Merge pull request #71 from eseiler/infra/benchmark

[INFRA] Add bin benchmark

.github/workflows/ci_linux.yml

@@ -96,7 +96,7 @@ jobs:
         run: |
           mkdir build
           cd build
-          cmake ../raptor -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} -DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }}"
+          cmake ../raptor -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} -DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }}" -DRAPTOR_NATIVE_BUILD=OFF
 
       - name: Build tests
         env:

.github/workflows/ci_macos.yml

@@ -83,7 +83,7 @@ jobs:
         run: |
           mkdir build
           cd build
-          cmake ../raptor -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} -DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }}"
+          cmake ../raptor -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} -DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }}" -DRAPTOR_NATIVE_BUILD=OFF
 
       - name: Build application
         env:

.github/workflows/ci_misc.yml

@@ -91,7 +91,7 @@ jobs:
         run: |
           mkdir build
           cd build
-          cmake ../raptor -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} -DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }}"
+          cmake ../raptor -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} -DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }}" -DRAPTOR_NATIVE_BUILD=OFF
 
       - name: Build tests
         if: ${{!matrix.skip_build_tests}}

CMakeLists.txt

@@ -97,5 +97,7 @@ add_subdirectory (doc EXCLUDE_FROM_ALL)
 
 ## TEST
 
+set (RAPTOR_ENABLE_BENCHMARK OFF CACHE BOOL "Compile benchmarks as cli tests.")
+
 enable_testing ()
 add_subdirectory (test EXCLUDE_FROM_ALL)

test/CMakeLists.txt

@@ -53,13 +53,17 @@ macro (add_app_test test_filename test_alternative)
     target_link_libraries (${target} "${PROJECT_NAME}_lib" seqan3::seqan3 gtest gtest_main)
 
     # Make seqan3::test available for both cli and api tests.
-    target_include_directories(${target} PUBLIC "${SEQAN3_CLONE_DIR}/test/include")
-    target_include_directories(${target} PUBLIC "${SEQAN3_TEST_CLONE_DIR}/googletest/include/")
+    target_include_directories (${target} PUBLIC "${SEQAN3_CLONE_DIR}/test/include")
+    target_include_directories (${target} PUBLIC "${SEQAN3_TEST_CLONE_DIR}/googletest/include/")
 
     # Add the test to its general target (cli or api).
     if (${test_alternative} STREQUAL "CLI_TEST")
         add_dependencies (${target} "${PROJECT_NAME}") # cli test needs the application executable
         add_dependencies (cli_test ${target})
+        if (RAPTOR_ENABLE_BENCHMARK)
+            target_include_directories (${target} PUBLIC "${SEQAN3_BENCHMARK_CLONE_DIR}/include/")
+            target_link_libraries (${target} gbenchmark)
+        endif ()
     elseif (${test_alternative} STREQUAL "API_TEST")
         add_dependencies (api_test ${target})
     endif ()
@@ -94,4 +98,11 @@ add_subdirectory (api)
 add_subdirectory (cli)
 add_subdirectory (coverage)
 
+if (RAPTOR_ENABLE_BENCHMARK)
+    set (SEQAN3_BENCHMARK_CLONE_DIR "${PROJECT_BINARY_DIR}/vendor/benchmark")
+    include ("${SEQAN3_CLONE_DIR}/test/cmake/seqan3_require_benchmark.cmake")
+    seqan3_require_benchmark ()
+    add_subdirectory (benchmark)
+endif ()
+
 message (STATUS "${FontBold}You can run `make test` to build and run tests.${FontReset}")

test/benchmark/CMakeLists.txt

@@ -0,0 +1,3 @@
+cmake_minimum_required (VERSION 3.8)
+
+add_cli_test (bin_influence_benchmark.cpp)

test/benchmark/bin_influence_benchmark.cpp

@@ -0,0 +1,58 @@
+// -----------------------------------------------------------------------------------------------------
+// Copyright (c) 2006-2021, Knut Reinert & Freie Universität Berlin
+// Copyright (c) 2016-2021, 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/raptor/blob/master/LICENSE.md
+// -----------------------------------------------------------------------------------------------------
+
+#include <benchmark/benchmark.h>
+
+#include <seqan3/alphabet/nucleotide/dna4.hpp>
+#include <seqan3/utility/views/slice.hpp>
+
+#include <seqan3/search/dream_index/interleaved_bloom_filter.hpp>
+#include <seqan3/search/views/kmer_hash.hpp>
+#include <seqan3/test/performance/sequence_generator.hpp>
+
+static constexpr size_t const genome_size{5000}; // 4'300'000'000
+static constexpr size_t const read_size{100};
+static constexpr size_t const read_count{1000}; // 1'000'000
+static constexpr size_t const ibf_size{8'388'608/*=1MiB*/}; // 34'359'738'368/*=4GiB*/
+
+static std::vector<seqan3::dna4> const genome{seqan3::test::generate_sequence<seqan3::dna4>(genome_size, 0, 0)};
+static std::vector<std::vector<seqan3::dna4>> const reads{[] (auto const & genome) {
+    std::vector<std::vector<seqan3::dna4>> result(read_count);
+    size_t i{};
+    for (auto && read_start : seqan3::test::generate_numeric_sequence<size_t>(read_count, 0, genome_size - read_size + 1, 0))
+    {
+        auto v = genome | seqan3::views::slice(read_start, read_start + read_size);
+        result[i++].assign(v.begin(), v.end());
+    }
+    return result;
+    } (genome)};
+
+static void search_benchmark(benchmark::State & state)
+{
+    size_t const bin_count = static_cast<size_t>(state.range(0));
+    size_t const hash_num{2u};
+    size_t const bin_size{ibf_size / bin_count};
+    size_t const chunk_size{(genome_size + bin_count - 1) / bin_count};
+
+    seqan3::interleaved_bloom_filter<seqan3::data_layout::uncompressed> ibf{seqan3::bin_count{bin_count},
+                                                                            seqan3::bin_size{bin_size},
+                                                                            seqan3::hash_function_count{hash_num}};
+
+    size_t bin_counter{};
+    for (auto && sequence : genome | seqan3::views::chunk(chunk_size))
+        for (auto && hash : sequence | seqan3::views::kmer_hash(seqan3::ungapped{19u}))
+            ibf.emplace(hash, seqan3::bin_index{bin_counter++});
+
+    auto agent = ibf.counting_agent<uint16_t>();
+    for (auto _ : state)
+        for (auto && query : reads)
+            benchmark::DoNotOptimize(agent.bulk_count(query | seqan3::views::kmer_hash(seqan3::ungapped{19u})));
+}
+
+BENCHMARK(search_benchmark)->RangeMultiplier(2)->Range(64, 65536);
+
+BENCHMARK_MAIN();