peacock-data-public-datasets-idc-cronscript
/
venv
/lib
/python3.10
/site-packages
/joblib
/test
/test_memmapping.py
import os | |
import mmap | |
import sys | |
import platform | |
import gc | |
import pickle | |
import itertools | |
from time import sleep | |
import subprocess | |
import threading | |
import faulthandler | |
import pytest | |
from joblib.test.common import with_numpy, np | |
from joblib.test.common import with_multiprocessing | |
from joblib.test.common import with_dev_shm | |
from joblib.testing import raises, parametrize, skipif | |
from joblib.backports import make_memmap | |
from joblib.parallel import Parallel, delayed | |
from joblib.pool import MemmappingPool | |
from joblib.executor import _TestingMemmappingExecutor as TestExecutor | |
from joblib._memmapping_reducer import has_shareable_memory | |
from joblib._memmapping_reducer import ArrayMemmapForwardReducer | |
from joblib._memmapping_reducer import _strided_from_memmap | |
from joblib._memmapping_reducer import _get_temp_dir | |
from joblib._memmapping_reducer import _WeakArrayKeyMap | |
from joblib._memmapping_reducer import _get_backing_memmap | |
import joblib._memmapping_reducer as jmr | |
def setup_module(): | |
faulthandler.dump_traceback_later(timeout=300, exit=True) | |
def teardown_module(): | |
faulthandler.cancel_dump_traceback_later() | |
def check_memmap_and_send_back(array): | |
assert _get_backing_memmap(array) is not None | |
return array | |
def check_array(args): | |
"""Dummy helper function to be executed in subprocesses | |
Check that the provided array has the expected values in the provided | |
range. | |
""" | |
data, position, expected = args | |
np.testing.assert_array_equal(data[position], expected) | |
def inplace_double(args): | |
"""Dummy helper function to be executed in subprocesses | |
Check that the input array has the right values in the provided range | |
and perform an inplace modification to double the values in the range by | |
two. | |
""" | |
data, position, expected = args | |
assert data[position] == expected | |
data[position] *= 2 | |
np.testing.assert_array_equal(data[position], 2 * expected) | |
def test_memmap_based_array_reducing(tmpdir): | |
"""Check that it is possible to reduce a memmap backed array""" | |
assert_array_equal = np.testing.assert_array_equal | |
filename = tmpdir.join('test.mmap').strpath | |
# Create a file larger than what will be used by a | |
buffer = np.memmap(filename, dtype=np.float64, shape=500, mode='w+') | |
# Fill the original buffer with negative markers to detect over of | |
# underflow in case of test failures | |
buffer[:] = - 1.0 * np.arange(buffer.shape[0], dtype=buffer.dtype) | |
buffer.flush() | |
# Memmap a 2D fortran array on a offsetted subsection of the previous | |
# buffer | |
a = np.memmap(filename, dtype=np.float64, shape=(3, 5, 4), | |
mode='r+', order='F', offset=4) | |
a[:] = np.arange(60).reshape(a.shape) | |
# Build various views that share the buffer with the original memmap | |
# b is an memmap sliced view on an memmap instance | |
b = a[1:-1, 2:-1, 2:4] | |
# c and d are array views | |
c = np.asarray(b) | |
d = c.T | |
# Array reducer with auto dumping disabled | |
reducer = ArrayMemmapForwardReducer(None, tmpdir.strpath, 'c', True) | |
def reconstruct_array_or_memmap(x): | |
cons, args = reducer(x) | |
return cons(*args) | |
# Reconstruct original memmap | |
a_reconstructed = reconstruct_array_or_memmap(a) | |
assert has_shareable_memory(a_reconstructed) | |
assert isinstance(a_reconstructed, np.memmap) | |
assert_array_equal(a_reconstructed, a) | |
# Reconstruct strided memmap view | |
b_reconstructed = reconstruct_array_or_memmap(b) | |
assert has_shareable_memory(b_reconstructed) | |
assert_array_equal(b_reconstructed, b) | |
# Reconstruct arrays views on memmap base | |
c_reconstructed = reconstruct_array_or_memmap(c) | |
assert not isinstance(c_reconstructed, np.memmap) | |
assert has_shareable_memory(c_reconstructed) | |
assert_array_equal(c_reconstructed, c) | |
d_reconstructed = reconstruct_array_or_memmap(d) | |
assert not isinstance(d_reconstructed, np.memmap) | |
assert has_shareable_memory(d_reconstructed) | |
assert_array_equal(d_reconstructed, d) | |
# Test graceful degradation on fake memmap instances with in-memory | |
# buffers | |
a3 = a * 3 | |
assert not has_shareable_memory(a3) | |
a3_reconstructed = reconstruct_array_or_memmap(a3) | |
assert not has_shareable_memory(a3_reconstructed) | |
assert not isinstance(a3_reconstructed, np.memmap) | |
assert_array_equal(a3_reconstructed, a * 3) | |
# Test graceful degradation on arrays derived from fake memmap instances | |
b3 = np.asarray(a3) | |
assert not has_shareable_memory(b3) | |
b3_reconstructed = reconstruct_array_or_memmap(b3) | |
assert isinstance(b3_reconstructed, np.ndarray) | |
assert not has_shareable_memory(b3_reconstructed) | |
assert_array_equal(b3_reconstructed, b3) | |
def test_resource_tracker_retries_when_permissionerror(tmpdir): | |
# Test resource_tracker retry mechanism when unlinking memmaps. See more | |
# thorough information in the ``unlink_file`` documentation of joblib. | |
filename = tmpdir.join('test.mmap').strpath | |
cmd = """if 1: | |
import os | |
import numpy as np | |
import time | |
from joblib.externals.loky.backend import resource_tracker | |
resource_tracker.VERBOSE = 1 | |
# Start the resource tracker | |
resource_tracker.ensure_running() | |
time.sleep(1) | |
# Create a file containing numpy data | |
memmap = np.memmap(r"{filename}", dtype=np.float64, shape=10, mode='w+') | |
memmap[:] = np.arange(10).astype(np.int8).data | |
memmap.flush() | |
assert os.path.exists(r"{filename}") | |
del memmap | |
# Create a np.memmap backed by this file | |
memmap = np.memmap(r"{filename}", dtype=np.float64, shape=10, mode='w+') | |
resource_tracker.register(r"{filename}", "file") | |
# Ask the resource_tracker to delete the file backing the np.memmap , this | |
# should raise PermissionError that the resource_tracker will log. | |
resource_tracker.maybe_unlink(r"{filename}", "file") | |
# Wait for the resource_tracker to process the maybe_unlink before cleaning | |
# up the memmap | |
time.sleep(2) | |
""".format(filename=filename) | |
p = subprocess.Popen([sys.executable, '-c', cmd], stderr=subprocess.PIPE, | |
stdout=subprocess.PIPE) | |
p.wait() | |
out, err = p.communicate() | |
assert p.returncode == 0 | |
assert out == b'' | |
msg = 'tried to unlink {}, got PermissionError'.format(filename) | |
assert msg in err.decode() | |
def test_high_dimension_memmap_array_reducing(tmpdir): | |
assert_array_equal = np.testing.assert_array_equal | |
filename = tmpdir.join('test.mmap').strpath | |
# Create a high dimensional memmap | |
a = np.memmap(filename, dtype=np.float64, shape=(100, 15, 15, 3), | |
mode='w+') | |
a[:] = np.arange(100 * 15 * 15 * 3).reshape(a.shape) | |
# Create some slices/indices at various dimensions | |
b = a[0:10] | |
c = a[:, 5:10] | |
d = a[:, :, :, 0] | |
e = a[1:3:4] | |
# Array reducer with auto dumping disabled | |
reducer = ArrayMemmapForwardReducer(None, tmpdir.strpath, 'c', True) | |
def reconstruct_array_or_memmap(x): | |
cons, args = reducer(x) | |
return cons(*args) | |
a_reconstructed = reconstruct_array_or_memmap(a) | |
assert has_shareable_memory(a_reconstructed) | |
assert isinstance(a_reconstructed, np.memmap) | |
assert_array_equal(a_reconstructed, a) | |
b_reconstructed = reconstruct_array_or_memmap(b) | |
assert has_shareable_memory(b_reconstructed) | |
assert_array_equal(b_reconstructed, b) | |
c_reconstructed = reconstruct_array_or_memmap(c) | |
assert has_shareable_memory(c_reconstructed) | |
assert_array_equal(c_reconstructed, c) | |
d_reconstructed = reconstruct_array_or_memmap(d) | |
assert has_shareable_memory(d_reconstructed) | |
assert_array_equal(d_reconstructed, d) | |
e_reconstructed = reconstruct_array_or_memmap(e) | |
assert has_shareable_memory(e_reconstructed) | |
assert_array_equal(e_reconstructed, e) | |
def test__strided_from_memmap(tmpdir): | |
fname = tmpdir.join('test.mmap').strpath | |
size = 5 * mmap.ALLOCATIONGRANULARITY | |
offset = mmap.ALLOCATIONGRANULARITY + 1 | |
# This line creates the mmap file that is reused later | |
memmap_obj = np.memmap(fname, mode='w+', shape=size + offset) | |
# filename, dtype, mode, offset, order, shape, strides, total_buffer_len | |
memmap_obj = _strided_from_memmap(fname, dtype='uint8', mode='r', | |
offset=offset, order='C', shape=size, | |
strides=None, total_buffer_len=None, | |
unlink_on_gc_collect=False) | |
assert isinstance(memmap_obj, np.memmap) | |
assert memmap_obj.offset == offset | |
memmap_backed_obj = _strided_from_memmap( | |
fname, dtype='uint8', mode='r', offset=offset, order='C', | |
shape=(size // 2,), strides=(2,), total_buffer_len=size, | |
unlink_on_gc_collect=False | |
) | |
assert _get_backing_memmap(memmap_backed_obj).offset == offset | |
def test_pool_with_memmap(factory, tmpdir): | |
"""Check that subprocess can access and update shared memory memmap""" | |
assert_array_equal = np.testing.assert_array_equal | |
# Fork the subprocess before allocating the objects to be passed | |
pool_temp_folder = tmpdir.mkdir('pool').strpath | |
p = factory(10, max_nbytes=2, temp_folder=pool_temp_folder) | |
try: | |
filename = tmpdir.join('test.mmap').strpath | |
a = np.memmap(filename, dtype=np.float32, shape=(3, 5), mode='w+') | |
a.fill(1.0) | |
p.map(inplace_double, [(a, (i, j), 1.0) | |
for i in range(a.shape[0]) | |
for j in range(a.shape[1])]) | |
assert_array_equal(a, 2 * np.ones(a.shape)) | |
# Open a copy-on-write view on the previous data | |
b = np.memmap(filename, dtype=np.float32, shape=(5, 3), mode='c') | |
p.map(inplace_double, [(b, (i, j), 2.0) | |
for i in range(b.shape[0]) | |
for j in range(b.shape[1])]) | |
# Passing memmap instances to the pool should not trigger the creation | |
# of new files on the FS | |
assert os.listdir(pool_temp_folder) == [] | |
# the original data is untouched | |
assert_array_equal(a, 2 * np.ones(a.shape)) | |
assert_array_equal(b, 2 * np.ones(b.shape)) | |
# readonly maps can be read but not updated | |
c = np.memmap(filename, dtype=np.float32, shape=(10,), mode='r', | |
offset=5 * 4) | |
with raises(AssertionError): | |
p.map(check_array, [(c, i, 3.0) for i in range(c.shape[0])]) | |
# depending on the version of numpy one can either get a RuntimeError | |
# or a ValueError | |
with raises((RuntimeError, ValueError)): | |
p.map(inplace_double, [(c, i, 2.0) for i in range(c.shape[0])]) | |
finally: | |
# Clean all filehandlers held by the pool | |
p.terminate() | |
del p | |
def test_pool_with_memmap_array_view(factory, tmpdir): | |
"""Check that subprocess can access and update shared memory array""" | |
assert_array_equal = np.testing.assert_array_equal | |
# Fork the subprocess before allocating the objects to be passed | |
pool_temp_folder = tmpdir.mkdir('pool').strpath | |
p = factory(10, max_nbytes=2, temp_folder=pool_temp_folder) | |
try: | |
filename = tmpdir.join('test.mmap').strpath | |
a = np.memmap(filename, dtype=np.float32, shape=(3, 5), mode='w+') | |
a.fill(1.0) | |
# Create an ndarray view on the memmap instance | |
a_view = np.asarray(a) | |
assert not isinstance(a_view, np.memmap) | |
assert has_shareable_memory(a_view) | |
p.map(inplace_double, [(a_view, (i, j), 1.0) | |
for i in range(a.shape[0]) | |
for j in range(a.shape[1])]) | |
# Both a and the a_view have been updated | |
assert_array_equal(a, 2 * np.ones(a.shape)) | |
assert_array_equal(a_view, 2 * np.ones(a.shape)) | |
# Passing memmap array view to the pool should not trigger the | |
# creation of new files on the FS | |
assert os.listdir(pool_temp_folder) == [] | |
finally: | |
p.terminate() | |
del p | |
def test_permission_error_windows_reference_cycle(backend): | |
# Non regression test for: | |
# https://github.com/joblib/joblib/issues/806 | |
# | |
# The issue happens when trying to delete a memory mapped file that has | |
# not yet been closed by one of the worker processes. | |
cmd = """if 1: | |
import numpy as np | |
from joblib import Parallel, delayed | |
data = np.random.rand(int(2e6)).reshape((int(1e6), 2)) | |
# Build a complex cyclic reference that is likely to delay garbage | |
# collection of the memmapped array in the worker processes. | |
first_list = current_list = [data] | |
for i in range(10): | |
current_list = [current_list] | |
first_list.append(current_list) | |
if __name__ == "__main__": | |
results = Parallel(n_jobs=2, backend="{b}")( | |
delayed(len)(current_list) for i in range(10)) | |
assert results == [1] * 10 | |
""".format(b=backend) | |
p = subprocess.Popen([sys.executable, '-c', cmd], stderr=subprocess.PIPE, | |
stdout=subprocess.PIPE) | |
p.wait() | |
out, err = p.communicate() | |
assert p.returncode == 0, out.decode() + "\n\n" + err.decode() | |
def test_permission_error_windows_memmap_sent_to_parent(backend): | |
# Second non-regression test for: | |
# https://github.com/joblib/joblib/issues/806 | |
# previously, child process would not convert temporary memmaps to numpy | |
# arrays when sending the data back to the parent process. This would lead | |
# to permission errors on windows when deleting joblib's temporary folder, | |
# as the memmaped files handles would still opened in the parent process. | |
cmd = '''if 1: | |
import os | |
import time | |
import numpy as np | |
from joblib import Parallel, delayed | |
from testutils import return_slice_of_data | |
data = np.ones(int(2e6)) | |
if __name__ == '__main__': | |
# warm-up call to launch the workers and start the resource_tracker | |
_ = Parallel(n_jobs=2, verbose=5, backend='{b}')( | |
delayed(id)(i) for i in range(20)) | |
time.sleep(0.5) | |
slice_of_data = Parallel(n_jobs=2, verbose=5, backend='{b}')( | |
delayed(return_slice_of_data)(data, 0, 20) for _ in range(10)) | |
'''.format(b=backend) | |
for _ in range(3): | |
env = os.environ.copy() | |
env['PYTHONPATH'] = os.path.dirname(__file__) | |
p = subprocess.Popen([sys.executable, '-c', cmd], | |
stderr=subprocess.PIPE, | |
stdout=subprocess.PIPE, env=env) | |
p.wait() | |
out, err = p.communicate() | |
assert p.returncode == 0, err | |
assert out == b'' | |
if sys.version_info[:3] not in [(3, 8, 0), (3, 8, 1)]: | |
# In early versions of Python 3.8, a reference leak | |
# https://github.com/cloudpipe/cloudpickle/issues/327, holds | |
# references to pickled objects, generating race condition during | |
# cleanup finalizers of joblib and noisy resource_tracker outputs. | |
assert b'resource_tracker' not in err | |
def test_parallel_isolated_temp_folders(backend): | |
# Test that consecutive Parallel call use isolated subfolders, even | |
# for the loky backend that reuses its executor instance across calls. | |
array = np.arange(int(1e2)) | |
[filename_1] = Parallel(n_jobs=2, backend=backend, max_nbytes=10)( | |
delayed(getattr)(array, 'filename') for _ in range(1) | |
) | |
[filename_2] = Parallel(n_jobs=2, backend=backend, max_nbytes=10)( | |
delayed(getattr)(array, 'filename') for _ in range(1) | |
) | |
assert os.path.dirname(filename_2) != os.path.dirname(filename_1) | |
def test_managed_backend_reuse_temp_folder(backend): | |
# Test that calls to a managed parallel object reuse the same memmaps. | |
array = np.arange(int(1e2)) | |
with Parallel(n_jobs=2, backend=backend, max_nbytes=10) as p: | |
[filename_1] = p( | |
delayed(getattr)(array, 'filename') for _ in range(1) | |
) | |
[filename_2] = p( | |
delayed(getattr)(array, 'filename') for _ in range(1) | |
) | |
assert os.path.dirname(filename_2) == os.path.dirname(filename_1) | |
def test_memmapping_temp_folder_thread_safety(): | |
# Concurrent calls to Parallel with the loky backend will use the same | |
# executor, and thus the same reducers. Make sure that those reducers use | |
# different temporary folders depending on which Parallel objects called | |
# them, which is necessary to limit potential race conditions during the | |
# garbage collection of temporary memmaps. | |
array = np.arange(int(1e2)) | |
temp_dirs_thread_1 = set() | |
temp_dirs_thread_2 = set() | |
def concurrent_get_filename(array, temp_dirs): | |
with Parallel(backend='loky', n_jobs=2, max_nbytes=10) as p: | |
for i in range(10): | |
[filename] = p( | |
delayed(getattr)(array, 'filename') for _ in range(1) | |
) | |
temp_dirs.add(os.path.dirname(filename)) | |
t1 = threading.Thread( | |
target=concurrent_get_filename, args=(array, temp_dirs_thread_1) | |
) | |
t2 = threading.Thread( | |
target=concurrent_get_filename, args=(array, temp_dirs_thread_2) | |
) | |
t1.start() | |
t2.start() | |
t1.join() | |
t2.join() | |
assert len(temp_dirs_thread_1) == 1 | |
assert len(temp_dirs_thread_2) == 1 | |
assert temp_dirs_thread_1 != temp_dirs_thread_2 | |
def test_multithreaded_parallel_termination_resource_tracker_silent(): | |
# test that concurrent termination attempts of a same executor does not | |
# emit any spurious error from the resource_tracker. We test various | |
# situations making 0, 1 or both parallel call sending a task that will | |
# make the worker (and thus the whole Parallel call) error out. | |
cmd = '''if 1: | |
import os | |
import numpy as np | |
from joblib import Parallel, delayed | |
from joblib.externals.loky.backend import resource_tracker | |
from concurrent.futures import ThreadPoolExecutor, wait | |
resource_tracker.VERBOSE = 0 | |
array = np.arange(int(1e2)) | |
temp_dirs_thread_1 = set() | |
temp_dirs_thread_2 = set() | |
def raise_error(array): | |
raise ValueError | |
def parallel_get_filename(array, temp_dirs): | |
with Parallel(backend="loky", n_jobs=2, max_nbytes=10) as p: | |
for i in range(10): | |
[filename] = p( | |
delayed(getattr)(array, "filename") for _ in range(1) | |
) | |
temp_dirs.add(os.path.dirname(filename)) | |
def parallel_raise(array, temp_dirs): | |
with Parallel(backend="loky", n_jobs=2, max_nbytes=10) as p: | |
for i in range(10): | |
[filename] = p( | |
delayed(raise_error)(array) for _ in range(1) | |
) | |
temp_dirs.add(os.path.dirname(filename)) | |
executor = ThreadPoolExecutor(max_workers=2) | |
# both function calls will use the same loky executor, but with a | |
# different Parallel object. | |
future_1 = executor.submit({f1}, array, temp_dirs_thread_1) | |
future_2 = executor.submit({f2}, array, temp_dirs_thread_2) | |
# Wait for both threads to terminate their backend | |
wait([future_1, future_2]) | |
future_1.result() | |
future_2.result() | |
''' | |
functions_and_returncodes = [ | |
("parallel_get_filename", "parallel_get_filename", 0), | |
("parallel_get_filename", "parallel_raise", 1), | |
("parallel_raise", "parallel_raise", 1) | |
] | |
for f1, f2, returncode in functions_and_returncodes: | |
p = subprocess.Popen([sys.executable, '-c', cmd.format(f1=f1, f2=f2)], | |
stderr=subprocess.PIPE, stdout=subprocess.PIPE) | |
p.wait() | |
out, err = p.communicate() | |
assert p.returncode == returncode, out.decode() | |
assert b"resource_tracker" not in err, err.decode() | |
def test_many_parallel_calls_on_same_object(backend): | |
# After #966 got merged, consecutive Parallel objects were sharing temp | |
# folder, which would lead to race conditions happening during the | |
# temporary resources management with the resource_tracker. This is a | |
# non-regression test that makes sure that consecutive Parallel operations | |
# on the same object do not error out. | |
cmd = '''if 1: | |
import os | |
import time | |
import numpy as np | |
from joblib import Parallel, delayed | |
from testutils import return_slice_of_data | |
data = np.ones(100) | |
if __name__ == '__main__': | |
for i in range(5): | |
slice_of_data = Parallel( | |
n_jobs=2, max_nbytes=1, backend='{b}')( | |
delayed(return_slice_of_data)(data, 0, 20) | |
for _ in range(10) | |
) | |
'''.format(b=backend) | |
env = os.environ.copy() | |
env['PYTHONPATH'] = os.path.dirname(__file__) | |
p = subprocess.Popen( | |
[sys.executable, '-c', cmd], | |
stderr=subprocess.PIPE, | |
stdout=subprocess.PIPE, | |
env=env, | |
) | |
p.wait() | |
out, err = p.communicate() | |
assert p.returncode == 0, err | |
assert out == b'' | |
if sys.version_info[:3] not in [(3, 8, 0), (3, 8, 1)]: | |
# In early versions of Python 3.8, a reference leak | |
# https://github.com/cloudpipe/cloudpickle/issues/327, holds | |
# references to pickled objects, generating race condition during | |
# cleanup finalizers of joblib and noisy resource_tracker outputs. | |
assert b'resource_tracker' not in err | |
def test_memmap_returned_as_regular_array(backend): | |
data = np.ones(int(1e3)) | |
# Check that child processes send temporary memmaps back as numpy arrays. | |
[result] = Parallel(n_jobs=2, backend=backend, max_nbytes=100)( | |
delayed(check_memmap_and_send_back)(data) for _ in range(1)) | |
assert _get_backing_memmap(result) is None | |
def test_resource_tracker_silent_when_reference_cycles(backend): | |
# There is a variety of reasons that can make joblib with loky backend | |
# output noisy warnings when a reference cycle is preventing a memmap from | |
# being garbage collected. Especially, joblib's main process finalizer | |
# deletes the temporary folder if it was not done before, which can | |
# interact badly with the resource_tracker. We don't risk leaking any | |
# resources, but this will likely make joblib output a lot of low-level | |
# confusing messages. | |
# | |
# This test makes sure that the resource_tracker is silent when a reference | |
# has been collected concurrently on non-Windows platforms. | |
# | |
# Note that the script in ``cmd`` is the exact same script as in | |
# test_permission_error_windows_reference_cycle. | |
if backend == "loky" and sys.platform.startswith('win'): | |
# XXX: on Windows, reference cycles can delay timely garbage collection | |
# and make it impossible to properly delete the temporary folder in the | |
# main process because of permission errors. | |
pytest.xfail( | |
"The temporary folder cannot be deleted on Windows in the " | |
"presence of a reference cycle" | |
) | |
cmd = """if 1: | |
import numpy as np | |
from joblib import Parallel, delayed | |
data = np.random.rand(int(2e6)).reshape((int(1e6), 2)) | |
# Build a complex cyclic reference that is likely to delay garbage | |
# collection of the memmapped array in the worker processes. | |
first_list = current_list = [data] | |
for i in range(10): | |
current_list = [current_list] | |
first_list.append(current_list) | |
if __name__ == "__main__": | |
results = Parallel(n_jobs=2, backend="{b}")( | |
delayed(len)(current_list) for i in range(10)) | |
assert results == [1] * 10 | |
""".format(b=backend) | |
p = subprocess.Popen([sys.executable, '-c', cmd], stderr=subprocess.PIPE, | |
stdout=subprocess.PIPE) | |
p.wait() | |
out, err = p.communicate() | |
out = out.decode() | |
err = err.decode() | |
assert p.returncode == 0, out + "\n\n" + err | |
assert "resource_tracker" not in err, err | |
def test_memmapping_pool_for_large_arrays(factory, tmpdir): | |
"""Check that large arrays are not copied in memory""" | |
# Check that the tempfolder is empty | |
assert os.listdir(tmpdir.strpath) == [] | |
# Build an array reducers that automatically dump large array content | |
# to filesystem backed memmap instances to avoid memory explosion | |
p = factory(3, max_nbytes=40, temp_folder=tmpdir.strpath, verbose=2) | |
try: | |
# The temporary folder for the pool is not provisioned in advance | |
assert os.listdir(tmpdir.strpath) == [] | |
assert not os.path.exists(p._temp_folder) | |
small = np.ones(5, dtype=np.float32) | |
assert small.nbytes == 20 | |
p.map(check_array, [(small, i, 1.0) for i in range(small.shape[0])]) | |
# Memory has been copied, the pool filesystem folder is unused | |
assert os.listdir(tmpdir.strpath) == [] | |
# Try with a file larger than the memmap threshold of 40 bytes | |
large = np.ones(100, dtype=np.float64) | |
assert large.nbytes == 800 | |
p.map(check_array, [(large, i, 1.0) for i in range(large.shape[0])]) | |
# The data has been dumped in a temp folder for subprocess to share it | |
# without per-child memory copies | |
assert os.path.isdir(p._temp_folder) | |
dumped_filenames = os.listdir(p._temp_folder) | |
assert len(dumped_filenames) == 1 | |
# Check that memory mapping is not triggered for arrays with | |
# dtype='object' | |
objects = np.array(['abc'] * 100, dtype='object') | |
results = p.map(has_shareable_memory, [objects]) | |
assert not results[0] | |
finally: | |
# check FS garbage upon pool termination | |
p.terminate() | |
for i in range(10): | |
sleep(.1) | |
if not os.path.exists(p._temp_folder): | |
break | |
else: # pragma: no cover | |
raise AssertionError( | |
'temporary folder {} was not deleted'.format(p._temp_folder) | |
) | |
del p | |
def test_child_raises_parent_exits_cleanly(backend): | |
# When a task executed by a child process raises an error, the parent | |
# process's backend is notified, and calls abort_everything. | |
# In loky, abort_everything itself calls shutdown(kill_workers=True) which | |
# sends SIGKILL to the worker, preventing it from running the finalizers | |
# supposed to signal the resource_tracker when the worker is done using | |
# objects relying on a shared resource (e.g np.memmaps). Because this | |
# behavior is prone to : | |
# - cause a resource leak | |
# - make the resource tracker emit noisy resource warnings | |
# we explicitly test that, when the said situation occurs: | |
# - no resources are actually leaked | |
# - the temporary resources are deleted as soon as possible (typically, at | |
# the end of the failing Parallel call) | |
# - the resource_tracker does not emit any warnings. | |
cmd = """if 1: | |
import os | |
from pathlib import Path | |
from time import sleep | |
import numpy as np | |
from joblib import Parallel, delayed | |
from testutils import print_filename_and_raise | |
data = np.random.rand(1000) | |
def get_temp_folder(parallel_obj, backend): | |
if "{b}" == "loky": | |
return Path(parallel_obj._backend._workers._temp_folder) | |
else: | |
return Path(parallel_obj._backend._pool._temp_folder) | |
if __name__ == "__main__": | |
try: | |
with Parallel(n_jobs=2, backend="{b}", max_nbytes=100) as p: | |
temp_folder = get_temp_folder(p, "{b}") | |
p(delayed(print_filename_and_raise)(data) | |
for i in range(1)) | |
except ValueError as e: | |
# the temporary folder should be deleted by the end of this | |
# call but apparently on some file systems, this takes | |
# some time to be visible. | |
# | |
# We attempt to write into the temporary folder to test for | |
# its existence and we wait for a maximum of 10 seconds. | |
for i in range(100): | |
try: | |
with open(temp_folder / "some_file.txt", "w") as f: | |
f.write("some content") | |
except FileNotFoundError: | |
# temp_folder has been deleted, all is fine | |
break | |
# ... else, wait a bit and try again | |
sleep(.1) | |
else: | |
raise AssertionError( | |
str(temp_folder) + " was not deleted" | |
) from e | |
""".format(b=backend) | |
env = os.environ.copy() | |
env['PYTHONPATH'] = os.path.dirname(__file__) | |
p = subprocess.Popen([sys.executable, '-c', cmd], stderr=subprocess.PIPE, | |
stdout=subprocess.PIPE, env=env) | |
p.wait() | |
out, err = p.communicate() | |
out, err = out.decode(), err.decode() | |
filename = out.split('\n')[0] | |
assert p.returncode == 0, err or out | |
assert err == '' # no resource_tracker warnings. | |
assert not os.path.exists(filename) | |
def test_memmapping_pool_for_large_arrays_disabled(factory, tmpdir): | |
"""Check that large arrays memmapping can be disabled""" | |
# Set max_nbytes to None to disable the auto memmapping feature | |
p = factory(3, max_nbytes=None, temp_folder=tmpdir.strpath) | |
try: | |
# Check that the tempfolder is empty | |
assert os.listdir(tmpdir.strpath) == [] | |
# Try with a file largish than the memmap threshold of 40 bytes | |
large = np.ones(100, dtype=np.float64) | |
assert large.nbytes == 800 | |
p.map(check_array, [(large, i, 1.0) for i in range(large.shape[0])]) | |
# Check that the tempfolder is still empty | |
assert os.listdir(tmpdir.strpath) == [] | |
finally: | |
# Cleanup open file descriptors | |
p.terminate() | |
del p | |
def test_memmapping_on_large_enough_dev_shm(factory): | |
"""Check that memmapping uses /dev/shm when possible""" | |
orig_size = jmr.SYSTEM_SHARED_MEM_FS_MIN_SIZE | |
try: | |
# Make joblib believe that it can use /dev/shm even when running on a | |
# CI container where the size of the /dev/shm is not very large (that | |
# is at least 32 MB instead of 2 GB by default). | |
jmr.SYSTEM_SHARED_MEM_FS_MIN_SIZE = int(32e6) | |
p = factory(3, max_nbytes=10) | |
try: | |
# Check that the pool has correctly detected the presence of the | |
# shared memory filesystem. | |
pool_temp_folder = p._temp_folder | |
folder_prefix = '/dev/shm/joblib_memmapping_folder_' | |
assert pool_temp_folder.startswith(folder_prefix) | |
assert os.path.exists(pool_temp_folder) | |
# Try with a file larger than the memmap threshold of 10 bytes | |
a = np.ones(100, dtype=np.float64) | |
assert a.nbytes == 800 | |
p.map(id, [a] * 10) | |
# a should have been memmapped to the pool temp folder: the joblib | |
# pickling procedure generate one .pkl file: | |
assert len(os.listdir(pool_temp_folder)) == 1 | |
# create a new array with content that is different from 'a' so | |
# that it is mapped to a different file in the temporary folder of | |
# the pool. | |
b = np.ones(100, dtype=np.float64) * 2 | |
assert b.nbytes == 800 | |
p.map(id, [b] * 10) | |
# A copy of both a and b are now stored in the shared memory folder | |
assert len(os.listdir(pool_temp_folder)) == 2 | |
finally: | |
# Cleanup open file descriptors | |
p.terminate() | |
del p | |
for i in range(100): | |
# The temp folder is cleaned up upon pool termination | |
if not os.path.exists(pool_temp_folder): | |
break | |
sleep(.1) | |
else: # pragma: no cover | |
raise AssertionError('temporary folder of pool was not deleted') | |
finally: | |
jmr.SYSTEM_SHARED_MEM_FS_MIN_SIZE = orig_size | |
def test_memmapping_on_too_small_dev_shm(factory): | |
orig_size = jmr.SYSTEM_SHARED_MEM_FS_MIN_SIZE | |
try: | |
# Make joblib believe that it cannot use /dev/shm unless there is | |
# 42 exabytes of available shared memory in /dev/shm | |
jmr.SYSTEM_SHARED_MEM_FS_MIN_SIZE = int(42e18) | |
p = factory(3, max_nbytes=10) | |
try: | |
# Check that the pool has correctly detected the presence of the | |
# shared memory filesystem. | |
pool_temp_folder = p._temp_folder | |
assert not pool_temp_folder.startswith('/dev/shm') | |
finally: | |
# Cleanup open file descriptors | |
p.terminate() | |
del p | |
# The temp folder is cleaned up upon pool termination | |
assert not os.path.exists(pool_temp_folder) | |
finally: | |
jmr.SYSTEM_SHARED_MEM_FS_MIN_SIZE = orig_size | |
def test_memmapping_pool_for_large_arrays_in_return(factory, tmpdir): | |
"""Check that large arrays are not copied in memory in return""" | |
assert_array_equal = np.testing.assert_array_equal | |
# Build an array reducers that automatically dump large array content | |
# but check that the returned datastructure are regular arrays to avoid | |
# passing a memmap array pointing to a pool controlled temp folder that | |
# might be confusing to the user | |
# The MemmappingPool user can always return numpy.memmap object explicitly | |
# to avoid memory copy | |
p = factory(3, max_nbytes=10, temp_folder=tmpdir.strpath) | |
try: | |
res = p.apply_async(np.ones, args=(1000,)) | |
large = res.get() | |
assert not has_shareable_memory(large) | |
assert_array_equal(large, np.ones(1000)) | |
finally: | |
p.terminate() | |
del p | |
def _worker_multiply(a, n_times): | |
"""Multiplication function to be executed by subprocess""" | |
assert has_shareable_memory(a) | |
return a * n_times | |
def test_workaround_against_bad_memmap_with_copied_buffers(factory, tmpdir): | |
"""Check that memmaps with a bad buffer are returned as regular arrays | |
Unary operations and ufuncs on memmap instances return a new memmap | |
instance with an in-memory buffer (probably a numpy bug). | |
""" | |
assert_array_equal = np.testing.assert_array_equal | |
p = factory(3, max_nbytes=10, temp_folder=tmpdir.strpath) | |
try: | |
# Send a complex, large-ish view on a array that will be converted to | |
# a memmap in the worker process | |
a = np.asarray(np.arange(6000).reshape((1000, 2, 3)), | |
order='F')[:, :1, :] | |
# Call a non-inplace multiply operation on the worker and memmap and | |
# send it back to the parent. | |
b = p.apply_async(_worker_multiply, args=(a, 3)).get() | |
assert not has_shareable_memory(b) | |
assert_array_equal(b, 3 * a) | |
finally: | |
p.terminate() | |
del p | |
def identity(arg): | |
return arg | |
def test_pool_memmap_with_big_offset(factory, retry_no, tmpdir): | |
# Test that numpy memmap offset is set correctly if greater than | |
# mmap.ALLOCATIONGRANULARITY, see | |
# https://github.com/joblib/joblib/issues/451 and | |
# https://github.com/numpy/numpy/pull/8443 for more details. | |
fname = tmpdir.join('test.mmap').strpath | |
size = 5 * mmap.ALLOCATIONGRANULARITY | |
offset = mmap.ALLOCATIONGRANULARITY + 1 | |
obj = make_memmap(fname, mode='w+', shape=size, dtype='uint8', | |
offset=offset) | |
p = factory(2, temp_folder=tmpdir.strpath) | |
result = p.apply_async(identity, args=(obj,)).get() | |
assert isinstance(result, np.memmap) | |
assert result.offset == offset | |
np.testing.assert_array_equal(obj, result) | |
p.terminate() | |
def test_pool_get_temp_dir(tmpdir): | |
pool_folder_name = 'test.tmpdir' | |
pool_folder, shared_mem = _get_temp_dir(pool_folder_name, tmpdir.strpath) | |
assert shared_mem is False | |
assert pool_folder == tmpdir.join('test.tmpdir').strpath | |
pool_folder, shared_mem = _get_temp_dir(pool_folder_name, temp_folder=None) | |
if sys.platform.startswith('win'): | |
assert shared_mem is False | |
assert pool_folder.endswith(pool_folder_name) | |
def test_pool_get_temp_dir_no_statvfs(tmpdir, monkeypatch): | |
"""Check that _get_temp_dir works when os.statvfs is not defined | |
Regression test for #902 | |
""" | |
pool_folder_name = 'test.tmpdir' | |
import joblib._memmapping_reducer | |
if hasattr(joblib._memmapping_reducer.os, 'statvfs'): | |
# We are on Unix, since Windows doesn't have this function | |
monkeypatch.delattr(joblib._memmapping_reducer.os, 'statvfs') | |
pool_folder, shared_mem = _get_temp_dir(pool_folder_name, temp_folder=None) | |
if sys.platform.startswith('win'): | |
assert shared_mem is False | |
assert pool_folder.endswith(pool_folder_name) | |
def test_numpy_arrays_use_different_memory(mmap_mode): | |
def func(arr, value): | |
arr[:] = value | |
return arr | |
arrays = [np.zeros((10, 10), dtype='float64') for i in range(10)] | |
results = Parallel(mmap_mode=mmap_mode, max_nbytes=0, n_jobs=2)( | |
delayed(func)(arr, i) for i, arr in enumerate(arrays)) | |
for i, arr in enumerate(results): | |
np.testing.assert_array_equal(arr, i) | |
def test_weak_array_key_map(): | |
def assert_empty_after_gc_collect(container, retries=100): | |
for i in range(retries): | |
if len(container) == 0: | |
return | |
gc.collect() | |
sleep(.1) | |
assert len(container) == 0 | |
a = np.ones(42) | |
m = _WeakArrayKeyMap() | |
m.set(a, 'a') | |
assert m.get(a) == 'a' | |
b = a | |
assert m.get(b) == 'a' | |
m.set(b, 'b') | |
assert m.get(a) == 'b' | |
del a | |
gc.collect() | |
assert len(m._data) == 1 | |
assert m.get(b) == 'b' | |
del b | |
assert_empty_after_gc_collect(m._data) | |
c = np.ones(42) | |
m.set(c, 'c') | |
assert len(m._data) == 1 | |
assert m.get(c) == 'c' | |
with raises(KeyError): | |
m.get(np.ones(42)) | |
del c | |
assert_empty_after_gc_collect(m._data) | |
# Check that creating and dropping numpy arrays with potentially the same | |
# object id will not cause the map to get confused. | |
def get_set_get_collect(m, i): | |
a = np.ones(42) | |
with raises(KeyError): | |
m.get(a) | |
m.set(a, i) | |
assert m.get(a) == i | |
return id(a) | |
unique_ids = set([get_set_get_collect(m, i) for i in range(1000)]) | |
if platform.python_implementation() == 'CPython': | |
# On CPython (at least) the same id is often reused many times for the | |
# temporary arrays created under the local scope of the | |
# get_set_get_collect function without causing any spurious lookups / | |
# insertions in the map. Apparently on Python nogil, the id is not | |
# reused as often. | |
max_len_unique_ids = 400 if getattr(sys.flags, 'nogil', False) else 100 | |
assert len(unique_ids) < max_len_unique_ids | |
def test_weak_array_key_map_no_pickling(): | |
m = _WeakArrayKeyMap() | |
with raises(pickle.PicklingError): | |
pickle.dumps(m) | |
def test_direct_mmap(tmpdir): | |
testfile = str(tmpdir.join('arr.dat')) | |
a = np.arange(10, dtype='uint8') | |
a.tofile(testfile) | |
def _read_array(): | |
with open(testfile) as fd: | |
mm = mmap.mmap(fd.fileno(), 0, access=mmap.ACCESS_READ, offset=0) | |
return np.ndarray((10,), dtype=np.uint8, buffer=mm, offset=0) | |
def func(x): | |
return x**2 | |
arr = _read_array() | |
# this is expected to work and gives the reference | |
ref = Parallel(n_jobs=2)(delayed(func)(x) for x in [a]) | |
# now test that it work with the mmap array | |
results = Parallel(n_jobs=2)(delayed(func)(x) for x in [arr]) | |
np.testing.assert_array_equal(results, ref) | |
# also test with a mmap array read in the subprocess | |
def worker(): | |
return _read_array() | |
results = Parallel(n_jobs=2)(delayed(worker)() for _ in range(1)) | |
np.testing.assert_array_equal(results[0], arr) | |