import sqlalchemy
from sqlalchemy import Table, Column, Integer, DateTime, String, Boolean, ForeignKey
from sqlalchemy.orm import backref
from sqlalchemy.ext.declarative import declarative_base
from .tools import Enum, relationship
import os
import sys
from datetime import datetime
if sys.version_info[0] >= 3:
from pickle import dumps, loads
else:
from cPickle import dumps, loads
from .tools import logger
Base = declarative_base()
Status = ('submitted', 'queued', 'waiting', 'executing', 'success', 'failure')
[docs]class ArrayJob(Base):
"""This class defines one element of an array job."""
__tablename__ = 'ArrayJob'
unique = Column(Integer, primary_key = True)
id = Column(Integer)
job_id = Column(Integer, ForeignKey('Job.unique'))
status = Column(Enum(*Status))
result = Column(Integer)
machine_name = Column(String(10))
submit_time = Column(DateTime)
start_time = Column(DateTime)
finish_time = Column(DateTime)
job = relationship("Job", backref='array', order_by=id)
def __init__(self, id, job_id):
self.id = id
self.job_id = job_id
self.status = Status[0]
self.result = None
self.machine_name = None # will be set later, by the Job class
self.submit_time = datetime.now()
self.start_time = None
self.finish_time = None
[docs] def std_out_file(self):
return self.job.std_out_file() + "." + str(self.id) if self.job.log_dir else None
[docs] def std_err_file(self):
return self.job.std_err_file() + "." + str(self.id) if self.job.log_dir else None
def __str__(self):
n = "<ArrayJob %d> of <Job %d>" % (self.id, self.job.id)
if self.result is not None: r = "%s (%d)" % (self.status, self.result)
else: r = "%s" % self.status
return "%s : %s" % (n, r)
[docs]class Job(Base):
"""This class defines one Job that was submitted to the Job Manager."""
__tablename__ = 'Job'
unique = Column(Integer, primary_key = True) # The unique ID of the job (not corresponding to the grid ID)
command_line = Column(String(255)) # The command line to execute, converted to one string
name = Column(String(20)) # A hand-chosen name for the task
queue_name = Column(String(20)) # The name of the queue
machine_name = Column(String(10)) # The name of the machine in which the job is run
grid_arguments = Column(String(255)) # The kwargs arguments for the job submission (e.g. in the grid)
id = Column(Integer) # The ID of the job as given from the grid
exec_dir = Column(String(255)) # The directory in which the command should be executed
log_dir = Column(String(255)) # The directory where the log files will be put to
array_string = Column(String(255)) # The array string (only needed for re-submission)
stop_on_failure = Column(Boolean) # An indicator whether to stop depending jobs when this job finishes with an error
submit_time = Column(DateTime)
start_time = Column(DateTime)
finish_time = Column(DateTime)
status = Column(Enum(*Status))
result = Column(Integer)
def __init__(self, command_line, name = None, exec_dir = None, log_dir = None, array_string = None, queue_name = 'local', machine_name = None, stop_on_failure = False, **kwargs):
"""Constructs a Job object without an ID (needs to be set later)."""
self.command_line = dumps(command_line)
self.name = name
self.queue_name = queue_name # will be set during the queue command later
self.machine_name = machine_name # will be set during the execute command later
self.grid_arguments = dumps(kwargs)
self.exec_dir = exec_dir
self.log_dir = log_dir
self.stop_on_failure = stop_on_failure
self.array_string = dumps(array_string)
self.submit()
[docs] def submit(self, new_queue = None):
"""Sets the status of this job to 'submitted'."""
self.status = 'submitted'
self.result = None
self.machine_name = None
if new_queue is not None:
self.queue_name = new_queue
for array_job in self.array:
array_job.status = 'submitted'
array_job.result = None
array_job.machine_name = None
self.submit_time = datetime.now()
self.start_time = None
self.finish_time = None
[docs] def queue(self, new_job_id = None, new_job_name = None, queue_name = None):
"""Sets the status of this job to 'queued' or 'waiting'."""
# update the job id (i.e., when the job is executed in the grid)
if new_job_id is not None:
self.id = new_job_id
if new_job_name is not None:
self.name = new_job_name
if queue_name is not None:
self.queue_name = queue_name
new_status = 'queued'
self.result = None
# check if we have to wait for another job to finish
for job in self.get_jobs_we_wait_for():
if job.status not in ('success', 'failure'):
new_status = 'waiting'
elif self.stop_on_failure and job.status == 'failure':
new_status = 'failure'
# reset the queued jobs that depend on us to waiting status
for job in self.get_jobs_waiting_for_us():
if job.status == 'queued':
job.status = 'failure' if new_status == 'failure' else 'waiting'
self.status = new_status
for array_job in self.array:
if array_job.status not in ('success', 'failure'):
array_job.status = new_status
[docs] def execute(self, array_id = None, machine_name = None):
"""Sets the status of this job to 'executing'."""
self.status = 'executing'
if array_id is not None:
for array_job in self.array:
if array_job.id == array_id:
array_job.status = 'executing'
if machine_name is not None:
array_job.machine_name = machine_name
array_job.start_time = datetime.now()
elif machine_name is not None:
self.machine_name = machine_name
if self.start_time is None:
self.start_time = datetime.now()
# sometimes, the 'finish' command did not work for array jobs,
# so check if any old job still has the 'executing' flag set
for job in self.get_jobs_we_wait_for():
if job.array and job.status == 'executing':
job.finish(0, -1)
[docs] def finish(self, result, array_id = None):
"""Sets the status of this job to 'success' or 'failure'."""
# check if there is any array job still running
new_status = 'success' if result == 0 else 'failure'
new_result = result
finished = True
if array_id is not None:
for array_job in self.array:
if array_job.id == array_id:
array_job.status = new_status
array_job.result = result
array_job.finish_time = datetime.now()
if array_job.status not in ('success', 'failure'):
finished = False
elif new_result == 0:
new_result = array_job.result
if finished:
# There was no array job, or all array jobs finished
self.status = 'success' if new_result == 0 else 'failure'
self.result = new_result
self.finish_time = datetime.now()
# update all waiting jobs
for job in self.get_jobs_waiting_for_us():
if job.status == 'waiting':
job.queue()
[docs] def refresh(self):
"""Refreshes the status information."""
if self.status == 'executing' and self.array:
new_result = 0
for array_job in self.array:
if array_job.status == 'failure' and new_result is not None:
new_result = array_job.result
elif array_job.status not in ('success', 'failure'):
new_result = None
if new_result is not None:
self.status = 'success' if new_result == 0 else 'failure'
self.result = new_result
[docs] def get_command_line(self):
"""Returns the command line for the job."""
# In python 2, the command line is unicode, which needs to be converted to string before pickling;
# In python 3, the command line is bytes, which can be pickled directly
return loads(self.command_line) if isinstance(self.command_line, bytes) else loads(self.command_line.encode())
[docs] def set_command_line(self, command_line):
"""Sets / overwrites the command line for the job."""
self.command_line = dumps(command_line)
[docs] def get_exec_dir(self):
"""Returns the command line for the job."""
# In python 2, the command line is unicode, which needs to be converted to string before pickling;
# In python 3, the command line is bytes, which can be pickled directly
return str(os.path.realpath(self.exec_dir)) if self.exec_dir is not None else None
[docs] def get_array(self):
"""Returns the array arguments for the job; usually a string."""
# In python 2, the command line is unicode, which needs to be converted to string before pickling;
# In python 3, the command line is bytes, which can be pickled directly
return loads(self.array_string) if isinstance(self.array_string, bytes) else loads(self.array_string.encode())
[docs] def get_arguments(self):
"""Returns the additional options for the grid (such as the queue, memory requirements, ...)."""
# In python 2, the command line is unicode, which needs to be converted to string before pickling;
# In python 3, the command line is bytes, which can be pickled directly
args = loads(self.grid_arguments)['kwargs'] if isinstance(self.grid_arguments, bytes) else loads(self.grid_arguments.encode())['kwargs']
# in any case, the commands have to be converted to str
retval = {}
if 'pe_opt' in args:
retval['pe_opt'] = args['pe_opt']
if 'memfree' in args and args['memfree'] is not None:
retval['memfree'] = args['memfree']
if 'hvmem' in args and args['hvmem'] is not None:
retval['hvmem'] = args['hvmem']
if 'gpumem' in args and args['gpumem'] is not None:
retval['gpumem'] = args['gpumem']
if 'env' in args and len(args['env']) > 0:
retval['env'] = args['env']
if 'io_big' in args and args['io_big']:
retval['io_big'] = True
# also add the queue
if self.queue_name is not None:
retval['queue'] = str(self.queue_name)
return retval
[docs] def set_arguments(self, **kwargs):
self.grid_arguments = dumps(kwargs)
[docs] def get_jobs_we_wait_for(self):
return [j.waited_for_job for j in self.jobs_we_have_to_wait_for if j.waited_for_job is not None]
[docs] def get_jobs_waiting_for_us(self):
return [j.waiting_job for j in self.jobs_that_wait_for_us if j.waiting_job is not None]
[docs] def std_out_file(self, array_id = None):
return os.path.join(self.log_dir, (self.name if self.name else 'job') + ".o" + str(self.id)) if self.log_dir else None
[docs] def std_err_file(self, array_id = None):
return os.path.join(self.log_dir, (self.name if self.name else 'job') + ".e" + str(self.id)) if self.log_dir else None
def _cmdline(self):
cmdline = self.get_command_line()
c = ""
for cmd in cmdline:
if cmd[0] == '-':
c += "%s " % cmd
else:
c += "'%s' " % cmd
return c
def __str__(self):
id = "%d (%d)" % (self.unique, self.id)
if self.machine_name: m = "%s - %s" % (self.queue_name, self.machine_name)
else: m = self.queue_name
if self.array: a = "[%d-%d:%d]" % self.get_array()
else: a = ""
if self.name is not None: n = "<Job: %s %s - '%s'>" % (id, a, self.name)
else: n = "<Job: %s>" % id
if self.result is not None: r = "%s (%d)" % (self.status, self.result)
else: r = "%s" % self.status
return "%s | %s : %s -- %s" % (n, m, r, self._cmdline())
[docs]class JobDependence(Base):
"""This table defines a many-to-many relationship between Jobs."""
__tablename__ = 'JobDependence'
id = Column(Integer, primary_key=True)
waiting_job_id = Column(Integer, ForeignKey('Job.unique')) # The ID of the waiting job
waited_for_job_id = Column(Integer, ForeignKey('Job.unique')) # The ID of the job to wait for
# This is twisted: The 'jobs_we_have_to_wait_for' field in the Job class needs to be joined with the waiting job id, so that jobs_we_have_to_wait_for.waiting_job is correct
# Honestly, I am lost but it seems to work...
waiting_job = relationship('Job', backref = 'jobs_we_have_to_wait_for', primaryjoin=(Job.unique == waiting_job_id), order_by=id) # The job that is waited for
waited_for_job = relationship('Job', backref = 'jobs_that_wait_for_us', primaryjoin=(Job.unique == waited_for_job_id), order_by=id) # The job that waits
def __init__(self, waiting_job_id, waited_for_job_id):
self.waiting_job_id = waiting_job_id
self.waited_for_job_id = waited_for_job_id
[docs]def add_job(session, command_line, name = 'job', dependencies = [], array = None, exec_dir=None, log_dir = None, stop_on_failure = False, **kwargs):
"""Helper function to create a job, add the dependencies and the array jobs."""
job = Job(command_line=command_line, name=name, exec_dir=exec_dir, log_dir=log_dir, array_string=array, stop_on_failure=stop_on_failure, kwargs=kwargs)
session.add(job)
session.flush()
session.refresh(job)
# by default id and unique id are identical, but the id might be overwritten later on
job.id = job.unique
for d in dependencies:
if d == job.unique:
logger.warn("Adding self-dependency of job %d is not allowed" % d)
continue
depending = list(session.query(Job).filter(Job.unique == d))
if len(depending):
session.add(JobDependence(job.unique, depending[0].unique))
else:
logger.warn("Could not find dependent job with id %d in database" % d)
if array:
(start, stop, step) = array
# add array jobs
for i in range(start, stop+1, step):
session.add(ArrayJob(i, job.unique))
session.commit()
return job
[docs]def times(job):
"""Returns a string containing timing information for teh given job, which might be a :py:class:`Job` or an :py:class:`ArrayJob`."""
timing = "Submitted: %s" % job.submit_time.ctime()
if job.start_time is not None:
timing += "\nStarted : %s \t Job waited : %s" % (job.start_time.ctime(), job.start_time - job.submit_time)
if job.finish_time is not None:
timing += "\nFinished : %s \t Job executed: %s" % (job.finish_time.ctime(), job.finish_time - job.start_time)
return timing