Completion profiling

Links: notebook, html, PDF, python, slides, GitHub

Profiling avec cProfile, memory_profiler, pyinstrument, snakeviz.

line_profiler ne semble pas plus être maintenu.

%matplotlib inline
import matplotlib.pyplot as plt
plt.style.use('ggplot')
from jyquickhelper import add_notebook_menu
add_notebook_menu()

Setup

Function to profile

from mlstatpy.nlp.completion import CompletionTrieNode

def gain_dynamique_moyen_par_mot(queries, weights):
    per = list(zip(weights, queries))
    total = sum(weights) * 1.0
    res = []
    trie = CompletionTrieNode.build([(None, q) for _, q in per])
    trie.precompute_stat()
    trie.update_stat_dynamic()
    wks = [(w, p, len(w) - trie.min_keystroke0(w)[0]) for p, w in per]
    wks_dyn = [(w, p, len(w) - trie.min_dynamic_keystroke(w)[0])
               for p, w in per]
    wks_dyn2 = [(w, p, len(w) - trie.min_dynamic_keystroke2(w)[0])
                for p, w in per]
    gain = sum(g * p / total for w, p, g in wks)
    gain_dyn = sum(g * p / total for w, p, g in wks_dyn)
    gain_dyn2 = sum(g * p / total for w, p, g in wks_dyn2)
    ave_length = sum(len(w) * p / total for p, w in per)
    return gain, gain_dyn, gain_dyn2, ave_length

Data

from mlstatpy.data.wikipedia import download_titles
file_titles = download_titles(country='fr')
len(file_titles)
33
from mlstatpy.data.wikipedia import enumerate_titles
list_titles = list(sorted(set(_ for _ in enumerate_titles(file_titles) if 'A' <= _[0] <= 'Z')))
import random
sample1000 = random.sample(list_titles, 1000)
with open("sample1000.txt", "w", encoding="utf-8") as f:
    f.write("\n".join(sample1000))

Standard modules

cProfile

import cProfile, io, pstats, os

def toprofile0(lines):
    gain_dynamique_moyen_par_mot(lines, [1.0] * len(lines))

def doprofile(lines, filename):
    pr = cProfile.Profile()
    pr.enable()
    toprofile0(lines)
    pr.disable()
    s = io.StringIO()
    ps = pstats.Stats(pr, stream=s).sort_stats('cumulative')
    ps.print_stats()
    rem = os.path.normpath(os.path.join(os.getcwd(), "..", "..", ".."))
    res = s.getvalue().replace(rem, "")
    ps.dump_stats(filename)
    return res
r = doprofile(sample1000, "completion.prof")
print(r)
      1311797 function calls in 1.865 seconds
Ordered by: cumulative time
ncalls  tottime  percall  cumtime  percall filename:lineno(function)
     1    0.000    0.000    1.865    1.865 <ipython-input-7-d2b6d910fdd7>:3(toprofile0)
     1    0.000    0.000    1.865    1.865 <ipython-input-2-684f3e860cf5>:3(gain_dynamique_moyen_par_mot)
     1    0.241    0.241    1.232    1.232 srcmlstatpynlpcompletion.py:415(precompute_stat)
 15982    0.244    0.000    0.770    0.000 srcmlstatpynlpcompletion.py:503(merge_completions)
     1    0.088    0.088    0.366    0.366 srcmlstatpynlpcompletion.py:450(update_stat_dynamic)
 15982    0.307    0.000    0.314    0.000 {built-in method builtins.__build_class__}
     1    0.194    0.194    0.220    0.220 srcmlstatpynlpcompletion.py:203(build)
 16982    0.094    0.000    0.165    0.000 srcmlstatpynlpcompletion.py:555(update_dynamic_minimum_keystroke)
 36051    0.114    0.000    0.130    0.000 srcmlstatpynlpcompletion.py:523(<listcomp>)
 37609    0.035    0.000    0.071    0.000 {built-in method builtins.all}
 16982    0.051    0.000    0.058    0.000 srcmlstatpynlpcompletion.py:588(second_step)
314299    0.053    0.000    0.053    0.000 {built-in method builtins.len}
 15983    0.006    0.000    0.049    0.000 {method 'extend' of 'collections.deque' objects}
 16983    0.031    0.000    0.047    0.000 srcmlstatpynlpcompletion.py:97(unsorted_iter)
 15982    0.039    0.000    0.046    0.000 srcmlstatpynlpcompletion.py:542(update_minimum_keystroke)
 16982    0.041    0.000    0.044    0.000 srcmlstatpynlpcompletion.py:624(init_dynamic_minimum_keystroke)
  1001    0.028    0.000    0.043    0.000 srcmlstatpynlpcompletion.py:132(leaves)
115015    0.041    0.000    0.041    0.000 srcmlstatpynlpcompletion.py:435(<genexpr>)
 15982    0.024    0.000    0.032    0.000 {built-in method builtins.sorted}
  3000    0.031    0.000    0.031    0.000 srcmlstatpynlpcompletion.py:257(find)
110110    0.027    0.000    0.027    0.000 {built-in method builtins.hasattr}
117519    0.023    0.000    0.023    0.000 {method 'values' of 'dict' objects}
     1    0.001    0.001    0.017    0.017 <ipython-input-2-684f3e860cf5>:10(<listcomp>)
 16982    0.015    0.000    0.017    0.000 srcmlstatpynlpcompletion.py:20(__init__)
 47946    0.016    0.000    0.016    0.000 {method 'extend' of 'list' objects}
 23287    0.015    0.000    0.015    0.000 {built-in method builtins.min}
  1000    0.002    0.000    0.015    0.000 srcmlstatpynlpcompletion.py:321(min_keystroke0)
     1    0.001    0.001    0.013    0.013 <ipython-input-2-684f3e860cf5>:13(<listcomp>)
 50946    0.013    0.000    0.013    0.000 {method 'pop' of 'list' objects}
     1    0.001    0.001    0.013    0.013 <ipython-input-2-684f3e860cf5>:11(<listcomp>)
 20069    0.012    0.000    0.012    0.000 {built-in method builtins.max}
  1000    0.002    0.000    0.012    0.000 srcmlstatpynlpcompletion.py:382(min_dynamic_keystroke2)
  1000    0.002    0.000    0.012    0.000 srcmlstatpynlpcompletion.py:352(min_dynamic_keystroke)
 56589    0.011    0.000    0.011    0.000 {method 'popleft' of 'collections.deque' objects}
 52034    0.011    0.000    0.011    0.000 {method 'append' of 'list' objects}
 38608    0.009    0.000    0.009    0.000 {method 'append' of 'collections.deque' objects}
 16982    0.008    0.000    0.008    0.000 srcmlstatpynlpcompletion.py:517(<genexpr>)
 16981    0.007    0.000    0.007    0.000 srcmlstatpynlpcompletion.py:54(_add)
 15982    0.007    0.000    0.007    0.000 srcmlstatpynlpcompletion.py:511(<listcomp>)
 15982    0.007    0.000    0.007    0.000 srcmlstatpynlpcompletion.py:508(Fake)
 31964    0.006    0.000    0.006    0.000 {method 'items' of 'dict' objects}
     5    0.001    0.000    0.002    0.000 {built-in method builtins.sum}
 17982    0.002    0.000    0.002    0.000 {built-in method builtins.isinstance}
  1001    0.000    0.000    0.001    0.000 <ipython-input-2-684f3e860cf5>:18(<genexpr>)
  1001    0.001    0.000    0.001    0.000 <ipython-input-2-684f3e860cf5>:15(<genexpr>)
     1    0.000    0.000    0.000    0.000 <ipython-input-2-684f3e860cf5>:7(<listcomp>)
  1001    0.000    0.000    0.000    0.000 <ipython-input-2-684f3e860cf5>:16(<genexpr>)
  1001    0.000    0.000    0.000    0.000 <ipython-input-2-684f3e860cf5>:17(<genexpr>)
     1    0.000    0.000    0.000    0.000 {method 'disable' of '_lsprof.Profiler' objects}

Others informations when profiling

memory_profiler

See memory_profiler. Version 0.56 is bugged (see #258).

from memory_profiler import profile, __version__
%load_ext memory_profiler
%memit toprofile0(sample1000)
peak memory: 411.20 MiB, increment: 18.40 MiB
from io import StringIO
st = StringIO()
@profile(stream=st)
def toprofile(lines):
    gain_dynamique_moyen_par_mot(lines, [1.0] * len(lines))
toprofile(sample1000)
ERROR: Could not find file <ipython-input-11-7512ff5cdee3>
NOTE: %mprun can only be used on functions defined in physical files, and not in the IPython environment.
%%file temp_mem_profile.py

from mlstatpy.nlp.completion import CompletionTrieNode
from memory_profiler import profile

@profile(precision=4)
def gain_dynamique_moyen_par_mot(queries, weights):
    per = list(zip(weights, queries))
    total = sum(weights) * 1.0
    res = []
    trie = CompletionTrieNode.build([(None, q) for _, q in per])
    trie.precompute_stat()
    trie.update_stat_dynamic()
    wks = [(w, p, len(w) - trie.min_keystroke0(w)[0]) for p, w in per]
    wks_dyn = [(w, p, len(w) - trie.min_dynamic_keystroke(w)[0])
               for p, w in per]
    wks_dyn2 = [(w, p, len(w) - trie.min_dynamic_keystroke2(w)[0])
                for p, w in per]
    gain = sum(g * p / total for w, p, g in wks)
    gain_dyn = sum(g * p / total for w, p, g in wks_dyn)
    gain_dyn2 = sum(g * p / total for w, p, g in wks_dyn2)
    ave_length = sum(len(w) * p / total for p, w in per)
    return gain, gain_dyn, gain_dyn2, ave_length

@profile(precision=4)
def toprofile():
    with open("sample1000.txt", "r", encoding="utf-8") as f:
        lines = [_.strip("\n\r ") for _ in f.readlines()]
    gain_dynamique_moyen_par_mot(lines, [1.0] * len(lines))
toprofile()
Overwriting temp_mem_profile.py
import sys
cmd = sys.executable
from pyquickhelper.loghelper import run_cmd
cmd += " -m memory_profiler temp_mem_profile.py"
out, err = run_cmd(cmd, wait=True)
print(out)
Filename: temp_mem_profile.py
Line #    Mem usage    Increment   Line Contents
================================================
     5  56.7930 MiB  56.7930 MiB   @profile(precision=4)
     6                             def gain_dynamique_moyen_par_mot(queries, weights):
     7  56.7930 MiB   0.0000 MiB       per = list(zip(weights, queries))
     8  56.7930 MiB   0.0000 MiB       total = sum(weights) * 1.0
     9  56.7930 MiB   0.0000 MiB       res = []
    10  63.3047 MiB   6.4492 MiB       trie = CompletionTrieNode.build([(None, q) for _, q in per])
    11  71.0742 MiB   7.7695 MiB       trie.precompute_stat()
    12  80.6211 MiB   9.5469 MiB       trie.update_stat_dynamic()
    13  80.7305 MiB   0.1094 MiB       wks = [(w, p, len(w) - trie.min_keystroke0(w)[0]) for p, w in per]
    14  80.7930 MiB   0.0469 MiB       wks_dyn = [(w, p, len(w) - trie.min_dynamic_keystroke(w)[0])
    15  80.7930 MiB   0.0000 MiB                  for p, w in per]
    16  80.8398 MiB   0.0430 MiB       wks_dyn2 = [(w, p, len(w) - trie.min_dynamic_keystroke2(w)[0])
    17  80.8398 MiB   0.0000 MiB                   for p, w in per]
    18  80.8398 MiB   0.0000 MiB       gain = sum(g * p / total for w, p, g in wks)
    19  80.8398 MiB   0.0000 MiB       gain_dyn = sum(g * p / total for w, p, g in wks_dyn)
    20  80.8398 MiB   0.0000 MiB       gain_dyn2 = sum(g * p / total for w, p, g in wks_dyn2)
    21  80.8398 MiB   0.0000 MiB       ave_length = sum(len(w) * p / total for p, w in per)
    22  80.8398 MiB   0.0000 MiB       return gain, gain_dyn, gain_dyn2, ave_length

Filename: temp_mem_profile.py
Line #    Mem usage    Increment   Line Contents
================================================
    24  56.5820 MiB  56.5820 MiB   @profile(precision=4)
    25                             def toprofile():
    26  56.5820 MiB   0.0000 MiB       with open("sample1000.txt", "r", encoding="utf-8") as f:
    27  56.7930 MiB   0.0742 MiB           lines = [_.strip("nr ") for _ in f.readlines()]
    28  80.8398 MiB  24.0469 MiB       gain_dynamique_moyen_par_mot(lines, [1.0] * len(lines))

Static Visualization

pyinstrument

See pyinstrument.

from pyinstrument import Profiler

profiler = Profiler(use_signal=False)
profiler.start()

toprofile0(sample1000)

profiler.stop()
out = profiler.output_text(unicode=False, color=False)
print(out.replace("\\", "/"))
  _     ._   __/__   _ _  _  _ _/_   Recorded: 18:17:34  Samples:  1048
 /_//_/// /_/ / //_// / //_'/ //     Duration: 1.802     CPU time: 1.703
/   _/                      v3.0.1
Program:  -f pstats completion.prof -o completion.dot
1.799 run_code  IPython/core/interactiveshell.py:3288
`- 1.799 <module>  <ipython-input-18-f16978ea99ef>:6
   `- 1.799 toprofile0  <ipython-input-7-d2b6d910fdd7>:3
      `- 1.799 gain_dynamique_moyen_par_mot  <ipython-input-2-684f3e860cf5>:3
         |- 1.251 precompute_stat  mlstatpy/nlp/completion.py:415
         |  |- 0.917 merge_completions  mlstatpy/nlp/completion.py:503
         |  |  |- 0.771 [self]
         |  |  `- 0.136 <listcomp>  mlstatpy/nlp/completion.py:523
         |  |- 0.224 [self]
         |  |- 0.051 update_minimum_keystroke  mlstatpy/nlp/completion.py:542
         |  |- 0.037 <genexpr>  mlstatpy/nlp/completion.py:435
         |  `- 0.021 leaves  mlstatpy/nlp/completion.py:132
         |- 0.289 update_stat_dynamic  mlstatpy/nlp/completion.py:450
         |  |- 0.147 update_dynamic_minimum_keystroke  mlstatpy/nlp/completion.py:555
         |  |  |- 0.100 [self]
         |  |  `- 0.046 second_step  mlstatpy/nlp/completion.py:588
         |  |- 0.084 [self]
         |  |- 0.040 init_dynamic_minimum_keystroke  mlstatpy/nlp/completion.py:624
         |  `- 0.018 unsorted_iter  mlstatpy/nlp/completion.py:97
         |- 0.204 build  mlstatpy/nlp/completion.py:203
         |  `- 0.190 [self]
         |- 0.020 <listcomp>  <ipython-input-2-684f3e860cf5>:10
         |  `- 0.019 min_keystroke0  mlstatpy/nlp/completion.py:321
         `- 0.018 <listcomp>  <ipython-input-2-684f3e860cf5>:13

Javascript Visualization

SnakeViz

%load_ext snakeviz

L’instruction qui suit lance l’explorateur par défaut avec les données du profilage.

# %snakeviz toprofile0(sample1000)
from pyquickhelper.helpgen import NbImage
NbImage("images/func_info.jpg", width=400)
../_images/completion_profiling_29_0.jpeg

vprof, py-spy

See vprof or py-spy. The second one outputs a SVG file easy to handle.

# from vprof import profiler

# needs to be run from a file not from a notebook
# profiler.run(toprofile0, 'cmh', args=(sample1000,), host='localhost', port=8000)
from pyquickhelper.helpgen import NbImage
NbImage("images/vprof.jpg", width=800)
../_images/completion_profiling_32_0.jpeg