, 'executable', None)
jd.arguments = job_arguments
jd.working_directory = getattr(self.job_config, 'working_dir', None)
jd.output = getattr(self.job_config, 'stdout', None)
jd.error = getattr(self.job_config, 'stderr', None)
jd.wall_time_limit = getattr(self.job_config, 'time_limit_mins', 0)
#jd.number_of_processes = 4
#jd.processes_per_host = 1
#jd.total_physical_memory = "2400"
if not jd.output:
jd.output = 'std.out'
if not jd.error:
jd.error = 'std.err'
self.svc = saga.job.Service('ssh://%s/' %
self.running_nodes[0][0].public_ips[0],
session=self.session)
self.job = self.svc.create_job(jd)
self.job.run()
def run_job(self):
JobDeploymentBase.run_job(self)
# TODO: Should this be running/managing the job remotely via a SAGA
# SSH session or should we be expecting to communicate with a remote
# resource management service to handle this?
# This function could use the libhpc resource daemon client to talk to
# a resource daemon that is installed on the target resource, however,
# at present we simply use SSH (via SAGA Python) to trigger job
# execution and handle compressing and returning the output files.
LOG.debug('SSH Deployer: Run job...')
job_arguments = getattr(self.job_config, 'args', [])
input_files = getattr(self, 'transferred_input_files', [])
job_arguments += input_files
# Check if we have a JOB_ID variable in the arguments or input files.
# If so, replace this variable with the actual job ID.
job_arguments_tmp = job_arguments
job_arguments = []
for item in job_arguments_tmp:
# Can't do a replace on items that are not string types!
if isinstance(item, basestring):
job_arguments.append(
item.replace('$JOB_ID', self.job_config.job_id))
else:
job_arguments.append(item)
LOG.debug('Modified job arguments: %s' % job_arguments)
jd = saga.job.Description()
jd.environment = getattr(self.job_config, 'environment', {})
jd.executable = getattr(self.job_config, 'executable', None)
jd.arguments = job_arguments
jd.working_directory = getattr(self.job_config, 'working_dir', None)
jd.output = getattr(self.job_config, 'stdout', None)
jd.error = getattr(self.job_config, 'stderr', None)
jd.wall_time_limit = getattr(self.job_config, 'time_limit_mins', 0)
if not jd.output:
jd.output = 'std.out'
if not jd.error:
jd.error = 'std.err'
self.svc = saga.job.Service('ssh://%s/' % self.host,
session=self.session)
self.job = self.svc.create_job(jd)
self.job.run()
def run_job(self):
JobDeploymentBase.run_job(self)
# This function uses the libhpc resource daemon client to talk to the
# resource daemon that is installed on cloud resources. It uses this
# interface to run jobs and monitor their state to see when they are
# complete.
# TODO: Should this be running/managing the job remotely via a SAGA
# SSH session or should we be expecting to communicate with a remote
# resource management service to handle this?
LOG.debug('Run job...')
job_arguments = getattr(self.job_config, 'args', [])
input_files = getattr(self, 'transferred_input_files', [])
job_arguments += input_files
jd = Description()
jd.environment = getattr(self.job_config, 'environment', {})
if self.job_config.num_processes > 1:
jd.executable = ('mpirun -np %s -machinefile /tmp/machinefile' %
(self.job_config.num_processes))
executable = getattr(self.job_config, 'executable', None)
if executable:
job_arguments.insert(0, executable)
else:
jd.executable = getattr(self.job_config, 'executable', None)
jd.arguments = job_arguments
jd.working_directory = getattr(self.job_config, 'working_dir', None)
jd.output = getattr(self.job_config, 'stdout', None)
jd.error = getattr(self.job_config, 'stderr', None)
jd.wall_time_limit = getattr(self.job_config, 'time_limit_mins', 0)
#jd.number_of_processes = 4
#jd.processes_per_host = 1
#jd.total_physical_memory = "2400"
if not jd.output:
jd.output = 'std.out'
if not jd.error:
jd.error = 'std.err'
self.svc = Service('ssh://%s/' %
self.running_nodes[0][0].public_ips[0],
session=self.session)
self.job = self.svc.create_job(jd)
self.job.run()
def run_job(self, job_details=None):
JobDeploymentBase.run_job(self)