1 minute read

If you run cross_validate(n_jobs > 1) with your own estimator, pay attention that your estimator will be copied per job.


scores = parallel(
            clone(estimator), X, y, scorers, train, test, verbose, None,
            fit_params, return_train_score=return_train_score,
        for train, test in cv.split(X, y, groups))


estimator_type = type(estimator)
if estimator_type in (list, tuple, set, frozenset):
    return estimator_type([clone(e, safe=safe) for e in estimator])
elif not hasattr(estimator, 'get_params'):
    if not safe:
        return copy.deepcopy(estimator)

# Serveral lines omitted

new_object_params = estimator.get_params(deep=False)
for name, param in six.iteritems(new_object_params):
    new_object_params[name] = clone(param, safe=False)


init = getattr(cls.__init__, 'deprecated_original', cls.__init__)

So basically what you list in your estimator’s __init__ signature will be DEEP copied. Once I initialized my estimator with a 6GB matrix and run cross_validate(n_jobs = 10)…My workstation exploded that day.

If possible, put all those heavy parameters to your fit method. Afterall, we can call cross_validate(n_jobs > 1, fit_params=kwargs).

Update: It’s not enough. fit_params will be copied as well!

Solution: numpy.memmap. See discussions:

Update: Objects in fit_params won’t be copied, only references of them will be. By default, sklearn.externals.joblib.Parallel uses MultiprocessingBackend, so there would be $n$ python3 processes in the background. However, my ubuntu task manager showed that each python3 process had taken a big chunk of memory while the total memory usage had not boomed. It looked like each process copied the parameter objects.

On the other hand, a memory map is like an in-memory index of its .joblib file (and it’s much smaller!). The memory map will be read first to find the positions of data in that .joblib file, then the corresponding positions will be accessed.

The mmap_mode parameter of joblib.load(filename, mmap_mode) actually means:

  • If None, do not use memory mapping
  • If not None, use memory mapping with the mode of mmap_mode. Available modes are the the same with numpy.memmap:
    • 'r': Open existing file for reading only.
    • 'r+': Open existing file for reading and writing.
    • 'w+': Create or overwrite existing file for reading and writing.
    • 'c': Copy-on-write: assignments affect data in memory, but changes are not saved to disk. The file on disk is read-only.