Add comprehensive unit tests for core modules

.github/workflows/c-cpp.yml

@@ -14,6 +14,10 @@ jobs:
       env:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }}
+        OMP_NUM_THREADS: 1
+        OMP_DYNAMIC: FALSE
+        OPENBLAS_NUM_THREADS: 1
+        MKL_NUM_THREADS: 1
 
       steps:
       - uses: actions/checkout@v2
@@ -30,8 +34,6 @@ jobs:
           cd build
           ./unit_tests 
 
-          OMP_NUM_THREADS=1 ./unit_tests -r junit > unit_tests_report.xml
-
       - name: Code coverage
         run: |
-          cpp-coveralls -r . -b "build/" -i "src/" -i "include/" --exclude "ext/" --gcov-options "\-lp" --verbose
+          cpp-coveralls -r . -b "build/" -i "src/" -i "include/" --exclude "ext/" --gcov-options "\-lp" --verbose

CMakeLists.txt

@@ -45,7 +45,7 @@ include_directories( ${LAPACK_INCLUDE_DIR} )
 
 find_package( BLAS )
 
-find_package( VTK COMPONENTS vtkIOGeometry vtkFiltersCore REQUIRED )
+find_package( VTK COMPONENTS IOGeometry FiltersCore REQUIRED )
 
 add_compile_definitions( KITRT_PYTHON_PATH="${CMAKE_SOURCE_DIR}/python" )
 add_compile_definitions( BLAZE_USE_SHARED_MEMORY_PARALLELIZATION=0 )

include/common/mesh.hpp

@@ -133,7 +133,7 @@ class Mesh
      *  @return cell_idxs:   std::vector<unsigned> */
     std::vector<unsigned> GetCellsofBall( const double x, const double y, const double r ) const;
 
-    /*! @brief Returns index of cells contained in the rectangle with specified corner coordinates/*
+    /*! @brief Returns index of cells contained in the rectangle with specified corner coordinates
      *  @return cell_idxs:   std::vector<unsigned> */
     std::vector<unsigned> GetCellsofRectangle( const std::vector<std::vector<double>>& cornercoordinates ) const;
 

include/optimizers/neuralnetworkoptimizer.hpp

@@ -71,15 +71,15 @@ class NeuralNetworkOptimizer : public OptimizerBase
 
     inline ~NeuralNetworkOptimizer();
 
-    inline void Solve( Vector& alpha, const Vector& u, const VectorVector& moments, unsigned idx_cell = 0 ) override{};
+    inline void Solve( Vector&, const Vector&, const VectorVector&, unsigned = 0 ) override{};
 
-    inline void SolveMultiCell( VectorVector& alpha, const VectorVector& u, const VectorVector& moments, Vector& alpha_norms ) override{};
+    inline void SolveMultiCell( VectorVector&, const VectorVector&, const VectorVector&, Vector& ) override{};
 
     /*! @brief Reconstruct the moment sol from the Lagrange multiplier alpha
      *  @param sol moment vector
      *  @param alpha Lagrange multipliers
      *  @param moments Moment basis      */
-    inline void ReconstructMoments( Vector& sol, const Vector& alpha, const VectorVector& moments ) override{};
+    inline void ReconstructMoments( Vector&, const Vector&, const VectorVector& ) override{};
 };
 #endif
 #endif    // MLOPTIMIZER_H

include/solvers/snsolver_hpc.hpp

@@ -158,7 +158,8 @@ class SNSolverHPC
 
     void IterPostprocessing();
 
-    void SetGhostCells(); /*!< @brief Sets vector of ghost cells for
+    /*! @brief Sets vector of ghost cell values according to boundary conditions */
+    void SetGhostCells();
 
     // Helper
     /*! @brief ComputeTimeStep calculates the maximal stable time step using the

src/common/config.cpp

@@ -530,7 +530,7 @@ void Config::SetPostprocessing() {
     _dataDir           = std::filesystem::path( _inputDir ).append( _dataDir ).lexically_normal();
 
     // create directories if they dont exist
-    if( !std::filesystem::exists( _outputDir ) ) std::filesystem::create_directory( _outputDir );
+    if( !std::filesystem::exists( _outputDir ) ) std::filesystem::create_directories( _outputDir );
 
     // init logger
     InitLogger();
@@ -1249,7 +1249,7 @@ void Config::InitLogger() {
 
         // create log dir if not existent
         if( !std::filesystem::exists( _logDir ) ) {
-            std::filesystem::create_directory( _logDir );
+            std::filesystem::create_directories( _logDir );
         }
 
         if( !spdlog::get( "event" ) ) {
@@ -1398,4 +1398,4 @@ template <typename K, typename V> K Config::findKey( const std::map<K, V>& myMap
     }
     // If the value is not found, you can return a default value or throw an exception
     throw std::out_of_range( "Value not found in the map" );
-}
+}

src/common/io.cpp

@@ -51,11 +51,9 @@ void ExportVTK( const std::string fileName,
                 const std::vector<std::vector<std::vector<double>>>& outputFields,
                 const std::vector<std::vector<std::string>>& outputFieldNames,
                 const Mesh* mesh ) {
-    int rank   = 0;
-    int nprocs = 1;
+    int rank = 0;
 #ifdef IMPORT_MPI
     // Initialize MPI
-    MPI_Comm_size( MPI_COMM_WORLD, &nprocs );
     MPI_Comm_rank( MPI_COMM_WORLD, &rank );
 #endif
     if( rank == 0 ) {
@@ -152,7 +150,8 @@ void ExportVTK( const std::string fileName,
 Mesh* LoadSU2MeshFromFile( const Config* settings ) {
     auto log = spdlog::get( "event" );
     // log->info( "| Importing mesh. This may take a while for large meshes." );
-    unsigned dim;
+    unsigned dim = settings->GetDim();
+    bool foundDim = false;
     std::vector<Vector> nodes;
     std::vector<std::vector<unsigned>> cells;
     std::vector<std::pair<BOUNDARY_TYPE, std::vector<unsigned>>> boundaries;
@@ -166,12 +165,16 @@ Mesh* LoadSU2MeshFromFile( const Config* settings ) {
         while( getline( ifs, line ) ) {
             if( line.find( "NDIME", 0 ) != std::string::npos ) {
                 dim = static_cast<unsigned>( TextProcessingToolbox::GetTrailingNumber( line ) );
+                foundDim = true;
                 // if( settings->GetDim() != dim ) {
                 //     log->info( "Warning: Mesh dimension does not coinside with problem dimension! Proceed with caution!" );
                 // }
                 break;
             }
         }
+        if( !foundDim ) {
+            ErrorMessages::Error( "Invalid mesh file detected! Missing NDIME entry.", CURRENT_FUNCTION );
+        }
         ifs.clear();
         ifs.seekg( 0, std::ios::beg );
         while( getline( ifs, line ) ) {
@@ -682,4 +685,4 @@ Matrix createSU2MeshFromImage( std::string imageName, std::string SU2Filename )
 
     return gsImage.transpose();
 }
-*/
+*/

src/common/mesh.cpp

@@ -26,10 +26,8 @@ Mesh::Mesh( const Config* settings,
     else {
         ErrorMessages::Error( "Unsupported mesh dimension!", CURRENT_FUNCTION );
     }
-    int nprocs = 1;
     int rank   = 0;
 #ifdef IMPORT_MPI
-    MPI_Comm_size( MPI_COMM_WORLD, &nprocs );
     MPI_Comm_rank( MPI_COMM_WORLD, &rank );
 #endif
     if( rank == 0 ) {
@@ -93,18 +91,13 @@ Mesh::Mesh( const Config* settings,
 Mesh::~Mesh() {}
 
 void Mesh::ComputeConnectivity() {
-    int nprocs = 1;
     int rank   = 0;
 #ifdef IMPORT_MPI
-    MPI_Comm_size( MPI_COMM_WORLD, &nprocs );
     MPI_Comm_rank( MPI_COMM_WORLD, &rank );
 #endif
 
-    unsigned comm_size = 1;    // No MPI implementation right now
     // determine number/chunk size and indices of cells treated by each mpi thread (deactivated for now)
     unsigned chunkSize    = _numCells;    // std::ceil( static_cast<float>( _numCells ) / static_cast<float>( comm_size ) );
-    unsigned mpiCellStart = 0;            // comm_rank * chunkSize;
-    unsigned mpiCellEnd   = _numCells;    // std::min( ( comm_rank + 1 ) * chunkSize, _numCells );
 
     // 'flat' vectors are a flattened representation of the neighbors numCells<numNodesPerCell> nested vectors; easier for MPI
     // 'part' vectors store information for each single MPI thread

src/datagenerator/datageneratorbase.cpp

@@ -85,8 +85,10 @@ DataGeneratorBase::DataGeneratorBase( Config* settings ) {
 }
 
 DataGeneratorBase::~DataGeneratorBase() {
-    delete _quadrature;
     delete _entropy;
+    delete _optimizer;
+    delete _basisGenerator;
+    delete _quadrature;
 }
 
 DataGeneratorBase* DataGeneratorBase::Create( Config* settings ) {

src/solvers/mnsolver_normalized.cpp

@@ -29,7 +29,7 @@ MNSolverNormalized::MNSolverNormalized( Config* settings ) : MNSolver( settings
     _sol2 = VectorVector( _nCells, Vector( _nSystem, 0.0 ) );
 }
 
-MNSolverNormalized::~MNSolverNormalized() {}
+MNSolverNormalized::~MNSolverNormalized() { delete _optimizer2; }
 
 void MNSolverNormalized::IterPreprocessing( unsigned /*idx_pseudotime*/ ) {
     Vector alpha_norm_per_cell( _nCells, 0 );    // ONLY FOR DEBUGGING! THIS SLOWS DOWN THE CODE

src/solvers/snsolver_hpc.cpp

@@ -38,7 +38,7 @@ SNSolverHPC::SNSolverHPC( Config* settings ) {
     _nq   = static_cast<unsigned long>( quad->GetNq() );
     _nSys = _nq;
 
-    if( _numProcs > _nq ) {
+    if( static_cast<unsigned long>( _numProcs ) > _nq ) {
         ErrorMessages::Error( "The number of processors must be less than or equal to the number of quadrature points.", CURRENT_FUNCTION );
     }
 
@@ -287,7 +287,7 @@ void SNSolverHPC::Solve() {
         DrawPreSolverOutput();
     }
     _curSimTime = 0.0;
-    auto start = std::chrono::high_resolution_clock::now();    // Start timing
+    auto start  = std::chrono::high_resolution_clock::now();    // Start timing
 
     std::chrono::duration<double> duration;
     // Loop over energies (pseudo-time of continuous slowing down approach)
@@ -1487,7 +1487,6 @@ void SNSolverHPC::SetProbingCellsLineGreen() {
         double horizontalLineWidth = std::abs( p1[0] - p2[0] );
 
         double pt_ratio_h = horizontalLineWidth / ( horizontalLineWidth + verticalLineWidth );
-        double pt_ratio_v = verticalLineWidth / ( horizontalLineWidth + verticalLineWidth );
 
         unsigned nHorizontalProbingCells = (unsigned)std::ceil( _nProbingCellsLineGreen / 2 * pt_ratio_h );
         unsigned nVerticalProbingCells   = _nProbingCellsLineGreen / 2 - nHorizontalProbingCells;
@@ -1591,20 +1590,13 @@ void SNSolverHPC::SetProbingCellsLineGreen() {
         }
 
         // Compute the probing cells for each block
-        for( int i = 0; i < _nProbingCellsBlocksGreen; i++ ) {
+        for( unsigned i = 0; i < _nProbingCellsBlocksGreen; i++ ) {
             _probingCellsBlocksGreen.push_back( _mesh->GetCellsofRectangle( block_corners[i] ) );
         }
     }
 }
 
 void SNSolverHPC::ComputeQOIsGreenProbingLine() {
-    double verticalLineWidth   = std::abs( _cornerUpperLeftGreen[1] - _cornerLowerLeftGreen[1] - _thicknessGreen );
-    double horizontalLineWidth = std::abs( _cornerUpperLeftGreen[0] - _cornerUpperRightGreen[0] - _thicknessGreen );
-
-    double dl    = 2 * ( horizontalLineWidth + verticalLineWidth ) / ( (double)_nProbingCellsLineGreen );
-    double area  = dl * _thicknessGreen;
-    double l_max = _nProbingCellsLineGreen * dl;
-
 #pragma omp parallel for
     for( unsigned i = 0; i < _nProbingCellsLineGreen; i++ ) {    // Loop over probing cells
         _absorptionValsLineSegment[i] =
@@ -1694,4 +1686,4 @@ void SNSolverHPC::ComputeCellsPerimeterLattice() {
             }
         }
     }
-}
+}

tests/input/validation_tests/SN_solver_hpc/lattice_hpc_200.cfg

@@ -0,0 +1,45 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%  Lattice Validation SN-HPC           %
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% ---- File specifications ----
+%
+OUTPUT_DIR = ../../../result
+OUTPUT_FILE = lattice_hpc_200
+LOG_DIR = ../../../result/logs
+LOG_FILE = lattice_hpc_200_output
+MESH_FILE = lattice_hpc_200.mesh
+FORCE_CONNECTIVITY_RECOMPUTE = YES
+%
+% ---- Problem specifications ----
+%
+PROBLEM = LATTICE
+SPATIAL_DIM = 2
+SOURCE_MAGNITUDE = 1.0
+%
+% ---- Solver specifications ----
+%
+HPC_SOLVER = YES
+SOLVER = SN_SOLVER
+CFL_NUMBER = 0.5
+TIME_FINAL = 0.5
+RECONS_ORDER = 2
+TIME_INTEGRATION_ORDER = 2
+%
+% ---- Boundary Conditions ----
+%
+BC_NEUMANN = ( void )
+%
+% ---- Quadrature ----
+%
+QUAD_TYPE = GAUSS_LEGENDRE_TENSORIZED_2D
+QUAD_ORDER = 6
+%
+% ----- Output ----
+%
+VOLUME_OUTPUT = (MINIMAL)
+VOLUME_OUTPUT_FREQUENCY = 0
+SCREEN_OUTPUT = (ITER, WALL_TIME, MASS, RMS_FLUX, VTK_OUTPUT, CSV_OUTPUT)
+SCREEN_OUTPUT_FREQUENCY = 1
+HISTORY_OUTPUT = (ITER, SIM_TIME, WALL_TIME, MASS, RMS_FLUX, VTK_OUTPUT, CSV_OUTPUT, CUR_OUTFLOW, TOTAL_OUTFLOW, CUR_OUTFLOW_P1, TOTAL_OUTFLOW_P1, CUR_OUTFLOW_P2, TOTAL_OUTFLOW_P2, MAX_OUTFLOW, CUR_PARTICLE_ABSORPTION, TOTAL_PARTICLE_ABSORPTION, MAX_PARTICLE_ABSORPTION)
+HISTORY_OUTPUT_FREQUENCY = 1