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"""Testbed for open/close PyTables files.
This uses the HotShot profiler.
"""
import os
import sys
import getopt
import pstats
import cProfile
from time import perf_counter as clock
from pathlib import Path
import tables as tb
filename = None
niter = 1
def show_stats(explain, tref):
"Show the used memory"
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("WallClock time:", clock() - tref)
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")
def check_open_close():
for i in range(niter):
print(
"------------------ open_close #%s -------------------------" % i
)
tref = clock()
fileh = tb.open_file(filename)
fileh.close()
show_stats("After closing file", tref)
def check_only_open():
for i in range(niter):
print("------------------ only_open #%s -------------------------" % i)
tref = clock()
fileh = tb.open_file(filename)
show_stats("Before closing file", tref)
fileh.close()
def check_full_browse():
for i in range(niter):
print("------------------ full_browse #%s -----------------------" % i)
tref = clock()
fileh = tb.open_file(filename)
for node in fileh:
pass
fileh.close()
show_stats("After full browse", tref)
def check_partial_browse():
for i in range(niter):
print("------------------ partial_browse #%s --------------------" % i)
tref = clock()
fileh = tb.open_file(filename)
for node in fileh.root.ngroup0.ngroup1:
pass
fileh.close()
show_stats("After closing file", tref)
def check_full_browse_attrs():
for i in range(niter):
print("------------------ full_browse_attrs #%s -----------------" % i)
tref = clock()
fileh = tb.open_file(filename)
for node in fileh:
# Access to an attribute
_ = node._v_attrs.CLASS
fileh.close()
show_stats("After full browse", tref)
def check_partial_browse_attrs():
for i in range(niter):
print("------------------ partial_browse_attrs #%s --------------" % i)
tref = clock()
fileh = tb.open_file(filename)
for node in fileh.root.ngroup0.ngroup1:
# Access to an attribute
_ = node._v_attrs.CLASS
fileh.close()
show_stats("After closing file", tref)
def check_open_group():
for i in range(niter):
print("------------------ open_group #%s ------------------------" % i)
tref = clock()
fileh = tb.open_file(filename)
group = fileh.root.ngroup0.ngroup1
# Access to an attribute
_ = group._v_attrs.CLASS
fileh.close()
show_stats("After closing file", tref)
def check_open_leaf():
for i in range(niter):
print("------------------ open_leaf #%s -----------------------" % i)
tref = clock()
fileh = tb.open_file(filename)
leaf = fileh.root.ngroup0.ngroup1.array9
# Access to an attribute
_ = leaf._v_attrs.CLASS
fileh.close()
show_stats("After closing file", tref)
if __name__ == "__main__":
usage = (
"""usage: %s [-v] [-p] [-n niter] [-O] [-o] [-B] [-b] [-g] [-l] [-A] [-a] [-E] [-S] datafile
-v verbose (total dump of profiling)
-p do profiling
-n number of iterations for reading
-O Check open_close
-o Check only_open
-B Check full browse
-b Check partial browse
-A Check full browse and reading one attr each node
-a Check partial browse and reading one attr each node
-g Check open nested group
-l Check open nested leaf
-E Check everything
-S Check everything as subprocess
\n"""
% sys.argv[0]
)
try:
opts, pargs = getopt.getopt(sys.argv[1:], "vpn:OoBbAaglESs")
except Exception:
sys.stderr.write(usage)
sys.exit(0)
progname = sys.argv[0]
args = sys.argv[1:]
# if we pass too much parameters, abort
if len(pargs) != 1:
sys.stderr.write(usage)
sys.exit(0)
# default options
verbose = 0
silent = 0 # if silent, does not print the final statistics
profile = 0
all_checks = 0
all_system_checks = 0
func = []
# Checking options
options = ["-O", "-o", "-B", "-b", "-A", "-a", "-g", "-l"]
# Dict to map options to checking functions
option2func = {
"-O": "check_open_close",
"-o": "check_only_open",
"-B": "check_full_browse",
"-b": "check_partial_browse",
"-A": "check_full_browse_attrs",
"-a": "check_partial_browse_attrs",
"-g": "check_open_group",
"-l": "check_open_leaf",
}
# Get the options
for option in opts:
if option[0] == "-v":
verbose = 1
elif option[0] == "-p":
profile = 1
elif option[0] in option2func:
func.append(option2func[option[0]])
elif option[0] == "-E":
all_checks = 1
for opt in options:
func.append(option2func[opt])
elif option[0] == "-S":
all_system_checks = 1
elif option[0] == "-s":
silent = 1
elif option[0] == "-n":
niter = int(option[1])
filename = pargs[0]
tref = clock()
if all_system_checks:
args.remove("-S") # We don't want -S in the options list again
for opt in options:
opts = r"{} \-s {} {}".format(progname, opt, " ".join(args))
# print "opts-->", opts
os.system("python2.4 %s" % opts)
else:
if profile:
for ifunc in func:
cProfile.run(ifunc + "()", ifunc + ".prof")
stats = pstats.Stats(ifunc + ".prof")
stats.strip_dirs()
stats.sort_stats("time", "calls")
if verbose:
stats.print_stats()
else:
stats.print_stats(20)
else:
for ifunc in func:
eval(ifunc + "()")
if not silent:
print("------------------ End of run -------------------------")
show_stats("Final statistics (after closing everything)", tref)
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