[FEATURE] Add --timing-output and Output layout timings.

seqan · Nov 8, 2023 · be73b16 · be73b16
1 parent 74355cf
commit be73b16
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Showing 5 changed files with 39 additions and 2 deletions.
diff --git a/include/chopper/configuration.hpp b/include/chopper/configuration.hpp
@@ -29,6 +29,9 @@ struct configuration
 
     //!\brief Internal parameter that triggers some verbose debug output.
     bool debug{false};
+
+    //!\brief If specified, layout timings are written to the specified file.
+    std::filesystem::path output_timings{};
     //!\}
 
     /*!\name Configuration of size estimates (chopper::count)

diff --git a/lib/hibf b/lib/hibf
diff --git a/src/chopper.cpp b/src/chopper.cpp
@@ -39,6 +39,8 @@ int main(int argc, char const * argv[])
         else if (config.k > config.window_size)
             throw sharg::parser_error{"The k-mer size cannot be bigger than the window size."};
 
+        assert(parser.is_option_set("timing-output") && !config.output_timings.empty());
+
         config.disable_sketch_output = !parser.is_option_set("output-sketches-to");
     }
     catch (sharg::parser_error const & ext) // the user did something wrong

diff --git a/src/layout/execute.cpp b/src/layout/execute.cpp
@@ -61,6 +61,11 @@ int execute(chopper::configuration & config, std::vector<std::string> const & fi
     seqan::hibf::layout::layout hibf_layout;
     std::vector<seqan::hibf::sketch::hyperloglog> sketches;
 
+    seqan::hibf::concurrent_timer compute_sketches_timer{};
+    seqan::hibf::concurrent_timer union_estimation_timer{};
+    seqan::hibf::concurrent_timer rearrangement_timer{};
+    seqan::hibf::concurrent_timer dp_algorithm_timer{};
+
     if (config.determine_best_tmax)
     {
         std::tie(hibf_layout, sketches) = determine_best_number_of_technical_bins(config);
@@ -69,8 +74,16 @@ int execute(chopper::configuration & config, std::vector<std::string> const & fi
     {
         std::vector<size_t> kmer_counts;
 
+        compute_sketches_timer.start();
         seqan::hibf::sketch::compute_sketches(config.hibf_config, kmer_counts, sketches);
-        hibf_layout = seqan::hibf::layout::compute_layout(config.hibf_config, kmer_counts, sketches);
+        compute_sketches_timer.stop();
+        dp_algorithm_timer.start();
+        hibf_layout = seqan::hibf::layout::compute_layout(config.hibf_config,
+                                                          kmer_counts,
+                                                          sketches,
+                                                          union_estimation_timer,
+                                                          rearrangement_timer);
+        dp_algorithm_timer.stop();
 
         if (config.output_verbose_statistics)
         {
@@ -98,6 +111,20 @@ int execute(chopper::configuration & config, std::vector<std::string> const & fi
     config.write_to(fout);
     hibf_layout.write_to(fout);
 
+    if (!config.output_timings.empty())
+    {
+        std::ofstream output_stream{config.output_timings};
+        output_stream << std::fixed << std::setprecision(2);
+        output_stream << "sketching_in_seconds\t"
+                      << "layouting_in_seconds\t"
+                      << "union_estimation_in_seconds\t"
+                      << "rearrangement_in_seconds\n";
+        output_stream << compute_sketches_timer.in_seconds() << '\t';
+        output_stream << dp_algorithm_timer.in_seconds() << '\t';
+        output_stream << union_estimation_timer.in_seconds() << '\t';
+        output_stream << rearrangement_timer.in_seconds() << '\t';
+    }
+
     return 0;
 }
 

diff --git a/src/set_up_parser.cpp b/src/set_up_parser.cpp
@@ -78,6 +78,11 @@ void set_up_parser(sharg::parser & parser, configuration & config)
                 "accuracy.",
             .default_message = "k-mer size",
         });
+    parser.add_option(config.output_timings,
+                      sharg::config{.short_id = '\0',
+                                    .long_id = "timing-output",
+                                    .description = "Write time and memory usage to specified file (TSV format). ",
+                                    .default_message = ""});
 
     parser.add_option(
         config.hibf_config.tmax,
+1 −0		.github/workflows/ci_coverage.yml
+0 −3		.gitmodules
+4 −4		include/hibf/build/build_data.hpp
+1 −1		include/hibf/build/insert_into_ibf.hpp
+3 −2		include/hibf/build/update_parent_kmers.hpp
+156 −11		include/hibf/hierarchical_interleaved_bloom_filter.hpp
+36 −189		include/hibf/interleaved_bloom_filter.hpp
+10 −0		include/hibf/layout/compute_layout.hpp
+7 −0		include/hibf/layout/data_store.hpp
+2 −0		include/hibf/layout/layout.hpp
+968 −0		include/hibf/misc/bit_vector.hpp
+3 −2		include/hibf/misc/print.hpp
+236 −60		include/hibf/misc/timer.hpp
+7 −0		include/hibf/platform.hpp
+2 −1		src/build/compute_kmers.cpp
+2 −1		src/build/construct_ibf.cpp
+5 −4		src/build/insert_into_ibf.cpp
+24 −2		src/hierarchical_interleaved_bloom_filter.cpp
+70 −92		src/interleaved_bloom_filter.cpp
+1 −0		src/layout/compute_fpr_correction.cpp
+16 −1		src/layout/compute_layout.cpp
+10 −0		src/layout/hierarchical_binning.cpp
+3 −2		src/misc/print.cpp
+0 −1		submodules/sdsl-lite
+1 −1		test/documentation/hibf_doxygen_cfg.in
+1 −1		test/header/CMakeLists.txt
+69 −0		test/include/hibf/test/cereal.hpp
+784 −0		test/include/hibf/test/iterator_test_template.hpp
+1 −1		test/iwyu/CMakeLists.txt
+1 −1		test/performance/ibf/CMakeLists.txt
+0 −151		test/performance/ibf/binning_bitvector_benchmark.cpp
+140 −0		test/performance/ibf/bit_vector_benchmark.cpp
+4 −0		test/performance/ibf/interleaved_bloom_filter_benchmark.cpp
+2 −0		test/unit/hibf/CMakeLists.txt
+802 −0		test/unit/hibf/bit_vector_test.cpp
+102 −79		test/unit/hibf/hierarchical_interleaved_bloom_filter_test.cpp
+139 −186		test/unit/hibf/interleaved_bloom_filter_test.cpp
+1 −0		test/unit/hibf/layout/CMakeLists.txt
+39 −0		test/unit/hibf/layout/compute_layout_test.cpp
+5 −4		test/unit/hibf/print_test.cpp
+125 −0		test/unit/hibf/timer_test.cpp