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// -----------------------------------------------------------------------------------------------------
// Copyright (c) 2006-2020, Knut Reinert & Freie Universität Berlin
// Copyright (c) 2016-2020, Knut Reinert & MPI für molekulare Genetik
// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License
// shipped with this file and also available at: https://github.com/seqan/seqan3/blob/master/LICENSE.md
// -----------------------------------------------------------------------------------------------------
#include <benchmark/benchmark.h>
#include <tuple>
#include <utility>
#include <vector>
#include <seqan3/alignment/configuration/align_config_score_type.hpp>
#include <seqan3/alignment/pairwise/align_pairwise.hpp>
#include <seqan3/alphabet/aminoacid/aa20.hpp>
#include <seqan3/alphabet/nucleotide/dna4.hpp>
#include <seqan3/range/views/to.hpp>
#include <seqan3/range/views/zip.hpp>
#include <seqan3/test/performance/sequence_generator.hpp>
#include <seqan3/test/performance/units.hpp>
#include <seqan3/test/seqan2.hpp>
#include <seqan3/std/ranges>
#ifdef SEQAN3_HAS_SEQAN2
#include <seqan/align.h>
#include <seqan/align_parallel.h>
#endif
constexpr auto nt_score_scheme = seqan3::nucleotide_scoring_scheme{seqan3::match_score{4},
seqan3::mismatch_score{-5}};
constexpr auto affine_cfg = seqan3::align_cfg::method_global{} |
seqan3::align_cfg::gap_cost_affine{seqan3::align_cfg::open_score{-10},
seqan3::align_cfg::extension_score{-1}} |
seqan3::align_cfg::scoring_scheme{nt_score_scheme};
// Globally defined constants to ensure same test data.
inline constexpr size_t sequence_length = 150;
#ifndef NDEBUG
inline constexpr size_t set_size = 128;
#else // assume release
inline constexpr size_t set_size = 1024;
#endif // NDEBUG
// Range to test for sequence length variance
inline constexpr size_t deviation_begin = 0;
inline constexpr size_t deviation_end = 64;
inline constexpr size_t deviation_step = 8;
//We don't know if the system supports hyper-threading so we use only half the threads so that the
// simd benchmark is likely to run on physical cores only.
uint32_t get_number_of_threads()
{
uint32_t thread_count = std::thread::hardware_concurrency();
return (thread_count == 1) ? thread_count : thread_count >> 1;
}
// ============================================================================
// affine; score; dna4; collection
// ============================================================================
template <typename ...align_configs_t>
void seqan3_affine_dna4_accelerated(benchmark::State & state, align_configs_t && ...configs)
{
size_t sequence_length_variance = state.range(0);
auto data = seqan3::test::generate_sequence_pairs<seqan3::dna4>(sequence_length,
set_size,
sequence_length_variance);
int64_t total = 0;
auto accelerate_config = (affine_cfg | ... | configs);
for (auto _ : state)
{
for (auto && res : seqan3::align_pairwise(data, accelerate_config))
total += res.score();
}
state.counters["cells"] = seqan3::test::pairwise_cell_updates(data, affine_cfg);
state.counters["CUPS"] = seqan3::test::cell_updates_per_second(state.counters["cells"]);
state.counters["total"] = total;
}
BENCHMARK_CAPTURE(seqan3_affine_dna4_accelerated,
simd_with_score,
seqan3::align_cfg::output_score{},
seqan3::align_cfg::score_type<int16_t>{},
seqan3::align_cfg::vectorised{})
->UseRealTime()
->DenseRange(deviation_begin, deviation_end, deviation_step);
BENCHMARK_CAPTURE(seqan3_affine_dna4_accelerated,
simd_with_end_position,
seqan3::align_cfg::output_end_position{},
seqan3::align_cfg::output_score{},
seqan3::align_cfg::score_type<int16_t>{},
seqan3::align_cfg::vectorised{})
->UseRealTime()
->DenseRange(deviation_begin, deviation_end, deviation_step);
BENCHMARK_CAPTURE(seqan3_affine_dna4_accelerated,
simd_parallel_with_score,
seqan3::align_cfg::output_score{},
seqan3::align_cfg::score_type<int16_t>{},
seqan3::align_cfg::vectorised{},
seqan3::align_cfg::parallel{get_number_of_threads()})
->UseRealTime()
->DenseRange(deviation_begin, deviation_end, deviation_step);
BENCHMARK_CAPTURE(seqan3_affine_dna4_accelerated,
simd_parallel_with_end_position,
seqan3::align_cfg::output_end_position{},
seqan3::align_cfg::output_score{},
seqan3::align_cfg::score_type<int16_t>{},
seqan3::align_cfg::vectorised{},
seqan3::align_cfg::parallel{get_number_of_threads()})
->UseRealTime()
->DenseRange(deviation_begin, deviation_end, deviation_step);
#ifdef SEQAN3_HAS_SEQAN2
template <typename ...args_t>
void seqan2_affine_dna4_accelerated(benchmark::State & state, args_t && ...args)
{
std::tuple captured_args{args...};
size_t sequence_length_variance = state.range(0);
auto [vec1, vec2] = seqan3::test::generate_sequence_pairs_seqan2<seqan::Dna>(sequence_length,
set_size,
sequence_length_variance);
auto exec = std::get<0>(captured_args);
setNumThreads(exec, std::get<1>(captured_args));
int64_t total = 0;
for (auto _ : state)
{
// In SeqAn2 the gap open contains already the gap extension costs, that's why we use -11 here.
auto res = seqan::globalAlignmentScore(exec, vec1, vec2, seqan::Score<int16_t>{4, -5, -1, -11});
total = std::accumulate(seqan::begin(res), seqan::end(res), total);
}
state.counters["cells"] = seqan3::test::pairwise_cell_updates(seqan3::views::zip(vec1, vec2), affine_cfg);
state.counters["CUPS"] = seqan3::test::cell_updates_per_second(state.counters["cells"]);
state.counters["total"] = total;
}
// Note SeqAn2 has no parallel interface yet for computing the traceback as well.
BENCHMARK_CAPTURE(seqan2_affine_dna4_accelerated,
simd_with_score,
seqan::ExecutionPolicy<seqan::Serial, seqan::Vectorial>{},
1)
->UseRealTime()
->DenseRange(deviation_begin, deviation_end, deviation_step);
BENCHMARK_CAPTURE(seqan2_affine_dna4_accelerated,
simd_parallel_with_score,
seqan::ExecutionPolicy<seqan::Parallel, seqan::Vectorial>{},
get_number_of_threads())
->UseRealTime()
->DenseRange(deviation_begin, deviation_end, deviation_step);
#endif // SEQAN3_HAS_SEQAN2
// ============================================================================
// instantiate tests
// ============================================================================
BENCHMARK_MAIN();
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