在 joblib `Parallel` 上下文中腌制 `matlab` 对象时出错

Posted 2023-02-16

【中文标题】在 joblib `Parallel` 上下文中腌制 `matlab` 对象时出错

【英文标题】：Error pickling a `matlab` object in joblib `Parallel` context

【发布时间】：2019-08-20 18:54:52

【问题描述】：

我正在 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），并且遇到了涉及 matlab.double 的导入错误。相同的代码在multiprocessing.Pool 中运行良好，所以我无法找出问题所在。这是一个最小的重现测试用例。

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.

所以，唯一有问题的是使用'loky' 后端的那个。 完整的回溯是：

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.

查看回溯，似乎根本原因是在子进程中导入matlab 包时出现问题。

可能值得注意的是，如果我定义了x = np.array([[0.0]])（在导入numpy as np 之后），这一切都运行得很好。当然，主进程对任何 matlab 导入都没有问题，所以我不确定子进程为什么会这样。

我不确定这个错误是否与 matlab 包特别有关，或者是否与全局变量和 cloudpickle 或 loky 有关。在我的应用程序中，坚持使用loky 会有所帮助，因此我将不胜感激！

我还应该注意，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，所以我希望我可以用 matlab.double 以外的类型重现这个错误，但我还没有找到另一个。

深入研究，我注意到导入matlab 包的过程比我预期的更循环，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，首先导入了一些文件matlab/mlarray.py，该文件导入了一些其他文件，其中一个包含import matlab，这导致matlab/__init__.py运行，内部有from mlarray import double, single, uint8, ...，这是导致崩溃的行。

这种循环可能是问题所在吗？如果是这样，为什么我可以在主进程中导入这个模块，而不是在loky后端？

【问题讨论】：

你可能是对的。 import matlab 应该在任何事情之前先运行。尝试multiprocessing.pool.Pool 中的参数initializer。使用def initializer(): import matlab 验证假设。

看来there is no simple way to specify the initializer 没有破解joblib。

这些是很好的提示，不知道Pool 的初始化程序。太糟糕了 joblib 没有它。谢谢！

【参考方案1】：

该错误是由于子进程中全局对象的加载顺序不正确引起的。在traceback中可以清楚地看到 _ForkingPickler.loads(res) -> ... -> import matlab -> from mlarray import ... 当cloudpickle 加载全局变量x 时，matlab 尚未导入。

joblib 和 loky 似乎将模块视为普通的全局对象，并将它们动态地发送给子进程。 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腌制 matlab 对象并在您的函数中导入 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)

当然你也可以使用joblib.dumps和loads来序列化对象。

使用初始化器

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

Currently there's no simple API to specify initializer。于是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，但在当前版本的 joblib 和 loky 上运行良好。 然后你可以像这样使用它：

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

希望joblib的开发者以后在Parallel的构造函数中添加initializer参数。