Merge branch 'main' into 211-python-dependencies

Author: annette-lutz

cpp/CMakeLists.txt

@@ -6,6 +6,7 @@ option(MEMILIO_BUILD_TESTS "Build memilio unit tests." ON)
 option(MEMILIO_BUILD_EXAMPLES "Build memilio examples." ON)
 option(MEMILIO_BUILD_MODELS "Build memilio models." ON)
 option(MEMILIO_BUILD_SIMULATIONS "Build memilio simulations that were used for scientific articles." ON)
+option(MEMILIO_BUILD_BENCHMARKS "Build memilio benchmarks with google benchmark." OFF)
 option(MEMILIO_USE_BUNDLED_SPDLOG "Use spdlog bundled with epi" ON)
 option(MEMILIO_USE_BUNDLED_EIGEN "Use eigen bundled with epi" ON)
 option(MEMILIO_USE_BUNDLED_BOOST "Use boost bundled with epi (only for epi-io)" ON)
@@ -84,6 +85,9 @@ endif()
 if (MEMILIO_BUILD_SIMULATIONS)
     add_subdirectory(simulations)
 endif()
+if (MEMILIO_BUILD_BENCHMARKS)
+    add_subdirectory(benchmarks)
+endif()
 
 # install
 include(GNUInstallDirs)

cpp/benchmarks/CMakeLists.txt

@@ -0,0 +1,42 @@
+set(BENCHMARK_ENABLE_TESTING OFF CACHE BOOL "Disable benchmark testing" FORCE)
+#set(BENCHMARK_ENABLE_EXCEPTIONS OFF CACHE BOOL "Disable benchmark exceptions" FORCE)
+set(BENCHMARK_ENABLE_INSTALL OFF CACHE BOOL "Don't install benchmark" FORCE)
+set(BENCHMARK_DOWNLOAD_DEPENDENCIES OFF CACHE BOOL "Don't download dependencies" FORCE)
+set(BENCHMARK_ENABLE_GTEST_TESTS OFF CACHE BOOL "Disable Google Test in benchmark" FORCE)
+
+if(CMAKE_VERSION VERSION_LESS 3.11)
+    set(UPDATE_DISCONNECTED_IF_AVAILABLE "UPDATE_DISCONNECTED 1")
+
+    include(DownloadProject)
+    download_project(PROJ        benchmark
+		     GIT_REPOSITORY      https://github.com/google/benchmark.git
+		     GIT_TAG             v1.6.1
+		     UPDATE_DISCONNECTED 1
+		     QUIET
+    )
+
+    # CMake warning suppression will not be needed in version 1.9
+    set(CMAKE_SUPPRESS_DEVELOPER_WARNINGS 1 CACHE BOOL "")
+    add_subdirectory(${benchmark_SOURCE_DIR} ${benchmark_SOURCE_DIR} EXCLUDE_FROM_ALL)
+    unset(CMAKE_SUPPRESS_DEVELOPER_WARNINGS)
+else()
+    include(FetchContent)
+    FetchContent_Declare(benchmark
+        GIT_REPOSITORY      https://github.com/google/benchmark.git
+        GIT_TAG             v1.6.1)
+    FetchContent_GetProperties(benchmark)
+    if(NOT benchmark_POPULATED)
+        FetchContent_Populate(benchmark)
+        set(CMAKE_SUPPRESS_DEVELOPER_WARNINGS 1 CACHE BOOL "")
+        add_subdirectory(${benchmark_SOURCE_DIR} ${benchmark_BINARY_DIR} EXCLUDE_FROM_ALL)
+        unset(CMAKE_SUPPRESS_DEVELOPER_WARNINGS)
+    endif()
+endif()
+
+set_target_properties(benchmark PROPERTIES FOLDER "Extern")
+
+add_executable(simulation_benchmark simulation.cpp)
+target_link_libraries(simulation_benchmark PRIVATE memilio secir benchmark::benchmark)
+
+add_executable(integrator_step_benchmark integrator_step.cpp)
+target_link_libraries(integrator_step_benchmark PRIVATE memilio secir benchmark::benchmark)

cpp/benchmarks/integrator_step.config

@@ -0,0 +1,20 @@
+{
+        "abs_tol" : 1e-10,
+        "dt_init" : 1,
+        "dt_max" : 1.7976931348623157e+308,
+        "dt_min" : 2.2250738585072014e-308,
+        "num_agegroups" : 1,
+        "rel_tol" : 1e-5,
+        "t_init" : 50,
+        "yt" :
+        [
+                6377.873644,
+                35.24915600,
+                30.02961100,
+                182.1458650,
+                66.15305900,
+                79.53062100,
+                3069.383604,
+                159.6344400
+        ]
+}

cpp/benchmarks/integrator_step.cpp

@@ -0,0 +1,66 @@
+/* 
+* Copyright (cfg) 2020-2021 German Aerospace Center (DLR-SC)
+*
+* Authors: Rene Schmieding
+*
+* Contact: Martin J. Kuehn <[email protected]>
+*
+* Licensed under the Apache License, Version 2.0 (the "License");
+* you may not use this file except in compliance with the License.
+* You may obtain a copy of the License at
+*
+*     http://www.apache.org/licenses/LICENSE-2.0
+*
+* Unless required by applicable law or agreed to in writing, software
+* distributed under the License is distributed on an "AS IS" BASIS,
+* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+* See the License for the specific language governing permissions and
+* limitations under the License.
+*/
+#include "benchmarks/integrator_step.h"
+#include "benchmarks/secir_ageres_setups.h"
+
+#include "memilio/math/adapt_rk.h"
+#include "memilio/math/stepper_wrapper.h"
+
+template <class Integrator>
+void integrator_step(::benchmark::State& state)
+{
+    // suppress non-critical messages
+    mio::set_log_level(mio::LogLevel::critical);
+    // NOTE: make sure that yt has sensible values, e.g. by creating a simulation with the chosen model
+    // with "num_agegroups" agegroups, and taking "yt" as the state of the simulation at "t_init"
+    // NOTE: yt must have #agegroups * #compartments entries
+    // benchmark setup
+    auto cfg = mio::benchmark::IntegratorStepConfig::initialize("benchmarks/integrator_step.config");
+    //auto cfg = mio::benchmark::IntegratorStepConfig::initialize();
+    auto model = mio::benchmark::model::SecirAgeres(cfg.num_agegroups);
+    // set deriv function and integrator
+    mio::DerivFunction f = [model](Eigen::Ref<const Eigen::VectorXd> x, double s, Eigen::Ref<Eigen::VectorXd> dxds) {
+        model.eval_right_hand_side(x, x, s, dxds);
+    };
+    auto I = Integrator(cfg.abs_tol, cfg.rel_tol, cfg.dt_min, cfg.dt_max);
+
+    double t, dt;
+    for (auto _ : state) {
+        // This code gets timed
+        t  = cfg.t_init;
+        dt = cfg.dt_init;
+        I.step(f, cfg.yt, t, dt, cfg.ytp1);
+    }
+}
+
+// dummy runs to avoid large effects of cpu scaling on times of actual benchmarks
+BENCHMARK_TEMPLATE(integrator_step, mio::RKIntegratorCore)->Name("Dummy 1/3");
+BENCHMARK_TEMPLATE(integrator_step, mio::RKIntegratorCore)->Name("Dummy 2/3");
+BENCHMARK_TEMPLATE(integrator_step, mio::RKIntegratorCore)->Name("Dummy 3/3");
+// register functions as a benchmarks and set a name
+BENCHMARK_TEMPLATE(integrator_step, mio::RKIntegratorCore)->Name("simulate SecirModel adapt_rk");
+BENCHMARK_TEMPLATE(integrator_step, mio::ControlledStepperWrapper<boost::numeric::odeint::runge_kutta_cash_karp54>)
+    ->Name("simulate SecirModel boost rk_ck54");
+BENCHMARK_TEMPLATE(integrator_step, mio::ControlledStepperWrapper<boost::numeric::odeint::runge_kutta_dopri5>)
+    ->Name("simulate SecirModel boost rk_dopri5");
+BENCHMARK_TEMPLATE(integrator_step, mio::ControlledStepperWrapper<boost::numeric::odeint::runge_kutta_fehlberg78>)
+    ->Name("simulate SecirModel boost rkf78");
+// run all benchmarks
+BENCHMARK_MAIN();

cpp/benchmarks/integrator_step.h

@@ -0,0 +1,107 @@
+/* 
+* Copyright (C) 2020-2021 German Aerospace Center (DLR-SC)
+*
+* Authors: Rene Schmieding
+*
+* Contact: Martin J. Kuehn <[email protected]>
+*
+* Licensed under the Apache License, Version 2.0 (the "License");
+* you may not use this file except in compliance with the License.
+* You may obtain a copy of the License at
+*
+*     http://www.apache.org/licenses/LICENSE-2.0
+*
+* Unless required by applicable law or agreed to in writing, software
+* distributed under the License is distributed on an "AS IS" BASIS,
+* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+* See the License for the specific language governing permissions and
+* limitations under the License.
+*/
+#ifndef INTEGRATOR_STEP_H_
+#define INTEGRATOR_STEP_H_
+
+#include "memilio/io/json_serializer.h"
+#include "memilio/utils/logging.h"
+
+#include "benchmark/benchmark.h"
+
+namespace mio
+{
+namespace benchmark
+{
+    /// @brief parameters for integrator-step benchmark
+    struct IntegratorStepConfig {
+        int num_agegroups;
+        double t_init, dt_init, abs_tol, rel_tol, dt_min, dt_max;
+        Eigen::VectorXd yt, ytp1;
+        /**
+         * @brief creates configuration with default parameters for a secir model
+         * @return configuration for integrator-step benchmark
+         */
+        static IntegratorStepConfig initialize()
+        {
+            const double vals[8] = {6377.873644, 35.249156, 30.029611,   182.145865,
+                                    66.153059,   79.530621, 3069.383604, 159.634440};
+            return IntegratorStepConfig{1,
+                                        50,
+                                        1,
+                                        1e-10,
+                                        1e-5,
+                                        std::numeric_limits<double>::min(),
+                                        std::numeric_limits<double>::max(),
+                                        Eigen::Matrix<double, 8, 1>(vals),
+                                        Eigen::VectorXd::Zero(8)};
+        }
+        /**
+         * @brief reads configuration from json file
+         * @param path the path of the configfile
+         * @return configuration for integrator-step benchmark
+         */
+        static IntegratorStepConfig initialize(std::string path)
+        {
+            auto result = mio::read_json(path, mio::Tag<IntegratorStepConfig>{});
+            if (!result) { // failed to read config
+                mio::log(mio::LogLevel::critical, result.error().formatted_message());
+                abort();
+            }
+            return result.value();
+        }
+        /// @brief function implementing mio::deserialize, used by read_json in initialize
+        template <class IOContext>
+        static mio::IOResult<IntegratorStepConfig> deserialize(IOContext& io)
+        {
+            auto obj              = io.expect_object("integrator_step");
+            auto num_agegroups_io = obj.expect_element("num_agegroups", mio::Tag<int>{});
+            auto t_init_io        = obj.expect_element("t_init", mio::Tag<double>{});
+            auto dt_init_io       = obj.expect_element("dt_init", mio::Tag<double>{});
+            auto abs_tol_io       = obj.expect_element("abs_tol", mio::Tag<double>{});
+            auto rel_tol_io       = obj.expect_element("rel_tol", mio::Tag<double>{});
+            auto dt_min_io        = obj.expect_element("dt_min", mio::Tag<double>{});
+            auto dt_max_io        = obj.expect_element("dt_max", mio::Tag<double>{});
+            auto yt_io            = obj.expect_list("yt", mio::Tag<double>{});
+            return mio::apply(
+                io,
+                [](auto&& num_agegroups, auto&& t_init, auto&& dt_init, auto&& abs_tol, auto&& rel_tol, auto&& dt_min,
+                   auto&& dt_max, auto&& yt) {
+                    IntegratorStepConfig cfg{num_agegroups,
+                                             t_init,
+                                             dt_init,
+                                             abs_tol,
+                                             rel_tol,
+                                             dt_min,
+                                             dt_max,
+                                             Eigen::VectorXd::Zero(yt.size()),
+                                             Eigen::VectorXd::Zero(yt.size())};
+                    for (size_t i = 0; i < yt.size(); i++) {
+                        cfg.yt[i] = yt[i];
+                    }
+                    return cfg;
+                },
+                num_agegroups_io, t_init_io, dt_init_io, abs_tol_io, rel_tol_io, dt_min_io, dt_max_io, yt_io);
+        }
+    };
+} // namespace benchmark
+
+} // namespace mio
+
+#endif