SciCompMod · reneSchm · Apr 17, 2026 · Apr 17, 2026 · Apr 17, 2026 · Apr 17, 2026
diff --git a/.github/actions/sbml-test/action.yaml b/.github/actions/sbml-test/action.yaml
@@ -38,7 +38,7 @@ runs:
       shell: bash
       run: |
         cd cpp/build
-        cmake -DCMAKE_BUILD_TYPE=Release -DMEMILIO_ENABLE_SBML=ON -Dsbml_DIR=/usr/lib/x86_64-linux-gnu/cmake ..
+        cmake -DCMAKE_BUILD_TYPE=Release -DMEMILIO_BUILD_TESTS=OFF -DMEMILIO_ENABLE_SBML=ON -Dsbml_DIR=/usr/lib/x86_64-linux-gnu/cmake ..
         cmake --build . -j 4
     - name: Run SBML importer
       shell: bash
@@ -49,5 +49,5 @@ runs:
       shell: bash
       run: |
         cd cpp/build
-        cmake -DCMAKE_BUILD_TYPE=Release -DMEMILIO_ENABLE_SBML=ON -Dsbml_DIR=/usr/lib/x86_64-linux-gnu/cmake ..
+        cmake -DCMAKE_BUILD_TYPE=Release -DMEMILIO_BUILD_TESTS=OFF -DMEMILIO_ENABLE_SBML=ON -Dsbml_DIR=/usr/lib/x86_64-linux-gnu/cmake ..
         cmake --build . -j 4
diff --git a/cpp/CMakeLists.txt b/cpp/CMakeLists.txt
@@ -28,7 +28,21 @@ option(MEMILIO_ENABLE_IPOPT "Enable numerical optimization with Ipopt, requires
 option(MEMILIO_ENABLE_PROFILING "Enable runtime performance profiling of memilio." OFF)
 option(MEMILIO_ENABLE_LIKWID_MARKER "Enable performance measuring with likwid markers." OFF)
 
-mark_as_advanced(MEMILIO_USE_BUNDLED_SPDLOG MEMILIO_SANITIZE_ADDRESS MEMILIO_SANITIZE_UNDEFINED)
+cmake_path(CONVERT "${PROJECT_SOURCE_DIR}/.." TO_CMAKE_PATH_LIST PROJECT_ROOT_NORMALIZED NORMALIZE)
+set(MEMILIO_BASE_DIR "${PROJECT_ROOT_NORMALIZED}" CACHE PATH
+    "Path to the MEmilio project root, used for file I/O. Accessed via mio::base_dir().")
+set(MEMILIO_DATA_DIR "${PROJECT_ROOT_NORMALIZED}/data" CACHE PATH
+    "Path to the MEmilio data directory. Accessed via mio::data_dir().")
+
+mark_as_advanced(
+    MEMILIO_USE_BUNDLED_SPDLOG
+    MEMILIO_SANITIZE_ADDRESS
+    MEMILIO_SANITIZE_UNDEFINED
+    MEMILIO_BUILD_SHARED_LIBS
+    MEMILIO_BUILD_STATIC_LIBS
+    MEMILIO_BASE_DIR
+    MEMILIO_DATA_DIR
+    )
 
 # try to treat AppleClang as Clang, but warn about missing support
 if(CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang")
@@ -76,9 +90,6 @@ set(CMAKE_PDB_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/bin")
 set(CMAKE_RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/bin")
 set(CMAKE_INSTALL_RPATH "${CMAKE_BINARY_DIR}/lib" "${CMAKE_BINARY_DIR}/bin")
 
-# sets MEMILIO_BASE_DIR to the directory containing cpp (i.e., the root of the git repo)
-cmake_path(CONVERT "${PROJECT_SOURCE_DIR}/.." TO_CMAKE_PATH_LIST MEMILIO_BASE_DIR NORMALIZE)
-
 # code coverage analysis
 # Note: this only works under linux and with make
 # Ninja creates different directory names which do not work together with this scrupt

diff --git a/cpp/README.md b/cpp/README.md
@@ -28,7 +28,7 @@ The following table lists the dependencies that are used. Most of them are requi
 
 | Library | Version  | Required | Bundled               | Notes |
 |---------|----------|----------|-----------------------|-------|
-| spdlog  | 1.15.0   | Yes      | Yes (git repo)        | https://github.com/gabime/spdlog |
+| spdlog  | 1.17.0   | Yes      | Yes (git repo)        | https://github.com/gabime/spdlog |
 | Eigen   | 3.4.0    | Yes      | Yes (git repo)        | http://gitlab.com/libeigen/eigen |
 | Boost   | 1.84.0   | Yes      | Yes (git repo)        | https://github.com/boostorg/boost |
 | JsonCpp | 1.9.6    | No       | Yes (git repo)        | https://github.com/open-source-parsers/jsoncpp |

diff --git a/cpp/benchmarks/flow_simulation_ode_secirvvs.cpp b/cpp/benchmarks/flow_simulation_ode_secirvvs.cpp
@@ -21,11 +21,11 @@
 #include "benchmarks/flow_simulation_ode_secirvvs.h"
 #include "memilio/compartments/flow_simulation.h"
 #include "memilio/compartments/simulation.h"
-#include "memilio/utils/base_dir.h"
+#include "memilio/io/directories.h"
 #include "ode_secirvvs/model.h"
 #include <string>
 
-const std::string config_path = mio::base_dir() + "cpp/benchmarks/simulation.config";
+const std::string config_path = (mio::base_dir() / "cpp/benchmarks/simulation.config").string();
 
 // simulation without flows (not in Model definition and not calculated by Simulation)
 void flowless_sim(::benchmark::State& state)

diff --git a/cpp/benchmarks/flow_simulation_ode_seir.cpp b/cpp/benchmarks/flow_simulation_ode_seir.cpp
@@ -20,12 +20,12 @@
 #include "benchmarks/simulation.h"
 #include "memilio/compartments/flow_simulation.h"
 #include "memilio/compartments/simulation.h"
-#include "memilio/utils/base_dir.h"
+#include "memilio/io/directories.h"
 #include "ode_seir/model.h"
 
 #include <string>
 
-const std::string config_path = mio::base_dir() + "cpp/benchmarks/simulation.config";
+const std::string config_path = (mio::base_dir() / "cpp/benchmarks/simulation.config").string();
 
 namespace mio
 {

diff --git a/cpp/benchmarks/graph_simulation.cpp b/cpp/benchmarks/graph_simulation.cpp
@@ -22,11 +22,11 @@
 #include "memilio/compartments/simulation.h"
 #include "memilio/math/adapt_rk.h"
 #include "memilio/mobility/metapopulation_mobility_instant.h"
-#include "memilio/utils/base_dir.h"
+#include "memilio/io/directories.h"
 #include "ode_secirvvs/model.h"
 #include <string>
 
-const std::string config_path = mio::base_dir() + "cpp/benchmarks/graph_simulation.config";
+const std::string config_path = (mio::base_dir() / "cpp/benchmarks/graph_simulation.config").string();
 
 mio::osecirvvs::Model<ScalarType> create_model(size_t num_agegroups, const ScalarType tmax)
 {

diff --git a/cpp/benchmarks/integrator_step.cpp b/cpp/benchmarks/integrator_step.cpp
@@ -22,7 +22,7 @@
 
 #include "memilio/math/adapt_rk.h"
 #include "memilio/math/stepper_wrapper.h"
-#include "memilio/utils/base_dir.h"
+#include "memilio/io/directories.h"
 
 template <class Integrator>
 void integrator_step(::benchmark::State& state)
@@ -33,8 +33,8 @@ void integrator_step(::benchmark::State& state)
     // 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(mio::base_dir() + "cpp/benchmarks/integrator_step.config");
+    auto cfg = mio::benchmark::IntegratorStepConfig::initialize(
+        (mio::base_dir() / "cpp/benchmarks/integrator_step.config").string());
     //auto cfg = mio::benchmark::IntegratorStepConfig::initialize();
     auto model = mio::benchmark::model::SecirAgeres(cfg.num_agegroups);
     // set deriv function and integrator

diff --git a/cpp/benchmarks/simulation.cpp b/cpp/benchmarks/simulation.cpp
@@ -22,15 +22,16 @@
 
 #include "memilio/math/adapt_rk.h"
 #include "memilio/math/stepper_wrapper.h"
-#include "memilio/utils/base_dir.h"
+#include "memilio/io/directories.h"
 
 template <class Integrator>
 void simulation(::benchmark::State& state)
 {
     // suppress non-critical messages
     mio::set_log_level(mio::LogLevel::critical);
     // setup benchmark parameters
-    auto cfg = mio::benchmark::SimulationConfig::initialize(mio::base_dir() + "cpp/benchmarks/simulation.config");
+    auto cfg =
+        mio::benchmark::SimulationConfig::initialize((mio::base_dir() / "cpp/benchmarks/simulation.config").string());
     //auto cfg = mio::benchmark::SimulationConfig::initialize(10);
     auto model = mio::benchmark::model::SecirAgeres(cfg.num_agegroups);
 

diff --git a/cpp/examples/CMakeLists.txt b/cpp/examples/CMakeLists.txt
@@ -1,7 +1,3 @@
-# configure directory that contains the data files used by examples
-file(TO_CMAKE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/../../data" MEMILIO_DATA_DIR)
-configure_file(data_dir.h.in data_dir.h)
-
 add_executable(euler_example euler_test.cpp)
 target_link_libraries(euler_example PRIVATE memilio)
 target_compile_options(euler_example PRIVATE ${MEMILIO_CXX_FLAGS_ENABLE_WARNING_ERRORS})
@@ -18,17 +14,17 @@ add_executable(adapt_rk_example adapt_rk_test.cpp)
 target_link_libraries(adapt_rk_example PRIVATE memilio)
 target_compile_options(adapt_rk_example PRIVATE ${MEMILIO_CXX_FLAGS_ENABLE_WARNING_ERRORS})
 
-add_executable(ode_seir_example ode_seir.cpp)
-target_link_libraries(ode_seir_example PRIVATE memilio ode_seir)
-target_compile_options(ode_seir_example PRIVATE ${MEMILIO_CXX_FLAGS_ENABLE_WARNING_ERRORS})
-
-add_executable(ode_seirdb_example ode_seirdb.cpp)
-target_link_libraries(ode_seirdb_example PRIVATE memilio ode_seirdb)
-target_compile_options(ode_seirdb_example PRIVATE ${MEMILIO_CXX_FLAGS_ENABLE_WARNING_ERRORS})
-
-add_executable(ode_seir_ageres_example ode_seir_ageres.cpp)
-target_link_libraries(ode_seir_ageres_example PRIVATE memilio ode_seir)
-target_compile_options(ode_seir_ageres_example PRIVATE ${MEMILIO_CXX_FLAGS_ENABLE_WARNING_ERRORS})
+add_executable(ode_seir_example ode_seir.cpp)
+target_link_libraries(ode_seir_example PRIVATE memilio ode_seir)
+target_compile_options(ode_seir_example PRIVATE ${MEMILIO_CXX_FLAGS_ENABLE_WARNING_ERRORS})
+
+add_executable(ode_seirdb_example ode_seirdb.cpp)
+target_link_libraries(ode_seirdb_example PRIVATE memilio ode_seirdb)
+target_compile_options(ode_seirdb_example PRIVATE ${MEMILIO_CXX_FLAGS_ENABLE_WARNING_ERRORS})
+
+add_executable(ode_seir_ageres_example ode_seir_ageres.cpp)
+target_link_libraries(ode_seir_ageres_example PRIVATE memilio ode_seir)
+target_compile_options(ode_seir_ageres_example PRIVATE ${MEMILIO_CXX_FLAGS_ENABLE_WARNING_ERRORS})
 
 add_executable(ode_sir_example ode_sir.cpp)
 target_link_libraries(ode_sir_example PRIVATE memilio ode_sir)

diff --git a/cpp/examples/abm_history_object.cpp b/cpp/examples/abm_history_object.cpp
@@ -22,8 +22,10 @@
 #include "abm/simulation.h"
 #include "abm/model.h"
 #include "abm/location_type.h"
+#include "memilio/io/io.h"
 #include "memilio/utils/abstract_parameter_distribution.h"
 #include "memilio/io/history.h"
+#include "memilio/io/directories.h"
 #include "memilio/utils/parameter_distributions.h"
 
 #include <fstream>
@@ -43,7 +45,8 @@ void write_log_to_file(const T& history)
     auto loc_id      = std::get<1>(logg);
     auto time_points = std::get<0>(logg);
     std::string input;
-    std::ofstream myfile("test_output.txt");
+    std::ofstream myfile(mio::create_directories_or_exit(mio::example_results_dir("abm_history_object")) /
+                         "test_output.txt");
     myfile << "Locations as numbers:\n";
     for (auto&& id : loc_id[0]) {
         myfile << convert_loc_id_to_string(id) << "\n";

diff --git a/cpp/examples/abm_minimal.cpp b/cpp/examples/abm_minimal.cpp
@@ -21,6 +21,7 @@
 #include "abm/lockdown_rules.h"
 #include "abm/model.h"
 #include "abm/common_abm_loggers.h"
+#include "memilio/io/directories.h"
 
 #include <fstream>
 
@@ -165,10 +166,11 @@ int main()
     // The first column is Time. The other columns correspond to the number of people with a certain infection state at this Time:
     // Time = Time in days, S = Susceptible, E = Exposed, I_NS = InfectedNoSymptoms, I_Sy = InfectedSymptoms, I_Sev = InfectedSevere,
     // I_Crit = InfectedCritical, R = Recovered, D = Dead
-    std::ofstream outfile("abm_minimal.txt");
+    auto outpath = mio::create_directories_or_exit(mio::example_results_dir("abm_minimal")) / "history.txt";
+    std::ofstream outfile(outpath);
     std::get<0>(historyTimeSeries.get_log())
         .print_table(outfile, {"S", "E", "I_NS", "I_Sy", "I_Sev", "I_Crit", "R", "D"}, 7, 4);
-    std::cout << "Results written to abm_minimal.txt" << std::endl;
+    std::cout << "Results written to " << outpath << std::endl;
 
     return 0;
 }
diff --git a/cpp/examples/abm_parameter_study.cpp b/cpp/examples/abm_parameter_study.cpp
@@ -27,7 +27,7 @@
 #include "memilio/data/analyze_result.h"
 #include "memilio/io/io.h"
 #include "memilio/io/result_io.h"
-#include "memilio/utils/base_dir.h"
+#include "memilio/io/directories.h"
 #include "memilio/utils/logging.h"
 #include "memilio/utils/miompi.h"
 #include "memilio/utils/random_number_generator.h"
@@ -192,11 +192,7 @@ int main()
     mio::ParameterStudy study(std::move(model), t0, tmax, mio::abm::TimeSpan(0), num_runs);
     study.get_rng() = rng; // use the same RNG as the model
 
-    const std::string result_dir = mio::path_join(mio::base_dir(), "example_results");
-    if (!mio::create_directory(result_dir)) {
-        mio::log_error("Could not create result directory \"{}\".", result_dir);
-        return 1;
-    }
+    const auto result_dir = mio::create_directories_or_exit(mio::example_results_dir("abm_parameter_study"));
 
     // Run the study
     // The first lambda ("create_simulation" argument) sets up the simulation, the second ("process_simulation_result")
@@ -212,17 +208,17 @@ int main()
         },
         [&result_dir](auto&& sim, auto&& run_idx) {
             auto interpolated_result = mio::interpolate_simulation_result(sim.get_result());
-            std::string outpath = mio::path_join(result_dir, "abm_minimal_run_" + std::to_string(run_idx) + ".txt");
+            auto outpath             = result_dir / ("abm_minimal_run_" + std::to_string(run_idx) + ".txt");
             std::ofstream outfile_run(outpath);
             sim.get_result().print_table(outfile_run, {"S", "E", "I_NS", "I_Sy", "I_Sev", "I_Crit", "R", "D"}, 7, 4);
-            std::cout << "Results written to " << outpath << std::endl;
+            std::cout << "Results written to " << outpath.string() << std::endl;
             return std::vector{interpolated_result};
         });
 
     // The study collects all results on the root rank, so we only process the results there
     if (mio::mpi::is_root()) {
         const auto write_percentile = [&](double p) {
-            std::ofstream out(mio::path_join(result_dir, fmt::format("Results_p{:0<4.2}.txt", p)));
+            std::ofstream out(result_dir / fmt::format("Results_p{:0<4.2}.txt", p));
             auto ensemble_percentiles = ensemble_percentile(ensemble_results, p);
             ensemble_percentiles.front().print_table(out, {"S", "E", "I_NS", "I_Sy", "I_Sev", "I_Crit", "R", "D"}, 7,
                                                      4);

diff --git a/cpp/examples/data_dir.h.in b/cpp/examples/data_dir.h.in
diff --git a/cpp/examples/graph_abm.cpp b/cpp/examples/graph_abm.cpp
@@ -47,7 +47,7 @@ struct Logger : mio::LogAlways {
     */
     using Type = std::vector<std::tuple<int, mio::abm::LocationType, mio::abm::LocationId, size_t,
                                         std::map<mio::abm::InfectionState, size_t>>>;
-    static Type log(const mio::abm::Simulation<mio::GraphABModel>& sim)
+    static Type log(const mio::abm::Simulation<mio::abm::GraphABModel>& sim)
     {
         Type location_information{};
         location_information.reserve(size_t(mio::abm::LocationType::Count));
@@ -76,7 +76,7 @@ int main()
     const auto age_group_adults   = mio::AgeGroup(1);
     const auto age_group_seniors  = mio::AgeGroup(2);
 
-    auto model1 = mio::GraphABModel(num_age_groups, 0);
+    auto model1 = mio::abm::GraphABModel(num_age_groups, 0);
 
     //Set infection parameters
     model1.parameters.get<mio::abm::TimeExposedToNoSymptoms>()           = mio::ParameterDistributionConstant(4.);
@@ -134,7 +134,7 @@ int main()
     add_household_group_to_model(model1, single_hh_group_m1);
     add_household_group_to_model(model1, family_hh_group_m1);
 
-    auto model2 = mio::GraphABModel(num_age_groups, 1);
+    auto model2 = mio::abm::GraphABModel(num_age_groups, 1);
 
     //Set infection parameters
     model2.parameters.get<mio::abm::TimeExposedToNoSymptoms>()           = mio::ParameterDistributionConstant(4.);

diff --git a/cpp/examples/ode_mseirs4.cpp b/cpp/examples/ode_mseirs4.cpp
@@ -67,7 +67,7 @@ int main()
     // Compute S1 as residual to match N
     double assigned = 5000.0 + (300.0 + 150.0 + 80.0 + 70.0) + (200.0 + 100.0 + 50.0 + 50.0) +
                       (40000.0 + 30000.0 + 20000.0 + 10000.0) + (100000.0 + 50000.0 + 50000.0);
-    double S1 = N - assigned;
+    double S1       = N - assigned;
     if (S1 < 0)
         S1 = 0;
     model.populations[{mio::Index<mio::omseirs4::InfectionState>(mio::omseirs4::InfectionState::S1)}] = S1;
@@ -80,15 +80,8 @@ int main()
     double dt   = 1.0; // daily output
     auto result = mio::simulate(t0, tmax, dt, model);
 
-    // print header
-    std::cout << "t M S1 S2 S3 S4 E1 E2 E3 E4 I1 I2 I3 I4 R1 R2 R3 R4\n";
-    for (size_t i = 0; i < (size_t)result.get_num_time_points(); ++i) {
-        std::cout << result.get_time(i);
-        const auto& y = result.get_value(i);
-        for (size_t k = 0; k < (size_t)mio::omseirs4::InfectionState::Count; ++k) {
-            std::cout << ' ' << y[(Eigen::Index)k];
-        }
-        std::cout << '\n';
-    }
+    // print results
+    result.print_table(
+        {"M", "S1", "S2", "S3", "S4", "E1", "E2", "E3", "E4", "I1", "I2", "I3", "I4", "R1", "R2", "R3", "R4"}, 10, 2);
     return 0;
 }
diff --git a/cpp/examples/ode_seair_optimization.cpp b/cpp/examples/ode_seair_optimization.cpp
@@ -23,6 +23,8 @@
 
 #include "memilio/ad/ad.h"
 
+#include "memilio/io/directories.h"
+#include "memilio/io/io.h"
 #include "memilio/utils/compiler_diagnostics.h"
 #include "ode_seair/model.h"
 #include "ode_seair/infection_state.h"
@@ -512,18 +514,20 @@ void Seair_NLP::finalize_solution(Ipopt::SolverReturn status, Ipopt::Index n, co
     }
     mio::oseair::Model<FP> model;
 
+    const auto result_dir = mio::create_directories_or_exit(mio::example_results_dir("ode_seair_optimization"));
+
     //open files for parameter output
-    std::ofstream outFileSocialDistancing("SocialDistancing.txt");
-    std::ofstream outFileQuarantined("Quarantined.txt");
-    std::ofstream outFileTestingRate("TestingRate.txt");
+    std::ofstream outFileSocialDistancing(result_dir / "SocialDistancing.txt");
+    std::ofstream outFileQuarantined(result_dir / "Quarantined.txt");
+    std::ofstream outFileTestingRate(result_dir / "TestingRate.txt");
 
     //open files for state output
-    std::ofstream outFileSusceptible("Susceptible.txt");
-    std::ofstream outFileExposed("Exposed.txt");
-    std::ofstream outFileAsymptomatic("Asymptomatic.txt");
-    std::ofstream outFileInfected("Infected.txt");
-    std::ofstream outFileRecovered("Recovered.txt");
-    std::ofstream outFileDead("Dead.txt");
+    std::ofstream outFileSusceptible(result_dir / "Susceptible.txt");
+    std::ofstream outFileExposed(result_dir / "Exposed.txt");
+    std::ofstream outFileAsymptomatic(result_dir / "Asymptomatic.txt");
+    std::ofstream outFileInfected(result_dir / "Infected.txt");
+    std::ofstream outFileRecovered(result_dir / "Recovered.txt");
+    std::ofstream outFileDead(result_dir / "Dead.txt");
 
     set_initial_values(model);
     int gridindex = 0;