Merge pull request #6 from DamynChipman/develop

Bug fixes to merge into new release

.github/ISSUE_TEMPLATE/bug_report.md

@@ -25,13 +25,6 @@ If applicable, add screenshots to help explain your problem.
 
 **Desktop (please complete the following information):**
  - OS: [e.g. iOS]
- - Browser [e.g. chrome, safari]
- - Version [e.g. 22]
-
-**Smartphone (please complete the following information):**
- - Device: [e.g. iPhone6]
- - OS: [e.g. iOS8.1]
- - Browser [e.g. stock browser, safari]
  - Version [e.g. 22]
 
 **Additional context**

.github/workflows/cmake-multi-platform.yml

@@ -1,64 +1,59 @@
-# This starter workflow is for a CMake project running on multiple platforms. There is a different starter workflow if you just want a single platform.
-# See: https://github.com/actions/starter-workflows/blob/main/ci/cmake-single-platform.yml
 name: CMake on multiple platforms
-
 on:
   push:
     branches: [ "develop" ]
   pull_request:
     branches: [ "develop" ]
-
 jobs:
   build:
     runs-on: ${{ matrix.os }}
-
     strategy:
-      # Set fail-fast to false to ensure that feedback is delivered for all matrix combinations. Consider changing this to true when your workflow is stable.
       fail-fast: false
-
-      # Set up a matrix to run the following 3 configurations:
-      # 1. <Windows, Release, latest MSVC compiler toolchain on the default runner image, default generator>
-      # 2. <Linux, Release, latest GCC compiler toolchain on the default runner image, default generator>
-      # 3. <Linux, Release, latest Clang compiler toolchain on the default runner image, default generator>
-      #
-      # To add more build types (Release, Debug, RelWithDebInfo, etc.) customize the build_type list.
       matrix:
-        os: [macos-latest]
-        build_type: [Debug]
+        os: [macos-latest, ubuntu-latest]
+        build_type: [Release, Debug]
+        mpi: ['mpich', 'openmpi']
         c_compiler: [mpicc]
         cpp_compiler: [mpic++]
         fortran_compiler: [gfortran]
-
+        include:
+          - os: macos-latest
+            mpi_path: /usr/local
+          - os: ubuntu-latest
+            mpi_path: /usr
+            flags: -fno-lto
     steps:
     - uses: actions/checkout@v3
     - uses: mpi4py/setup-mpi@v1
+      with:
+        mpi: ${{ matrix.mpi }}
     - uses: modflowpy/install-gfortran-action@v1
-
     - name: Set reusable strings
-      # Turn repeated input strings (such as the build output directory) into step outputs. These step outputs can be used throughout the workflow file.
       id: strings
       shell: bash
       run: |
         echo "build-output-dir=${{ github.workspace }}/build" >> "$GITHUB_OUTPUT"
-
     - name: Configure CMake
-      # Configure CMake in a 'build' subdirectory. `CMAKE_BUILD_TYPE` is only required if you are using a single-configuration generator such as make.
-      # See https://cmake.org/cmake/help/latest/variable/CMAKE_BUILD_TYPE.html?highlight=cmake_build_type
       run: >
         cmake -B ${{ steps.strings.outputs.build-output-dir }}
         -DCMAKE_CXX_COMPILER=${{ matrix.cpp_compiler }}
+        -DCMAKE_CXX_FLAGS=${{ matrix.flags }}
         -DCMAKE_C_COMPILER=${{ matrix.c_compiler }}
+        -DCMAKE_C_FLAGS=${{ matrix.flags }}
         -DCMAKE_Fortran_COMPILER=${{ matrix.fortran_compiler }}
         -DCMAKE_BUILD_TYPE=${{ matrix.build_type }}
-        -DMPI_PATH=/usr/local
+        -DMPI_PATH=${{ matrix.mpi_path }}
         -S ${{ github.workspace }}
-
     - name: Build
-      # Build your program with the given configuration. Note that --config is needed because the default Windows generator is a multi-config generator (Visual Studio generator).
       run: cmake --build ${{ steps.strings.outputs.build-output-dir }} --config ${{ matrix.build_type }}
-
     - name: Test
       working-directory: ${{ steps.strings.outputs.build-output-dir }}
-      # Execute tests defined by the CMake configuration. Note that --build-config is needed because the default Windows generator is a multi-config generator (Visual Studio generator).
-      # See https://cmake.org/cmake/help/latest/manual/ctest.1.html for more detail
-      run: ctest --build-config ${{ matrix.build_type }}
+      run: ctest --build-config ${{ matrix.build_type }} --rerun-failed --output-on-failure
+    # - name: Run
+    #   working-directory: ${{ steps.strings.outputs.build-output-dir }}/examples/elliptic-single
+    #   run: |
+    #     mpiexec -n 2 elliptic-single
+    # - uses: actions/upload-artifact@v4
+    #   with:
+    #     name: elliptic-mesh
+    #     path: ${{ steps.strings.outputs.build-output-dir }}/examples/elliptic-single/*vtu

src/Patches/FiniteVolume/FiniteVolumeGrid.cpp

@@ -15,41 +15,11 @@ FiniteVolumeGrid::FiniteVolumeGrid(MPI::Communicator comm, int nx, double x_lowe
     ny_(ny),
     y_lower_(y_lower),
     y_upper_(y_upper),
-    dy_((y_upper - y_lower)/ny) {
-
-    //
-    // create();
-    // setFromOptions();
-    // setup();
-
-}
-
-FiniteVolumeGrid::~FiniteVolumeGrid() {
-    // if (dm == PETSC_NULLPTR) {
-    //     DMDestroy(&dm);
-    // }
-}
-
-Petsc::ErrorCode FiniteVolumeGrid::create() {
-    if (dm == PETSC_NULLPTR) {
-        int dof_vertex = 0;
-        int dof_face = 0;
-        int dof_element = 1;
-        int stencil_width = 1;
-        return DMStagCreate2d(this->getComm(), DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, nx_, ny_, PETSC_DECIDE, PETSC_DECIDE, dof_vertex, dof_face, dof_element, DMSTAG_STENCIL_STAR, stencil_width, nullptr, nullptr, &dm);
-    }
-    else {
-        return 0;
-    }
-}
-
-Petsc::ErrorCode FiniteVolumeGrid::setFromOptions() {
-    return DMSetFromOptions(dm);
-}
+    dy_((y_upper - y_lower)/ny)
+        {}
 
-Petsc::ErrorCode FiniteVolumeGrid::setup() {
-    return DMSetUp(dm);
-}
+FiniteVolumeGrid::~FiniteVolumeGrid()
+    {}
 
 double FiniteVolumeGrid::point(DimensionIndex dim, int index) {
     double p = 0;

src/Patches/FiniteVolume/FiniteVolumeGrid.hpp

@@ -3,9 +3,6 @@
 
 #include <string>
 
-#include <petsc.h>
-#include <petscdmda.h>
-
 #include "../../EllipticForestApp.hpp"
 #include "../../MPI.hpp"
 #include "../../PatchGrid.hpp"
@@ -21,11 +18,6 @@ enum DimensionIndex {
     Y = 1
 };
 
-namespace Petsc {
-    using DataManagement = DM;
-    using ErrorCode = PetscErrorCode;
-} // NAMESPACE : Petsc
-
 class FiniteVolumeGrid : public MPI::MPIObject, public PatchGridBase<double> {
 
 protected:
@@ -80,12 +72,6 @@ class FiniteVolumeGrid : public MPI::MPIObject, public PatchGridBase<double> {
 
 public:
 
-    /**
-     * @brief The PETSc data management handle
-     * 
-     */
-    Petsc::DataManagement dm = PETSC_NULLPTR;
-
     /**
      * @brief Construct a new FiniteVolumeGrid object (default)
      * 
@@ -111,27 +97,6 @@ class FiniteVolumeGrid : public MPI::MPIObject, public PatchGridBase<double> {
      */
     ~FiniteVolumeGrid();
 
-    /**
-     * @brief Creates the PETSc components of the grid
-     * 
-     * @return Petsc::ErrorCode 
-     */
-    Petsc::ErrorCode create();
-
-    /**
-     * @brief Sets the PETSc components from options of the grid
-     * 
-     * @return Petsc::ErrorCode 
-     */
-    Petsc::ErrorCode setFromOptions();
-
-    /**
-     * @brief Sets the grid up
-     * 
-     * @return Petsc::ErrorCode 
-     */
-    Petsc::ErrorCode setup();
-
     /**
      * @brief Returns the coordinate of the cell center at `index` for dimension `dim`
      * 

src/QuadNode.hpp

@@ -54,6 +54,12 @@ class Node : public MPI::MPIObject {
 	 */
 	MPI::Communicator node_comm;
 
+	/**
+	 * @brief Flag for if the node communicator has been set
+	 * 
+	 */
+	bool node_comm_set = false;
+
 	/**
 	 * @brief Construct a new Node object (default)
 	 * 
@@ -94,6 +100,12 @@ class Node : public MPI::MPIObject {
 
 	}
 
+	~Node() {
+		if (node_comm_set) {
+			MPI_Comm_free(&node_comm);
+		}
+	}
+
 	/**
 	 * @brief Checks if this node is owned by this rank
 	 * 

src/Quadtree.hpp

@@ -173,6 +173,7 @@ class Quadtree : public MPI::MPIObject {
 					// Additional info for node
 					node->leaf = local_num >= 0;
 					node->node_comm = node_comm;
+					node->node_comm_set = true;
 
 					// Put in map
 					map[path] = node;

src/Vector.hpp

@@ -4,6 +4,7 @@
 #include <iostream>
 #include <iomanip>
 #include <vector>
+#include <algorithm>
 #include <initializer_list>
 #include <string>
 

test/test_matrix.cpp

@@ -52,34 +52,6 @@ TEST(Matrix, range) {
 
 }
 
-TEST(Matrix, get_row_and_col) {
-
-    Matrix<double> m1(3, 4, {
-        1, 2, 3, 4,
-        5, 6, 7, 8,
-        9, 10, 11, 12
-    });
-
-    Vector<double> v1({9, 10, 11, 12});
-
-    Vector<double> v2 = m1.getRow(2);
-    EXPECT_EQ(v2.size(), v1.size());
-
-    for (auto i = 0; i < v2.size(); i++) {
-        EXPECT_EQ(v2[i], v1[i]);
-    }
-
-    Vector<double> v3({2, 6, 10});
-
-    Vector<double> v4 = m1.getCol(1);
-    EXPECT_EQ(v3.size(), v3.size());
-
-    for (auto i = 0; i < v4.size(); i++) {
-        EXPECT_EQ(v3[i], v4[i]);
-    }
-
-}
-
 TEST(Matrix, index_sets) {
 
     Matrix<double> m1(6, 8, {