def job_start(self, params):
work_dir = params['working_directory']
self.machine = self.get_machine()
use_machine(self.machine)
self.cdir = CreateDirectory("remote", work_dir)
trans = TransferFiles("remote",
params['input_directory'],
work_dir,
dependencies=[self.cdir])
self.job = PBSScript("remote",
params['command'],
work_dir,
dependencies=[trans],
**params['additional_arguments'])
self.job.run()
ret = self.job._ret
if ret:
try:
job_id = int(ret.split('\n')[0])
except ValueError:
end_machine()
raise ModuleError(self, "Error submitting job: %s" % ret)
self.set_job_machine(params, self.machine)
return params
def job_start(self, params):
work_dir = params['working_directory']
self.machine = self.get_machine()
use_machine(self.machine)
self.cdir = CreateDirectory("remote", work_dir)
trans = TransferFiles("remote", params['input_directory'], work_dir,
dependencies = [self.cdir])
self.job = PBSScript("remote", params['command'], work_dir,
dependencies = [trans], **params['additional_arguments'])
self.job.run()
ret = self.job._ret
if ret:
try:
job_id = int(ret.split('\n')[0])
except ValueError:
end_machine()
raise ModuleError(self, "Error submitting job: %s" % ret)
self.set_job_machine(params, self.machine)
return params
class RunPBSScript(RQModule):
""" Run a pbs script by submitting it to a PBS scheduler
"""
_input_ports = [('machine', Machine),
('command', '(edu.utah.sci.vistrails.basic:String)', True),
('working_directory', '(edu.utah.sci.vistrails.basic:String)'),
('input_directory', '(edu.utah.sci.vistrails.basic:String)'),
('processes', '(edu.utah.sci.vistrails.basic:Integer)', True),
('time', '(edu.utah.sci.vistrails.basic:String)', True),
('mpi', '(edu.utah.sci.vistrails.basic:Boolean)', True),
('threads', '(edu.utah.sci.vistrails.basic:Integer)', True),
('memory', '(edu.utah.sci.vistrails.basic:String)', True),
('diskspace', '(edu.utah.sci.vistrails.basic:String)', True),
]
_output_ports = [('stdout', '(edu.utah.sci.vistrails.basic:String)'),
('stderr', '(edu.utah.sci.vistrails.basic:String)'),
]
job = None
def job_read_inputs(self):
d = {}
if not self.has_input('command'):
raise ModuleError(self, "No command specified")
d['command'] = self.get_input('command').strip()
d['working_directory'] = self.get_input('working_directory') \
if self.has_input('working_directory') else '.'
if not self.has_input('input_directory'):
raise ModuleError(self, "No input directory specified")
d['input_directory'] = self.get_input('input_directory').strip()
d['additional_arguments'] = {'processes': 1, 'time': -1, 'mpi': False,
'threads': 1, 'memory':-1, 'diskspace': -1}
for k in d['additional_arguments']:
if self.has_input(k):
d['additional_arguments'][k] = self.get_input(k)
return d
def job_start(self, params):
work_dir = params['working_directory']
self.machine = self.get_machine()
use_machine(self.machine)
self.cdir = CreateDirectory("remote", work_dir)
trans = TransferFiles("remote", params['input_directory'], work_dir,
dependencies = [self.cdir])
self.job = PBSScript("remote", params['command'], work_dir,
dependencies = [trans], **params['additional_arguments'])
self.job.run()
ret = self.job._ret
if ret:
try:
job_id = int(ret.split('\n')[0])
except ValueError:
end_machine()
raise ModuleError(self, "Error submitting job: %s" % ret)
self.set_job_machine(params, self.machine)
return params
def job_get_handle(self, params):
if not self.job:
self.job_start(params)
return self.job
def job_finish(self, params):
job_info = self.job.get_job_info()
if job_info:
self.annotate({'job_info': job_info})
# copies the created files to the client
get_result = TransferFiles("local", params['input_directory'],
params['working_directory'],
dependencies = [self.cdir])
get_result.run()
end_machine()
params['stdout'] = self.job.standard_output()
params['stderr'] = self.job.standard_error()
return params
def job_set_results(self, params):
self.set_output('stdout', params['stdout'])
self.set_output('stderr', params['stderr'])
class RunPBSScript(RQModule):
""" Run a pbs script by submitting it to a PBS scheduler
"""
_input_ports = [
('machine', Machine),
('command', '(edu.utah.sci.vistrails.basic:String)', True),
('working_directory', '(edu.utah.sci.vistrails.basic:String)'),
('input_directory', '(edu.utah.sci.vistrails.basic:String)'),
('processes', '(edu.utah.sci.vistrails.basic:Integer)', True),
('time', '(edu.utah.sci.vistrails.basic:String)', True),
('mpi', '(edu.utah.sci.vistrails.basic:Boolean)', True),
('threads', '(edu.utah.sci.vistrails.basic:Integer)', True),
('memory', '(edu.utah.sci.vistrails.basic:String)', True),
('diskspace', '(edu.utah.sci.vistrails.basic:String)', True),
]
_output_ports = [
('stdout', '(edu.utah.sci.vistrails.basic:String)'),
('stderr', '(edu.utah.sci.vistrails.basic:String)'),
]
job = None
def job_read_inputs(self):
d = {}
if not self.has_input('command'):
raise ModuleError(self, "No command specified")
d['command'] = self.get_input('command').strip()
d['working_directory'] = self.get_input('working_directory') \
if self.has_input('working_directory') else '.'
if not self.has_input('input_directory'):
raise ModuleError(self, "No input directory specified")
d['input_directory'] = self.get_input('input_directory').strip()
d['additional_arguments'] = {
'processes': 1,
'time': -1,
'mpi': False,
'threads': 1,
'memory': -1,
'diskspace': -1
}
for k in d['additional_arguments']:
if self.has_input(k):
d['additional_arguments'][k] = self.get_input(k)
return d
def job_start(self, params):
work_dir = params['working_directory']
self.machine = self.get_machine()
use_machine(self.machine)
self.cdir = CreateDirectory("remote", work_dir)
trans = TransferFiles("remote",
params['input_directory'],
work_dir,
dependencies=[self.cdir])
self.job = PBSScript("remote",
params['command'],
work_dir,
dependencies=[trans],
**params['additional_arguments'])
self.job.run()
ret = self.job._ret
if ret:
try:
job_id = int(ret.split('\n')[0])
except ValueError:
end_machine()
raise ModuleError(self, "Error submitting job: %s" % ret)
self.set_job_machine(params, self.machine)
return params
def job_get_handle(self, params):
if not self.job:
self.job_start(params)
return self.job
def job_finish(self, params):
job_info = self.job.get_job_info()
if job_info:
self.annotate({'job_info': job_info})
# copies the created files to the client
get_result = TransferFiles("local",
params['input_directory'],
params['working_directory'],
dependencies=[self.cdir])
get_result.run()
end_machine()
params['stdout'] = self.job.standard_output()
params['stderr'] = self.job.standard_error()
return params
def job_set_results(self, params):
self.set_output('stdout', params['stdout'])
self.set_output('stderr', params['stderr'])