829 Optimization of TestingStrategy (#830)

Performance optimization of TestingStrategies
- vector instead of unordered_map for testing schemes): ~25% decrease of run time
- switch of ifs in testing strategy: additional ~8 % decrease of run time
- CustomIndexArray for GoToWork/GoToSchool paramater: no measureable change
- bitset for agegroups in TestingCriteria with fixed number of age groups: ~7% decrease of run time

Co-authored-by: DavidKerkmann <[email protected]>

Author: dabele

cpp/examples/abm_minimal.cpp

@@ -41,9 +41,12 @@ int main()
     world.parameters.get<mio::abm::IncubationPeriod>() = 4.;
 
     // Set the age group the can go to school is AgeGroup(1) (i.e. 5-14)
-    world.parameters.get<mio::abm::AgeGroupGotoSchool>() = {age_group_5_to_14};
+    world.parameters.get<mio::abm::AgeGroupGotoSchool>() = false;
+    world.parameters.get<mio::abm::AgeGroupGotoSchool>()[age_group_5_to_14] = true;
     // Set the age group the can go to work is AgeGroup(2) and AgeGroup(3) (i.e. 15-34 and 35-59)
-    world.parameters.get<mio::abm::AgeGroupGotoWork>() = {age_group_15_to_34, age_group_35_to_59};
+    world.parameters.get<mio::abm::AgeGroupGotoWork>() = false;
+    world.parameters.get<mio::abm::AgeGroupGotoWork>()[age_group_15_to_34] = true;
+    world.parameters.get<mio::abm::AgeGroupGotoWork>()[age_group_35_to_59] = true;
 
     // Check if the parameters satisfy their contraints.
     world.parameters.check_constraints();
@@ -169,4 +172,4 @@ int main()
     std::cout << "Results written to abm_minimal.txt" << std::endl;
 
     return 0;
-}
+}

cpp/models/abm/config.h

@@ -0,0 +1,36 @@
+/*
+* Copyright (C) 2020-2024 MEmilio
+*
+* Authors: Daniel Abele
+*
+* 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 MIO_ABM_CONFIG_H
+#define MIO_ABM_CONFIG_H
+
+namespace mio
+{
+namespace abm
+{
+
+/**
+ * Maximum number of age groups allowed in the model.
+ */
+const constexpr int MAX_NUM_AGE_GROUPS = 64;
+
+}
+} // namespace mio
+
+#endif

cpp/models/abm/migration_rules.cpp

@@ -56,7 +56,7 @@ LocationType go_to_school(Person::RandomNumberGenerator& /*rng*/, const Person&
     if (current_loc == LocationType::Home && t < params.get<LockdownDate>() && t.day_of_week() < 5 &&
         person.get_go_to_school_time(params) >= t.time_since_midnight() &&
         person.get_go_to_school_time(params) < t.time_since_midnight() + dt &&
-        params.get<mio::abm::AgeGroupGotoSchool>().count(person.get_age()) && person.goes_to_school(t, params) &&
+        params.get<mio::abm::AgeGroupGotoSchool>()[person.get_age()] && person.goes_to_school(t, params) &&
         !person.is_in_quarantine()) {
         return LocationType::School;
     }
@@ -73,7 +73,7 @@ LocationType go_to_work(Person::RandomNumberGenerator& /*rng*/, const Person& pe
     auto current_loc = person.get_location().get_type();
 
     if (current_loc == LocationType::Home && t < params.get<LockdownDate>() &&
-        params.get<mio::abm::AgeGroupGotoWork>().count(person.get_age()) && t.day_of_week() < 5 &&
+        params.get<mio::abm::AgeGroupGotoWork>()[person.get_age()] && t.day_of_week() < 5 &&
         t.time_since_midnight() + dt > person.get_go_to_work_time(params) &&
         t.time_since_midnight() <= person.get_go_to_work_time(params) && person.goes_to_work(t, params) &&
         !person.is_in_quarantine()) {

cpp/models/abm/parameters.h

@@ -497,10 +497,12 @@ struct GotoSchoolTimeMaximum {
  * @brief The set of AgeGroups that can go to school.
  */
 struct AgeGroupGotoSchool {
-    using Type = std::set<AgeGroup>;
-    static Type get_default(AgeGroup /*size*/)
+    using Type = CustomIndexArray<bool, AgeGroup>;
+    static Type get_default(AgeGroup num_agegroups)
     {
-        return std::set<AgeGroup>{AgeGroup(1)};
+        auto a = Type(num_agegroups, false);
+        a[AgeGroup(1)] = true;
+        return a;
     }
     static std::string name()
     {
@@ -512,10 +514,13 @@ struct AgeGroupGotoSchool {
  * @brief The set of AgeGroups that can go to work.
  */
 struct AgeGroupGotoWork {
-    using Type = std::set<AgeGroup>;
-    static Type get_default(AgeGroup /*size*/)
+    using Type = CustomIndexArray<bool, AgeGroup>;
+    static Type get_default(AgeGroup num_agegroups)
     {
-        return std::set<AgeGroup>{AgeGroup(2), AgeGroup(3)};
+        auto a = Type(num_agegroups, false);
+        a[AgeGroup(2)] = true;
+        a[AgeGroup(3)] = true;
+        return a;
     }
     static std::string name()
     {

cpp/models/abm/testing_strategy.cpp

@@ -29,7 +29,7 @@ namespace abm
 TestingCriteria::TestingCriteria(const std::vector<AgeGroup>& ages, const std::vector<InfectionState>& infection_states)
 {
     for (auto age : ages) {
-        m_ages.insert(static_cast<size_t>(age));
+        m_ages.set(static_cast<size_t>(age), true);
     }
     for (auto infection_state : infection_states) {
         m_infection_states.set(static_cast<size_t>(infection_state), true);
@@ -43,13 +43,12 @@ bool TestingCriteria::operator==(const TestingCriteria& other) const
 
 void TestingCriteria::add_age_group(const AgeGroup age_group)
 {
-    
-    m_ages.insert(static_cast<size_t>(age_group));
+    m_ages.set(static_cast<size_t>(age_group), true);
 }
 
 void TestingCriteria::remove_age_group(const AgeGroup age_group)
 {
-    m_ages.erase(static_cast<size_t>(age_group));
+    m_ages.set(static_cast<size_t>(age_group), false);
 }
 
 void TestingCriteria::add_infection_state(const InfectionState infection_state)
@@ -65,7 +64,7 @@ void TestingCriteria::remove_infection_state(const InfectionState infection_stat
 bool TestingCriteria::evaluate(const Person& p, TimePoint t) const
 {
     // An empty vector of ages or none bitset of #InfectionStates% means that no condition on the corresponding property is set. 
-    return (m_ages.empty() || m_ages.count(static_cast<size_t>(p.get_age()))) &&
+    return (m_ages.none() || m_ages[static_cast<size_t>(p.get_age())]) &&
            (m_infection_states.none() || m_infection_states[static_cast<size_t>(p.get_infection_state(t))]);
 }
 
@@ -104,9 +103,9 @@ void TestingScheme::update_activity_status(TimePoint t)
 bool TestingScheme::run_scheme(Person::RandomNumberGenerator& rng, Person& person, TimePoint t) const
 {
     if (person.get_time_since_negative_test() > m_minimal_time_since_last_test) {
-        double random = UniformDistribution<double>::get_instance()(rng);
-        if (random < m_probability) {
-            if (m_testing_criteria.evaluate(person, t)) {
+        if (m_testing_criteria.evaluate(person, t)) {
+            double random = UniformDistribution<double>::get_instance()(rng);
+            if (random < m_probability) {
                 return !person.get_tested(rng, t, m_test_type.get_default());
             }
         }
@@ -116,23 +115,45 @@ bool TestingScheme::run_scheme(Person::RandomNumberGenerator& rng, Person& perso
 
 TestingStrategy::TestingStrategy(
     const std::unordered_map<LocationId, std::vector<TestingScheme>>& location_to_schemes_map)
-    : m_location_to_schemes_map(location_to_schemes_map)
+    : m_location_to_schemes_map(location_to_schemes_map.begin(), location_to_schemes_map.end())
 {
 }
 
 void TestingStrategy::add_testing_scheme(const LocationId& loc_id, const TestingScheme& scheme)
 {
-    auto& schemes_vector = m_location_to_schemes_map[loc_id];
-    if (std::find(schemes_vector.begin(), schemes_vector.end(), scheme) == schemes_vector.end()) {
-        schemes_vector.emplace_back(scheme);
+    auto iter_schemes =
+        std::find_if(m_location_to_schemes_map.begin(), m_location_to_schemes_map.end(), [loc_id](auto& p) {
+            return p.first == loc_id;
+        });
+    if (iter_schemes == m_location_to_schemes_map.end()) {
+        //no schemes for this location yet, add a new list with one scheme
+        m_location_to_schemes_map.emplace_back(loc_id, std::vector<TestingScheme>(1, scheme));
+    }
+    else {
+        //add scheme to existing vector if the scheme doesn't exist yet
+        auto& schemes = iter_schemes->second;
+        if (std::find(schemes.begin(), schemes.end(), scheme) == schemes.end()) {
+            schemes.push_back(scheme);
+        }
     }
 }
 
 void TestingStrategy::remove_testing_scheme(const LocationId& loc_id, const TestingScheme& scheme)
 {
-    auto& schemes_vector = m_location_to_schemes_map[loc_id];
-    auto last            = std::remove(schemes_vector.begin(), schemes_vector.end(), scheme);
-    schemes_vector.erase(last, schemes_vector.end());
+    auto iter_schemes =
+        std::find_if(m_location_to_schemes_map.begin(), m_location_to_schemes_map.end(), [loc_id](auto& p) {
+            return p.first == loc_id;
+        });
+    if (iter_schemes != m_location_to_schemes_map.end()) {
+        //remove the scheme from the list
+        auto& schemes_vector = iter_schemes->second;
+        auto last            = std::remove(schemes_vector.begin(), schemes_vector.end(), scheme);
+        schemes_vector.erase(last, schemes_vector.end());
+        //delete the list of schemes for this location if no schemes left
+        if (schemes_vector.empty()) {
+            m_location_to_schemes_map.erase(iter_schemes);
+        }
+    }
 }
 
 void TestingStrategy::update_activity_status(TimePoint t)
@@ -152,16 +173,22 @@ bool TestingStrategy::run_strategy(Person::RandomNumberGenerator& rng, Person& p
         return true;
     }
 
-    // Combine two vectors of schemes at corresponding location and location stype
-    std::vector<TestingScheme>* schemes_vector[] = {
-        &m_location_to_schemes_map[LocationId{location.get_index(), location.get_type()}],
-        &m_location_to_schemes_map[LocationId{INVALID_LOCATION_INDEX, location.get_type()}]};
-
-    for (auto vec_ptr : schemes_vector) {
-        if (!std::all_of(vec_ptr->begin(), vec_ptr->end(), [&rng, &person, t](TestingScheme& ts) {
-                return !ts.is_active() || ts.run_scheme(rng, person, t);
-            })) {
-            return false;
+    //lookup schemes for this specific location as well as the location type
+    //lookup in std::vector instead of std::map should be much faster unless for large numbers of schemes
+    for (auto loc_key : {LocationId{location.get_index(), location.get_type()},
+                         LocationId{INVALID_LOCATION_INDEX, location.get_type()}}) {
+        auto iter_schemes =
+            std::find_if(m_location_to_schemes_map.begin(), m_location_to_schemes_map.end(), [loc_key](auto& p) {
+                return p.first == loc_key;
+            });
+        if (iter_schemes != m_location_to_schemes_map.end()) {
+            //apply all testing schemes that are found
+            auto& schemes = iter_schemes->second;
+            if (!std::all_of(schemes.begin(), schemes.end(), [&rng, &person, t](TestingScheme& ts) {
+                    return !ts.is_active() || ts.run_scheme(rng, person, t);
+                })) {
+                return false;
+            }
         }
     }
     return true;

cpp/models/abm/testing_strategy.h

@@ -20,6 +20,7 @@
 #ifndef EPI_ABM_TESTING_SCHEME_H
 #define EPI_ABM_TESTING_SCHEME_H
 
+#include "abm/config.h"
 #include "abm/parameters.h"
 #include "abm/person.h"
 #include "abm/location.h"
@@ -91,7 +92,7 @@ class TestingCriteria
     bool evaluate(const Person& p, TimePoint t) const;
 
 private:
-    std::unordered_set<size_t> m_ages; ///< Set of #AgeGroup%s that are either allowed or required to be tested.
+    std::bitset<MAX_NUM_AGE_GROUPS> m_ages; ///< Set of #AgeGroup%s that are either allowed or required to be tested.
     std::bitset<(size_t)InfectionState::Count>
         m_infection_states; /**< BitSet of #InfectionState%s that are either allowed or required to
     be tested.*/
@@ -221,7 +222,7 @@ class TestingStrategy
     bool run_strategy(Person::RandomNumberGenerator& rng, Person& person, const Location& location, TimePoint t);
 
 private:
-    std::unordered_map<LocationId, std::vector<TestingScheme>>
+    std::vector<std::pair<LocationId, std::vector<TestingScheme>>>
         m_location_to_schemes_map; ///< Set of schemes that are checked for testing.
 };
 

cpp/models/abm/world.h

@@ -20,6 +20,7 @@
 #ifndef EPI_ABM_WORLD_H
 #define EPI_ABM_WORLD_H
 
+#include "abm/config.h"
 #include "abm/location_type.h"
 #include "abm/parameters.h"
 #include "abm/location.h"
@@ -55,14 +56,15 @@ class World
 
     /**
      * @brief Create a World.
-     * @param[in] num_agegroups The number of AgeGroup%s in the simulated World.
+     * @param[in] num_agegroups The number of AgeGroup%s in the simulated World. Must be less than MAX_NUM_AGE_GROUPS.
      */
     World(size_t num_agegroups)
         : parameters(num_agegroups)
         , m_trip_list()
         , m_use_migration_rules(true)
         , m_cemetery_id(add_location(LocationType::Cemetery))
     {
+        assert(num_agegroups < MAX_NUM_AGE_GROUPS && "MAX_NUM_AGE_GROUPS exceeded.");
     }
 
     /**

cpp/tests/test_abm_lockdown_rules.cpp

@@ -53,9 +53,12 @@ TEST(TestLockdownRules, school_closure)
     p2.set_assigned_location(school);
     mio::abm::Parameters params = mio::abm::Parameters(num_age_groups);
     // Set the age group the can go to school is AgeGroup(1) (i.e. 5-14)
-    params.get<mio::abm::AgeGroupGotoSchool>() = {age_group_5_to_14};
+    params.get<mio::abm::AgeGroupGotoSchool>() = false;
+    params.get<mio::abm::AgeGroupGotoSchool>()[age_group_5_to_14] = true;
     // Set the age group the can go to work is AgeGroup(2) and AgeGroup(3) (i.e. 15-34 or 35-59)
-    params.get<mio::abm::AgeGroupGotoWork>() = {age_group_15_to_34, age_group_35_to_59};
+    params.get<mio::abm::AgeGroupGotoWork>() = false;
+    params.get<mio::abm::AgeGroupGotoWork>()[age_group_15_to_34] = true;
+    params.get<mio::abm::AgeGroupGotoWork>()[age_group_35_to_59] = true;
     mio::abm::set_school_closure(t, 0.7, params);
 
     auto p1_rng = mio::abm::Person::RandomNumberGenerator(rng, p1);
@@ -88,9 +91,12 @@ TEST(TestLockdownRules, school_opening)
     p.set_assigned_location(school);
     mio::abm::Parameters params = mio::abm::Parameters(num_age_groups);
     // Set the age group the can go to school is AgeGroup(1) (i.e. 5-14)
-    params.get<mio::abm::AgeGroupGotoSchool>() = {age_group_5_to_14};
+    params.get<mio::abm::AgeGroupGotoSchool>() = false;
+    params.get<mio::abm::AgeGroupGotoSchool>()[age_group_5_to_14] = true;
     // Set the age group the can go to work is AgeGroup(2) and AgeGroup(3) (i.e. 15-34 or 35-59)
-    params.get<mio::abm::AgeGroupGotoWork>() = {age_group_15_to_34, age_group_35_to_59};
+    params.get<mio::abm::AgeGroupGotoWork>() = false;
+    params.get<mio::abm::AgeGroupGotoWork>()[age_group_15_to_34] = true;
+    params.get<mio::abm::AgeGroupGotoWork>()[age_group_35_to_59] = true;
     mio::abm::set_school_closure(t_closing, 1., params);
     mio::abm::set_school_closure(t_opening, 0., params);
 
@@ -110,9 +116,12 @@ TEST(TestLockdownRules, home_office)
     mio::abm::Parameters params(num_age_groups);
 
     // Set the age group the can go to school is AgeGroup(1) (i.e. 5-14)
-    params.get<mio::abm::AgeGroupGotoSchool>() = {age_group_5_to_14};
+    params.get<mio::abm::AgeGroupGotoSchool>() = false;
+    params.get<mio::abm::AgeGroupGotoSchool>()[age_group_5_to_14] = true;
     // Set the age group the can go to work is AgeGroup(2) and AgeGroup(3) (i.e. 15-34 or 35-59)
-    params.get<mio::abm::AgeGroupGotoWork>() = {age_group_15_to_34, age_group_35_to_59};
+    params.get<mio::abm::AgeGroupGotoWork>() = false;
+    params.get<mio::abm::AgeGroupGotoWork>()[age_group_15_to_34] = true;
+    params.get<mio::abm::AgeGroupGotoWork>()[age_group_35_to_59] = true;
 
     mio::abm::set_home_office(t, 0.4, params);
 
@@ -164,9 +173,12 @@ TEST(TestLockdownRules, no_home_office)
     p.set_assigned_location(work);
     mio::abm::Parameters params = mio::abm::Parameters(num_age_groups);
     // Set the age group the can go to school is AgeGroup(1) (i.e. 5-14)
-    params.get<mio::abm::AgeGroupGotoSchool>() = {age_group_5_to_14};
+    params.get<mio::abm::AgeGroupGotoSchool>() = false;
+    params.get<mio::abm::AgeGroupGotoSchool>()[age_group_5_to_14] = true;
     // Set the age group the can go to work is AgeGroup(2) and AgeGroup(3) (i.e. 15-34 or 35-59)
-    params.get<mio::abm::AgeGroupGotoWork>() = {age_group_15_to_34, age_group_35_to_59};
+    params.get<mio::abm::AgeGroupGotoWork>() = false;
+    params.get<mio::abm::AgeGroupGotoWork>()[age_group_15_to_34] = true;
+    params.get<mio::abm::AgeGroupGotoWork>()[age_group_35_to_59] = true;
 
     mio::abm::set_home_office(t_closing, 0.5, params);
     mio::abm::set_home_office(t_opening, 0., params);