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#!/usr/bin/env python3
"""This script allows to create arbitrarily large files with the desired
combination of groups, tables per group and rows per table.
Issue "python stress-test3.py" without parameters for a help on usage.
"""
import gc
import sys
from time import perf_counter as clock
from time import process_time as cpuclock
import tables as tb
class Test(tb.IsDescription):
ngroup = tb.Int32Col(pos=1)
ntable = tb.Int32Col(pos=2)
nrow = tb.Int32Col(pos=3)
float_ = tb.Float32Col(pos=3)
# string = tb.StringCol(500, pos=4)
def create_file(
filename, ngroups, ntables, nrows, complevel, complib, recsize
):
# First, create the groups
# Open a file in "w"rite mode
fileh = tb.open_file(filename, mode="w", title="PyTables Stress Test")
for k in range(ngroups):
# Create the group
group = fileh.create_group("/", "group%04d" % k, "Group %d" % k)
fileh.close()
# Now, create the tables
rowswritten = 0
rowsize = 0
for k in range(ngroups):
fileh = tb.open_file(filename, mode="a", root_uep="group%04d" % k)
# Get the group
group = fileh.root
for j in range(ntables):
# Create a table
table = fileh.create_table(
group,
"table%04d" % j,
Test,
"Table%04d" % j,
tb.Filters(complevel, complib),
nrows,
)
rowsize = table.rowsize
# Get the row object associated with the new table
row = table.row
# Fill the table
for i in range(nrows):
row["ngroup"] = k
row["ntable"] = j
row["nrow"] = i
row.append()
rowswritten += nrows
table.flush()
# Close the file
fileh.close()
return (rowswritten, rowsize)
def read_file(filename, ngroups, recsize, verbose):
# Open the HDF5 file in read-only mode
rowsread = 0
rowsize = 0
buffersize = 0
for ngroup in range(ngroups):
fileh = tb.open_file(filename, mode="r")
# Get the group
group = fileh.get_node(fileh.root, "group%04d" % ngroup)
ntable = 0
if verbose:
print("Group ==>", group)
for table in fileh.list_nodes(group, "Leaf"):
rowsize = table.rowsize
buffersize = table.rowsize * table.nrowsinbuf
if verbose > 1:
print("Table ==>", table)
print("Max rows in buf:", table.nrowsinbuf)
print("Rows in", table._v_pathname, ":", table.nrows)
print("Buffersize:", table.rowsize * table.nrowsinbuf)
print("MaxTuples:", table.nrowsinbuf)
nrow = 0
for row in table:
try:
assert row["ngroup"] == ngroup
assert row["ntable"] == ntable
assert row["nrow"] == nrow
except Exception:
print(
"Error in group: %d, table: %d, row: %d"
% (ngroup, ntable, nrow)
)
print("Record ==>", row)
nrow += 1
assert nrow == table.nrows
rowsread += table.nrows
ntable += 1
# Close the file (eventually destroy the extended type)
fileh.close()
return (rowsread, rowsize, buffersize)
def dump_garbage():
"""show us what the garbage is about."""
# Force collection
print("\nGARBAGE:")
gc.collect()
print("\nGARBAGE OBJECTS:")
for x in gc.garbage:
s = str(x)
# if len(s) > 80: s = s[:77] + "..."
print(type(x), "\n ", s)
if __name__ == "__main__":
import getopt
usage = """usage: %s [-d debug] [-v level] [-p] [-r] [-w] [-l complib] [-c complevel] [-g ngroups] [-t ntables] [-i nrows] file
-d debugging level
-v verbosity level
-r only read test
-w only write test
-l sets the compression library to be used ("zlib", "bzip2", "blosc", "blosc:codec")
-c sets a compression level (do not set it or 0 for no compression)
-g number of groups hanging from "/"
-t number of tables per group
-i number of rows per table
"""
try:
opts, pargs = getopt.getopt(sys.argv[1:], "d:v:parwl:c:g:t:i:")
except Exception:
sys.stderr.write(usage)
sys.exit(0)
# if we pass too much parameters, abort
if len(pargs) != 1:
sys.stderr.write(usage)
sys.exit(0)
# default options
ngroups = 5
ntables = 5
nrows = 100
verbose = 0
debug = 0
recsize = "medium"
testread = 1
testwrite = 1
complevel = 0
complib = "zlib"
# Get the options
for option in opts:
if option[0] == "-d":
debug = int(option[1])
if option[0] == "-v":
verbose = int(option[1])
elif option[0] == "-r":
testwrite = 0
elif option[0] == "-w":
testread = 0
elif option[0] == "-l":
complib = option[1]
elif option[0] == "-c":
complevel = int(option[1])
elif option[0] == "-g":
ngroups = int(option[1])
elif option[0] == "-t":
ntables = int(option[1])
elif option[0] == "-i":
nrows = int(option[1])
if debug:
gc.enable()
gc.set_debug(gc.DEBUG_LEAK)
# Catch the hdf5 file passed as the last argument
file = pargs[0]
print("Compression level:", complevel)
if complevel > 0:
print("Compression library:", complib)
rowsw = 0
if testwrite:
t1 = clock()
cpu1 = cpuclock()
(rowsw, rowsz) = create_file(
file, ngroups, ntables, nrows, complevel, complib, recsize
)
t2 = clock()
cpu2 = cpuclock()
tapprows = t2 - t1
cpuapprows = cpu2 - cpu1
print(f"Rows written: {rowsw} Row size: {rowsz}")
print(
f"Time writing rows: {tapprows:.3f} s (real) "
f"{cpuapprows:.3f} s (cpu) {cpuapprows / tapprows:.0%}"
)
print(f"Write Krows/sec: {rowsw / (tapprows * 1000):.3f}")
print(f"Write MB/s : {rowsw * rowsz / (tapprows * 2**20):.3f}")
if testread:
t1 = clock()
cpu1 = cpuclock()
(rowsr, rowsz, bufsz) = read_file(file, ngroups, recsize, verbose)
t2 = clock()
cpu2 = cpuclock()
treadrows = t2 - t1
cpureadrows = cpu2 - cpu1
print(f"Rows read: {rowsw} Row size: {rowsz}, Buf size: {bufsz}")
print(
f"Time reading rows: {treadrows:.3f} s (real) "
f"{cpureadrows:.3f} s (cpu) {cpureadrows / treadrows:.0%}"
)
print(f"Read Krows/sec: {rowsr / (treadrows * 1000):.3f}")
print(f"Read MB/s : {rowsr * rowsz / (treadrows * 2**20):.3f}")
# Show the dirt
if debug > 1:
dump_garbage()
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