1080 lines
46 KiB
Python
1080 lines
46 KiB
Python
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"""
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Helpers for embarrassingly parallel code.
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"""
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# Author: Gael Varoquaux < gael dot varoquaux at normalesup dot org >
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# Copyright: 2010, Gael Varoquaux
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# License: BSD 3 clause
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from __future__ import division
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import os
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import sys
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from math import sqrt
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import functools
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import time
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import threading
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import itertools
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from uuid import uuid4
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from numbers import Integral
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import warnings
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import queue
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from ._multiprocessing_helpers import mp
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from .logger import Logger, short_format_time
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from .disk import memstr_to_bytes
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from ._parallel_backends import (FallbackToBackend, MultiprocessingBackend,
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ThreadingBackend, SequentialBackend,
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LokyBackend)
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from .externals.cloudpickle import dumps, loads
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from .externals import loky
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# Make sure that those two classes are part of the public joblib.parallel API
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# so that 3rd party backend implementers can import them from here.
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from ._parallel_backends import AutoBatchingMixin # noqa
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from ._parallel_backends import ParallelBackendBase # noqa
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BACKENDS = {
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'multiprocessing': MultiprocessingBackend,
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'threading': ThreadingBackend,
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'sequential': SequentialBackend,
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'loky': LokyBackend,
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}
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# name of the backend used by default by Parallel outside of any context
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# managed by ``parallel_backend``.
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DEFAULT_BACKEND = 'loky'
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DEFAULT_N_JOBS = 1
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DEFAULT_THREAD_BACKEND = 'threading'
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# Thread local value that can be overridden by the ``parallel_backend`` context
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# manager
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_backend = threading.local()
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VALID_BACKEND_HINTS = ('processes', 'threads', None)
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VALID_BACKEND_CONSTRAINTS = ('sharedmem', None)
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def _register_dask():
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""" Register Dask Backend if called with parallel_backend("dask") """
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try:
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from ._dask import DaskDistributedBackend
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register_parallel_backend('dask', DaskDistributedBackend)
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except ImportError as e:
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msg = ("To use the dask.distributed backend you must install both "
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"the `dask` and distributed modules.\n\n"
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"See https://dask.pydata.org/en/latest/install.html for more "
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"information.")
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raise ImportError(msg) from e
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EXTERNAL_BACKENDS = {
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'dask': _register_dask,
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}
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def get_active_backend(prefer=None, require=None, verbose=0):
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"""Return the active default backend"""
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if prefer not in VALID_BACKEND_HINTS:
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raise ValueError("prefer=%r is not a valid backend hint, "
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"expected one of %r" % (prefer, VALID_BACKEND_HINTS))
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if require not in VALID_BACKEND_CONSTRAINTS:
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raise ValueError("require=%r is not a valid backend constraint, "
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"expected one of %r"
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% (require, VALID_BACKEND_CONSTRAINTS))
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if prefer == 'processes' and require == 'sharedmem':
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raise ValueError("prefer == 'processes' and require == 'sharedmem'"
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" are inconsistent settings")
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backend_and_jobs = getattr(_backend, 'backend_and_jobs', None)
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if backend_and_jobs is not None:
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# Try to use the backend set by the user with the context manager.
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backend, n_jobs = backend_and_jobs
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nesting_level = backend.nesting_level
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supports_sharedmem = getattr(backend, 'supports_sharedmem', False)
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if require == 'sharedmem' and not supports_sharedmem:
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# This backend does not match the shared memory constraint:
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# fallback to the default thead-based backend.
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sharedmem_backend = BACKENDS[DEFAULT_THREAD_BACKEND](
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nesting_level=nesting_level)
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if verbose >= 10:
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print("Using %s as joblib.Parallel backend instead of %s "
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"as the latter does not provide shared memory semantics."
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% (sharedmem_backend.__class__.__name__,
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backend.__class__.__name__))
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return sharedmem_backend, DEFAULT_N_JOBS
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else:
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return backend_and_jobs
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# We are outside of the scope of any parallel_backend context manager,
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# create the default backend instance now.
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backend = BACKENDS[DEFAULT_BACKEND](nesting_level=0)
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supports_sharedmem = getattr(backend, 'supports_sharedmem', False)
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uses_threads = getattr(backend, 'uses_threads', False)
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if ((require == 'sharedmem' and not supports_sharedmem) or
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(prefer == 'threads' and not uses_threads)):
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# Make sure the selected default backend match the soft hints and
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# hard constraints:
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backend = BACKENDS[DEFAULT_THREAD_BACKEND](nesting_level=0)
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return backend, DEFAULT_N_JOBS
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class parallel_backend(object):
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"""Change the default backend used by Parallel inside a with block.
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If ``backend`` is a string it must match a previously registered
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implementation using the ``register_parallel_backend`` function.
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By default the following backends are available:
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- 'loky': single-host, process-based parallelism (used by default),
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- 'threading': single-host, thread-based parallelism,
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- 'multiprocessing': legacy single-host, process-based parallelism.
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'loky' is recommended to run functions that manipulate Python objects.
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'threading' is a low-overhead alternative that is most efficient for
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functions that release the Global Interpreter Lock: e.g. I/O-bound code or
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CPU-bound code in a few calls to native code that explicitly releases the
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GIL.
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In addition, if the `dask` and `distributed` Python packages are installed,
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it is possible to use the 'dask' backend for better scheduling of nested
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parallel calls without over-subscription and potentially distribute
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parallel calls over a networked cluster of several hosts.
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It is also possible to use the distributed 'ray' backend for distributing
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the workload to a cluster of nodes. To use the 'ray' joblib backend add
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the following lines:
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>> from ray.util.joblib import register_ray
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>> register_ray()
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>> with parallel_backend("ray"):
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.. print(Parallel()(delayed(neg)(i + 1) for i in range(5)))
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[-1, -2, -3, -4, -5]
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Alternatively the backend can be passed directly as an instance.
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By default all available workers will be used (``n_jobs=-1``) unless the
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caller passes an explicit value for the ``n_jobs`` parameter.
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This is an alternative to passing a ``backend='backend_name'`` argument to
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the ``Parallel`` class constructor. It is particularly useful when calling
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into library code that uses joblib internally but does not expose the
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backend argument in its own API.
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>>> from operator import neg
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>>> with parallel_backend('threading'):
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... print(Parallel()(delayed(neg)(i + 1) for i in range(5)))
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...
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[-1, -2, -3, -4, -5]
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Warning: this function is experimental and subject to change in a future
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version of joblib.
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Joblib also tries to limit the oversubscription by limiting the number of
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threads usable in some third-party library threadpools like OpenBLAS, MKL
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or OpenMP. The default limit in each worker is set to
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``max(cpu_count() // effective_n_jobs, 1)`` but this limit can be
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overwritten with the ``inner_max_num_threads`` argument which will be used
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to set this limit in the child processes.
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.. versionadded:: 0.10
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"""
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def __init__(self, backend, n_jobs=-1, inner_max_num_threads=None,
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**backend_params):
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if isinstance(backend, str):
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if backend not in BACKENDS and backend in EXTERNAL_BACKENDS:
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register = EXTERNAL_BACKENDS[backend]
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register()
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backend = BACKENDS[backend](**backend_params)
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if inner_max_num_threads is not None:
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msg = ("{} does not accept setting the inner_max_num_threads "
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"argument.".format(backend.__class__.__name__))
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assert backend.supports_inner_max_num_threads, msg
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backend.inner_max_num_threads = inner_max_num_threads
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# If the nesting_level of the backend is not set previously, use the
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# nesting level from the previous active_backend to set it
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current_backend_and_jobs = getattr(_backend, 'backend_and_jobs', None)
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if backend.nesting_level is None:
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if current_backend_and_jobs is None:
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nesting_level = 0
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else:
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nesting_level = current_backend_and_jobs[0].nesting_level
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backend.nesting_level = nesting_level
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# Save the backends info and set the active backend
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self.old_backend_and_jobs = current_backend_and_jobs
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self.new_backend_and_jobs = (backend, n_jobs)
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_backend.backend_and_jobs = (backend, n_jobs)
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def __enter__(self):
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return self.new_backend_and_jobs
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def __exit__(self, type, value, traceback):
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self.unregister()
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def unregister(self):
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if self.old_backend_and_jobs is None:
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if getattr(_backend, 'backend_and_jobs', None) is not None:
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del _backend.backend_and_jobs
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else:
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_backend.backend_and_jobs = self.old_backend_and_jobs
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# Under Linux or OS X the default start method of multiprocessing
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# can cause third party libraries to crash. Under Python 3.4+ it is possible
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# to set an environment variable to switch the default start method from
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# 'fork' to 'forkserver' or 'spawn' to avoid this issue albeit at the cost
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# of causing semantic changes and some additional pool instantiation overhead.
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DEFAULT_MP_CONTEXT = None
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if hasattr(mp, 'get_context'):
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method = os.environ.get('JOBLIB_START_METHOD', '').strip() or None
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if method is not None:
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DEFAULT_MP_CONTEXT = mp.get_context(method=method)
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class BatchedCalls(object):
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"""Wrap a sequence of (func, args, kwargs) tuples as a single callable"""
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def __init__(self, iterator_slice, backend_and_jobs, reducer_callback=None,
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pickle_cache=None):
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self.items = list(iterator_slice)
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self._size = len(self.items)
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self._reducer_callback = reducer_callback
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if isinstance(backend_and_jobs, tuple):
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self._backend, self._n_jobs = backend_and_jobs
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else:
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# this is for backward compatibility purposes. Before 0.12.6,
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# nested backends were returned without n_jobs indications.
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self._backend, self._n_jobs = backend_and_jobs, None
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self._pickle_cache = pickle_cache if pickle_cache is not None else {}
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def __call__(self):
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# Set the default nested backend to self._backend but do not set the
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# change the default number of processes to -1
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with parallel_backend(self._backend, n_jobs=self._n_jobs):
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return [func(*args, **kwargs)
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for func, args, kwargs in self.items]
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def __reduce__(self):
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if self._reducer_callback is not None:
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self._reducer_callback()
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# no need pickle the callback.
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return (
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BatchedCalls,
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(self.items, (self._backend, self._n_jobs), None,
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self._pickle_cache)
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)
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def __len__(self):
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return self._size
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###############################################################################
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# CPU count that works also when multiprocessing has been disabled via
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# the JOBLIB_MULTIPROCESSING environment variable
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def cpu_count(only_physical_cores=False):
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"""Return the number of CPUs.
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This delegates to loky.cpu_count that takes into account additional
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constraints such as Linux CFS scheduler quotas (typically set by container
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runtimes such as docker) and CPU affinity (for instance using the taskset
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command on Linux).
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If only_physical_cores is True, do not take hyperthreading / SMT logical
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cores into account.
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"""
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if mp is None:
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return 1
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return loky.cpu_count(only_physical_cores=only_physical_cores)
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###############################################################################
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# For verbosity
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def _verbosity_filter(index, verbose):
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""" Returns False for indices increasingly apart, the distance
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depending on the value of verbose.
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We use a lag increasing as the square of index
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"""
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if not verbose:
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return True
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elif verbose > 10:
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return False
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if index == 0:
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return False
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verbose = .5 * (11 - verbose) ** 2
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scale = sqrt(index / verbose)
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next_scale = sqrt((index + 1) / verbose)
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return (int(next_scale) == int(scale))
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###############################################################################
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def delayed(function, check_pickle=None):
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"""Decorator used to capture the arguments of a function."""
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if check_pickle is not None:
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warnings.warn('check_pickle is deprecated in joblib 0.12 and will be'
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' removed in 0.13', DeprecationWarning)
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# Try to pickle the input function, to catch the problems early when
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# using with multiprocessing:
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if check_pickle:
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dumps(function)
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def delayed_function(*args, **kwargs):
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return function, args, kwargs
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try:
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delayed_function = functools.wraps(function)(delayed_function)
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except AttributeError:
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" functools.wraps fails on some callable objects "
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return delayed_function
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###############################################################################
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class BatchCompletionCallBack(object):
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"""Callback used by joblib.Parallel's multiprocessing backend.
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This callable is executed by the parent process whenever a worker process
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has returned the results of a batch of tasks.
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It is used for progress reporting, to update estimate of the batch
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processing duration and to schedule the next batch of tasks to be
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processed.
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"""
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def __init__(self, dispatch_timestamp, batch_size, parallel):
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self.dispatch_timestamp = dispatch_timestamp
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self.batch_size = batch_size
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self.parallel = parallel
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def __call__(self, out):
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self.parallel.n_completed_tasks += self.batch_size
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this_batch_duration = time.time() - self.dispatch_timestamp
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self.parallel._backend.batch_completed(self.batch_size,
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this_batch_duration)
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self.parallel.print_progress()
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||
|
|
with self.parallel._lock:
|
||
|
|
if self.parallel._original_iterator is not None:
|
||
|
|
self.parallel.dispatch_next()
|
||
|
|
|
||
|
|
|
||
|
|
###############################################################################
|
||
|
|
def register_parallel_backend(name, factory, make_default=False):
|
||
|
|
"""Register a new Parallel backend factory.
|
||
|
|
|
||
|
|
The new backend can then be selected by passing its name as the backend
|
||
|
|
argument to the Parallel class. Moreover, the default backend can be
|
||
|
|
overwritten globally by setting make_default=True.
|
||
|
|
|
||
|
|
The factory can be any callable that takes no argument and return an
|
||
|
|
instance of ``ParallelBackendBase``.
|
||
|
|
|
||
|
|
Warning: this function is experimental and subject to change in a future
|
||
|
|
version of joblib.
|
||
|
|
|
||
|
|
.. versionadded:: 0.10
|
||
|
|
|
||
|
|
"""
|
||
|
|
BACKENDS[name] = factory
|
||
|
|
if make_default:
|
||
|
|
global DEFAULT_BACKEND
|
||
|
|
DEFAULT_BACKEND = name
|
||
|
|
|
||
|
|
|
||
|
|
def effective_n_jobs(n_jobs=-1):
|
||
|
|
"""Determine the number of jobs that can actually run in parallel
|
||
|
|
|
||
|
|
n_jobs is the number of workers requested by the callers. Passing n_jobs=-1
|
||
|
|
means requesting all available workers for instance matching the number of
|
||
|
|
CPU cores on the worker host(s).
|
||
|
|
|
||
|
|
This method should return a guesstimate of the number of workers that can
|
||
|
|
actually perform work concurrently with the currently enabled default
|
||
|
|
backend. The primary use case is to make it possible for the caller to know
|
||
|
|
in how many chunks to slice the work.
|
||
|
|
|
||
|
|
In general working on larger data chunks is more efficient (less scheduling
|
||
|
|
overhead and better use of CPU cache prefetching heuristics) as long as all
|
||
|
|
the workers have enough work to do.
|
||
|
|
|
||
|
|
Warning: this function is experimental and subject to change in a future
|
||
|
|
version of joblib.
|
||
|
|
|
||
|
|
.. versionadded:: 0.10
|
||
|
|
|
||
|
|
"""
|
||
|
|
backend, backend_n_jobs = get_active_backend()
|
||
|
|
if n_jobs is None:
|
||
|
|
n_jobs = backend_n_jobs
|
||
|
|
return backend.effective_n_jobs(n_jobs=n_jobs)
|
||
|
|
|
||
|
|
|
||
|
|
###############################################################################
|
||
|
|
class Parallel(Logger):
|
||
|
|
''' Helper class for readable parallel mapping.
|
||
|
|
|
||
|
|
Read more in the :ref:`User Guide <parallel>`.
|
||
|
|
|
||
|
|
Parameters
|
||
|
|
-----------
|
||
|
|
n_jobs: int, default: None
|
||
|
|
The maximum number of concurrently running jobs, such as the number
|
||
|
|
of Python worker processes when backend="multiprocessing"
|
||
|
|
or the size of the thread-pool when backend="threading".
|
||
|
|
If -1 all CPUs are used. If 1 is given, no parallel computing code
|
||
|
|
is used at all, which is useful for debugging. For n_jobs below -1,
|
||
|
|
(n_cpus + 1 + n_jobs) are used. Thus for n_jobs = -2, all
|
||
|
|
CPUs but one are used.
|
||
|
|
None is a marker for 'unset' that will be interpreted as n_jobs=1
|
||
|
|
(sequential execution) unless the call is performed under a
|
||
|
|
parallel_backend context manager that sets another value for
|
||
|
|
n_jobs.
|
||
|
|
backend: str, ParallelBackendBase instance or None, default: 'loky'
|
||
|
|
Specify the parallelization backend implementation.
|
||
|
|
Supported backends are:
|
||
|
|
|
||
|
|
- "loky" used by default, can induce some
|
||
|
|
communication and memory overhead when exchanging input and
|
||
|
|
output data with the worker Python processes.
|
||
|
|
- "multiprocessing" previous process-based backend based on
|
||
|
|
`multiprocessing.Pool`. Less robust than `loky`.
|
||
|
|
- "threading" is a very low-overhead backend but it suffers
|
||
|
|
from the Python Global Interpreter Lock if the called function
|
||
|
|
relies a lot on Python objects. "threading" is mostly useful
|
||
|
|
when the execution bottleneck is a compiled extension that
|
||
|
|
explicitly releases the GIL (for instance a Cython loop wrapped
|
||
|
|
in a "with nogil" block or an expensive call to a library such
|
||
|
|
as NumPy).
|
||
|
|
- finally, you can register backends by calling
|
||
|
|
register_parallel_backend. This will allow you to implement
|
||
|
|
a backend of your liking.
|
||
|
|
|
||
|
|
It is not recommended to hard-code the backend name in a call to
|
||
|
|
Parallel in a library. Instead it is recommended to set soft hints
|
||
|
|
(prefer) or hard constraints (require) so as to make it possible
|
||
|
|
for library users to change the backend from the outside using the
|
||
|
|
parallel_backend context manager.
|
||
|
|
prefer: str in {'processes', 'threads'} or None, default: None
|
||
|
|
Soft hint to choose the default backend if no specific backend
|
||
|
|
was selected with the parallel_backend context manager. The
|
||
|
|
default process-based backend is 'loky' and the default
|
||
|
|
thread-based backend is 'threading'. Ignored if the ``backend``
|
||
|
|
parameter is specified.
|
||
|
|
require: 'sharedmem' or None, default None
|
||
|
|
Hard constraint to select the backend. If set to 'sharedmem',
|
||
|
|
the selected backend will be single-host and thread-based even
|
||
|
|
if the user asked for a non-thread based backend with
|
||
|
|
parallel_backend.
|
||
|
|
verbose: int, optional
|
||
|
|
The verbosity level: if non zero, progress messages are
|
||
|
|
printed. Above 50, the output is sent to stdout.
|
||
|
|
The frequency of the messages increases with the verbosity level.
|
||
|
|
If it more than 10, all iterations are reported.
|
||
|
|
timeout: float, optional
|
||
|
|
Timeout limit for each task to complete. If any task takes longer
|
||
|
|
a TimeOutError will be raised. Only applied when n_jobs != 1
|
||
|
|
pre_dispatch: {'all', integer, or expression, as in '3*n_jobs'}
|
||
|
|
The number of batches (of tasks) to be pre-dispatched.
|
||
|
|
Default is '2*n_jobs'. When batch_size="auto" this is reasonable
|
||
|
|
default and the workers should never starve.
|
||
|
|
batch_size: int or 'auto', default: 'auto'
|
||
|
|
The number of atomic tasks to dispatch at once to each
|
||
|
|
worker. When individual evaluations are very fast, dispatching
|
||
|
|
calls to workers can be slower than sequential computation because
|
||
|
|
of the overhead. Batching fast computations together can mitigate
|
||
|
|
this.
|
||
|
|
The ``'auto'`` strategy keeps track of the time it takes for a batch
|
||
|
|
to complete, and dynamically adjusts the batch size to keep the time
|
||
|
|
on the order of half a second, using a heuristic. The initial batch
|
||
|
|
size is 1.
|
||
|
|
``batch_size="auto"`` with ``backend="threading"`` will dispatch
|
||
|
|
batches of a single task at a time as the threading backend has
|
||
|
|
very little overhead and using larger batch size has not proved to
|
||
|
|
bring any gain in that case.
|
||
|
|
temp_folder: str, optional
|
||
|
|
Folder to be used by the pool for memmapping large arrays
|
||
|
|
for sharing memory with worker processes. If None, this will try in
|
||
|
|
order:
|
||
|
|
|
||
|
|
- a folder pointed by the JOBLIB_TEMP_FOLDER environment
|
||
|
|
variable,
|
||
|
|
- /dev/shm if the folder exists and is writable: this is a
|
||
|
|
RAM disk filesystem available by default on modern Linux
|
||
|
|
distributions,
|
||
|
|
- the default system temporary folder that can be
|
||
|
|
overridden with TMP, TMPDIR or TEMP environment
|
||
|
|
variables, typically /tmp under Unix operating systems.
|
||
|
|
|
||
|
|
Only active when backend="loky" or "multiprocessing".
|
||
|
|
max_nbytes int, str, or None, optional, 1M by default
|
||
|
|
Threshold on the size of arrays passed to the workers that
|
||
|
|
triggers automated memory mapping in temp_folder. Can be an int
|
||
|
|
in Bytes, or a human-readable string, e.g., '1M' for 1 megabyte.
|
||
|
|
Use None to disable memmapping of large arrays.
|
||
|
|
Only active when backend="loky" or "multiprocessing".
|
||
|
|
mmap_mode: {None, 'r+', 'r', 'w+', 'c'}
|
||
|
|
Memmapping mode for numpy arrays passed to workers.
|
||
|
|
See 'max_nbytes' parameter documentation for more details.
|
||
|
|
|
||
|
|
Notes
|
||
|
|
-----
|
||
|
|
|
||
|
|
This object uses workers to compute in parallel the application of a
|
||
|
|
function to many different arguments. The main functionality it brings
|
||
|
|
in addition to using the raw multiprocessing or concurrent.futures API
|
||
|
|
are (see examples for details):
|
||
|
|
|
||
|
|
* More readable code, in particular since it avoids
|
||
|
|
constructing list of arguments.
|
||
|
|
|
||
|
|
* Easier debugging:
|
||
|
|
- informative tracebacks even when the error happens on
|
||
|
|
the client side
|
||
|
|
- using 'n_jobs=1' enables to turn off parallel computing
|
||
|
|
for debugging without changing the codepath
|
||
|
|
- early capture of pickling errors
|
||
|
|
|
||
|
|
* An optional progress meter.
|
||
|
|
|
||
|
|
* Interruption of multiprocesses jobs with 'Ctrl-C'
|
||
|
|
|
||
|
|
* Flexible pickling control for the communication to and from
|
||
|
|
the worker processes.
|
||
|
|
|
||
|
|
* Ability to use shared memory efficiently with worker
|
||
|
|
processes for large numpy-based datastructures.
|
||
|
|
|
||
|
|
Examples
|
||
|
|
--------
|
||
|
|
|
||
|
|
A simple example:
|
||
|
|
|
||
|
|
>>> from math import sqrt
|
||
|
|
>>> from joblib import Parallel, delayed
|
||
|
|
>>> Parallel(n_jobs=1)(delayed(sqrt)(i**2) for i in range(10))
|
||
|
|
[0.0, 1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0, 9.0]
|
||
|
|
|
||
|
|
Reshaping the output when the function has several return
|
||
|
|
values:
|
||
|
|
|
||
|
|
>>> from math import modf
|
||
|
|
>>> from joblib import Parallel, delayed
|
||
|
|
>>> r = Parallel(n_jobs=1)(delayed(modf)(i/2.) for i in range(10))
|
||
|
|
>>> res, i = zip(*r)
|
||
|
|
>>> res
|
||
|
|
(0.0, 0.5, 0.0, 0.5, 0.0, 0.5, 0.0, 0.5, 0.0, 0.5)
|
||
|
|
>>> i
|
||
|
|
(0.0, 0.0, 1.0, 1.0, 2.0, 2.0, 3.0, 3.0, 4.0, 4.0)
|
||
|
|
|
||
|
|
The progress meter: the higher the value of `verbose`, the more
|
||
|
|
messages:
|
||
|
|
|
||
|
|
>>> from time import sleep
|
||
|
|
>>> from joblib import Parallel, delayed
|
||
|
|
>>> r = Parallel(n_jobs=2, verbose=10)(delayed(sleep)(.2) for _ in range(10)) #doctest: +SKIP
|
||
|
|
[Parallel(n_jobs=2)]: Done 1 tasks | elapsed: 0.6s
|
||
|
|
[Parallel(n_jobs=2)]: Done 4 tasks | elapsed: 0.8s
|
||
|
|
[Parallel(n_jobs=2)]: Done 10 out of 10 | elapsed: 1.4s finished
|
||
|
|
|
||
|
|
Traceback example, note how the line of the error is indicated
|
||
|
|
as well as the values of the parameter passed to the function that
|
||
|
|
triggered the exception, even though the traceback happens in the
|
||
|
|
child process:
|
||
|
|
|
||
|
|
>>> from heapq import nlargest
|
||
|
|
>>> from joblib import Parallel, delayed
|
||
|
|
>>> Parallel(n_jobs=2)(delayed(nlargest)(2, n) for n in (range(4), 'abcde', 3)) #doctest: +SKIP
|
||
|
|
#...
|
||
|
|
---------------------------------------------------------------------------
|
||
|
|
Sub-process traceback:
|
||
|
|
---------------------------------------------------------------------------
|
||
|
|
TypeError Mon Nov 12 11:37:46 2012
|
||
|
|
PID: 12934 Python 2.7.3: /usr/bin/python
|
||
|
|
...........................................................................
|
||
|
|
/usr/lib/python2.7/heapq.pyc in nlargest(n=2, iterable=3, key=None)
|
||
|
|
419 if n >= size:
|
||
|
|
420 return sorted(iterable, key=key, reverse=True)[:n]
|
||
|
|
421
|
||
|
|
422 # When key is none, use simpler decoration
|
||
|
|
423 if key is None:
|
||
|
|
--> 424 it = izip(iterable, count(0,-1)) # decorate
|
||
|
|
425 result = _nlargest(n, it)
|
||
|
|
426 return map(itemgetter(0), result) # undecorate
|
||
|
|
427
|
||
|
|
428 # General case, slowest method
|
||
|
|
TypeError: izip argument #1 must support iteration
|
||
|
|
___________________________________________________________________________
|
||
|
|
|
||
|
|
|
||
|
|
Using pre_dispatch in a producer/consumer situation, where the
|
||
|
|
data is generated on the fly. Note how the producer is first
|
||
|
|
called 3 times before the parallel loop is initiated, and then
|
||
|
|
called to generate new data on the fly:
|
||
|
|
|
||
|
|
>>> from math import sqrt
|
||
|
|
>>> from joblib import Parallel, delayed
|
||
|
|
>>> def producer():
|
||
|
|
... for i in range(6):
|
||
|
|
... print('Produced %s' % i)
|
||
|
|
... yield i
|
||
|
|
>>> out = Parallel(n_jobs=2, verbose=100, pre_dispatch='1.5*n_jobs')(
|
||
|
|
... delayed(sqrt)(i) for i in producer()) #doctest: +SKIP
|
||
|
|
Produced 0
|
||
|
|
Produced 1
|
||
|
|
Produced 2
|
||
|
|
[Parallel(n_jobs=2)]: Done 1 jobs | elapsed: 0.0s
|
||
|
|
Produced 3
|
||
|
|
[Parallel(n_jobs=2)]: Done 2 jobs | elapsed: 0.0s
|
||
|
|
Produced 4
|
||
|
|
[Parallel(n_jobs=2)]: Done 3 jobs | elapsed: 0.0s
|
||
|
|
Produced 5
|
||
|
|
[Parallel(n_jobs=2)]: Done 4 jobs | elapsed: 0.0s
|
||
|
|
[Parallel(n_jobs=2)]: Done 6 out of 6 | elapsed: 0.0s remaining: 0.0s
|
||
|
|
[Parallel(n_jobs=2)]: Done 6 out of 6 | elapsed: 0.0s finished
|
||
|
|
|
||
|
|
'''
|
||
|
|
def __init__(self, n_jobs=None, backend=None, verbose=0, timeout=None,
|
||
|
|
pre_dispatch='2 * n_jobs', batch_size='auto',
|
||
|
|
temp_folder=None, max_nbytes='1M', mmap_mode='r',
|
||
|
|
prefer=None, require=None):
|
||
|
|
active_backend, context_n_jobs = get_active_backend(
|
||
|
|
prefer=prefer, require=require, verbose=verbose)
|
||
|
|
nesting_level = active_backend.nesting_level
|
||
|
|
if backend is None and n_jobs is None:
|
||
|
|
# If we are under a parallel_backend context manager, look up
|
||
|
|
# the default number of jobs and use that instead:
|
||
|
|
n_jobs = context_n_jobs
|
||
|
|
if n_jobs is None:
|
||
|
|
# No specific context override and no specific value request:
|
||
|
|
# default to 1.
|
||
|
|
n_jobs = 1
|
||
|
|
self.n_jobs = n_jobs
|
||
|
|
self.verbose = verbose
|
||
|
|
self.timeout = timeout
|
||
|
|
self.pre_dispatch = pre_dispatch
|
||
|
|
self._ready_batches = queue.Queue()
|
||
|
|
self._id = uuid4().hex
|
||
|
|
self._reducer_callback = None
|
||
|
|
|
||
|
|
if isinstance(max_nbytes, str):
|
||
|
|
max_nbytes = memstr_to_bytes(max_nbytes)
|
||
|
|
|
||
|
|
self._backend_args = dict(
|
||
|
|
max_nbytes=max_nbytes,
|
||
|
|
mmap_mode=mmap_mode,
|
||
|
|
temp_folder=temp_folder,
|
||
|
|
prefer=prefer,
|
||
|
|
require=require,
|
||
|
|
verbose=max(0, self.verbose - 50),
|
||
|
|
)
|
||
|
|
if DEFAULT_MP_CONTEXT is not None:
|
||
|
|
self._backend_args['context'] = DEFAULT_MP_CONTEXT
|
||
|
|
elif hasattr(mp, "get_context"):
|
||
|
|
self._backend_args['context'] = mp.get_context()
|
||
|
|
|
||
|
|
if backend is None:
|
||
|
|
backend = active_backend
|
||
|
|
|
||
|
|
elif isinstance(backend, ParallelBackendBase):
|
||
|
|
# Use provided backend as is, with the current nesting_level if it
|
||
|
|
# is not set yet.
|
||
|
|
if backend.nesting_level is None:
|
||
|
|
backend.nesting_level = nesting_level
|
||
|
|
|
||
|
|
elif hasattr(backend, 'Pool') and hasattr(backend, 'Lock'):
|
||
|
|
# Make it possible to pass a custom multiprocessing context as
|
||
|
|
# backend to change the start method to forkserver or spawn or
|
||
|
|
# preload modules on the forkserver helper process.
|
||
|
|
self._backend_args['context'] = backend
|
||
|
|
backend = MultiprocessingBackend(nesting_level=nesting_level)
|
||
|
|
else:
|
||
|
|
try:
|
||
|
|
backend_factory = BACKENDS[backend]
|
||
|
|
except KeyError as e:
|
||
|
|
raise ValueError("Invalid backend: %s, expected one of %r"
|
||
|
|
% (backend, sorted(BACKENDS.keys()))) from e
|
||
|
|
backend = backend_factory(nesting_level=nesting_level)
|
||
|
|
|
||
|
|
if (require == 'sharedmem' and
|
||
|
|
not getattr(backend, 'supports_sharedmem', False)):
|
||
|
|
raise ValueError("Backend %s does not support shared memory"
|
||
|
|
% backend)
|
||
|
|
|
||
|
|
if (batch_size == 'auto' or isinstance(batch_size, Integral) and
|
||
|
|
batch_size > 0):
|
||
|
|
self.batch_size = batch_size
|
||
|
|
else:
|
||
|
|
raise ValueError(
|
||
|
|
"batch_size must be 'auto' or a positive integer, got: %r"
|
||
|
|
% batch_size)
|
||
|
|
|
||
|
|
self._backend = backend
|
||
|
|
self._output = None
|
||
|
|
self._jobs = list()
|
||
|
|
self._managed_backend = False
|
||
|
|
|
||
|
|
# This lock is used coordinate the main thread of this process with
|
||
|
|
# the async callback thread of our the pool.
|
||
|
|
self._lock = threading.RLock()
|
||
|
|
|
||
|
|
def __enter__(self):
|
||
|
|
self._managed_backend = True
|
||
|
|
self._initialize_backend()
|
||
|
|
return self
|
||
|
|
|
||
|
|
def __exit__(self, exc_type, exc_value, traceback):
|
||
|
|
self._terminate_backend()
|
||
|
|
self._managed_backend = False
|
||
|
|
|
||
|
|
def _initialize_backend(self):
|
||
|
|
"""Build a process or thread pool and return the number of workers"""
|
||
|
|
try:
|
||
|
|
n_jobs = self._backend.configure(n_jobs=self.n_jobs, parallel=self,
|
||
|
|
**self._backend_args)
|
||
|
|
if self.timeout is not None and not self._backend.supports_timeout:
|
||
|
|
warnings.warn(
|
||
|
|
'The backend class {!r} does not support timeout. '
|
||
|
|
"You have set 'timeout={}' in Parallel but "
|
||
|
|
"the 'timeout' parameter will not be used.".format(
|
||
|
|
self._backend.__class__.__name__,
|
||
|
|
self.timeout))
|
||
|
|
|
||
|
|
except FallbackToBackend as e:
|
||
|
|
# Recursively initialize the backend in case of requested fallback.
|
||
|
|
self._backend = e.backend
|
||
|
|
n_jobs = self._initialize_backend()
|
||
|
|
|
||
|
|
return n_jobs
|
||
|
|
|
||
|
|
def _effective_n_jobs(self):
|
||
|
|
if self._backend:
|
||
|
|
return self._backend.effective_n_jobs(self.n_jobs)
|
||
|
|
return 1
|
||
|
|
|
||
|
|
def _terminate_backend(self):
|
||
|
|
if self._backend is not None:
|
||
|
|
self._backend.terminate()
|
||
|
|
|
||
|
|
def _dispatch(self, batch):
|
||
|
|
"""Queue the batch for computing, with or without multiprocessing
|
||
|
|
|
||
|
|
WARNING: this method is not thread-safe: it should be only called
|
||
|
|
indirectly via dispatch_one_batch.
|
||
|
|
|
||
|
|
"""
|
||
|
|
# If job.get() catches an exception, it closes the queue:
|
||
|
|
if self._aborting:
|
||
|
|
return
|
||
|
|
|
||
|
|
self.n_dispatched_tasks += len(batch)
|
||
|
|
self.n_dispatched_batches += 1
|
||
|
|
|
||
|
|
dispatch_timestamp = time.time()
|
||
|
|
cb = BatchCompletionCallBack(dispatch_timestamp, len(batch), self)
|
||
|
|
with self._lock:
|
||
|
|
job_idx = len(self._jobs)
|
||
|
|
job = self._backend.apply_async(batch, callback=cb)
|
||
|
|
# A job can complete so quickly than its callback is
|
||
|
|
# called before we get here, causing self._jobs to
|
||
|
|
# grow. To ensure correct results ordering, .insert is
|
||
|
|
# used (rather than .append) in the following line
|
||
|
|
self._jobs.insert(job_idx, job)
|
||
|
|
|
||
|
|
def dispatch_next(self):
|
||
|
|
"""Dispatch more data for parallel processing
|
||
|
|
|
||
|
|
This method is meant to be called concurrently by the multiprocessing
|
||
|
|
callback. We rely on the thread-safety of dispatch_one_batch to protect
|
||
|
|
against concurrent consumption of the unprotected iterator.
|
||
|
|
|
||
|
|
"""
|
||
|
|
if not self.dispatch_one_batch(self._original_iterator):
|
||
|
|
self._iterating = False
|
||
|
|
self._original_iterator = None
|
||
|
|
|
||
|
|
def dispatch_one_batch(self, iterator):
|
||
|
|
"""Prefetch the tasks for the next batch and dispatch them.
|
||
|
|
|
||
|
|
The effective size of the batch is computed here.
|
||
|
|
If there are no more jobs to dispatch, return False, else return True.
|
||
|
|
|
||
|
|
The iterator consumption and dispatching is protected by the same
|
||
|
|
lock so calling this function should be thread safe.
|
||
|
|
|
||
|
|
"""
|
||
|
|
if self.batch_size == 'auto':
|
||
|
|
batch_size = self._backend.compute_batch_size()
|
||
|
|
else:
|
||
|
|
# Fixed batch size strategy
|
||
|
|
batch_size = self.batch_size
|
||
|
|
|
||
|
|
with self._lock:
|
||
|
|
# to ensure an even distribution of the workolad between workers,
|
||
|
|
# we look ahead in the original iterators more than batch_size
|
||
|
|
# tasks - However, we keep consuming only one batch at each
|
||
|
|
# dispatch_one_batch call. The extra tasks are stored in a local
|
||
|
|
# queue, _ready_batches, that is looked-up prior to re-consuming
|
||
|
|
# tasks from the origal iterator.
|
||
|
|
try:
|
||
|
|
tasks = self._ready_batches.get(block=False)
|
||
|
|
except queue.Empty:
|
||
|
|
# slice the iterator n_jobs * batchsize items at a time. If the
|
||
|
|
# slice returns less than that, then the current batchsize puts
|
||
|
|
# too much weight on a subset of workers, while other may end
|
||
|
|
# up starving. So in this case, re-scale the batch size
|
||
|
|
# accordingly to distribute evenly the last items between all
|
||
|
|
# workers.
|
||
|
|
n_jobs = self._cached_effective_n_jobs
|
||
|
|
big_batch_size = batch_size * n_jobs
|
||
|
|
|
||
|
|
islice = list(itertools.islice(iterator, big_batch_size))
|
||
|
|
if len(islice) == 0:
|
||
|
|
return False
|
||
|
|
elif (iterator is self._original_iterator
|
||
|
|
and len(islice) < big_batch_size):
|
||
|
|
# We reached the end of the original iterator (unless
|
||
|
|
# iterator is the ``pre_dispatch``-long initial slice of
|
||
|
|
# the original iterator) -- decrease the batch size to
|
||
|
|
# account for potential variance in the batches running
|
||
|
|
# time.
|
||
|
|
final_batch_size = max(1, len(islice) // (10 * n_jobs))
|
||
|
|
else:
|
||
|
|
final_batch_size = max(1, len(islice) // n_jobs)
|
||
|
|
|
||
|
|
# enqueue n_jobs batches in a local queue
|
||
|
|
for i in range(0, len(islice), final_batch_size):
|
||
|
|
tasks = BatchedCalls(islice[i:i + final_batch_size],
|
||
|
|
self._backend.get_nested_backend(),
|
||
|
|
self._reducer_callback,
|
||
|
|
self._pickle_cache)
|
||
|
|
self._ready_batches.put(tasks)
|
||
|
|
|
||
|
|
# finally, get one task.
|
||
|
|
tasks = self._ready_batches.get(block=False)
|
||
|
|
if len(tasks) == 0:
|
||
|
|
# No more tasks available in the iterator: tell caller to stop.
|
||
|
|
return False
|
||
|
|
else:
|
||
|
|
self._dispatch(tasks)
|
||
|
|
return True
|
||
|
|
|
||
|
|
def _print(self, msg, msg_args):
|
||
|
|
"""Display the message on stout or stderr depending on verbosity"""
|
||
|
|
# XXX: Not using the logger framework: need to
|
||
|
|
# learn to use logger better.
|
||
|
|
if not self.verbose:
|
||
|
|
return
|
||
|
|
if self.verbose < 50:
|
||
|
|
writer = sys.stderr.write
|
||
|
|
else:
|
||
|
|
writer = sys.stdout.write
|
||
|
|
msg = msg % msg_args
|
||
|
|
writer('[%s]: %s\n' % (self, msg))
|
||
|
|
|
||
|
|
def print_progress(self):
|
||
|
|
"""Display the process of the parallel execution only a fraction
|
||
|
|
of time, controlled by self.verbose.
|
||
|
|
"""
|
||
|
|
if not self.verbose:
|
||
|
|
return
|
||
|
|
elapsed_time = time.time() - self._start_time
|
||
|
|
|
||
|
|
# Original job iterator becomes None once it has been fully
|
||
|
|
# consumed : at this point we know the total number of jobs and we are
|
||
|
|
# able to display an estimation of the remaining time based on already
|
||
|
|
# completed jobs. Otherwise, we simply display the number of completed
|
||
|
|
# tasks.
|
||
|
|
if self._original_iterator is not None:
|
||
|
|
if _verbosity_filter(self.n_dispatched_batches, self.verbose):
|
||
|
|
return
|
||
|
|
self._print('Done %3i tasks | elapsed: %s',
|
||
|
|
(self.n_completed_tasks,
|
||
|
|
short_format_time(elapsed_time), ))
|
||
|
|
else:
|
||
|
|
index = self.n_completed_tasks
|
||
|
|
# We are finished dispatching
|
||
|
|
total_tasks = self.n_dispatched_tasks
|
||
|
|
# We always display the first loop
|
||
|
|
if not index == 0:
|
||
|
|
# Display depending on the number of remaining items
|
||
|
|
# A message as soon as we finish dispatching, cursor is 0
|
||
|
|
cursor = (total_tasks - index + 1 -
|
||
|
|
self._pre_dispatch_amount)
|
||
|
|
frequency = (total_tasks // self.verbose) + 1
|
||
|
|
is_last_item = (index + 1 == total_tasks)
|
||
|
|
if (is_last_item or cursor % frequency):
|
||
|
|
return
|
||
|
|
remaining_time = (elapsed_time / index) * \
|
||
|
|
(self.n_dispatched_tasks - index * 1.0)
|
||
|
|
# only display status if remaining time is greater or equal to 0
|
||
|
|
self._print('Done %3i out of %3i | elapsed: %s remaining: %s',
|
||
|
|
(index,
|
||
|
|
total_tasks,
|
||
|
|
short_format_time(elapsed_time),
|
||
|
|
short_format_time(remaining_time),
|
||
|
|
))
|
||
|
|
|
||
|
|
def retrieve(self):
|
||
|
|
self._output = list()
|
||
|
|
while self._iterating or len(self._jobs) > 0:
|
||
|
|
if len(self._jobs) == 0:
|
||
|
|
# Wait for an async callback to dispatch new jobs
|
||
|
|
time.sleep(0.01)
|
||
|
|
continue
|
||
|
|
# We need to be careful: the job list can be filling up as
|
||
|
|
# we empty it and Python list are not thread-safe by default hence
|
||
|
|
# the use of the lock
|
||
|
|
with self._lock:
|
||
|
|
job = self._jobs.pop(0)
|
||
|
|
|
||
|
|
try:
|
||
|
|
if getattr(self._backend, 'supports_timeout', False):
|
||
|
|
self._output.extend(job.get(timeout=self.timeout))
|
||
|
|
else:
|
||
|
|
self._output.extend(job.get())
|
||
|
|
|
||
|
|
except BaseException as exception:
|
||
|
|
# Note: we catch any BaseException instead of just Exception
|
||
|
|
# instances to also include KeyboardInterrupt.
|
||
|
|
|
||
|
|
# Stop dispatching any new job in the async callback thread
|
||
|
|
self._aborting = True
|
||
|
|
|
||
|
|
# If the backend allows it, cancel or kill remaining running
|
||
|
|
# tasks without waiting for the results as we will raise
|
||
|
|
# the exception we got back to the caller instead of returning
|
||
|
|
# any result.
|
||
|
|
backend = self._backend
|
||
|
|
if (backend is not None and
|
||
|
|
hasattr(backend, 'abort_everything')):
|
||
|
|
# If the backend is managed externally we need to make sure
|
||
|
|
# to leave it in a working state to allow for future jobs
|
||
|
|
# scheduling.
|
||
|
|
ensure_ready = self._managed_backend
|
||
|
|
backend.abort_everything(ensure_ready=ensure_ready)
|
||
|
|
raise
|
||
|
|
|
||
|
|
def __call__(self, iterable):
|
||
|
|
if self._jobs:
|
||
|
|
raise ValueError('This Parallel instance is already running')
|
||
|
|
# A flag used to abort the dispatching of jobs in case an
|
||
|
|
# exception is found
|
||
|
|
self._aborting = False
|
||
|
|
|
||
|
|
if not self._managed_backend:
|
||
|
|
n_jobs = self._initialize_backend()
|
||
|
|
else:
|
||
|
|
n_jobs = self._effective_n_jobs()
|
||
|
|
|
||
|
|
if isinstance(self._backend, LokyBackend):
|
||
|
|
# For the loky backend, we add a callback executed when reducing
|
||
|
|
# BatchCalls, that makes the loky executor use a temporary folder
|
||
|
|
# specific to this Parallel object when pickling temporary memmaps.
|
||
|
|
# This callback is necessary to ensure that several Parallel
|
||
|
|
# objects using the same resuable executor don't use the same
|
||
|
|
# temporary resources.
|
||
|
|
|
||
|
|
def _batched_calls_reducer_callback():
|
||
|
|
# Relevant implementation detail: the following lines, called
|
||
|
|
# when reducing BatchedCalls, are called in a thread-safe
|
||
|
|
# situation, meaning that the context of the temporary folder
|
||
|
|
# manager will not be changed in between the callback execution
|
||
|
|
# and the end of the BatchedCalls pickling. The reason is that
|
||
|
|
# pickling (the only place where set_current_context is used)
|
||
|
|
# is done from a single thread (the queue_feeder_thread).
|
||
|
|
self._backend._workers._temp_folder_manager.set_current_context( # noqa
|
||
|
|
self._id
|
||
|
|
)
|
||
|
|
self._reducer_callback = _batched_calls_reducer_callback
|
||
|
|
|
||
|
|
# self._effective_n_jobs should be called in the Parallel.__call__
|
||
|
|
# thread only -- store its value in an attribute for further queries.
|
||
|
|
self._cached_effective_n_jobs = n_jobs
|
||
|
|
|
||
|
|
backend_name = self._backend.__class__.__name__
|
||
|
|
if n_jobs == 0:
|
||
|
|
raise RuntimeError("%s has no active worker." % backend_name)
|
||
|
|
|
||
|
|
self._print("Using backend %s with %d concurrent workers.",
|
||
|
|
(backend_name, n_jobs))
|
||
|
|
if hasattr(self._backend, 'start_call'):
|
||
|
|
self._backend.start_call()
|
||
|
|
iterator = iter(iterable)
|
||
|
|
pre_dispatch = self.pre_dispatch
|
||
|
|
|
||
|
|
if pre_dispatch == 'all' or n_jobs == 1:
|
||
|
|
# prevent further dispatch via multiprocessing callback thread
|
||
|
|
self._original_iterator = None
|
||
|
|
self._pre_dispatch_amount = 0
|
||
|
|
else:
|
||
|
|
self._original_iterator = iterator
|
||
|
|
if hasattr(pre_dispatch, 'endswith'):
|
||
|
|
pre_dispatch = eval(pre_dispatch)
|
||
|
|
self._pre_dispatch_amount = pre_dispatch = int(pre_dispatch)
|
||
|
|
|
||
|
|
# The main thread will consume the first pre_dispatch items and
|
||
|
|
# the remaining items will later be lazily dispatched by async
|
||
|
|
# callbacks upon task completions.
|
||
|
|
|
||
|
|
# TODO: this iterator should be batch_size * n_jobs
|
||
|
|
iterator = itertools.islice(iterator, self._pre_dispatch_amount)
|
||
|
|
|
||
|
|
self._start_time = time.time()
|
||
|
|
self.n_dispatched_batches = 0
|
||
|
|
self.n_dispatched_tasks = 0
|
||
|
|
self.n_completed_tasks = 0
|
||
|
|
# Use a caching dict for callables that are pickled with cloudpickle to
|
||
|
|
# improve performances. This cache is used only in the case of
|
||
|
|
# functions that are defined in the __main__ module, functions that are
|
||
|
|
# defined locally (inside another function) and lambda expressions.
|
||
|
|
self._pickle_cache = dict()
|
||
|
|
try:
|
||
|
|
# Only set self._iterating to True if at least a batch
|
||
|
|
# was dispatched. In particular this covers the edge
|
||
|
|
# case of Parallel used with an exhausted iterator. If
|
||
|
|
# self._original_iterator is None, then this means either
|
||
|
|
# that pre_dispatch == "all", n_jobs == 1 or that the first batch
|
||
|
|
# was very quick and its callback already dispatched all the
|
||
|
|
# remaining jobs.
|
||
|
|
self._iterating = False
|
||
|
|
if self.dispatch_one_batch(iterator):
|
||
|
|
self._iterating = self._original_iterator is not None
|
||
|
|
|
||
|
|
while self.dispatch_one_batch(iterator):
|
||
|
|
pass
|
||
|
|
|
||
|
|
if pre_dispatch == "all" or n_jobs == 1:
|
||
|
|
# The iterable was consumed all at once by the above for loop.
|
||
|
|
# No need to wait for async callbacks to trigger to
|
||
|
|
# consumption.
|
||
|
|
self._iterating = False
|
||
|
|
|
||
|
|
with self._backend.retrieval_context():
|
||
|
|
self.retrieve()
|
||
|
|
# Make sure that we get a last message telling us we are done
|
||
|
|
elapsed_time = time.time() - self._start_time
|
||
|
|
self._print('Done %3i out of %3i | elapsed: %s finished',
|
||
|
|
(len(self._output), len(self._output),
|
||
|
|
short_format_time(elapsed_time)))
|
||
|
|
finally:
|
||
|
|
if hasattr(self._backend, 'stop_call'):
|
||
|
|
self._backend.stop_call()
|
||
|
|
if not self._managed_backend:
|
||
|
|
self._terminate_backend()
|
||
|
|
self._jobs = list()
|
||
|
|
self._pickle_cache = None
|
||
|
|
output = self._output
|
||
|
|
self._output = None
|
||
|
|
return output
|
||
|
|
|
||
|
|
def __repr__(self):
|
||
|
|
return '%s(n_jobs=%s)' % (self.__class__.__name__, self.n_jobs)
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