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332 | from zlib import crc32
import numpy as np
import pytest
from distributed.protocol import (
serialize,
deserialize,
decompress,
dumps,
loads,
to_serialize,
msgpack,
)
from distributed.protocol.utils import BIG_BYTES_SHARD_SIZE
from distributed.protocol.numpy import itemsize
from distributed.protocol.pickle import HIGHEST_PROTOCOL
from distributed.protocol.compression import maybe_compress
from distributed.system import MEMORY_LIMIT
from distributed.utils import ensure_bytes, tmpfile, nbytes
from distributed.utils_test import gen_cluster
def test_serialize():
x = np.ones((5, 5))
header, frames = serialize(x)
assert header["type"]
assert len(frames) == 1
if "compression" in header:
frames = decompress(header, frames)
result = deserialize(header, frames)
assert (result == x).all()
@pytest.mark.parametrize(
"x",
[
np.ones(5),
np.array(5),
np.random.random((5, 5)),
np.random.random((5, 5))[::2, :],
np.random.random((5, 5))[:, ::2],
np.asfortranarray(np.random.random((5, 5))),
np.asfortranarray(np.random.random((5, 5)))[::2, :],
np.asfortranarray(np.random.random((5, 5)))[:, ::2],
np.random.random(5).astype("f4"),
np.random.random(5).astype(">i8"),
np.random.random(5).astype("<i8"),
np.arange(5).astype("M8[us]"),
np.arange(5).astype("M8[ms]"),
np.arange(5).astype("m8"),
np.arange(5).astype("m8[s]"),
np.arange(5).astype("c16"),
np.arange(5).astype("c8"),
np.array([True, False, True]),
np.ones(shape=5, dtype=[("a", "i4"), ("b", "M8[us]")]),
np.array(["abc"], dtype="S3"),
np.array(["abc"], dtype="U3"),
np.array(["abc"], dtype=object),
np.array([np.arange(3), np.arange(4, 6)], dtype=object),
np.ones(shape=(5,), dtype=("f8", 32)),
np.ones(shape=(5,), dtype=[("x", "f8", 32)]),
np.ones(shape=(5,), dtype=np.dtype([("a", "i1"), ("b", "f8")], align=False)),
np.ones(shape=(5,), dtype=np.dtype([("a", "i1"), ("b", "f8")], align=True)),
np.ones(shape=(5,), dtype=np.dtype([("a", "m8[us]")], align=False)),
# this dtype fails unpickling
np.ones(shape=(5,), dtype=np.dtype([("a", "m8")], align=False)),
np.array([(1, "abc")], dtype=[("x", "i4"), ("s", object)]),
np.zeros(5000, dtype=[("x%d" % i, "<f8") for i in range(4)]),
np.zeros(5000, dtype="S32"),
np.zeros((1, 1000, 1000)),
np.arange(12)[::2], # non-contiguous array
np.ones(shape=(5, 6)).astype(dtype=[("total", "<f8"), ("n", "<f8")]),
np.broadcast_to(np.arange(3), shape=(10, 3)), # zero-strided array
],
)
def test_dumps_serialize_numpy(x):
header, frames = serialize(x)
if "compression" in header:
frames = decompress(header, frames)
for frame in frames:
assert isinstance(frame, (bytes, memoryview))
if x.dtype.char == "O" and any(isinstance(e, np.ndarray) for e in x.flat):
if HIGHEST_PROTOCOL >= 5:
assert len(frames) > 1
else:
assert len(frames) == 1
y = deserialize(header, frames)
assert x.shape == y.shape
assert x.dtype == y.dtype
if x.flags.c_contiguous or x.flags.f_contiguous:
assert x.strides == y.strides
if x.dtype.char == "O":
for e_x, e_y in zip(x.flat, y.flat):
np.testing.assert_equal(e_x, e_y)
else:
np.testing.assert_equal(x, y)
@pytest.mark.parametrize("writeable", [True, False])
def test_dumps_numpy_writable(writeable):
a1 = np.arange(1000)
a1.flags.writeable = writeable
fs = dumps([to_serialize(a1)])
# Make all frames read-only
fs = list(map(ensure_bytes, fs))
(a2,) = loads(fs)
assert (a1 == a2).all()
assert a2.flags.writeable == a1.flags.writeable
@pytest.mark.parametrize(
"x",
[
np.ma.masked_array([5, 6], mask=[True, False], fill_value=10, dtype="i4"),
np.ma.masked_array([5.0, 6.0], mask=[True, False], fill_value=10, dtype="f4"),
np.ma.masked_array(
[5.0, 6.0], mask=[True, False], fill_value=np.nan, dtype="f8"
),
np.ma.masked_array(
[5.0, 6.0], mask=np.ma.nomask, fill_value=np.nan, dtype="f8"
),
np.ma.masked_array(
[True, False], mask=np.ma.nomask, fill_value=True, dtype="bool"
),
np.ma.masked_array(["a", "b"], mask=[True, False], fill_value="c", dtype="O"),
],
)
def test_serialize_numpy_ma_masked_array(x):
(y,) = loads(dumps([to_serialize(x)]))
assert x.data.dtype == y.data.dtype
np.testing.assert_equal(x.data, y.data)
np.testing.assert_equal(x.mask, y.mask)
np.testing.assert_equal(x.fill_value, y.fill_value)
def test_serialize_numpy_ma_masked():
(y,) = loads(dumps([to_serialize(np.ma.masked)]))
assert y is np.ma.masked
def test_dumps_serialize_numpy_custom_dtype():
import builtins
test_rational = pytest.importorskip("numpy.core.test_rational")
rational = test_rational.rational
try:
builtins.rational = (
rational # Work around https://github.com/numpy/numpy/issues/9160
)
x = np.array([1], dtype=rational)
header, frames = serialize(x)
y = deserialize(header, frames)
np.testing.assert_equal(x, y)
finally:
del builtins.rational
def test_memmap():
with tmpfile("npy") as fn:
with open(fn, "wb") as f: # touch file
pass
x = np.memmap(fn, shape=(5, 5), dtype="i4", mode="readwrite")
x[:] = 5
header, frames = serialize(x)
if "compression" in header:
frames = decompress(header, frames)
y = deserialize(header, frames)
np.testing.assert_equal(x, y)
@pytest.mark.slow
def test_dumps_serialize_numpy_large():
if MEMORY_LIMIT < 2e9:
pytest.skip("insufficient memory")
x = np.random.random(size=int(BIG_BYTES_SHARD_SIZE * 2 // 8)).view("u1")
assert x.nbytes == BIG_BYTES_SHARD_SIZE * 2
frames = dumps([to_serialize(x)])
dtype, shape = x.dtype, x.shape
checksum = crc32(x)
del x
[y] = loads(frames)
assert (y.dtype, y.shape) == (dtype, shape)
assert crc32(y) == checksum, "Arrays are unequal"
@pytest.mark.parametrize(
"dt,size",
[
("f8", 8),
("i4", 4),
("c16", 16),
("b", 1),
("S3", 3),
("M8[us]", 8),
("M8[s]", 8),
("U3", 12),
([("a", "i4"), ("b", "f8")], 12),
(("i4", 100), 4),
([("a", "i4", 100)], 8),
([("a", "i4", 20), ("b", "f8")], 20 * 4 + 8),
([("a", "i4", 200), ("b", "f8")], 8),
],
)
def test_itemsize(dt, size):
assert itemsize(np.dtype(dt)) == size
def test_compress_numpy():
pytest.importorskip("lz4")
x = np.ones(10000000, dtype="i4")
frames = dumps({"x": to_serialize(x)})
assert sum(map(nbytes, frames)) < x.nbytes
header = msgpack.loads(frames[2], raw=False, use_list=False, strict_map_key=False)
try:
import blosc # noqa: F401
except ImportError:
pass
else:
assert all(c == "blosc" for c in header["headers"][("x",)]["compression"])
def test_compress_memoryview():
mv = memoryview(b"0" * 1000000)
compression, compressed = maybe_compress(mv)
if compression:
assert len(compressed) < len(mv)
@pytest.mark.skip
def test_dont_compress_uncompressable_data():
blosc = pytest.importorskip("blosc")
x = np.random.randint(0, 255, size=100000).astype("uint8")
header, [data] = serialize(x)
assert "compression" not in header
assert data == x.data
x = np.ones(1000000)
header, [data] = serialize(x)
assert header["compression"] == ["blosc"]
assert data != x.data
x = np.ones(100)
header, [data] = serialize(x)
assert "compression" not in header
if isinstance(data, memoryview):
assert data.obj.ctypes.data == x.ctypes.data
@gen_cluster(client=True, timeout=60)
async def test_dumps_large_blosc(c, s, a, b):
x = c.submit(np.ones, BIG_BYTES_SHARD_SIZE * 2, dtype="u1")
await x
def test_compression_takes_advantage_of_itemsize():
pytest.importorskip("lz4")
blosc = pytest.importorskip("blosc")
x = np.arange(1000000, dtype="i8")
assert len(blosc.compress(x.data, typesize=8)) < len(
blosc.compress(x.data, typesize=1)
)
_, a = serialize(x)
aa = [maybe_compress(frame)[1] for frame in a]
_, b = serialize(x.view("u1"))
bb = [maybe_compress(frame)[1] for frame in b]
assert sum(map(nbytes, aa)) < sum(map(nbytes, bb))
def test_large_numpy_array():
x = np.ones((100000000,), dtype="u4")
header, frames = serialize(x)
assert sum(header["lengths"]) == sum(map(nbytes, frames))
@pytest.mark.parametrize(
"x",
[
np.broadcast_to(np.arange(10), (20, 10)), # Some strides are 0
np.broadcast_to(1, (3, 4, 2)), # All strides are 0
np.broadcast_to(np.arange(100)[:1], 5), # x.base is larger than x
np.broadcast_to(np.arange(5), (4, 5))[:, ::-1],
],
)
@pytest.mark.parametrize("writeable", [True, False])
def test_zero_strided_numpy_array(x, writeable):
assert 0 in x.strides
x.setflags(write=writeable)
header, frames = serialize(x)
y = deserialize(header, frames)
np.testing.assert_equal(x, y)
# Ensure we transmit fewer bytes than the full array
assert sum(map(nbytes, frames)) < x.nbytes
# Ensure both x and y are have same write flag
assert x.flags.writeable == y.flags.writeable
def test_non_zero_strided_array():
x = np.arange(10)
header, frames = serialize(x)
assert "broadcast_to" not in header
assert sum(map(nbytes, frames)) == x.nbytes
def test_serialize_writeable_array_readonly_base_object():
# Regression test for https://github.com/dask/distributed/issues/3252
x = np.arange(3)
# Create array which doesn't own it's own memory
y = np.broadcast_to(x, (3, 3))
# Make y writeable and it's base object (x) read-only
y.setflags(write=True)
x.setflags(write=False)
# Serialize / deserialize y
z = deserialize(*serialize(y))
np.testing.assert_equal(z, y)
# Ensure z and y have the same flags (including WRITEABLE)
assert z.flags == y.flags
|