feat(benchmarks): added memory and timing benchmarks
This commit is contained in:
151
benchmarks/Memory/main.cpp
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151
benchmarks/Memory/main.cpp
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@@ -0,0 +1,151 @@
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// ReSharper disable CppUnusedIncludeDirective
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#include <iostream>
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#include <fstream>
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#include <chrono>
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#include <thread>
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#include <format>
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#include <cppad/utility/thread_alloc.hpp> // Required for parallel_setup
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#include "fourdst/logging/logging.h"
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#include "fourdst/atomic/species.h"
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#include "fourdst/composition/utils.h"
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#include "quill/Logger.h"
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#include "quill/Backend.h"
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#include "CLI/CLI.hpp"
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#include <clocale>
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#include "gridfire/gridfire.h"
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#include "fourdst/composition/composition.h"
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#include "gridfire/utils/gf_omp.h"
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#include <atomic>
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#include <new>
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#include <cstdlib>
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static std::atomic<size_t> g_allocated_bytes{0};
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void* operator new(std::size_t size) {
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g_allocated_bytes += size;
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if (void* ptr = std::malloc(size)) {
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return ptr;
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}
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throw std::bad_alloc();
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}
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void operator delete(void* ptr, std::size_t size) {
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g_allocated_bytes -= size;
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std::free(ptr);
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}
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void operator delete(void* ptr) {
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std::free(ptr);
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}
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struct MemoryScopeTracker {
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size_t start_bytes;
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MemoryScopeTracker() : start_bytes(g_allocated_bytes.load()) {}
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size_t bytes_allocated() const {
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return g_allocated_bytes.load() - start_bytes;
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}
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void reset_tracking() {
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start_bytes = 0;
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g_allocated_bytes = 0;
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}
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};
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static std::terminate_handler g_previousHandler = nullptr;
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void quill_terminate_handler();
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gridfire::NetIn init(const double temp, const double rho, const double tMax) {
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std::setlocale(LC_ALL, "");
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g_previousHandler = std::set_terminate(quill_terminate_handler);
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quill::Logger* logger = fourdst::logging::LogManager::getInstance().getLogger("log");
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logger->set_log_level(quill::LogLevel::Info);
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using namespace gridfire;
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const std::vector<double> X = {0.7081145999999999, 2.94e-5, 0.276, 0.003, 0.0011, 9.62e-3, 1.62e-3, 5.16e-4};
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const std::vector<std::string> symbols = {"H-1", "He-3", "He-4", "C-12", "N-14", "O-16", "Ne-20", "Mg-24"};
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const fourdst::composition::Composition composition = fourdst::composition::buildCompositionFromMassFractions(symbols, X);
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NetIn netIn;
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netIn.composition = composition;
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netIn.temperature = temp;
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netIn.density = rho;
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netIn.energy = 0;
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netIn.tMax = tMax;
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netIn.dt0 = 1e-12;
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return netIn;
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}
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void quill_terminate_handler()
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{
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quill::Backend::stop();
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if (g_previousHandler)
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g_previousHandler();
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else
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std::abort();
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}
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int main(int argc, char* argv[]) {
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using namespace gridfire;
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double temp = 1.5e7;
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double rho = 1.6e2;
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double tMax = 3e17;
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std::string output_filename = "gf_mem.csv";
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CLI::App app("GridFire Memory Benchmarks");
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app.add_option("--temperature", temp, "Temperature in degrees")->default_val(std::format("{:5.2E}", temp));
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app.add_option("--density", rho, "Density in Kg")->default_val(std::format("{:5.2E}", rho));
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app.add_option("--tmax", tMax, "Maximum time in seconds")->default_val(std::format("{:5.2E}", tMax));
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app.add_option("--output", output_filename, "Output filename for intermediate results")->default_val("gf_mem.csv");
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CLI11_PARSE(app, argc, argv);
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const NetIn netIn = init(temp, rho, tMax);
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std::unique_ptr<engine::GraphEngine> engine;
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int prev_reactions = 0;
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int prev_species = 0;
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engine = std::make_unique<engine::GraphEngine>(netIn.composition, 1);
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MemoryScopeTracker tracker;
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std::ofstream mem_file(output_filename, std::ios::out);
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mem_file << "depth,species,reactions,engine_memory_bytes,solver_memory_bytes\n";
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for (int depth = 1; depth <= 100; depth++) {
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tracker.reset_tracking();
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engine = std::make_unique<engine::GraphEngine>(netIn.composition, depth);
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auto blob = engine->constructStateBlob();
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size_t engine_usage = tracker.bytes_allocated();
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size_t current_num_species = engine->getNetworkSpecies(*blob).size();
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size_t current_num_reactions = engine->getNetworkReactions(*blob).size();
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if (prev_reactions == current_num_reactions && prev_species == current_num_species) {
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std::println("Found end of useful graph traversal at a depth of {}", depth);
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break;
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}
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tracker.reset_tracking();
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const solver::PointSolver localSolver(*engine);
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solver::PointSolverContext solverCtx(*blob);
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size_t solver_usage = tracker.bytes_allocated();
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mem_file << std::format("{},{},{},{},{}\n", depth, current_num_species, current_num_reactions, engine_usage, solver_usage);
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prev_reactions = current_num_reactions;
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prev_species = current_num_species;
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}
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mem_file.close();
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std::println("Memory benchmarks results written to {}", output_filename);
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}
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5
benchmarks/Memory/meson.build
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5
benchmarks/Memory/meson.build
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@@ -0,0 +1,5 @@
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executable(
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'gf_bench_memory',
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'main.cpp',
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dependencies: [gridfire_dep, cli11_dep],
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)
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@@ -98,7 +98,7 @@ int main() {
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metadata["Compiler"] = "Unknown";
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#endif
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metadata["Threads"] = omp_get_max_threads();
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// metadata["Threads"] = omp_get_max_threads();
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metadata["Runs"] = runs;
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metadata["Temperature"] = temp;
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metadata["Density"] = rho;
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147
benchmarks/Timing/main.cpp
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147
benchmarks/Timing/main.cpp
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@@ -0,0 +1,147 @@
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// ReSharper disable CppUnusedIncludeDirective
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#include <iostream>
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#include <fstream>
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#include <chrono>
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#include <thread>
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#include <format>
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#include "fourdst/logging/logging.h"
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#include "fourdst/atomic/species.h"
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#include "fourdst/composition/utils.h"
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#include "quill/Logger.h"
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#include "quill/Backend.h"
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#include "CLI/CLI.hpp"
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#include <clocale>
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#include "gridfire/gridfire.h"
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#include "fourdst/composition/composition.h"
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#include "gridfire/utils/gf_omp.h"
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#include <atomic>
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#include <new>
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#include <cstdlib>
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static std::terminate_handler g_previousHandler = nullptr;
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void quill_terminate_handler();
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gridfire::NetIn init(const double temp, const double rho, const double tMax) {
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std::setlocale(LC_ALL, "");
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g_previousHandler = std::set_terminate(quill_terminate_handler);
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quill::Logger* logger = fourdst::logging::LogManager::getInstance().getLogger("log");
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logger->set_log_level(quill::LogLevel::Info);
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using namespace gridfire;
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const std::vector<double> X = {0.7081145999999999, 2.94e-5, 0.276, 0.003, 0.0011, 9.62e-3, 1.62e-3, 5.16e-4};
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const std::vector<std::string> symbols = {"H-1", "He-3", "He-4", "C-12", "N-14", "O-16", "Ne-20", "Mg-24"};
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const fourdst::composition::Composition composition = fourdst::composition::buildCompositionFromMassFractions(symbols, X);
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NetIn netIn;
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netIn.composition = composition;
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netIn.temperature = temp;
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netIn.density = rho;
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netIn.energy = 0;
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netIn.tMax = tMax;
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netIn.dt0 = 1e-12;
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return netIn;
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}
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void quill_terminate_handler()
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{
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quill::Backend::stop();
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if (g_previousHandler)
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g_previousHandler();
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else
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std::abort();
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}
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int main(int argc, char* argv[]) {
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using namespace gridfire;
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double temp = 1.5e7;
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double rho = 1.6e2;
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double tMax = 3e17;
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std::string output_filename = "gridfire_timings.csv";
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CLI::App app("GridFire Timeing Benchmarks");
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app.add_option("--temperature", temp, "Temperature in degrees")->default_val(std::format("{:5.2E}", temp));
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app.add_option("--density", rho, "Density in Kg")->default_val(std::format("{:5.2E}", rho));
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app.add_option("--tmax", tMax, "Maximum time in seconds")->default_val(std::format("{:5.2E}", tMax));
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app.add_option("--output", output_filename, "Output filename for intermediate results")->default_val("gridfire_timings.csv");
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CLI11_PARSE(app, argc, argv);
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const NetIn netIn = init(temp, rho, tMax);
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std::unique_ptr<engine::GraphEngine> engine;
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struct TimingInfo {
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double depth;
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int num_reactions;
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int num_species;
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double timing;
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};
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std::vector<TimingInfo> timings;
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int prev_reactions = 0;
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int prev_species = 0;
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engine = std::make_unique<engine::GraphEngine>(netIn.composition, 1);
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for (int depth = 1; depth <= 100; depth++) {
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engine = std::make_unique<engine::GraphEngine>(netIn.composition, depth);
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auto blob = engine->constructStateBlob();
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TimingInfo info;
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info.depth = depth;
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info.num_species = engine->getNetworkSpecies(*blob).size();
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info.num_reactions = engine->getNetworkReactions(*blob).size();
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if (prev_reactions == info.num_reactions && prev_species == info.num_species) {
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std::println("Found end of useful graph traversal at a depth of {}", depth);
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break;
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}
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const solver::PointSolver localSolver(*engine);
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solver::PointSolverContext solverCtx(*blob);
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solverCtx.stdout_logging = true;
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try {
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auto start = std::chrono::high_resolution_clock::now();
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auto result = localSolver.evaluate(solverCtx, netIn, false, false);
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auto end = std::chrono::high_resolution_clock::now();
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double ns = std::chrono::duration<double>(end - start).count();
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info.timing = ns;
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prev_reactions = info.num_reactions;
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prev_species = info.num_species;
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timings.push_back(info);
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} catch (gridfire::exceptions::CVODESolverFailureError& e) {
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continue;
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}
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}
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std::ofstream csvFile(output_filename, std::ios::out);
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csvFile << std::format("# Temperature (K): {}", temp);
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csvFile << std::format("# Density: {}", rho);
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csvFile << std::format("# TMax: {}", tMax);
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csvFile << "depth,reactions,species,time\n";
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for (const auto& [depth, numReactions, numSpecies, ns]: timings) {
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std::string line = std::format("{},{},{},{}\n", depth, numReactions, numSpecies, ns);
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csvFile << line;
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}
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csvFile.close();
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std::println("Timeing Benchmarks results written to {}", output_filename);
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}
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5
benchmarks/Timing/meson.build
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5
benchmarks/Timing/meson.build
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@@ -0,0 +1,5 @@
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executable(
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'gf_bench_timeing',
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'main.cpp',
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dependencies: [gridfire_dep, cli11_dep],
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)
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@@ -1,3 +1,5 @@
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if get_option('build_benchmarks')
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subdir('SingleZoneSolver')
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subdir('Memory')
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subdir('Timing')
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endif
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0
src/include/gridfire/io/generative/mesa.h
Normal file
0
src/include/gridfire/io/generative/mesa.h
Normal file
0
src/lib/io/generative/mesa.cpp
Normal file
0
src/lib/io/generative/mesa.cpp
Normal file
@@ -1,249 +0,0 @@
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// ReSharper disable CppUnusedIncludeDirective
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#include <iostream>
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#include <fstream>
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#include <chrono>
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#include <thread>
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#include <format>
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#include <cppad/utility/thread_alloc.hpp> // Required for parallel_setup
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#include "fourdst/logging/logging.h"
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#include "fourdst/atomic/species.h"
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#include "fourdst/composition/utils.h"
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#include "quill/Logger.h"
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#include "quill/Backend.h"
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#include "CLI/CLI.hpp"
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#include <clocale>
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#include "gridfire/gridfire.h"
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#include "fourdst/composition/composition.h"
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#include "gridfire/utils/gf_omp.h"
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static std::terminate_handler g_previousHandler = nullptr;
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static std::vector<std::pair<double, std::unordered_map<std::string, std::pair<double, double>>>> g_callbackHistory;
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static bool s_wrote_abundance_history = false;
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void quill_terminate_handler();
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gridfire::NetIn init(const double temp, const double rho, const double tMax) {
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std::setlocale(LC_ALL, "");
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g_previousHandler = std::set_terminate(quill_terminate_handler);
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quill::Logger* logger = fourdst::logging::LogManager::getInstance().getLogger("log");
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logger->set_log_level(quill::LogLevel::Info);
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using namespace gridfire;
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const std::vector<double> X = {0.7081145999999999, 2.94e-5, 0.276, 0.003, 0.0011, 9.62e-3, 1.62e-3, 5.16e-4};
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const std::vector<std::string> symbols = {"H-1", "He-3", "He-4", "C-12", "N-14", "O-16", "Ne-20", "Mg-24"};
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const fourdst::composition::Composition composition = fourdst::composition::buildCompositionFromMassFractions(symbols, X);
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NetIn netIn;
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netIn.composition = composition;
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netIn.temperature = temp;
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netIn.density = rho;
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netIn.energy = 0;
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netIn.tMax = tMax;
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netIn.dt0 = 1e-12;
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return netIn;
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}
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void log_results(const gridfire::NetOut& netOut, const gridfire::NetIn& netIn) {
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std::vector<fourdst::atomic::Species> logSpecies = {
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fourdst::atomic::H_1,
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fourdst::atomic::He_3,
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fourdst::atomic::He_4,
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fourdst::atomic::C_12,
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fourdst::atomic::N_14,
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fourdst::atomic::O_16,
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fourdst::atomic::Ne_20,
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fourdst::atomic::Mg_24
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};
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std::vector<double> initial;
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std::vector<double> final;
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std::vector<double> delta;
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std::vector<double> fractional;
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for (const auto& species : logSpecies) {
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double initial_X = netIn.composition.getMassFraction(species);
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double final_X = netOut.composition.getMassFraction(species);
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double delta_X = final_X - initial_X;
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double fractionalChange = (delta_X) / initial_X * 100.0;
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initial.push_back(initial_X);
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final.push_back(final_X);
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delta.push_back(delta_X);
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fractional.push_back(fractionalChange);
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}
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initial.push_back(0.0); // Placeholder for energy
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final.push_back(netOut.energy);
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delta.push_back(netOut.energy);
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fractional.push_back(0.0); // Placeholder for energy
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initial.push_back(0.0);
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final.push_back(netOut.dEps_dT);
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delta.push_back(netOut.dEps_dT);
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fractional.push_back(0.0);
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initial.push_back(0.0);
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final.push_back(netOut.dEps_dRho);
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delta.push_back(netOut.dEps_dRho);
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fractional.push_back(0.0);
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initial.push_back(0.0);
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final.push_back(netOut.specific_neutrino_energy_loss);
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delta.push_back(netOut.specific_neutrino_energy_loss);
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fractional.push_back(0.0);
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initial.push_back(0.0);
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final.push_back(netOut.specific_neutrino_flux);
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delta.push_back(netOut.specific_neutrino_flux);
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fractional.push_back(0.0);
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initial.push_back(netIn.composition.getMeanParticleMass());
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final.push_back(netOut.composition.getMeanParticleMass());
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delta.push_back(final.back() - initial.back());
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fractional.push_back((final.back() - initial.back()) / initial.back() * 100.0);
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std::vector<std::string> rowLabels = [&]() -> std::vector<std::string> {
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std::vector<std::string> labels;
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for (const auto& species : logSpecies) {
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labels.emplace_back(species.name());
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}
|
||||
labels.emplace_back("ε");
|
||||
labels.emplace_back("dε/dT");
|
||||
labels.emplace_back("dε/dρ");
|
||||
labels.emplace_back("Eν");
|
||||
labels.emplace_back("Fν");
|
||||
labels.emplace_back("<μ>");
|
||||
return labels;
|
||||
}();
|
||||
|
||||
|
||||
gridfire::utils::Column<std::string> paramCol("Parameter", rowLabels);
|
||||
gridfire::utils::Column<double> initialCol("Initial", initial);
|
||||
gridfire::utils::Column<double> finalCol ("Final", final);
|
||||
gridfire::utils::Column<double> deltaCol ("δ", delta);
|
||||
gridfire::utils::Column<double> percentCol("% Change", fractional);
|
||||
|
||||
std::vector<std::unique_ptr<gridfire::utils::ColumnBase>> columns;
|
||||
columns.push_back(std::make_unique<gridfire::utils::Column<std::string>>(paramCol));
|
||||
columns.push_back(std::make_unique<gridfire::utils::Column<double>>(initialCol));
|
||||
columns.push_back(std::make_unique<gridfire::utils::Column<double>>(finalCol));
|
||||
columns.push_back(std::make_unique<gridfire::utils::Column<double>>(deltaCol));
|
||||
columns.push_back(std::make_unique<gridfire::utils::Column<double>>(percentCol));
|
||||
|
||||
|
||||
gridfire::utils::print_table("Simulation Results", columns);
|
||||
}
|
||||
|
||||
|
||||
void record_abundance_history_callback(const gridfire::solver::PointSolverTimestepContext& ctx) {
|
||||
s_wrote_abundance_history = true;
|
||||
const auto& engine = ctx.engine;
|
||||
// std::unordered_map<std::string, std::pair<double, double>> abundances;
|
||||
std::vector<double> Y;
|
||||
for (const auto& species : engine.getNetworkSpecies(ctx.state_ctx)) {
|
||||
const size_t sid = engine.getSpeciesIndex(ctx.state_ctx, species);
|
||||
double y = N_VGetArrayPointer(ctx.state)[sid];
|
||||
Y.push_back(y > 0.0 ? y : 0.0); // Regularize tiny negative abundances to zero
|
||||
}
|
||||
|
||||
fourdst::composition::Composition comp(engine.getNetworkSpecies(ctx.state_ctx), Y);
|
||||
|
||||
|
||||
std::unordered_map<std::string, std::pair<double, double>> abundances;
|
||||
for (const auto& sp : comp | std::views::keys) {
|
||||
abundances.emplace(std::string(sp.name()), std::make_pair(sp.mass(), comp.getMolarAbundance(sp)));
|
||||
}
|
||||
g_callbackHistory.emplace_back(ctx.t, abundances);
|
||||
}
|
||||
|
||||
|
||||
void save_callback_data(const std::string_view filename) {
|
||||
std::set<std::string> unique_species;
|
||||
for (const auto &abundances: g_callbackHistory | std::views::values) {
|
||||
for (const auto &species_name: abundances | std::views::keys) {
|
||||
unique_species.insert(species_name);
|
||||
}
|
||||
}
|
||||
std::ofstream csvFile(filename.data(), std::ios::out);
|
||||
csvFile << "t,";
|
||||
|
||||
size_t i = 0;
|
||||
for (const auto& species_name : unique_species) {
|
||||
csvFile << species_name;
|
||||
if (i < unique_species.size() - 1) {
|
||||
csvFile << ",";
|
||||
}
|
||||
i++;
|
||||
}
|
||||
|
||||
csvFile << "\n";
|
||||
|
||||
for (const auto& [time, data] : g_callbackHistory) {
|
||||
csvFile << time << ",";
|
||||
size_t j = 0;
|
||||
for (const auto& species_name : unique_species) {
|
||||
if (!data.contains(species_name)) {
|
||||
csvFile << "0.0";
|
||||
} else {
|
||||
csvFile << data.at(species_name).second;
|
||||
}
|
||||
if (j < unique_species.size() - 1) {
|
||||
csvFile << ",";
|
||||
}
|
||||
++j;
|
||||
}
|
||||
csvFile << "\n";
|
||||
}
|
||||
|
||||
csvFile.close();
|
||||
}
|
||||
|
||||
void log_callback_data(const double temp) {
|
||||
if (s_wrote_abundance_history) {
|
||||
std::cout << "Saving abundance history to abundance_history.csv" << std::endl;
|
||||
save_callback_data("abundance_history_" + std::to_string(temp) + ".csv");
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
void quill_terminate_handler()
|
||||
{
|
||||
log_callback_data(1.5e7);
|
||||
quill::Backend::stop();
|
||||
if (g_previousHandler)
|
||||
g_previousHandler();
|
||||
else
|
||||
std::abort();
|
||||
}
|
||||
|
||||
void callback_main(const gridfire::solver::PointSolverTimestepContext& ctx) {
|
||||
record_abundance_history_callback(ctx);
|
||||
}
|
||||
|
||||
int main() {
|
||||
using namespace gridfire;
|
||||
|
||||
constexpr double temp = 1.5e7;
|
||||
constexpr double rho = 1.6e2;
|
||||
constexpr double tMax = 3e17;
|
||||
|
||||
const NetIn netIn = init(temp, rho, tMax);
|
||||
|
||||
|
||||
auto engine = engine::GraphEngine(netIn.composition, engine::NetworkBuildDepth::Full);
|
||||
auto blob = engine.constructStateBlob();
|
||||
|
||||
const solver::PointSolver localSolver(engine);
|
||||
solver::PointSolverContext solverCtx(*blob);
|
||||
|
||||
auto result = localSolver.evaluate(solverCtx, netIn, false, false);
|
||||
std::cout << result << std::endl;
|
||||
}
|
||||
37
validation/vv/figures.ipynb
Normal file
37
validation/vv/figures.ipynb
Normal file
@@ -0,0 +1,37 @@
|
||||
{
|
||||
"cells": [
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"id": "initial_id",
|
||||
"metadata": {
|
||||
"collapsed": true
|
||||
},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
""
|
||||
]
|
||||
}
|
||||
],
|
||||
"metadata": {
|
||||
"kernelspec": {
|
||||
"display_name": "Python 3",
|
||||
"language": "python",
|
||||
"name": "python3"
|
||||
},
|
||||
"language_info": {
|
||||
"codemirror_mode": {
|
||||
"name": "ipython",
|
||||
"version": 2
|
||||
},
|
||||
"file_extension": ".py",
|
||||
"mimetype": "text/x-python",
|
||||
"name": "python",
|
||||
"nbconvert_exporter": "python",
|
||||
"pygments_lexer": "ipython2",
|
||||
"version": "2.7.6"
|
||||
}
|
||||
},
|
||||
"nbformat": 4,
|
||||
"nbformat_minor": 5
|
||||
}
|
||||
Reference in New Issue
Block a user