MikkelSchubert / adapterremoval / #46

Committed 27 Nov 2024 03:10PM UTC coverage: 27.245% (+1.0%) from 26.244%

Build # #46

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travis-ci

Committed by

MikkelSchubert

Commit Message

fix convenience executable make target

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0.0

/src/benchmarking.cpp

/*************************************************************************\
 * AdapterRemoval - cleaning next-generation sequencing reads            *
 *                                                                       *
 * Copyright (C) 2024 by Mikkel Schubert - mikkelsch@gmail.com           *
 *                                                                       *
 * This program is free software: you can redistribute it and/or modify  *
 * it under the terms of the GNU General Public License as published by  *
 * the Free Software Foundation, either version 3 of the License, or     *
 * (at your option) any later version.                                   *
 *                                                                       *
 * This program is distributed in the hope that it will be useful,       *
 * but WITHOUT ANY WARRANTY; without even the implied warranty of        *
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the         *
 * GNU General Public License for more details.                          *
 *                                                                       *
 * You should have received a copy of the GNU General Public License     *
 * along with this program.  If not, see <http://www.gnu.org/licenses/>. *
\*************************************************************************/
#include "benchmarking.hpp" // for benchmark_toggles, benchmarker
#include "debug.hpp"        // for AR_REQUIRE
#include "logging.hpp"      // for log
#include "mathutils.hpp"    // for arithmetic_mean, standard_deviation
#include "simd.hpp"         // for supported
#include "strutils.hpp"     // for to_lower
#include <algorithm>        // for find, accumulate
#include <array>            // for array
#include <cmath>            // for round
#include <iomanip>          // for fixed, setsetprecision
#include <iostream>         // for cout
#include <numeric>          // for accumulate

namespace adapterremoval {

namespace {

//! Number of loops to perform prior to benchmarking as burn-in
const size_t BENCHMARK_BURN_IN = 1;
//! Benchmarks must be repeated at least this number of times
const size_t BENCHMARK_MIN_LOOPS = 10;
//! Benchmarks must be repeated at most this number of times
const size_t BENCHMARK_MAX_LOOPS = 1000;
//! Benchmarks must run for at this this number of nano-seconds
const double BENCHMARK_MIN_TIME_NS = 5'000'000'000;
//! Benchmark loops shorter than this number of nano-seconds cannot be measured
const double BENCHMARK_CUTOFF_TIME_NS = 10'000;
//! Number of NS between terminal updates
const size_t BENCHMARK_UPDATE_INTERVAL = 50'000'000;

} // namespace

benchmark_toggles::benchmark_toggles(string_vec keys)
  : m_toggles(std::move(keys))
  , m_enabled(m_toggles.size(), false)
  , m_defaults()
{
}

bool
benchmark_toggles::update_toggles(const string_vec& keys)
{
  bool any_errors = false;
  m_defaults = keys.empty();
  for (const auto& key : keys) {
    const auto it =
      std::find(m_toggles.begin(), m_toggles.end(), to_lower(key));

    if (it == m_toggles.end()) {
      log::error() << "Unknown benchmarking toggle '" << key << "'";
      any_errors = true;
    } else {
      m_enabled.at(it - m_toggles.begin()) = true;
    }
  }

  if (any_errors) {
    auto msg = log::error();
    msg << "Valid toggles are ";
    for (size_t i = 0; i < m_toggles.size() - 1; ++i) {
      msg << m_toggles.at(i) << ", ";
    }
    msg << " and " << m_toggles.back();
  }

  return !any_errors;
}

bool
benchmark_toggles::is_set(const std::string& key) const
{
  const auto it = std::find(m_toggles.begin(), m_toggles.end(), to_lower(key));

  AR_REQUIRE(it != m_toggles.end());
  return m_enabled.at(it - m_toggles.begin());
}

benchmarker::benchmarker(std::string desc, string_vec toggles)
  : m_description(std::move(desc))
  , m_toggles(std::move(toggles))
{
}

void
benchmarker::run_if_toggled(const benchmark_toggles& toggles)
{
  const auto s = enabled(toggles);
  if (s != strategy::skip) {
    run(s);
  }
}

/** Called before `setup` to perform any per batch setup */
void
benchmarker::setup() {};

strategy
benchmarker::enabled(const benchmark_toggles& toggles) const
{
  if (toggles.defaults()) {
    return strategy::benchmark;
  }

  for (const auto& toggle : m_toggles) {
    if (toggles.is_set(toggle)) {
      return strategy::benchmark;
    }
  }

  return m_required ? strategy::passthrough : strategy::skip;
}

void
benchmarker::run(const strategy s)
{
  static bool header = false;
  if (!header) {
    std::cout << "             Benchmark |       Min |      Mean |       Max | "
                 "SD (%) | Loops | Outliers"
              << std::endl;
    header = true;
  }

  if (s != strategy::passthrough) {
    log::cerr() << "\r\033[K" << std::setw(22) << m_description << " burn-in";

    for (size_t i = 1; i <= BENCHMARK_BURN_IN; ++i) {
      setup();
      execute();

      log::cerr() << ".";
    }
  } else {
    log::cerr() << "\r\033[K" << std::setw(22) << m_description << " (setup)";
  }

  size_t loops = 0;
  uint64_t next_update = 0;
  do {
    uint64_t elapsed =
      std::accumulate(m_durations.begin(), m_durations.end(), uint64_t());

    do {
      setup();
      const auto start = clock::now();
      execute();
      const auto duration = (clock::now() - start).count();

      loops++;
      elapsed += duration;
      m_durations.push_back(duration);

      if (elapsed >= next_update) {
        log::cerr() << "\r\033[K" << summarize(loops);
        next_update += BENCHMARK_UPDATE_INTERVAL;
      }
    } while (s == strategy::benchmark &&
             m_durations.size() < BENCHMARK_MAX_LOOPS &&
             (m_durations.size() < BENCHMARK_MIN_LOOPS ||
              (elapsed < BENCHMARK_MIN_TIME_NS &&
               elapsed / m_durations.size() >= BENCHMARK_CUTOFF_TIME_NS)));
  } while (s == strategy::benchmark && (loops < 2 * m_durations.size()) &&
           grubbs_test_prune(m_durations));

  log::cerr() << "\r\033[K";

  if (s != strategy::passthrough) {
    std::cout << summarize(loops) << std::endl;
  }
}

std::string
benchmarker::summarize(size_t loops) const
{
  const std::array<size_t, 7> COLUMN_WIDTHS{ 22, 9, 9, 9, 6, 5, 8 };
  std::array<std::string, COLUMN_WIDTHS.size()> values{
    m_description,
    "",
    "",
    "",
    "",
    std::to_string(m_durations.size()),
    std::to_string(loops - m_durations.size()),
  };

  if (!m_durations.empty()) {
    const auto min_max =
      std::minmax_element(m_durations.begin(), m_durations.end());
    const auto mean = arithmetic_mean(m_durations);

    values.at(1) = format_thousand_sep(*min_max.first / 1e3);
    values.at(2) = format_thousand_sep(std::round(mean / 1e3));
    values.at(3) = format_thousand_sep(*min_max.second / 1e3);

    if (m_durations.size() > 1) {
      const auto sd = standard_deviation(m_durations);
      values.at(4) = format_fraction(1e9 * sd, 1e7 * mean);
    }
  }

  std::ostringstream ss;
  for (size_t i = 0; i < values.size(); ++i) {
    if (i) {
      ss << " | ";
    }

    ss << std::setw(COLUMN_WIDTHS.at(i)) << values.at(i);
  }

  return ss.str();
}

} // namespace adapterremoval

1	/*************************************************************************\
2	* AdapterRemoval - cleaning next-generation sequencing reads *
3	* *
4	* Copyright (C) 2024 by Mikkel Schubert - mikkelsch@gmail.com *
5	* *
6	* This program is free software: you can redistribute it and/or modify *
7	* it under the terms of the GNU General Public License as published by *
8	* the Free Software Foundation, either version 3 of the License, or *
9	* (at your option) any later version. *
10	* *
11	* This program is distributed in the hope that it will be useful, *
12	* but WITHOUT ANY WARRANTY; without even the implied warranty of *
13	* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
14	* GNU General Public License for more details. *
15	* *
16	* You should have received a copy of the GNU General Public License *
17	* along with this program. If not, see <http://www.gnu.org/licenses/>. *
18	\*************************************************************************/
19	#include "benchmarking.hpp" // for benchmark_toggles, benchmarker
20	#include "debug.hpp" // for AR_REQUIRE
21	#include "logging.hpp" // for log
22	#include "mathutils.hpp" // for arithmetic_mean, standard_deviation
23	#include "simd.hpp" // for supported
24	#include "strutils.hpp" // for to_lower
25	#include <algorithm> // for find, accumulate
26	#include <array> // for array
27	#include <cmath> // for round
28	#include <iomanip> // for fixed, setsetprecision
29	#include <iostream> // for cout
30	#include <numeric> // for accumulate
31
32	namespace adapterremoval {
33
34	namespace {
35
36	//! Number of loops to perform prior to benchmarking as burn-in
37	const size_t BENCHMARK_BURN_IN = 1;
38	//! Benchmarks must be repeated at least this number of times
39	const size_t BENCHMARK_MIN_LOOPS = 10;
40	//! Benchmarks must be repeated at most this number of times
41	const size_t BENCHMARK_MAX_LOOPS = 1000;
42	//! Benchmarks must run for at this this number of nano-seconds
43	const double BENCHMARK_MIN_TIME_NS = 5'000'000'000;
44	//! Benchmark loops shorter than this number of nano-seconds cannot be measured
45	const double BENCHMARK_CUTOFF_TIME_NS = 10'000;
46	//! Number of NS between terminal updates
47	const size_t BENCHMARK_UPDATE_INTERVAL = 50'000'000;
48
49	} // namespace
50
51	benchmark_toggles::benchmark_toggles(string_vec keys)	×
52	: m_toggles(std::move(keys))	×
53	, m_enabled(m_toggles.size(), false)	×
54	, m_defaults()	×
55	{
56	}
57
58	bool
59	benchmark_toggles::update_toggles(const string_vec& keys)	×
60	{
61	bool any_errors = false;	×
62	m_defaults = keys.empty();	×
63	for (const auto& key : keys) {	×
64	const auto it =	×
65	std::find(m_toggles.begin(), m_toggles.end(), to_lower(key));	×
66
67	if (it == m_toggles.end()) {	×
68	log::error() << "Unknown benchmarking toggle '" << key << "'";	×
69	any_errors = true;	×
70	} else {
71	m_enabled.at(it - m_toggles.begin()) = true;	×
72	}
73	}
74
75	if (any_errors) {	×
76	auto msg = log::error();	×
77	msg << "Valid toggles are ";	×
78	for (size_t i = 0; i < m_toggles.size() - 1; ++i) {	×
79	msg << m_toggles.at(i) << ", ";	×
80	}
81	msg << " and " << m_toggles.back();	×
82	}
83
84	return !any_errors;	×
85	}
86
87	bool
88	benchmark_toggles::is_set(const std::string& key) const	×
89	{
90	const auto it = std::find(m_toggles.begin(), m_toggles.end(), to_lower(key));	×
91
92	AR_REQUIRE(it != m_toggles.end());	×
93	return m_enabled.at(it - m_toggles.begin());	×
94	}
95
96	benchmarker::benchmarker(std::string desc, string_vec toggles)	×
97	: m_description(std::move(desc))	×
98	, m_toggles(std::move(toggles))	×
99	{
100	}
101
102	void
103	benchmarker::run_if_toggled(const benchmark_toggles& toggles)	×
104	{
105	const auto s = enabled(toggles);	×
106	if (s != strategy::skip) {	×
107	run(s);	×
108	}
109	}
110
111	/** Called before `setup` to perform any per batch setup */
112	void
113	benchmarker::setup() {};	×
114
115	strategy
116	benchmarker::enabled(const benchmark_toggles& toggles) const	×
117	{
118	if (toggles.defaults()) {	×
119	return strategy::benchmark;
120	}
121
122	for (const auto& toggle : m_toggles) {	×
123	if (toggles.is_set(toggle)) {	×
124	return strategy::benchmark;	×
125	}
126	}
127
128	return m_required ? strategy::passthrough : strategy::skip;	×
129	}
130
131	void
132	benchmarker::run(const strategy s)	×
133	{
134	static bool header = false;
135	if (!header) {	×
136	std::cout << " Benchmark \| Min \| Mean \| Max \| "	×
137	"SD (%) \| Loops \| Outliers"	×
138	<< std::endl;	×
139	header = true;	×
140	}
141
142	if (s != strategy::passthrough) {	×
143	log::cerr() << "\r\033[K" << std::setw(22) << m_description << " burn-in";	×
144
145	for (size_t i = 1; i <= BENCHMARK_BURN_IN; ++i) {	×
146	setup();	×
147	execute();	×
148
149	log::cerr() << ".";	×
150	}
151	} else {
152	log::cerr() << "\r\033[K" << std::setw(22) << m_description << " (setup)";	×
153	}
154
155	size_t loops = 0;
156	uint64_t next_update = 0;
157	do {	×
158	uint64_t elapsed =	×
159	std::accumulate(m_durations.begin(), m_durations.end(), uint64_t());	×
160
161	do {	×
162	setup();	×
163	const auto start = clock::now();	×
164	execute();	×
165	const auto duration = (clock::now() - start).count();	×
166
167	loops++;	×
168	elapsed += duration;	×
169	m_durations.push_back(duration);	×
170
171	if (elapsed >= next_update) {	×
172	log::cerr() << "\r\033[K" << summarize(loops);	×
173	next_update += BENCHMARK_UPDATE_INTERVAL;	×
174	}
175	} while (s == strategy::benchmark &&	×
176	m_durations.size() < BENCHMARK_MAX_LOOPS &&	×
177	(m_durations.size() < BENCHMARK_MIN_LOOPS \|\|	×
178	(elapsed < BENCHMARK_MIN_TIME_NS &&	×
179	elapsed / m_durations.size() >= BENCHMARK_CUTOFF_TIME_NS)));	×
180	} while (s == strategy::benchmark && (loops < 2 * m_durations.size()) &&	×
181	grubbs_test_prune(m_durations));	×
182
183	log::cerr() << "\r\033[K";	×
184
185	if (s != strategy::passthrough) {	×
186	std::cout << summarize(loops) << std::endl;	×
187	}
188	}
189
190	std::string
191	benchmarker::summarize(size_t loops) const	×
192	{
193	const std::array<size_t, 7> COLUMN_WIDTHS{ 22, 9, 9, 9, 6, 5, 8 };	×
194	std::array<std::string, COLUMN_WIDTHS.size()> values{	×
195	m_description,	×
196	"",
197	"",
198	"",
199	"",
200	std::to_string(m_durations.size()),	×
201	std::to_string(loops - m_durations.size()),	×
202	};
203
204	if (!m_durations.empty()) {	×
205	const auto min_max =	×
206	std::minmax_element(m_durations.begin(), m_durations.end());	×
207	const auto mean = arithmetic_mean(m_durations);	×
208
209	values.at(1) = format_thousand_sep(*min_max.first / 1e3);	×
210	values.at(2) = format_thousand_sep(std::round(mean / 1e3));	×
211	values.at(3) = format_thousand_sep(*min_max.second / 1e3);	×
212
213	if (m_durations.size() > 1) {	×
214	const auto sd = standard_deviation(m_durations);	×
215	values.at(4) = format_fraction(1e9 * sd, 1e7 * mean);	×
216	}
217	}
218
219	std::ostringstream ss;	×
220	for (size_t i = 0; i < values.size(); ++i) {	×
221	if (i) {	×
222	ss << " \| ";	×
223	}
224
225	ss << std::setw(COLUMN_WIDTHS.at(i)) << values.at(i);	×
226	}
227
228	return ss.str();	×
229	}
230
231	} // namespace adapterremoval

MikkelSchubert / adapterremoval / #46

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