错误在joblib`Parallel`上下文中挑选一个`matlab`对象

Question

我在Python上下文中并行运行一些Matlab代码（我知道，但这就是正在发生的事情），而且我遇到了涉及matlab.double的导入错误。相同的代码在multiprocessing.Pool中工作正常，所以我无法弄清问题是什么。这是一个最小的再现测试用例。

import matlab
from multiprocessing import Pool
from joblib import Parallel, delayed

# A global object that I would like to be available in the parallel subroutine
x = matlab.double([[0.0]])

def f(i):
    print(i, x)

with Pool(4) as p:
    p.map(f, range(10))
    # This prints 1, [[0.0]]\n2, [[0.0]]\n... as expected

for _ in Parallel(4, backend='multiprocessing')(delayed(f)(i) for i in range(10)):
    pass
# This also prints 1, [[0.0]]\n2, [[0.0]]\n... as expected

# Now run with default `backend='loky'`
for _ in Parallel(4)(delayed(f)(i) for i in range(10)):
    pass
# ^ this crashes.

因此，唯一有问题的是使用'loky'后端的那个。完整的追溯是：

exception calling callback for <Future at 0x7f63b5a57358 state=finished raised BrokenProcessPool>
joblib.externals.loky.process_executor._RemoteTraceback: 
'''
Traceback (most recent call last):
  File "~/miniconda3/envs/myenv/lib/python3.6/site-packages/joblib/externals/loky/process_executor.py", line 391, in _process_worker
    call_item = call_queue.get(block=True, timeout=timeout)
  File "~/miniconda3/envs/myenv/lib/python3.6/multiprocessing/queues.py", line 113, in get
    return _ForkingPickler.loads(res)
  File "~/miniconda3/envs/myenv/lib/python3.6/site-packages/matlab/mlarray.py", line 31, in <module>
    from _internal.mlarray_sequence import _MLArrayMetaClass
  File "~/miniconda3/envs/myenv/lib/python3.6/site-packages/matlab/_internal/mlarray_sequence.py", line 3, in <module>
    from _internal.mlarray_utils import _get_strides, _get_size, \
  File "~/miniconda3/envs/myenv/lib/python3.6/site-packages/matlab/_internal/mlarray_utils.py", line 4, in <module>
    import matlab
  File "~/miniconda3/envs/myenv/lib/python3.6/site-packages/matlab/__init__.py", line 24, in <module>
    from mlarray import double, single, uint8, int8, uint16, \
ImportError: cannot import name 'double'
'''

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "~/miniconda3/envs/myenv/lib/python3.6/site-packages/joblib/externals/loky/_base.py", line 625, in _invoke_callbacks
    callback(self)
  File "~/miniconda3/envs/myenv/lib/python3.6/site-packages/joblib/parallel.py", line 309, in __call__
    self.parallel.dispatch_next()
  File "~/miniconda3/envs/myenv/lib/python3.6/site-packages/joblib/parallel.py", line 731, in dispatch_next
    if not self.dispatch_one_batch(self._original_iterator):
  File "~/miniconda3/envs/myenv/lib/python3.6/site-packages/joblib/parallel.py", line 759, in dispatch_one_batch
    self._dispatch(tasks)
  File "~/miniconda3/envs/myenv/lib/python3.6/site-packages/joblib/parallel.py", line 716, in _dispatch
    job = self._backend.apply_async(batch, callback=cb)
  File "~/miniconda3/envs/myenv/lib/python3.6/site-packages/joblib/_parallel_backends.py", line 510, in apply_async
    future = self._workers.submit(SafeFunction(func))
  File "~/miniconda3/envs/myenv/lib/python3.6/site-packages/joblib/externals/loky/reusable_executor.py", line 151, in submit
    fn, *args, **kwargs)
  File "~/miniconda3/envs/myenv/lib/python3.6/site-packages/joblib/externals/loky/process_executor.py", line 1022, in submit
    raise self._flags.broken
joblib.externals.loky.process_executor.BrokenProcessPool: A task has failed to un-serialize. Please ensure that the arguments of the function are all picklable.
joblib.externals.loky.process_executor._RemoteTraceback: 
'''
Traceback (most recent call last):
  File "~/miniconda3/envs/myenv/lib/python3.6/site-packages/joblib/externals/loky/process_executor.py", line 391, in _process_worker
    call_item = call_queue.get(block=True, timeout=timeout)
  File "~/miniconda3/envs/myenv/lib/python3.6/multiprocessing/queues.py", line 113, in get
    return _ForkingPickler.loads(res)
  File "~/miniconda3/envs/myenv/lib/python3.6/site-packages/matlab/mlarray.py", line 31, in <module>
    from _internal.mlarray_sequence import _MLArrayMetaClass
  File "~/miniconda3/envs/myenv/lib/python3.6/site-packages/matlab/_internal/mlarray_sequence.py", line 3, in <module>
    from _internal.mlarray_utils import _get_strides, _get_size, \
  File "~/miniconda3/envs/myenv/lib/python3.6/site-packages/matlab/_internal/mlarray_utils.py", line 4, in <module>
    import matlab
  File "~/miniconda3/envs/myenv/lib/python3.6/site-packages/matlab/__init__.py", line 24, in <module>
    from mlarray import double, single, uint8, int8, uint16, \
ImportError: cannot import name 'double'
'''

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "test.py", line 20, in <module>
    for _ in Parallel(4)(delayed(f)(i) for i in range(10)):
  File "~/miniconda3/envs/myenv/lib/python3.6/site-packages/joblib/parallel.py", line 934, in __call__
    self.retrieve()
  File "~/miniconda3/envs/myenv/lib/python3.6/site-packages/joblib/parallel.py", line 833, in retrieve
    self._output.extend(job.get(timeout=self.timeout))
  File "~/miniconda3/envs/myenv/lib/python3.6/site-packages/joblib/_parallel_backends.py", line 521, in wrap_future_result
    return future.result(timeout=timeout)
  File "~/miniconda3/envs/myenv/lib/python3.6/concurrent/futures/_base.py", line 432, in result
    return self.__get_result()
  File "~/miniconda3/envs/myenv/lib/python3.6/concurrent/futures/_base.py", line 384, in __get_result
    raise self._exception
  File "~/miniconda3/envs/myenv/lib/python3.6/site-packages/joblib/externals/loky/_base.py", line 625, in _invoke_callbacks
    callback(self)
  File "~/miniconda3/envs/myenv/lib/python3.6/site-packages/joblib/parallel.py", line 309, in __call__
    self.parallel.dispatch_next()
  File "~/miniconda3/envs/myenv/lib/python3.6/site-packages/joblib/parallel.py", line 731, in dispatch_next
    if not self.dispatch_one_batch(self._original_iterator):
  File "~/miniconda3/envs/myenv/lib/python3.6/site-packages/joblib/parallel.py", line 759, in dispatch_one_batch
    self._dispatch(tasks)
  File "~/miniconda3/envs/myenv/lib/python3.6/site-packages/joblib/parallel.py", line 716, in _dispatch
    job = self._backend.apply_async(batch, callback=cb)
  File "~/miniconda3/envs/myenv/lib/python3.6/site-packages/joblib/_parallel_backends.py", line 510, in apply_async
    future = self._workers.submit(SafeFunction(func))
  File "~/miniconda3/envs/myenv/lib/python3.6/site-packages/joblib/externals/loky/reusable_executor.py", line 151, in submit
    fn, *args, **kwargs)
  File "~/miniconda3/envs/myenv/lib/python3.6/site-packages/joblib/externals/loky/process_executor.py", line 1022, in submit
    raise self._flags.broken
joblib.externals.loky.process_executor.BrokenProcessPool: A task has failed to un-serialize. Please ensure that the arguments of the function are all picklable.

看一下追溯，似乎根本原因是在子进程中导入matlab包的问题。

值得注意的是，如果相反我已经定义了x = np.array([[0.0]])（在导入numpy as np之后），这一切都运行得很好。当然主要过程对任何matlab进口没有问题，所以我不确定为什么子进程会。

我不确定这个错误是否与matlab包有任何关系，或者它是否与全局变量和cloudpickle或loky有关。在我的应用程序中，它将有助于坚持使用loky，所以我很感激任何见解！

我还应该注意到我正在使用Python的官方Matlab引擎：https://www.mathworks.com/help/matlab/matlab-engine-for-python.html。我想这可能会让其他人难以尝试测试用例，所以我希望我能用matlab.double以外的类型重现这个错误，但我还没有找到另一个。

挖掘更多，我注意到导入matlab包的过程比我预期的更圆，我推测这可能是问题的一部分？问题是，当import matlab由loky的_ForkingPickler运行时，首先导入一些文件matlab/mlarray.py，导入一些其他文件，其中一个包含import matlab，这导致matlab/__init__.py运行，其内部有from mlarray import double, single, uint8, ...，这是导致崩溃。

这种循环可能成为问题吗？如果是这样，为什么我可以在主进程中导入此模块，但不能在loky后端导入？

Answer 1

该错误是由子进程中全局对象的不正确加载顺序引起的。在追溯_ForkingPickler.loads(res) -> ... -> import matlab -> from mlarray import ...中可以清楚地看到，当全球变量matlab由x加载时，cloudpickle尚未导入。

joblib与loky似乎将模块视为普通的全局对象，并将它们动态发送到子进程。 joblib不记录定义这些对象/模块的顺序。因此，它们在子进程中以随机顺序加载（初始化）。

一个简单的解决方法是手动挑选matlab对象并在函数内导入matlab后加载它。

import matlab
import pickle

px = pickle.dumps(matlab.double([[0.0]]))

def f(i):
    import matlab
    x=pickle.loads(px)
    print(i, x)

当然，您也可以使用joblib.dumps和loads来序列化对象。

使用初始化程序

感谢@Aaron的建议，您还可以在加载initializer之前使用for loky（x）导入Matlab。

Currently there's no simple API to specify initializer。所以我写了一个简单的函数：

def with_initializer(self, f_init):
    # Overwrite initializer hook in the Loky ProcessPoolExecutor
    # https://github.com/tomMoral/loky/blob/f4739e123acb711781e46581d5ed31ed8201c7a9/loky/process_executor.py#L850
    hasattr(self._backend, '_workers') or self.__enter__()
    origin_init = self._backend._workers._initializer
    def new_init():
        origin_init()
        f_init()
    self._backend._workers._initializer = new_init if callable(origin_init) else f_init
    return self

它有点hacky但适用于当前版本的joblib和loky。然后你就可以使用它：

import matlab
from joblib import Parallel, delayed

x = matlab.double([[0.0]])

def f(i):
    print(i, x)

def _init_matlab():
    import matlab

with Parallel(4) as p:
    for _ in with_initializer(p, _init_matlab)(delayed(f)(i) for i in range(10)):
        pass

我希望joblib的开发人员将来会在initializer的构造函数中添加Parallel参数。