Introduce static TimePartition struct for Iterator

core/src/Iterator.cpp

@@ -1,5 +1,6 @@
 /*!
  * @author  Tim Spain <timothy.spain@nersc.no>
+ * @author  Joe Wallwork <jw2423@cam.ac.uk>
  */
 
 #include "include/Iterator.hpp"
@@ -10,37 +11,43 @@ namespace Nextsim {
 
 void Iterator::setStartStopStep(TimePoint startTime, TimePoint stopTime, Duration timestep)
 {
-    this->startTime = startTime;
-    this->stopTime = stopTime;
-    this->timestep = timestep;
+    TimePartition& timePartition = Iterator::getTimePartition();
+    timePartition.startTime = startTime;
+    timePartition.stopTime = stopTime;
+    timePartition.timestep = timestep;
 }
 
 TimePoint Iterator::parseAndSet(const std::string& startTimeStr, const std::string& stopTimeStr,
     const std::string& durationStr, const std::string& stepStr)
 {
+    TimePartition& timePartition = Iterator::getTimePartition();
+
     std::stringstream ss(startTimeStr);
-    ss >> startTime;
+    ss >> timePartition.startTime;
     ss = std::stringstream(stepStr);
-    ss >> timestep;
+    ss >> timePartition.timestep;
     if (!durationStr.empty()) {
         ss = std::stringstream(durationStr);
         Duration duration;
         ss >> duration;
-        stopTime = startTime + duration;
+        timePartition.stopTime = timePartition.startTime + duration;
     } else {
         ss = std::stringstream(stopTimeStr);
-        ss >> stopTime;
+        ss >> timePartition.stopTime;
     }
 
-    return startTime;
+    return timePartition.startTime;
 }
 
 void Iterator::run()
 {
-    iterant.start(startTime);
+    TimePartition& timePartition = Iterator::getTimePartition();
+
+    iterant.start(timePartition.startTime);
 
-    for (auto t = startTime; t < stopTime; t += timestep) {
-        TimestepTime tsTime = { t, timestep };
+    for (auto t = timePartition.startTime; t < timePartition.stopTime;
+         t += timePartition.timestep) {
+        TimestepTime tsTime = { t, timePartition.timestep };
         try {
             iterant.iterate(tsTime);
         } catch (const std::exception& e) {
@@ -50,7 +57,7 @@ void Iterator::run()
         }
     }
 
-    iterant.stop(stopTime);
+    iterant.stop(timePartition.stopTime);
 }
 
 } /* namespace Nextsim */

core/src/Model.cpp

@@ -58,11 +58,8 @@ Model::Model()
 
 Model::~Model() { }
 
-void Model::configure()
+void Model::configureTime()
 {
-    // Configure logging
-    Logged::configure();
-
     // Store the start/stop/step configuration directly in ModelConfig before
     // parsing these values to the numerical time values used by the model.
     ModelConfig::startTimeStr
@@ -76,6 +73,14 @@ void Model::configure()
     TimePoint timeNow = iterator.parseAndSet(ModelConfig::startTimeStr, ModelConfig::stopTimeStr,
         ModelConfig::durationStr, ModelConfig::stepStr);
     m_etadata.setTime(timeNow);
+}
+
+void Model::configure()
+{
+    // Configure logging
+    Logged::configure();
+
+    configureTime();
 
     // Configure the missing data value
     MissingData::setValue(

core/src/Xios.cpp

@@ -188,50 +188,21 @@ void Xios::finalize()
 }
 
 /*!
- * Overrides `Configure` method from `Configured`
- *
- * Configure the XIOS server if XIOS is enabled in the settings.
+ * @brief   Overrides `Configure` method from `Configured`
  *
+ * @details Configure the XIOS server if XIOS is enabled in the settings.
  */
 void Xios::configure()
 {
     // Check if XIOS is enabled in the nextSIM-DG configuration
     istringstream(Configured::getConfiguration(keyMap.at(ENABLED_KEY), std::string()))
         >> std::boolalpha >> isEnabled;
 
-    // Extract the start time from the model configuration
-    // TODO: Deduce from Model.iterator rather than duplicating here?
-    std::string startTimeStr;
-    istringstream(Configured::getConfiguration(keyMap.at(STARTTIME_KEY), std::string()))
-        >> startTimeStr;
-    if (startTimeStr.length() == 0) {
-        Logged::warning("Xios: Setting default start: 1970-01-01T00:00:00Z");
-        startTimeStr = "1970-01-01T00:00:00Z";
-    }
-    startTime = TimePoint(startTimeStr);
-
-    // Extract the timestep from the model configuration
-    // TODO: Deduce from Model.iterator rather than duplicating here?
-    std::string timeStepStr;
-    istringstream(Configured::getConfiguration(keyMap.at(TIME_STEP_KEY), std::string()))
-        >> timeStepStr;
-    if (timeStepStr.length() == 0) {
-        Logged::warning("Xios: Setting default time_step: P0-0T01:00:00");
-        timeStepStr = "P0-0T01:00:00";
-    }
-    timestep = Duration(timeStepStr);
-
-    // Extract the stop time from the model configuration
-    // TODO: Deduce from Model.iterator rather than duplicating here?
-    std::string stopTimeStr;
-    istringstream(Configured::getConfiguration(keyMap.at(STOPTIME_KEY), std::string()))
-        >> stopTimeStr;
-    if (stopTimeStr.length() == 0) {
-        Logged::warning("Xios: Setting default stop: start time plus P0-0T01:00:00");
-        stopTime = startTime + timestep;
-    } else {
-        stopTime = TimePoint(stopTimeStr);
-    }
+    // Extract the time partition information from the Iterator class
+    Iterator::TimePartition& timePartition = Iterator::getTimePartition();
+    startTime = timePartition.startTime;
+    timestep = timePartition.timestep;
+    stopTime = timePartition.stopTime;
 
     if (isEnabled) {
         configureServer();

core/src/include/Iterator.hpp

@@ -1,5 +1,6 @@
 /*!
  * @author  Tim Spain <timothy.spain@nersc.no>
+ * @author  Joe Wallwork <jw2423@cam.ac.uk>
  */
 
 #ifndef SRC_INCLUDE_ITERATOR_HPP
@@ -34,7 +35,7 @@ class Iterator {
      * @param stopTime Stop time point.
      * @param timestep Timestep length.
      */
-    void setStartStopStep(TimePoint startTime, TimePoint stopTime, Duration timestep);
+    static void setStartStopStep(TimePoint startTime, TimePoint stopTime, Duration timestep);
     /*!
      * @brief Sets the time parameters as a start time, run length and timestep
      * length.
@@ -57,16 +58,27 @@ class Iterator {
      * @param durationStr string to parse for the model run duration.
      * @param stepStr string to parse for the model time step length.
      */
-    TimePoint parseAndSet(const std::string& startTimeStr, const std::string& stopTimeStr,
+    static TimePoint parseAndSet(const std::string& startTimeStr, const std::string& stopTimeStr,
         const std::string& durationStr, const std::string& stepStr);
     //! Run the Iterant over the specified time period.
     void run();
 
+    // A struct to hold information related to the time partition.
+    struct TimePartition {
+        TimePoint startTime;
+        TimePoint stopTime;
+        Duration timestep;
+    };
+
+    //! Returns a reference to the static TimePartition instance.
+    static TimePartition& getTimePartition()
+    {
+        static TimePartition instance;
+        return instance;
+    }
+
 private:
     Iterant& iterant;
-    TimePoint startTime;
-    TimePoint stopTime;
-    Duration timestep;
 
 public:
     //! A base class for classes that specify what happens during one timestep.

core/src/include/Model.hpp

@@ -31,6 +31,8 @@ class Model : public Configured<Model> {
 #endif
     ~Model(); // Finalize the model. Collect data and so on.
 
+    void configureTime();
+
     void configure() override;
 
     enum {

core/src/include/Xios.hpp

@@ -15,6 +15,7 @@
 #if USE_XIOS
 
 #include "include/Configured.hpp"
+#include "include/Iterator.hpp"
 #include "include/Logged.hpp"
 #include "include/ModelArray.hpp"
 #include "include/ModelConfig.hpp"

core/test/CMakeLists.txt

@@ -83,39 +83,59 @@ if(ENABLE_MPI)
         target_compile_definitions(testXiosCalendar_MPI1 PRIVATE USE_XIOS)
         target_include_directories(
             testXiosCalendar_MPI1
-            PRIVATE "${MODEL_INCLUDE_DIR}" "${XIOS_INCLUDE_LIST}" "${ModulesRoot}/StructureModule"
+            PRIVATE
+                ${PHYSICS_INCLUDE_DIRS}
+                "${MODEL_INCLUDE_DIR}"
+                "${XIOS_INCLUDE_LIST}"
+                "${ModulesRoot}/StructureModule"
         )
         target_link_libraries(testXiosCalendar_MPI1 PRIVATE nextsimlib doctest::doctest)
 
         add_executable(testXiosAxis_MPI3 "XiosAxis_test.cpp" "MainMPI.cpp")
         target_compile_definitions(testXiosAxis_MPI3 PRIVATE USE_XIOS)
         target_include_directories(
             testXiosAxis_MPI3
-            PRIVATE "${MODEL_INCLUDE_DIR}" "${XIOS_INCLUDE_LIST}" "${ModulesRoot}/StructureModule"
+            PRIVATE
+                ${PHYSICS_INCLUDE_DIRS}
+                "${MODEL_INCLUDE_DIR}"
+                "${XIOS_INCLUDE_LIST}"
+                "${ModulesRoot}/StructureModule"
         )
         target_link_libraries(testXiosAxis_MPI3 PRIVATE nextsimlib doctest::doctest)
 
         add_executable(testXiosGrid_MPI2 "XiosGrid_test.cpp" "MainMPI.cpp")
         target_compile_definitions(testXiosGrid_MPI2 PRIVATE USE_XIOS)
         target_include_directories(
             testXiosGrid_MPI2
-            PRIVATE "${MODEL_INCLUDE_DIR}" "${XIOS_INCLUDE_LIST}" "${ModulesRoot}/StructureModule"
+            PRIVATE
+                ${PHYSICS_INCLUDE_DIRS}
+                "${MODEL_INCLUDE_DIR}"
+                "${XIOS_INCLUDE_LIST}"
+                "${ModulesRoot}/StructureModule"
         )
         target_link_libraries(testXiosGrid_MPI2 PRIVATE nextsimlib doctest::doctest)
 
         add_executable(testXiosField_MPI3 "XiosField_test.cpp" "MainMPI.cpp")
         target_compile_definitions(testXiosField_MPI3 PRIVATE USE_XIOS)
         target_include_directories(
             testXiosField_MPI3
-            PRIVATE "${MODEL_INCLUDE_DIR}" "${XIOS_INCLUDE_LIST}" "${ModulesRoot}/StructureModule"
+            PRIVATE
+                ${PHYSICS_INCLUDE_DIRS}
+                "${MODEL_INCLUDE_DIR}"
+                "${XIOS_INCLUDE_LIST}"
+                "${ModulesRoot}/StructureModule"
         )
         target_link_libraries(testXiosField_MPI3 PRIVATE nextsimlib doctest::doctest)
 
         add_executable(testXiosFile_MPI2 "XiosFile_test.cpp" "MainMPI.cpp")
         target_compile_definitions(testXiosFile_MPI2 PRIVATE USE_XIOS)
         target_include_directories(
             testXiosFile_MPI2
-            PRIVATE "${MODEL_INCLUDE_DIR}" "${XIOS_INCLUDE_LIST}" "${ModulesRoot}/StructureModule"
+            PRIVATE
+                ${PHYSICS_INCLUDE_DIRS}
+                "${MODEL_INCLUDE_DIR}"
+                "${XIOS_INCLUDE_LIST}"
+                "${ModulesRoot}/StructureModule"
         )
         target_link_libraries(testXiosFile_MPI2 PRIVATE nextsimlib doctest::doctest)
 
@@ -127,15 +147,23 @@ if(ENABLE_MPI)
         )
         target_include_directories(
             testXiosRead_MPI2
-            PRIVATE "${MODEL_INCLUDE_DIR}" "${XIOS_INCLUDE_LIST}" "${ModulesRoot}/StructureModule"
+            PRIVATE
+                ${PHYSICS_INCLUDE_DIRS}
+                "${MODEL_INCLUDE_DIR}"
+                "${XIOS_INCLUDE_LIST}"
+                "${ModulesRoot}/StructureModule"
         )
         target_link_libraries(testXiosRead_MPI2 PRIVATE nextsimlib doctest::doctest)
 
         add_executable(testXiosWrite_MPI2 "XiosWrite_test.cpp" "MainMPI.cpp")
         target_compile_definitions(testXiosWrite_MPI2 PRIVATE USE_XIOS)
         target_include_directories(
             testXiosWrite_MPI2
-            PRIVATE "${MODEL_INCLUDE_DIR}" "${XIOS_INCLUDE_LIST}" "${ModulesRoot}/StructureModule"
+            PRIVATE
+                ${PHYSICS_INCLUDE_DIRS}
+                "${MODEL_INCLUDE_DIR}"
+                "${XIOS_INCLUDE_LIST}"
+                "${ModulesRoot}/StructureModule"
         )
         target_link_libraries(testXiosWrite_MPI2 PRIVATE nextsimlib doctest::doctest)
 

core/test/Iterator_test.cpp

@@ -52,7 +52,7 @@ TEST_CASE("Count iterator testing")
     Duration overall(dt);
     overall *= nSteps;
     TimePoint stop = start + overall;
-    iterator.setStartStopStep(start, start + overall, dt);
+    Iterator::setStartStopStep(start, start + overall, dt);
     iterator.run();
 
     REQUIRE(dt.seconds() == 1);

core/test/XiosAxis_test.cpp

@@ -12,8 +12,11 @@
 
 #include "StructureModule/include/ParametricGrid.hpp"
 #include "include/Finalizer.hpp"
+#include "include/Model.hpp"
 #include "include/Xios.hpp"
 
+#include <mpi.h>
+
 namespace Nextsim {
 
 /*!
@@ -27,7 +30,19 @@ namespace Nextsim {
  */
 MPI_TEST_CASE("TestXiosAxis", 3)
 {
+    // Enable XIOS in the 'config' and provide parameters to configure it
     enableXios();
+    std::stringstream config;
+    config << "[model]" << std::endl;
+    config << "start = 2023-03-17T17:11:00Z" << std::endl;
+    config << "stop = 2023-03-17T18:11:00Z" << std::endl;
+    config << "time_step = P0-0T01:00:00" << std::endl;
+    std::unique_ptr<std::istream> pcstream(new std::stringstream(config.str()));
+    Configurator::addStream(std::move(pcstream));
+
+    // Create a Model and configure it so that time partition options are parsed
+    Model model(MPI_COMM_WORLD);
+    model.configureTime();
 
     // Get the Xios singleton instance and check it's initialized
     Xios& xiosHandler = Xios::getInstance();

core/test/XiosCalendar_test.cpp

@@ -13,8 +13,11 @@
 #include "StructureModule/include/ParametricGrid.hpp"
 #include "include/Configurator.hpp"
 #include "include/Finalizer.hpp"
+#include "include/Model.hpp"
 #include "include/Xios.hpp"
 
+#include <mpi.h>
+
 namespace Nextsim {
 
 /*!
@@ -33,10 +36,15 @@ MPI_TEST_CASE("TestXiosCalendar", 1)
     std::stringstream config;
     config << "[model]" << std::endl;
     config << "start = 2023-03-17T17:11:00Z" << std::endl;
+    config << "stop = 2023-03-17T18:11:00Z" << std::endl;
     config << "time_step = P0-0T01:00:00" << std::endl;
     std::unique_ptr<std::istream> pcstream(new std::stringstream(config.str()));
     Configurator::addStream(std::move(pcstream));
 
+    // Create a Model and configure it so that time partition options are parsed
+    Model model(MPI_COMM_WORLD);
+    model.configureTime();
+
     // Get the Xios singleton instance and check it's initialized
     Xios& xiosHandler = Xios::getInstance();
     REQUIRE(xiosHandler.isInitialized());