File size: 8,560 Bytes
dee9fba | 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 | """Script comparing different pickling strategies."""
from joblib.numpy_pickle import NumpyPickler, NumpyUnpickler
from joblib.numpy_pickle_utils import BinaryZlibFile, BinaryGzipFile
from pickle import _Pickler, _Unpickler, Pickler, Unpickler
import numpy as np
import bz2
import lzma
import time
import io
import sys
import os
from collections import OrderedDict
def fileobj(obj, fname, mode, kwargs):
"""Create a file object."""
return obj(fname, mode, **kwargs)
def bufferize(f, buf):
"""Bufferize a fileobject using buf."""
if buf is None:
return f
else:
if (buf.__name__ == io.BufferedWriter.__name__ or
buf.__name__ == io.BufferedReader.__name__):
return buf(f, buffer_size=10 * 1024 ** 2)
return buf(f)
def _load(unpickler, fname, f):
if unpickler.__name__ == NumpyUnpickler.__name__:
p = unpickler(fname, f)
else:
p = unpickler(f)
return p.load()
def print_line(obj, strategy, buffer, pickler, dump, load, disk_used):
"""Nice printing function."""
print('% 20s | %6s | % 14s | % 7s | % 5.1f | % 5.1f | % 5s' % (
obj, strategy, buffer, pickler, dump, load, disk_used))
class PickleBufferedWriter():
"""Protect the underlying fileobj against numerous calls to write
This is achieved by internally keeping a list of small chunks and
only flushing to the backing fileobj if passed a large chunk or
after a threshold on the number of small chunks.
"""
def __init__(self, fileobj,
max_buffer_size=10 * 1024 ** 2):
self._fileobj = fileobj
self._chunks = chunks = []
# As the `write` method is called many times by the pickler,
# attribute look ups on the self's __dict__ are too expensive
# hence we define a closure here with all the regularly
# accessed parameters
def _write(data):
chunks.append(data)
if len(chunks) > max_buffer_size:
self.flush()
self.write = _write
def flush(self):
self._fileobj.write(b''.join(self._chunks[:]))
del self._chunks[:]
def close(self):
self.flush()
self._fileobj.close()
def __enter__(self):
return self
def __exit__(self, *exc):
self.close()
return False
class PickleBufferedReader():
"""Protect the underlying fileobj against numerous calls to write
This is achieved by internally keeping a list of small chunks and
only flushing to the backing fileobj if passed a large chunk or
after a threshold on the number of small chunks.
"""
def __init__(self, fileobj,
max_buffer_size=10 * 1024 ** 2):
self._fileobj = fileobj
self._buffer = bytearray(max_buffer_size)
self.max_buffer_size = max_buffer_size
self._position = 0
def read(self, n=None):
data = b''
if n is None:
data = self._fileobj.read()
else:
while len(data) < n:
if self._position == 0:
self._buffer = self._fileobj.read(self.max_buffer_size)
elif self._position == self.max_buffer_size:
self._position = 0
continue
next_position = min(self.max_buffer_size,
self._position + n - len(data))
data += self._buffer[self._position:next_position]
self._position = next_position
return data
def readline(self):
line = []
while True:
c = self.read(1)
line.append(c)
if c == b'\n':
break
return b''.join(line)
def close(self):
self._fileobj.close()
def __enter__(self):
return self
def __exit__(self, *exc):
self.close()
return False
def run_bench():
print('% 20s | %10s | % 12s | % 8s | % 9s | % 9s | % 5s' % (
'Object', 'Compression', 'Buffer', 'Pickler/Unpickler',
'dump time (s)', 'load time (s)', 'Disk used (MB)'))
print("--- | --- | --- | --- | --- | --- | ---")
for oname, obj in objects.items():
# Looping over the objects (array, dict, etc)
if isinstance(obj, np.ndarray):
osize = obj.nbytes / 1e6
else:
osize = sys.getsizeof(obj) / 1e6
for cname, f in compressors.items():
fobj = f[0]
fname = f[1]
fmode = f[2]
fopts = f[3]
# Looping other defined compressors
for bname, buf in bufs.items():
writebuf = buf[0]
readbuf = buf[1]
# Looping other picklers
for pname, p in picklers.items():
pickler = p[0]
unpickler = p[1]
t0 = time.time()
# Now pickling the object in the file
if (writebuf is not None and
writebuf.__name__ == io.BytesIO.__name__):
b = writebuf()
p = pickler(b)
p.dump(obj)
with fileobj(fobj, fname, fmode, fopts) as f:
f.write(b.getvalue())
else:
with bufferize(fileobj(fobj, fname, fmode, fopts),
writebuf) as f:
p = pickler(f)
p.dump(obj)
dtime = time.time() - t0
t0 = time.time()
# Now loading the object from the file
obj_r = None
if (readbuf is not None and
readbuf.__name__ == io.BytesIO.__name__):
b = readbuf()
with fileobj(fobj, fname, 'rb', {}) as f:
b.write(f.read())
b.seek(0)
obj_r = _load(unpickler, fname, b)
else:
with bufferize(fileobj(fobj, fname, 'rb', {}),
readbuf) as f:
obj_r = _load(unpickler, fname, f)
ltime = time.time() - t0
if isinstance(obj, np.ndarray):
assert (obj == obj_r).all()
else:
assert obj == obj_r
print_line("{} ({:.1f}MB)".format(oname, osize),
cname,
bname,
pname,
dtime,
ltime,
"{:.2f}".format(os.path.getsize(fname) / 1e6))
# Defining objects used in this bench
DICT_SIZE = int(1e6)
ARRAY_SIZE = int(1e7)
arr = np.random.normal(size=(ARRAY_SIZE))
arr[::2] = 1
# Objects used for testing
objects = OrderedDict([
("dict", dict((i, str(i)) for i in range(DICT_SIZE))),
("list", [i for i in range(DICT_SIZE)]),
("array semi-random", arr),
("array random", np.random.normal(size=(ARRAY_SIZE))),
("array ones", np.ones((ARRAY_SIZE))), ])
# We test 3 different picklers
picklers = OrderedDict([
# Python implementation of Pickler/Unpickler
("Pickle", (_Pickler, _Unpickler)),
# C implementation of Pickler/Unpickler
("cPickle", (Pickler, Unpickler)),
# Joblib Pickler/Unpickler designed for numpy arrays.
("Joblib", (NumpyPickler, NumpyUnpickler)), ])
# The list of supported compressors used for testing
compressors = OrderedDict([
("No", (open, '/tmp/test_raw', 'wb', {})),
("Zlib", (BinaryZlibFile, '/tmp/test_zlib', 'wb', {'compresslevel': 3})),
("Gzip", (BinaryGzipFile, '/tmp/test_gzip', 'wb', {'compresslevel': 3})),
("Bz2", (bz2.BZ2File, '/tmp/test_bz2', 'wb', {'compresslevel': 3})),
("Xz", (lzma.LZMAFile, '/tmp/test_xz', 'wb',
{'preset': 3, 'check': lzma.CHECK_NONE})),
("Lzma", (lzma.LZMAFile, '/tmp/test_lzma', 'wb',
{'preset': 3, 'format': lzma.FORMAT_ALONE})), ])
# Test 3 buffering strategies
bufs = OrderedDict([
("None", (None, None)),
("io.BytesIO", (io.BytesIO, io.BytesIO)),
("io.Buffered", (io.BufferedWriter, io.BufferedReader)),
("PickleBuffered", (PickleBufferedWriter, PickleBufferedReader)), ])
if __name__ == "__main__":
run_bench()
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