test_memmapping.py
41.2 KB
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
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
1001
1002
1003
1004
1005
1006
1007
1008
1009
1010
1011
1012
1013
1014
1015
1016
1017
1018
1019
1020
1021
1022
1023
1024
1025
1026
1027
1028
1029
1030
1031
1032
1033
1034
1035
1036
1037
1038
1039
1040
1041
1042
1043
1044
1045
1046
1047
1048
1049
1050
1051
1052
1053
1054
1055
1056
1057
1058
1059
1060
1061
1062
1063
1064
1065
1066
1067
1068
1069
1070
1071
1072
1073
1074
1075
1076
1077
1078
1079
1080
1081
1082
1083
1084
1085
1086
1087
1088
1089
1090
1091
1092
1093
1094
1095
1096
1097
1098
1099
1100
1101
1102
1103
1104
1105
1106
1107
1108
1109
1110
1111
1112
1113
1114
1115
1116
1117
1118
1119
1120
1121
1122
1123
1124
1125
1126
1127
1128
1129
1130
1131
1132
1133
1134
1135
1136
1137
1138
1139
1140
1141
1142
1143
1144
1145
1146
1147
1148
1149
1150
1151
1152
1153
1154
1155
1156
1157
1158
1159
1160
1161
1162
import os
import mmap
import sys
import platform
import gc
import pickle
import itertools
from time import sleep
import subprocess
import threading
from joblib.test.common import with_numpy, np
from joblib.test.common import setup_autokill
from joblib.test.common import teardown_autokill
from joblib.test.common import with_multiprocessing
from joblib.test.common import with_dev_shm
from joblib.testing import raises, parametrize, skipif, xfail, param
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():
setup_autokill(__name__, timeout=300)
def teardown_module():
teardown_autokill(__name__)
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)
@with_numpy
@with_multiprocessing
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 offseted 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)
@skipif(sys.platform != "win32",
reason="PermissionError only easily triggerable on Windows")
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()
@with_numpy
@with_multiprocessing
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)
@with_numpy
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
@with_numpy
@with_multiprocessing
@parametrize("factory", [MemmappingPool, TestExecutor.get_memmapping_executor],
ids=["multiprocessing", "loky"])
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
@with_numpy
@with_multiprocessing
@parametrize("factory", [MemmappingPool, TestExecutor.get_memmapping_executor],
ids=["multiprocessing", "loky"])
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
@with_numpy
@parametrize("backend", ["multiprocessing", "loky"])
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()
@with_numpy
@parametrize("backend", ["multiprocessing", "loky"])
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
@with_numpy
@with_multiprocessing
@parametrize("backend", ["multiprocessing", "loky"])
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)
@with_numpy
@with_multiprocessing
@parametrize("backend", ["multiprocessing", "loky"])
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)
@with_numpy
@with_multiprocessing
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
@with_numpy
@with_multiprocessing
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()
@with_numpy
@with_multiprocessing
def test_nested_loop_error_in_grandchild_resource_tracker_silent():
# Safety smoke test: test that nested parallel calls using the loky backend
# don't yield noisy resource_tracker outputs when the grandchild errors
# out.
cmd = '''if 1:
from joblib import Parallel, delayed
def raise_error(i):
raise ValueError
def nested_loop(f):
Parallel(backend="loky", n_jobs=2)(
delayed(f)(i) for i in range(10)
)
if __name__ == "__main__":
Parallel(backend="loky", n_jobs=2)(
delayed(nested_loop)(func) for func in [raise_error]
)
'''
p = subprocess.Popen([sys.executable, '-c', cmd],
stderr=subprocess.PIPE, stdout=subprocess.PIPE)
p.wait()
out, err = p.communicate()
assert p.returncode == 1, out.decode()
assert b"resource_tracker" not in err, err.decode()
@with_numpy
@with_multiprocessing
@parametrize("backend", ["multiprocessing", "loky"])
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)
)
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)
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
@with_numpy
@with_multiprocessing
@parametrize("backend", ["multiprocessing", "loky"])
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
@with_numpy
@with_multiprocessing
@parametrize("backend", ["multiprocessing", param("loky", marks=xfail)])
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 is marked as xfail for now: but a next PR
# should fix this behavior.
# Note that the script in ``cmd`` is the exact same script as in
# test_permission_error_windows_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()
assert p.returncode == 0, out.decode()
assert b"resource_tracker" not in err, err.decode()
@with_numpy
@with_multiprocessing
@parametrize("factory", [MemmappingPool, TestExecutor.get_memmapping_executor],
ids=["multiprocessing", "loky"])
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 automaticaly 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 of {} was not deleted'.format(p)
)
del p
@with_numpy
@with_multiprocessing
@parametrize("backend", ["multiprocessing", "loky"])
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
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 p._backend._workers._temp_folder
else:
return p._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:
# the temporary folder should be deleted by the end of this
# call
assert not os.path.exists(temp_folder)
""".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, out
assert err == '' # no resource_tracker warnings.
assert not os.path.exists(filename)
@with_numpy
@with_multiprocessing
@parametrize("factory", [MemmappingPool, TestExecutor.get_memmapping_executor],
ids=["multiprocessing", "loky"])
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
@with_numpy
@with_multiprocessing
@with_dev_shm
@parametrize("factory", [MemmappingPool, TestExecutor.get_memmapping_executor],
ids=["multiprocessing", "loky"])
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
@with_numpy
@with_multiprocessing
@with_dev_shm
@parametrize("factory", [MemmappingPool, TestExecutor.get_memmapping_executor],
ids=["multiprocessing", "loky"])
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
@with_numpy
@with_multiprocessing
@parametrize("factory", [MemmappingPool, TestExecutor.get_memmapping_executor],
ids=["multiprocessing", "loky"])
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 automaticaly 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
@with_numpy
@with_multiprocessing
@parametrize("factory", [MemmappingPool, TestExecutor.get_memmapping_executor],
ids=["multiprocessing", "loky"])
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
@with_numpy
@with_multiprocessing
@parametrize(
"factory,retry_no",
list(itertools.product(
[MemmappingPool, TestExecutor.get_memmapping_executor], range(3))),
ids=['{}, {}'.format(x, y) for x, y in itertools.product(
["multiprocessing", "loky"], map(str, range(3)))])
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)
@with_numpy
@skipif(sys.platform == 'win32', reason='This test fails with a '
'PermissionError on Windows')
@parametrize("mmap_mode", ["r+", "w+"])
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)
@with_numpy
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.
assert len(unique_ids) < 100
def test_weak_array_key_map_no_pickling():
m = _WeakArrayKeyMap()
with raises(pickle.PicklingError):
pickle.dumps(m)
@with_numpy
@with_multiprocessing
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)