1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
|
from __future__ import annotations
from zlib import crc32
import pytest
np = pytest.importorskip("numpy")
from dask.utils import ensure_bytes, tmpfile
from distributed.protocol import (
decompress,
deserialize,
dumps,
loads,
msgpack,
serialize,
to_serialize,
)
from distributed.protocol.compression import maybe_compress
from distributed.protocol.numpy import itemsize
from distributed.protocol.utils import BIG_BYTES_SHARD_SIZE
from distributed.system import MEMORY_LIMIT
from distributed.utils import 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):
assert len(frames) > 1 # pickle protocol >= 5
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)
[y] = loads(frames)
assert (y.dtype, y.shape) == (dtype, shape)
assert crc32(y) == checksum, "Arrays are unequal"
x[:] = 2 # shared buffer; serialization is zero-copy
assert (x == y).all(), "Data was copied"
@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[1], raw=False, use_list=False, strict_map_key=False)
def test_compress_memoryview():
mv = memoryview(b"0" * 1000000)
compression, compressed = maybe_compress(mv)
if compression:
assert len(compressed) < len(mv)
@gen_cluster(client=True, timeout=60)
async def test_dumps_large(c, s, a, b):
x = c.submit(np.ones, BIG_BYTES_SHARD_SIZE * 2, dtype="u1")
await x
@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
|
