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#!/usr/bin/env python
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# encoding: utf-8
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"""
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Facilities for launching IPython processes asynchronously.
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"""
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#-----------------------------------------------------------------------------
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# Copyright (C) 2008-2009 The IPython Development Team
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#
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# Distributed under the terms of the BSD License. The full license is in
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# the file COPYING, distributed as part of this software.
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#-----------------------------------------------------------------------------
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#-----------------------------------------------------------------------------
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# Imports
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#-----------------------------------------------------------------------------
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import copy
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import logging
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import os
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import re
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import stat
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from signal import SIGINT, SIGTERM
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try:
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from signal import SIGKILL
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except ImportError:
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SIGKILL=SIGTERM
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from subprocess import Popen, PIPE, STDOUT
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try:
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from subprocess import check_output
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except ImportError:
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# pre-2.7, define check_output with Popen
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def check_output(*args, **kwargs):
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kwargs.update(dict(stdout=PIPE))
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p = Popen(*args, **kwargs)
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out,err = p.communicate()
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return out
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from zmq.eventloop import ioloop
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from IPython.external import Itpl
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# from IPython.config.configurable import Configurable
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from IPython.utils.traitlets import Any, Str, Int, List, Unicode, Dict, Instance, CUnicode
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from IPython.utils.path import get_ipython_module_path
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from IPython.utils.process import find_cmd, pycmd2argv, FindCmdError
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from IPython.parallel.factory import LoggingFactory
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# load winhpcjob only on Windows
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try:
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from .winhpcjob import (
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IPControllerTask, IPEngineTask,
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IPControllerJob, IPEngineSetJob
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)
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except ImportError:
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pass
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#-----------------------------------------------------------------------------
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# Paths to the kernel apps
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#-----------------------------------------------------------------------------
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ipcluster_cmd_argv = pycmd2argv(get_ipython_module_path(
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'IPython.parallel.apps.ipclusterapp'
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))
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ipengine_cmd_argv = pycmd2argv(get_ipython_module_path(
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'IPython.parallel.apps.ipengineapp'
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))
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ipcontroller_cmd_argv = pycmd2argv(get_ipython_module_path(
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'IPython.parallel.apps.ipcontrollerapp'
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))
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#-----------------------------------------------------------------------------
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# Base launchers and errors
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#-----------------------------------------------------------------------------
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class LauncherError(Exception):
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pass
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class ProcessStateError(LauncherError):
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pass
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class UnknownStatus(LauncherError):
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pass
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class BaseLauncher(LoggingFactory):
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"""An asbtraction for starting, stopping and signaling a process."""
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# In all of the launchers, the work_dir is where child processes will be
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# run. This will usually be the cluster_dir, but may not be. any work_dir
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# passed into the __init__ method will override the config value.
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# This should not be used to set the work_dir for the actual engine
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# and controller. Instead, use their own config files or the
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# controller_args, engine_args attributes of the launchers to add
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# the --work-dir option.
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work_dir = Unicode(u'.')
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loop = Instance('zmq.eventloop.ioloop.IOLoop')
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start_data = Any()
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stop_data = Any()
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def _loop_default(self):
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return ioloop.IOLoop.instance()
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def __init__(self, work_dir=u'.', config=None, **kwargs):
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super(BaseLauncher, self).__init__(work_dir=work_dir, config=config, **kwargs)
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self.state = 'before' # can be before, running, after
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self.stop_callbacks = []
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self.start_data = None
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self.stop_data = None
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@property
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def args(self):
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"""A list of cmd and args that will be used to start the process.
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This is what is passed to :func:`spawnProcess` and the first element
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will be the process name.
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"""
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return self.find_args()
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def find_args(self):
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"""The ``.args`` property calls this to find the args list.
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Subcommand should implement this to construct the cmd and args.
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"""
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raise NotImplementedError('find_args must be implemented in a subclass')
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@property
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def arg_str(self):
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"""The string form of the program arguments."""
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return ' '.join(self.args)
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@property
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def running(self):
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"""Am I running."""
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if self.state == 'running':
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return True
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else:
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return False
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def start(self):
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"""Start the process.
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This must return a deferred that fires with information about the
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process starting (like a pid, job id, etc.).
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"""
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raise NotImplementedError('start must be implemented in a subclass')
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def stop(self):
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"""Stop the process and notify observers of stopping.
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This must return a deferred that fires with information about the
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processing stopping, like errors that occur while the process is
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attempting to be shut down. This deferred won't fire when the process
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actually stops. To observe the actual process stopping, see
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:func:`observe_stop`.
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"""
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raise NotImplementedError('stop must be implemented in a subclass')
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def on_stop(self, f):
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"""Get a deferred that will fire when the process stops.
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The deferred will fire with data that contains information about
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the exit status of the process.
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"""
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if self.state=='after':
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return f(self.stop_data)
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else:
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self.stop_callbacks.append(f)
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def notify_start(self, data):
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"""Call this to trigger startup actions.
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This logs the process startup and sets the state to 'running'. It is
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a pass-through so it can be used as a callback.
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"""
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self.log.info('Process %r started: %r' % (self.args[0], data))
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self.start_data = data
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self.state = 'running'
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return data
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def notify_stop(self, data):
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"""Call this to trigger process stop actions.
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This logs the process stopping and sets the state to 'after'. Call
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this to trigger all the deferreds from :func:`observe_stop`."""
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self.log.info('Process %r stopped: %r' % (self.args[0], data))
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self.stop_data = data
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self.state = 'after'
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for i in range(len(self.stop_callbacks)):
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d = self.stop_callbacks.pop()
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d(data)
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return data
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def signal(self, sig):
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"""Signal the process.
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Return a semi-meaningless deferred after signaling the process.
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Parameters
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----------
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sig : str or int
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'KILL', 'INT', etc., or any signal number
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"""
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raise NotImplementedError('signal must be implemented in a subclass')
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#-----------------------------------------------------------------------------
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# Local process launchers
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#-----------------------------------------------------------------------------
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class LocalProcessLauncher(BaseLauncher):
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"""Start and stop an external process in an asynchronous manner.
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This will launch the external process with a working directory of
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``self.work_dir``.
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"""
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# This is used to to construct self.args, which is passed to
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# spawnProcess.
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cmd_and_args = List([])
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poll_frequency = Int(100) # in ms
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def __init__(self, work_dir=u'.', config=None, **kwargs):
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super(LocalProcessLauncher, self).__init__(
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work_dir=work_dir, config=config, **kwargs
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)
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self.process = None
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self.start_deferred = None
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self.poller = None
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def find_args(self):
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return self.cmd_and_args
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def start(self):
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if self.state == 'before':
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self.process = Popen(self.args,
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stdout=PIPE,stderr=PIPE,stdin=PIPE,
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env=os.environ,
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cwd=self.work_dir
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)
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self.loop.add_handler(self.process.stdout.fileno(), self.handle_stdout, self.loop.READ)
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self.loop.add_handler(self.process.stderr.fileno(), self.handle_stderr, self.loop.READ)
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self.poller = ioloop.PeriodicCallback(self.poll, self.poll_frequency, self.loop)
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self.poller.start()
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self.notify_start(self.process.pid)
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else:
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s = 'The process was already started and has state: %r' % self.state
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raise ProcessStateError(s)
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def stop(self):
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return self.interrupt_then_kill()
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def signal(self, sig):
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if self.state == 'running':
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self.process.send_signal(sig)
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def interrupt_then_kill(self, delay=2.0):
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"""Send INT, wait a delay and then send KILL."""
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self.signal(SIGINT)
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self.killer = ioloop.DelayedCallback(lambda : self.signal(SIGKILL), delay*1000, self.loop)
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self.killer.start()
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# callbacks, etc:
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def handle_stdout(self, fd, events):
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line = self.process.stdout.readline()
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# a stopped process will be readable but return empty strings
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if line:
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self.log.info(line[:-1])
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else:
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self.poll()
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def handle_stderr(self, fd, events):
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line = self.process.stderr.readline()
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# a stopped process will be readable but return empty strings
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if line:
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self.log.error(line[:-1])
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else:
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self.poll()
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def poll(self):
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status = self.process.poll()
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if status is not None:
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self.poller.stop()
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self.loop.remove_handler(self.process.stdout.fileno())
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self.loop.remove_handler(self.process.stderr.fileno())
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self.notify_stop(dict(exit_code=status, pid=self.process.pid))
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return status
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class LocalControllerLauncher(LocalProcessLauncher):
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"""Launch a controller as a regular external process."""
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controller_cmd = List(ipcontroller_cmd_argv, config=True)
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# Command line arguments to ipcontroller.
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controller_args = List(['--log-to-file','--log-level', str(logging.INFO)], config=True)
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def find_args(self):
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return self.controller_cmd + self.controller_args
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def start(self, cluster_dir):
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"""Start the controller by cluster_dir."""
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self.controller_args.extend(['--cluster-dir', cluster_dir])
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self.cluster_dir = unicode(cluster_dir)
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self.log.info("Starting LocalControllerLauncher: %r" % self.args)
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return super(LocalControllerLauncher, self).start()
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class LocalEngineLauncher(LocalProcessLauncher):
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"""Launch a single engine as a regular externall process."""
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engine_cmd = List(ipengine_cmd_argv, config=True)
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# Command line arguments for ipengine.
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engine_args = List(
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['--log-to-file','--log-level', str(logging.INFO)], config=True
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)
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def find_args(self):
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return self.engine_cmd + self.engine_args
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def start(self, cluster_dir):
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"""Start the engine by cluster_dir."""
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self.engine_args.extend(['--cluster-dir', cluster_dir])
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self.cluster_dir = unicode(cluster_dir)
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return super(LocalEngineLauncher, self).start()
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class LocalEngineSetLauncher(BaseLauncher):
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"""Launch a set of engines as regular external processes."""
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# Command line arguments for ipengine.
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engine_args = List(
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['--log-to-file','--log-level', str(logging.INFO)], config=True
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)
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# launcher class
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launcher_class = LocalEngineLauncher
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launchers = Dict()
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stop_data = Dict()
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def __init__(self, work_dir=u'.', config=None, **kwargs):
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super(LocalEngineSetLauncher, self).__init__(
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work_dir=work_dir, config=config, **kwargs
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)
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self.stop_data = {}
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def start(self, n, cluster_dir):
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"""Start n engines by profile or cluster_dir."""
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self.cluster_dir = unicode(cluster_dir)
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dlist = []
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for i in range(n):
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el = self.launcher_class(work_dir=self.work_dir, config=self.config, logname=self.log.name)
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# Copy the engine args over to each engine launcher.
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el.engine_args = copy.deepcopy(self.engine_args)
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el.on_stop(self._notice_engine_stopped)
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d = el.start(cluster_dir)
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if i==0:
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self.log.info("Starting LocalEngineSetLauncher: %r" % el.args)
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self.launchers[i] = el
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dlist.append(d)
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self.notify_start(dlist)
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# The consumeErrors here could be dangerous
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# dfinal = gatherBoth(dlist, consumeErrors=True)
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# dfinal.addCallback(self.notify_start)
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return dlist
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def find_args(self):
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return ['engine set']
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def signal(self, sig):
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dlist = []
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for el in self.launchers.itervalues():
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d = el.signal(sig)
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dlist.append(d)
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# dfinal = gatherBoth(dlist, consumeErrors=True)
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return dlist
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def interrupt_then_kill(self, delay=1.0):
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dlist = []
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for el in self.launchers.itervalues():
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d = el.interrupt_then_kill(delay)
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dlist.append(d)
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# dfinal = gatherBoth(dlist, consumeErrors=True)
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return dlist
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def stop(self):
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return self.interrupt_then_kill()
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def _notice_engine_stopped(self, data):
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pid = data['pid']
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for idx,el in self.launchers.iteritems():
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if el.process.pid == pid:
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break
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self.launchers.pop(idx)
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self.stop_data[idx] = data
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if not self.launchers:
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self.notify_stop(self.stop_data)
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#-----------------------------------------------------------------------------
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# MPIExec launchers
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#-----------------------------------------------------------------------------
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class MPIExecLauncher(LocalProcessLauncher):
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"""Launch an external process using mpiexec."""
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# The mpiexec command to use in starting the process.
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mpi_cmd = List(['mpiexec'], config=True)
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# The command line arguments to pass to mpiexec.
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mpi_args = List([], config=True)
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# The program to start using mpiexec.
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program = List(['date'], config=True)
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# The command line argument to the program.
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program_args = List([], config=True)
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# The number of instances of the program to start.
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n = Int(1, config=True)
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def find_args(self):
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"""Build self.args using all the fields."""
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return self.mpi_cmd + ['-n', str(self.n)] + self.mpi_args + \
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self.program + self.program_args
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def start(self, n):
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"""Start n instances of the program using mpiexec."""
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self.n = n
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return super(MPIExecLauncher, self).start()
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class MPIExecControllerLauncher(MPIExecLauncher):
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"""Launch a controller using mpiexec."""
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controller_cmd = List(ipcontroller_cmd_argv, config=True)
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# Command line arguments to ipcontroller.
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controller_args = List(['--log-to-file','--log-level', str(logging.INFO)], config=True)
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n = Int(1, config=False)
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def start(self, cluster_dir):
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"""Start the controller by cluster_dir."""
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self.controller_args.extend(['--cluster-dir', cluster_dir])
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self.cluster_dir = unicode(cluster_dir)
|
|
|
self.log.info("Starting MPIExecControllerLauncher: %r" % self.args)
|
|
|
return super(MPIExecControllerLauncher, self).start(1)
|
|
|
|
|
|
def find_args(self):
|
|
|
return self.mpi_cmd + ['-n', self.n] + self.mpi_args + \
|
|
|
self.controller_cmd + self.controller_args
|
|
|
|
|
|
|
|
|
class MPIExecEngineSetLauncher(MPIExecLauncher):
|
|
|
|
|
|
program = List(ipengine_cmd_argv, config=True)
|
|
|
# Command line arguments for ipengine.
|
|
|
program_args = List(
|
|
|
['--log-to-file','--log-level', str(logging.INFO)], config=True
|
|
|
)
|
|
|
n = Int(1, config=True)
|
|
|
|
|
|
def start(self, n, cluster_dir):
|
|
|
"""Start n engines by profile or cluster_dir."""
|
|
|
self.program_args.extend(['--cluster-dir', cluster_dir])
|
|
|
self.cluster_dir = unicode(cluster_dir)
|
|
|
self.n = n
|
|
|
self.log.info('Starting MPIExecEngineSetLauncher: %r' % self.args)
|
|
|
return super(MPIExecEngineSetLauncher, self).start(n)
|
|
|
|
|
|
#-----------------------------------------------------------------------------
|
|
|
# SSH launchers
|
|
|
#-----------------------------------------------------------------------------
|
|
|
|
|
|
# TODO: Get SSH Launcher working again.
|
|
|
|
|
|
class SSHLauncher(LocalProcessLauncher):
|
|
|
"""A minimal launcher for ssh.
|
|
|
|
|
|
To be useful this will probably have to be extended to use the ``sshx``
|
|
|
idea for environment variables. There could be other things this needs
|
|
|
as well.
|
|
|
"""
|
|
|
|
|
|
ssh_cmd = List(['ssh'], config=True)
|
|
|
ssh_args = List(['-tt'], config=True)
|
|
|
program = List(['date'], config=True)
|
|
|
program_args = List([], config=True)
|
|
|
hostname = CUnicode('', config=True)
|
|
|
user = CUnicode('', config=True)
|
|
|
location = CUnicode('')
|
|
|
|
|
|
def _hostname_changed(self, name, old, new):
|
|
|
if self.user:
|
|
|
self.location = u'%s@%s' % (self.user, new)
|
|
|
else:
|
|
|
self.location = new
|
|
|
|
|
|
def _user_changed(self, name, old, new):
|
|
|
self.location = u'%s@%s' % (new, self.hostname)
|
|
|
|
|
|
def find_args(self):
|
|
|
return self.ssh_cmd + self.ssh_args + [self.location] + \
|
|
|
self.program + self.program_args
|
|
|
|
|
|
def start(self, cluster_dir, hostname=None, user=None):
|
|
|
self.cluster_dir = unicode(cluster_dir)
|
|
|
if hostname is not None:
|
|
|
self.hostname = hostname
|
|
|
if user is not None:
|
|
|
self.user = user
|
|
|
|
|
|
return super(SSHLauncher, self).start()
|
|
|
|
|
|
def signal(self, sig):
|
|
|
if self.state == 'running':
|
|
|
# send escaped ssh connection-closer
|
|
|
self.process.stdin.write('~.')
|
|
|
self.process.stdin.flush()
|
|
|
|
|
|
|
|
|
|
|
|
class SSHControllerLauncher(SSHLauncher):
|
|
|
|
|
|
program = List(ipcontroller_cmd_argv, config=True)
|
|
|
# Command line arguments to ipcontroller.
|
|
|
program_args = List(['-r', '--log-to-file','--log-level', str(logging.INFO)], config=True)
|
|
|
|
|
|
|
|
|
class SSHEngineLauncher(SSHLauncher):
|
|
|
program = List(ipengine_cmd_argv, config=True)
|
|
|
# Command line arguments for ipengine.
|
|
|
program_args = List(
|
|
|
['--log-to-file','--log-level', str(logging.INFO)], config=True
|
|
|
)
|
|
|
|
|
|
class SSHEngineSetLauncher(LocalEngineSetLauncher):
|
|
|
launcher_class = SSHEngineLauncher
|
|
|
engines = Dict(config=True)
|
|
|
|
|
|
def start(self, n, cluster_dir):
|
|
|
"""Start engines by profile or cluster_dir.
|
|
|
`n` is ignored, and the `engines` config property is used instead.
|
|
|
"""
|
|
|
|
|
|
self.cluster_dir = unicode(cluster_dir)
|
|
|
dlist = []
|
|
|
for host, n in self.engines.iteritems():
|
|
|
if isinstance(n, (tuple, list)):
|
|
|
n, args = n
|
|
|
else:
|
|
|
args = copy.deepcopy(self.engine_args)
|
|
|
|
|
|
if '@' in host:
|
|
|
user,host = host.split('@',1)
|
|
|
else:
|
|
|
user=None
|
|
|
for i in range(n):
|
|
|
el = self.launcher_class(work_dir=self.work_dir, config=self.config, logname=self.log.name)
|
|
|
|
|
|
# Copy the engine args over to each engine launcher.
|
|
|
i
|
|
|
el.program_args = args
|
|
|
el.on_stop(self._notice_engine_stopped)
|
|
|
d = el.start(cluster_dir, user=user, hostname=host)
|
|
|
if i==0:
|
|
|
self.log.info("Starting SSHEngineSetLauncher: %r" % el.args)
|
|
|
self.launchers[host+str(i)] = el
|
|
|
dlist.append(d)
|
|
|
self.notify_start(dlist)
|
|
|
return dlist
|
|
|
|
|
|
|
|
|
|
|
|
#-----------------------------------------------------------------------------
|
|
|
# Windows HPC Server 2008 scheduler launchers
|
|
|
#-----------------------------------------------------------------------------
|
|
|
|
|
|
|
|
|
# This is only used on Windows.
|
|
|
def find_job_cmd():
|
|
|
if os.name=='nt':
|
|
|
try:
|
|
|
return find_cmd('job')
|
|
|
except FindCmdError:
|
|
|
return 'job'
|
|
|
else:
|
|
|
return 'job'
|
|
|
|
|
|
|
|
|
class WindowsHPCLauncher(BaseLauncher):
|
|
|
|
|
|
# A regular expression used to get the job id from the output of the
|
|
|
# submit_command.
|
|
|
job_id_regexp = Str(r'\d+', config=True)
|
|
|
# The filename of the instantiated job script.
|
|
|
job_file_name = CUnicode(u'ipython_job.xml', config=True)
|
|
|
# The full path to the instantiated job script. This gets made dynamically
|
|
|
# by combining the work_dir with the job_file_name.
|
|
|
job_file = CUnicode(u'')
|
|
|
# The hostname of the scheduler to submit the job to
|
|
|
scheduler = CUnicode('', config=True)
|
|
|
job_cmd = CUnicode(find_job_cmd(), config=True)
|
|
|
|
|
|
def __init__(self, work_dir=u'.', config=None, **kwargs):
|
|
|
super(WindowsHPCLauncher, self).__init__(
|
|
|
work_dir=work_dir, config=config, **kwargs
|
|
|
)
|
|
|
|
|
|
@property
|
|
|
def job_file(self):
|
|
|
return os.path.join(self.work_dir, self.job_file_name)
|
|
|
|
|
|
def write_job_file(self, n):
|
|
|
raise NotImplementedError("Implement write_job_file in a subclass.")
|
|
|
|
|
|
def find_args(self):
|
|
|
return [u'job.exe']
|
|
|
|
|
|
def parse_job_id(self, output):
|
|
|
"""Take the output of the submit command and return the job id."""
|
|
|
m = re.search(self.job_id_regexp, output)
|
|
|
if m is not None:
|
|
|
job_id = m.group()
|
|
|
else:
|
|
|
raise LauncherError("Job id couldn't be determined: %s" % output)
|
|
|
self.job_id = job_id
|
|
|
self.log.info('Job started with job id: %r' % job_id)
|
|
|
return job_id
|
|
|
|
|
|
def start(self, n):
|
|
|
"""Start n copies of the process using the Win HPC job scheduler."""
|
|
|
self.write_job_file(n)
|
|
|
args = [
|
|
|
'submit',
|
|
|
'/jobfile:%s' % self.job_file,
|
|
|
'/scheduler:%s' % self.scheduler
|
|
|
]
|
|
|
self.log.info("Starting Win HPC Job: %s" % (self.job_cmd + ' ' + ' '.join(args),))
|
|
|
# Twisted will raise DeprecationWarnings if we try to pass unicode to this
|
|
|
output = check_output([self.job_cmd]+args,
|
|
|
env=os.environ,
|
|
|
cwd=self.work_dir,
|
|
|
stderr=STDOUT
|
|
|
)
|
|
|
job_id = self.parse_job_id(output)
|
|
|
self.notify_start(job_id)
|
|
|
return job_id
|
|
|
|
|
|
def stop(self):
|
|
|
args = [
|
|
|
'cancel',
|
|
|
self.job_id,
|
|
|
'/scheduler:%s' % self.scheduler
|
|
|
]
|
|
|
self.log.info("Stopping Win HPC Job: %s" % (self.job_cmd + ' ' + ' '.join(args),))
|
|
|
try:
|
|
|
output = check_output([self.job_cmd]+args,
|
|
|
env=os.environ,
|
|
|
cwd=self.work_dir,
|
|
|
stderr=STDOUT
|
|
|
)
|
|
|
except:
|
|
|
output = 'The job already appears to be stoppped: %r' % self.job_id
|
|
|
self.notify_stop(dict(job_id=self.job_id, output=output)) # Pass the output of the kill cmd
|
|
|
return output
|
|
|
|
|
|
|
|
|
class WindowsHPCControllerLauncher(WindowsHPCLauncher):
|
|
|
|
|
|
job_file_name = CUnicode(u'ipcontroller_job.xml', config=True)
|
|
|
extra_args = List([], config=False)
|
|
|
|
|
|
def write_job_file(self, n):
|
|
|
job = IPControllerJob(config=self.config)
|
|
|
|
|
|
t = IPControllerTask(config=self.config)
|
|
|
# The tasks work directory is *not* the actual work directory of
|
|
|
# the controller. It is used as the base path for the stdout/stderr
|
|
|
# files that the scheduler redirects to.
|
|
|
t.work_directory = self.cluster_dir
|
|
|
# Add the --cluster-dir and from self.start().
|
|
|
t.controller_args.extend(self.extra_args)
|
|
|
job.add_task(t)
|
|
|
|
|
|
self.log.info("Writing job description file: %s" % self.job_file)
|
|
|
job.write(self.job_file)
|
|
|
|
|
|
@property
|
|
|
def job_file(self):
|
|
|
return os.path.join(self.cluster_dir, self.job_file_name)
|
|
|
|
|
|
def start(self, cluster_dir):
|
|
|
"""Start the controller by cluster_dir."""
|
|
|
self.extra_args = ['--cluster-dir', cluster_dir]
|
|
|
self.cluster_dir = unicode(cluster_dir)
|
|
|
return super(WindowsHPCControllerLauncher, self).start(1)
|
|
|
|
|
|
|
|
|
class WindowsHPCEngineSetLauncher(WindowsHPCLauncher):
|
|
|
|
|
|
job_file_name = CUnicode(u'ipengineset_job.xml', config=True)
|
|
|
extra_args = List([], config=False)
|
|
|
|
|
|
def write_job_file(self, n):
|
|
|
job = IPEngineSetJob(config=self.config)
|
|
|
|
|
|
for i in range(n):
|
|
|
t = IPEngineTask(config=self.config)
|
|
|
# The tasks work directory is *not* the actual work directory of
|
|
|
# the engine. It is used as the base path for the stdout/stderr
|
|
|
# files that the scheduler redirects to.
|
|
|
t.work_directory = self.cluster_dir
|
|
|
# Add the --cluster-dir and from self.start().
|
|
|
t.engine_args.extend(self.extra_args)
|
|
|
job.add_task(t)
|
|
|
|
|
|
self.log.info("Writing job description file: %s" % self.job_file)
|
|
|
job.write(self.job_file)
|
|
|
|
|
|
@property
|
|
|
def job_file(self):
|
|
|
return os.path.join(self.cluster_dir, self.job_file_name)
|
|
|
|
|
|
def start(self, n, cluster_dir):
|
|
|
"""Start the controller by cluster_dir."""
|
|
|
self.extra_args = ['--cluster-dir', cluster_dir]
|
|
|
self.cluster_dir = unicode(cluster_dir)
|
|
|
return super(WindowsHPCEngineSetLauncher, self).start(n)
|
|
|
|
|
|
|
|
|
#-----------------------------------------------------------------------------
|
|
|
# Batch (PBS) system launchers
|
|
|
#-----------------------------------------------------------------------------
|
|
|
|
|
|
class BatchSystemLauncher(BaseLauncher):
|
|
|
"""Launch an external process using a batch system.
|
|
|
|
|
|
This class is designed to work with UNIX batch systems like PBS, LSF,
|
|
|
GridEngine, etc. The overall model is that there are different commands
|
|
|
like qsub, qdel, etc. that handle the starting and stopping of the process.
|
|
|
|
|
|
This class also has the notion of a batch script. The ``batch_template``
|
|
|
attribute can be set to a string that is a template for the batch script.
|
|
|
This template is instantiated using Itpl. Thus the template can use
|
|
|
${n} fot the number of instances. Subclasses can add additional variables
|
|
|
to the template dict.
|
|
|
"""
|
|
|
|
|
|
# Subclasses must fill these in. See PBSEngineSet
|
|
|
# The name of the command line program used to submit jobs.
|
|
|
submit_command = List([''], config=True)
|
|
|
# The name of the command line program used to delete jobs.
|
|
|
delete_command = List([''], config=True)
|
|
|
# A regular expression used to get the job id from the output of the
|
|
|
# submit_command.
|
|
|
job_id_regexp = CUnicode('', config=True)
|
|
|
# The string that is the batch script template itself.
|
|
|
batch_template = CUnicode('', config=True)
|
|
|
# The file that contains the batch template
|
|
|
batch_template_file = CUnicode(u'', config=True)
|
|
|
# The filename of the instantiated batch script.
|
|
|
batch_file_name = CUnicode(u'batch_script', config=True)
|
|
|
# The PBS Queue
|
|
|
queue = CUnicode(u'', config=True)
|
|
|
|
|
|
# not configurable, override in subclasses
|
|
|
# PBS Job Array regex
|
|
|
job_array_regexp = CUnicode('')
|
|
|
job_array_template = CUnicode('')
|
|
|
# PBS Queue regex
|
|
|
queue_regexp = CUnicode('')
|
|
|
queue_template = CUnicode('')
|
|
|
# The default batch template, override in subclasses
|
|
|
default_template = CUnicode('')
|
|
|
# The full path to the instantiated batch script.
|
|
|
batch_file = CUnicode(u'')
|
|
|
# the format dict used with batch_template:
|
|
|
context = Dict()
|
|
|
|
|
|
|
|
|
def find_args(self):
|
|
|
return self.submit_command + [self.batch_file]
|
|
|
|
|
|
def __init__(self, work_dir=u'.', config=None, **kwargs):
|
|
|
super(BatchSystemLauncher, self).__init__(
|
|
|
work_dir=work_dir, config=config, **kwargs
|
|
|
)
|
|
|
self.batch_file = os.path.join(self.work_dir, self.batch_file_name)
|
|
|
|
|
|
def parse_job_id(self, output):
|
|
|
"""Take the output of the submit command and return the job id."""
|
|
|
m = re.search(self.job_id_regexp, output)
|
|
|
if m is not None:
|
|
|
job_id = m.group()
|
|
|
else:
|
|
|
raise LauncherError("Job id couldn't be determined: %s" % output)
|
|
|
self.job_id = job_id
|
|
|
self.log.info('Job submitted with job id: %r' % job_id)
|
|
|
return job_id
|
|
|
|
|
|
def write_batch_script(self, n):
|
|
|
"""Instantiate and write the batch script to the work_dir."""
|
|
|
self.context['n'] = n
|
|
|
self.context['queue'] = self.queue
|
|
|
print self.context
|
|
|
# first priority is batch_template if set
|
|
|
if self.batch_template_file and not self.batch_template:
|
|
|
# second priority is batch_template_file
|
|
|
with open(self.batch_template_file) as f:
|
|
|
self.batch_template = f.read()
|
|
|
if not self.batch_template:
|
|
|
# third (last) priority is default_template
|
|
|
self.batch_template = self.default_template
|
|
|
|
|
|
regex = re.compile(self.job_array_regexp)
|
|
|
# print regex.search(self.batch_template)
|
|
|
if not regex.search(self.batch_template):
|
|
|
self.log.info("adding job array settings to batch script")
|
|
|
firstline, rest = self.batch_template.split('\n',1)
|
|
|
self.batch_template = u'\n'.join([firstline, self.job_array_template, rest])
|
|
|
|
|
|
regex = re.compile(self.queue_regexp)
|
|
|
# print regex.search(self.batch_template)
|
|
|
if self.queue and not regex.search(self.batch_template):
|
|
|
self.log.info("adding PBS queue settings to batch script")
|
|
|
firstline, rest = self.batch_template.split('\n',1)
|
|
|
self.batch_template = u'\n'.join([firstline, self.queue_template, rest])
|
|
|
|
|
|
script_as_string = Itpl.itplns(self.batch_template, self.context)
|
|
|
self.log.info('Writing instantiated batch script: %s' % self.batch_file)
|
|
|
|
|
|
with open(self.batch_file, 'w') as f:
|
|
|
f.write(script_as_string)
|
|
|
os.chmod(self.batch_file, stat.S_IRUSR | stat.S_IWUSR | stat.S_IXUSR)
|
|
|
|
|
|
def start(self, n, cluster_dir):
|
|
|
"""Start n copies of the process using a batch system."""
|
|
|
# Here we save profile and cluster_dir in the context so they
|
|
|
# can be used in the batch script template as ${profile} and
|
|
|
# ${cluster_dir}
|
|
|
self.context['cluster_dir'] = cluster_dir
|
|
|
self.cluster_dir = unicode(cluster_dir)
|
|
|
self.write_batch_script(n)
|
|
|
output = check_output(self.args, env=os.environ)
|
|
|
|
|
|
job_id = self.parse_job_id(output)
|
|
|
self.notify_start(job_id)
|
|
|
return job_id
|
|
|
|
|
|
def stop(self):
|
|
|
output = check_output(self.delete_command+[self.job_id], env=os.environ)
|
|
|
self.notify_stop(dict(job_id=self.job_id, output=output)) # Pass the output of the kill cmd
|
|
|
return output
|
|
|
|
|
|
|
|
|
class PBSLauncher(BatchSystemLauncher):
|
|
|
"""A BatchSystemLauncher subclass for PBS."""
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submit_command = List(['qsub'], config=True)
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delete_command = List(['qdel'], config=True)
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job_id_regexp = CUnicode(r'\d+', config=True)
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batch_file = CUnicode(u'')
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job_array_regexp = CUnicode('#PBS\W+-t\W+[\w\d\-\$]+')
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job_array_template = CUnicode('#PBS -t 1-$n')
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queue_regexp = CUnicode('#PBS\W+-q\W+\$?\w+')
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queue_template = CUnicode('#PBS -q $queue')
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class PBSControllerLauncher(PBSLauncher):
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"""Launch a controller using PBS."""
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batch_file_name = CUnicode(u'pbs_controller', config=True)
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default_template= CUnicode("""#!/bin/sh
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#PBS -V
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#PBS -N ipcontroller
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%s --log-to-file --cluster-dir $cluster_dir
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"""%(' '.join(ipcontroller_cmd_argv)))
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def start(self, cluster_dir):
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"""Start the controller by profile or cluster_dir."""
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self.log.info("Starting PBSControllerLauncher: %r" % self.args)
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return super(PBSControllerLauncher, self).start(1, cluster_dir)
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class PBSEngineSetLauncher(PBSLauncher):
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"""Launch Engines using PBS"""
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batch_file_name = CUnicode(u'pbs_engines', config=True)
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default_template= CUnicode(u"""#!/bin/sh
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#PBS -V
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#PBS -N ipengine
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%s --cluster-dir $cluster_dir
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"""%(' '.join(ipengine_cmd_argv)))
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def start(self, n, cluster_dir):
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"""Start n engines by profile or cluster_dir."""
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self.log.info('Starting %i engines with PBSEngineSetLauncher: %r' % (n, self.args))
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return super(PBSEngineSetLauncher, self).start(n, cluster_dir)
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#SGE is very similar to PBS
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class SGELauncher(PBSLauncher):
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"""Sun GridEngine is a PBS clone with slightly different syntax"""
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job_array_regexp = CUnicode('#$$\W+-t\W+[\w\d\-\$]+')
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job_array_template = CUnicode('#$$ -t 1-$n')
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queue_regexp = CUnicode('#$$\W+-q\W+\$?\w+')
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queue_template = CUnicode('#$$ -q $queue')
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class SGEControllerLauncher(SGELauncher):
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"""Launch a controller using SGE."""
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batch_file_name = CUnicode(u'sge_controller', config=True)
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default_template= CUnicode(u"""#$$ -V
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#$$ -S /bin/sh
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#$$ -N ipcontroller
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%s --log-to-file --cluster-dir $cluster_dir
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"""%(' '.join(ipcontroller_cmd_argv)))
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def start(self, cluster_dir):
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"""Start the controller by profile or cluster_dir."""
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self.log.info("Starting PBSControllerLauncher: %r" % self.args)
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return super(PBSControllerLauncher, self).start(1, cluster_dir)
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class SGEEngineSetLauncher(SGELauncher):
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"""Launch Engines with SGE"""
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batch_file_name = CUnicode(u'sge_engines', config=True)
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default_template = CUnicode("""#$$ -V
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#$$ -S /bin/sh
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#$$ -N ipengine
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%s --cluster-dir $cluster_dir
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"""%(' '.join(ipengine_cmd_argv)))
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def start(self, n, cluster_dir):
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"""Start n engines by profile or cluster_dir."""
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self.log.info('Starting %i engines with SGEEngineSetLauncher: %r' % (n, self.args))
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return super(SGEEngineSetLauncher, self).start(n, cluster_dir)
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#-----------------------------------------------------------------------------
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# A launcher for ipcluster itself!
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#-----------------------------------------------------------------------------
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class IPClusterLauncher(LocalProcessLauncher):
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"""Launch the ipcluster program in an external process."""
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ipcluster_cmd = List(ipcluster_cmd_argv, config=True)
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# Command line arguments to pass to ipcluster.
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ipcluster_args = List(
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['--clean-logs', '--log-to-file', '--log-level', str(logging.INFO)], config=True)
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ipcluster_subcommand = Str('start')
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ipcluster_n = Int(2)
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def find_args(self):
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return self.ipcluster_cmd + [self.ipcluster_subcommand] + \
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['-n', repr(self.ipcluster_n)] + self.ipcluster_args
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def start(self):
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self.log.info("Starting ipcluster: %r" % self.args)
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return super(IPClusterLauncher, self).start()
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