Align update of nextSIM-DG and XIOS calendars

.github/workflows/test_suite.yml

@@ -50,9 +50,43 @@ jobs:
         cd test
         python3 ThermoIntegration_test.py
         ./run_test_jan2010_integration_test.sh python3
-        cd -
 
-  test-ubuntu-mpi:
+  test-ubuntu-mpi-noxios:
+
+    runs-on: ubuntu-22.04
+    container:
+      image: ghcr.io/nextsimhub/nextsimdg-dev-env:latest
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: build and compile with MPI but not XIOS
+      run: |
+        . /opt/spack-environment/activate.sh
+        mkdir -p build && cd build
+        cmake -DENABLE_MPI=ON -DENABLE_XIOS=OFF -DCMAKE_CXX_COMPILER="$(which mpic++)" ..
+        make -j 4
+
+    - name: run MPI tests
+      run: |
+        . /opt/spack-environment/activate.sh
+        apt update
+        apt install -y wget
+        cd build
+        (cd core/test && wget "ftp://ftp.nersc.no/nextsim/netCDF/partition_metadata_1.nc")
+        for component in core physics dynamics
+        do
+            cd $component/test
+            for file in $(find test* -maxdepth 0 -type f)
+            do
+              echo $file
+              nprocs=$(echo $file | sed -r "s/.*MPI([0-9]+)/\1/")
+              mpirun --allow-run-as-root --oversubscribe -n $nprocs ./$file
+            done
+            cd -
+        done
+
+  test-ubuntu-mpi-xios:
 
     runs-on: ubuntu-22.04
     container:
@@ -86,7 +120,6 @@ jobs:
             done
             cd -
         done
-        cd -
 
   test-mac-serial:
 
@@ -138,4 +171,3 @@ jobs:
         cd test
         python ThermoIntegration_test.py
         ./run_test_jan2010_integration_test.sh python
-        cd -

Dockerfiles/install-xios.sh

@@ -69,7 +69,12 @@ cat <<EOF >arch/arch-GCC_LINUX.fcm
 %MAKE           gmake
 EOF
 
-./make_xios --arch GCC_LINUX --job 8 --full --debug
+# Hack to remove a line that stops calendar attributes being accessed after the
+# context definition has been closed.
+# This should be fixed when we update to XIOS3 (see #761).
+sed -i "s/if (hasClient) CleanTree/\/\/if (hasClient) CleanTree/" src/node/context.cpp
+
+./make_xios --arch GCC_LINUX --job 8 --debug
 rm -r /xios/obj /xios/bin/generic_testcase.exe /xios/src /xios/tools \
   /xios/inputs /xios/doc /xios/arch /xios/xios_test_suite /xios/flags \
   /xios/generic_testcase /xios/ppsrc /xios/done

core/src/CMakeLists.txt

@@ -1,5 +1,14 @@
 # Sources for the main neXtSIM model
 
+if(ENABLE_XIOS)
+    set(XIOS_INCLUDE_LIST
+        "${xios_INCLUDES}"
+        "${xios_EXTERNS}/blitz/"
+        "${xios_EXTERNS}/rapidxml/include"
+    )
+    set(NextsimIncludeDirs "${NextsimIncludeDirs}" "${XIOS_INCLUDE_LIST}")
+endif()
+
 set(BaseSources
     "Logged.cpp"
     "ModelConfig.cpp"

core/src/ModelMetadata.cpp

@@ -1,7 +1,7 @@
 /*!
  * @file ModelMetadata.cpp
  *
- * @date 21 August 2024
+ * @date 10 Dec 2024
  * @author Tim Spain <[email protected]>
  */
 
@@ -103,4 +103,28 @@ ModelState& ModelMetadata::affixCoordinates(ModelState& state) const
     }
     return state;
 }
+
+void ModelMetadata::setTime(const TimePoint& time)
+{
+    m_time = time;
+#ifdef USE_XIOS
+    if (!xiosHandler->isInitialized()) {
+        throw std::runtime_error("ModelMetadata: Xios handler has not been initialized");
+    }
+    xiosHandler->setCalendarStep(0);
+    xiosHandler->setCalendarStart(time);
+#endif
+}
+
+void ModelMetadata::incrementTime(const Duration& step)
+{
+    m_time += step;
+#ifdef USE_XIOS
+    if (!xiosHandler->isInitialized()) {
+        throw std::runtime_error("ModelMetadata: Xios handler has not been initialized");
+    }
+    xiosHandler->incrementCalendar();
+#endif
+}
+
 } /* namespace Nextsim */

core/src/ParaGridIO.cpp

@@ -1,7 +1,7 @@
 /*!
  * @file ParaGridIO.cpp
  *
- * @date Oct 24, 2022
+ * @date 09 Dec 2024
  * @author Tim Spain <[email protected]>
  */
 
@@ -227,7 +227,7 @@ ModelState ParaGridIO::readForcingTimeStatic(
         std::vector<double> timeVec(timeDim.getSize());
         timeVar.getVar(timeVec.data());
         // Get the index of the largest TimePoint less than the target.
-        targetTIndex = std::find_if(begin(timeVec), end(timeVec), [time](double t) {
+        targetTIndex = std::find_if(std::begin(timeVec), std::end(timeVec), [time](double t) {
             return (TimePoint() + Duration(t)) > time;
         }) - timeVec.begin();
         // Rather than the first that is greater than, get the last that is less

core/src/Xios.cpp

@@ -2,7 +2,7 @@
  * @file    Xios.cpp
  * @author  Tom Meltzer <[email protected]>
  * @author  Joe Wallwork <[email protected]>
- * @date    09 Dec 2024
+ * @date    10 Dec 2024
  * @brief   XIOS interface implementation
  * @details
  *
@@ -37,7 +37,6 @@ static const std::map<int, std::string> keyMap = { { Xios::ENABLED_KEY, "xios.en
 //! Enable XIOS in the 'config'
 void enableXios()
 {
-    Configurator::clearStreams();
     std::stringstream config;
     config << "[xios]" << std::endl << "enable = true" << std::endl;
     std::unique_ptr<std::istream> pcstream(new std::stringstream(config.str()));
@@ -271,6 +270,18 @@ void Xios::setCalendarTimestep(const Duration timestep)
     cxios_update_calendar_timestep(clientCalendar);
 }
 
+/*!
+ * Update XIOS calendar iteration/step number to some value
+ *
+ * @param Step number to update to
+ */
+void Xios::setCalendarStep(const int stepNumber) { cxios_update_calendar(stepNumber); }
+
+/*!
+ * Increment XIOS' calendar iteration/step number by one.
+ */
+void Xios::incrementCalendar() { setCalendarStep(getCalendarStep() + 1); }
+
 /*!
  * Get calendar type
  *
@@ -347,13 +358,6 @@ std::string Xios::getCurrentDate(const bool isoFormat)
     return convertXiosDatetimeToString(xiosDate, isoFormat);
 }
 
-/*!
- * Update XIOS calendar iteration/step number
- *
- * @param current step number
- */
-void Xios::updateCalendar(const int stepNumber) { cxios_update_calendar(stepNumber); }
-
 /*!
  * Get the axis_definition group
  *

core/src/include/ModelMetadata.hpp

@@ -1,7 +1,7 @@
 /*!
  * @file ModelMetadata.hpp
  *
- * @date Jun 29, 2022
+ * @date 09 Dec 2024
  * @author Tim Spain <[email protected]>
  */
 
@@ -12,6 +12,9 @@
 #include "include/ModelArray.hpp"
 #include "include/ModelState.hpp"
 #include "include/Time.hpp"
+#ifdef USE_XIOS
+#include "include/Xios.hpp"
+#endif
 
 #include <string>
 
@@ -47,13 +50,13 @@ class ModelMetadata {
      *
      * @param time TimePoint instance encoding the current time.
      */
-    inline void setTime(const TimePoint& time) { m_time = time; }
+    void setTime(const TimePoint& time);
     /*!
      * @brief Increments the model time metadata value.
      *
      * @param step Duration of the time increment to add.
      */
-    inline void incrementTime(const Duration& step) { m_time += step; }
+    void incrementTime(const Duration& step);
     //! Returns the current model time.
     inline const TimePoint& time() const { return m_time; }
 
@@ -99,6 +102,15 @@ class ModelMetadata {
     int localCornerX, localCornerY, localExtentX, localExtentY, globalExtentX, globalExtentY;
 #endif
 
+#ifdef USE_XIOS
+    /*
+     * @brief Set pointer to Xios handler instance.
+     *
+     * @param xiosPtr Pointer to set
+     */
+    inline void setXiosHandler(Xios* xiosPtr) { xiosHandler = xiosPtr; }
+#endif
+
 private:
     TimePoint m_time;
     ConfigMap m_config;
@@ -117,6 +129,9 @@ class ModelMetadata {
 #ifdef USE_MPI
     const std::string bboxName = "bounding_boxes";
 #endif
+#ifdef USE_XIOS
+    Xios* xiosHandler = nullptr;
+#endif
 };
 
 } /* namespace Nextsim */

core/src/include/Xios.hpp

@@ -2,7 +2,7 @@
  * @file    Xios.hpp
  * @author  Tom Meltzer <[email protected]>
  * @author  Joe Wallwork <[email protected]>
- * @date    04 Dec 2024
+ * @date    10 Dec 2024
  * @brief   XIOS interface header
  * @details
  *
@@ -55,13 +55,14 @@ class Xios : public Configured<Xios> {
     void setCalendarOrigin(const TimePoint origin);
     void setCalendarStart(const TimePoint start);
     void setCalendarTimestep(const Duration timestep);
+    void setCalendarStep(const int stepNumber);
+    void incrementCalendar();
     std::string getCalendarType();
     TimePoint getCalendarOrigin();
     TimePoint getCalendarStart();
     Duration getCalendarTimestep();
     int getCalendarStep();
     std::string getCurrentDate(const bool isoFormat = true);
-    void updateCalendar(const int stepNumber);
 
     /* Axis */
     void createAxis(const std::string axisId);