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"""Script comparing different pickling strategies."""
import bz2
import io
import lzma
import os
import sys
import time
from collections import OrderedDict
from pickle import Pickler, Unpickler, _Pickler, _Unpickler
import numpy as np
from joblib.numpy_pickle import NumpyPickler, NumpyUnpickler
from joblib.numpy_pickle_utils import BinaryGzipFile, BinaryZlibFile
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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