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
|
# Small benchmark for compare creation times with parameter
# PYTABLES_SYS_ATTRS active or not.
import random
from time import perf_counter as clock
from pathlib import Path
import tables as tb
random.seed(2)
def show_stats(explain, tref):
"Show the used memory (only works for Linux 2.6.x)."
for line in Path("/proc/self/status").read_text().splitlines():
if line.startswith("VmSize:"):
vmsize = int(line.split()[1])
elif line.startswith("VmRSS:"):
vmrss = int(line.split()[1])
elif line.startswith("VmData:"):
vmdata = int(line.split()[1])
elif line.startswith("VmStk:"):
vmstk = int(line.split()[1])
elif line.startswith("VmExe:"):
vmexe = int(line.split()[1])
elif line.startswith("VmLib:"):
vmlib = int(line.split()[1])
print("Memory usage: ******* %s *******" % explain)
print(f"VmSize: {vmsize:>7} kB\tVmRSS: {vmrss:>7} kB")
print(f"VmData: {vmdata:>7} kB\tVmStk: {vmstk:>7} kB")
print(f"VmExe: {vmexe:>7} kB\tVmLib: {vmlib:>7} kB")
tnow = clock()
print(f"WallClock time: {tnow - tref:.3f}")
return tnow
def populate(f, nlevels):
g = f.root
# arr = np.zeros((10,), "f4")
# descr = {'f0': tables.Int32Col(), 'f1': tables.Float32Col()}
for i in range(nlevels):
# dset = f.create_array(g, "DS1", arr)
# dset = f.create_array(g, "DS2", arr)
f.create_carray(g, "DS1", tb.IntAtom(), (10,))
f.create_carray(g, "DS2", tb.IntAtom(), (10,))
# dset = f.create_table(g, "DS1", descr)
# dset = f.create_table(g, "DS2", descr)
f.create_group(g, "group2_")
g = f.create_group(g, "group")
def getnode(f, nlevels, niter, range_):
for i in range(niter):
nlevel = random.randrange(
(nlevels - range_) / 2, (nlevels + range_) / 2
)
groupname = ""
for i in range(nlevel):
groupname += "/group"
groupname += "/DS1"
f.get_node(groupname)
if __name__ == "__main__":
nlevels = 1024
niter = 256
range_ = 128
node_cache_slots = 64
pytables_sys_attrs = True
profile = True
doprofile = True
verbose = False
if doprofile:
import pstats
import cProfile
if profile:
tref = clock()
if profile:
show_stats("Abans de crear...", tref)
f = tb.open_file(
"/tmp/PTdeep-tree.h5",
"w",
node_cache_slots=node_cache_slots,
pytables_sys_attrs=pytables_sys_attrs,
)
if doprofile:
cProfile.run("populate(f, nlevels)", "populate.prof")
stats = pstats.Stats("populate.prof")
stats.strip_dirs()
stats.sort_stats("time", "calls")
if verbose:
stats.print_stats()
else:
stats.print_stats(20)
else:
populate(f, nlevels)
f.close()
if profile:
show_stats("Despres de crear", tref)
if profile:
tref = clock()
if profile:
show_stats("Abans d'obrir...", tref)
f = tb.open_file(
"/tmp/PTdeep-tree.h5",
"r",
node_cache_slots=node_cache_slots,
pytables_sys_attrs=pytables_sys_attrs,
)
if profile:
show_stats("Abans d'accedir...", tref)
if doprofile:
cProfile.run("getnode(f, nlevels, niter, range_)", "getnode.prof")
stats = pstats.Stats("getnode.prof")
stats.strip_dirs()
stats.sort_stats("time", "calls")
if verbose:
stats.print_stats()
else:
stats.print_stats(20)
else:
getnode(f, nlevels, niter, range_)
if profile:
show_stats("Despres d'accedir", tref)
f.close()
if profile:
show_stats("Despres de tancar", tref)
|
