This section describes some known problems that can arise when using MPIRE.
When using the progress bar in a Jupyter notebook you might encounter some issues. A few of these are described below, together with possible solutions.
When you something like
ImportError: IProgress not found. Please update jupyter and ipywidgets., this means
ipywidgets is not installed. You can install it using
pip install ipywidgets
conda install -c conda-forge ipywidgets
Have a look at the ipywidgets documentation for more information.
When you see something like
jupyter nbextension enable --py --sys-prefix widgetsnbextension
Note that you have to restart your notebook server after enabling the extension, simply restarting the kernel won’t be enough.
When using the
'forkserver' method you’ll probably run into one or two issues when running
unittests in your own package. One problem that might occur is that your unittests will restart whenever the piece of
code containing such a start method is called, leading to very funky terminal output. To remedy this problem make sure
setup call in
setup.py is surrounded by an
if __name__ == '__main__': clause:
from setuptools import setup if __name__ == '__main__': # Call setup and install any dependencies you have inside the if-clause setup(...)
See the ‘Safe importing of main module’ section at caveats.
The second problem you might encounter is that the semaphore tracker of multiprocessing will complain when you run
individual (or a selection of) unittests using
python setup.py test -s tests.some_test. At the end of the tests you
will see errors like:
Traceback (most recent call last): File ".../site-packages/multiprocess/semaphore_tracker.py", line 132, in main cache.remove(name) KeyError: b'/mp-d3i13qd5' .../site-packages/multiprocess/semaphore_tracker.py:146: UserWarning: semaphore_tracker: There appear to be 58 leaked semaphores to clean up at shutdown len(cache)) .../site-packages/multiprocess/semaphore_tracker.py:158: UserWarning: semaphore_tracker: '/mp-f45dt4d6': [Errno 2] No such file or directory warnings.warn('semaphore_tracker: %r: %s' % (name, e)) ...
Your unittests will still succeed and run OK. Unfortunately, I’ve not found a remedy to this problem using
python setup.py test yet. What you can use instead is something like the following:
python -m unittest tests.some_test
This will work just fine. See the unittest documentation for more information.
When you issue a
KeyboardInterrupt or when an error occured in the function that’s run in parallel, there are
situations where MPIRE needs a few seconds to gracefully shutdown. This has to do with the fact that in these situations
the task or results queue can be quite full, still. MPIRE drains these queues until they’re completely empty, as to
properly shutdown and clean up every communication channel.
To remedy this issue you can use the
max_tasks_active parameter and set it to
n_jobs * 2, or similar. Aside
from the added benefit that the workers can start more quickly, the queues won’t get that full anymore and shutting down
will be much quicker. See Maximum number of active tasks for more information.
When you’re using a lazy map function also be sure to iterate through the results, otherwise that queue will be full and draining it will take a longer time.
Sometimes you can encounter deadlocks in your code when using MPIRE. When you encounter this, chances are some tasks or results from your script can’t be pickled. MPIRE makes use of multiprocessing queues for inter-process communication and if your function returns unpicklable results the queue will unfortunately deadlock.
The only way to remedy this problem in MPIRE would be to manually pickle objects before sending it to a queue and quit gracefully when encountering a pickle error. However, this would mean objects would always be pickled twice. This would add a heavy performance penalty and is therefore not an acceptable solution.
Instead, the user should make sure their tasks and results are always picklable (which in most cases won’t be a
problem), or resort to setting
use_dill=True. The latter is capable of pickling a lot more exotic types. See
Dill for more information.
This error can occur when inside an iPython or Jupyter notebook session and the function to parallelize is defined in
that session. This is often the result of using
spawn as start method (the default on Windows), which starts a new
process without copying the function in question.
This error is actually related to the Unpicklable tasks/results problem and can be solved in a similar way. I.e., you can
define your function in a file that can be imported by the child process, or you can resort to using
dill by setting
use_dill=True. See Dill for more information.
Windows support has some caveats:
When using worker insights the arguments of the top 5 longest tasks are not available;
Progress bar is not supported when using threading as start method;
dilland an exception occurs, or when the exception occurs in an exit function, it can print additional
OSErrormessages in the terminal, but they can be safely ignored.
macOS is not yet officially supported. It seems to work mostly fine, with these caveats:
ulimit -n <number>to increase the limit of the number of open files. This is required because mpire uses a lot of file-descriptor based synchronization primitives. <Number> should be large enough to accomodate all of mpire’s file descriptors, eg. <number> = 65536.