def startJob(self, params):
work_dir = params['working_directory']
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()
try:
ret = self.job._ret
if ret:
job_id = int(ret)
except ValueError:
end_machine()
raise ModuleError(self, "Error submitting job: %s" % ret)
return params
def startJob(self, params):
work_dir = params['working_directory']
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()
try:
ret = self.job._ret
if ret:
job_id = int(ret)
except ValueError:
end_machine()
raise ModuleError(self, "Error submitting job: %s" % ret)
return params
class RunPBSScript(JobMixin,Module):
_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)'),
]
def getId(self, params):
return hashlib.md5(params['input_directory'] +
params['command'] +
params['working_directory']).hexdigest()
def readInputs(self):
self.job = None
d = {}
if not self.hasInputFromPort('machine'):
raise ModuleError(self, "No machine specified")
self.machine = self.getInputFromPort('machine').machine
if not self.hasInputFromPort('command'):
raise ModuleError(self, "No command specified")
d['command'] = self.getInputFromPort('command').strip()
d['working_directory'] = self.getInputFromPort('working_directory') \
if self.hasInputFromPort('working_directory') else '.'
if not self.hasInputFromPort('input_directory'):
raise ModuleError(self, "No input directory specified")
d['input_directory'] = self.getInputFromPort('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.hasInputFromPort(k):
d['additional_arguments'][k] = self.getInputFromPort(k)
return d
def startJob(self, params):
work_dir = params['working_directory']
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()
try:
ret = self.job._ret
if ret:
job_id = int(ret)
except ValueError:
end_machine()
raise ModuleError(self, "Error submitting job: %s" % ret)
return params
def getMonitor(self, params):
if not self.job:
self.startJob(params)
return self.job
def finishJob(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()
stdout = self.job.standard_output()
stderr = self.job.standard_error()
return {'stdout':stdout, 'stderr':stderr}
def setResults(self, params):
self.setResult('stdout', params['stdout'])
self.setResult('stderr', params['stderr'])
class RunPBSScript(JobMixin, Module):
_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)'),
]
def getId(self, params):
return hashlib.md5(params['input_directory'] + params['command'] +
params['working_directory']).hexdigest()
def readInputs(self):
self.job = None
d = {}
if not self.hasInputFromPort('machine'):
raise ModuleError(self, "No machine specified")
self.machine = self.getInputFromPort('machine').machine
if not self.hasInputFromPort('command'):
raise ModuleError(self, "No command specified")
d['command'] = self.getInputFromPort('command').strip()
d['working_directory'] = self.getInputFromPort('working_directory') \
if self.hasInputFromPort('working_directory') else '.'
if not self.hasInputFromPort('input_directory'):
raise ModuleError(self, "No input directory specified")
d['input_directory'] = self.getInputFromPort('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.hasInputFromPort(k):
d['additional_arguments'][k] = self.getInputFromPort(k)
return d
def startJob(self, params):
work_dir = params['working_directory']
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()
try:
ret = self.job._ret
if ret:
job_id = int(ret)
except ValueError:
end_machine()
raise ModuleError(self, "Error submitting job: %s" % ret)
return params
def getMonitor(self, params):
if not self.job:
self.startJob(params)
return self.job
def finishJob(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()
stdout = self.job.standard_output()
stderr = self.job.standard_error()
return {'stdout': stdout, 'stderr': stderr}
def setResults(self, params):
self.setResult('stdout', params['stdout'])
self.setResult('stderr', params['stderr'])
