Finished first phase of code refactoring to allow for multiple coarse space in...

Finished first phase of code refactoring to allow for multiple coarse space in domain decomposition methods.

AMDiS/src/parallel/ParallelCoarseSpaceMatVec.cc

@@ -19,32 +19,47 @@ namespace AMDiS {
   using namespace std;
 
   ParallelCoarseSpaceMatVec::ParallelCoarseSpaceMatVec()
-    : rStartInterior(0),
-      nGlobalOverallInterior(0),
+    : interiorMap(NULL),
       lastMeshNnz(0),
-      alwaysCreateNnzStructure(false)
+      alwaysCreateNnzStructure(false),
+      meshDistributor(NULL),
+      subdomainLevel(0),
+      rStartInterior(0),
+      nGlobalOverallInterior(0)
   {
     Parameters::get("parallel->always create nnz structure", 
 		    alwaysCreateNnzStructure);
   }
 
 
-  void ParallelCoarseSpaceMatVec::init(ParallelDofMapping *iMap,
-				       map<int, ParallelDofMapping*> cMap,
-				       int sdLevel,
-				       MPI::Intracomm mcLocal,
-				       MPI::Intracomm mcGlobal,
-				       MeshDistributor *meshDist)
+  void ParallelCoarseSpaceMatVec::setCoarseSpaceDofMapping(ParallelDofMapping *coarseDofs, 
+							   int component)
   {
-    FUNCNAME("ParallelCoarseSpaceMatVec:init()");
-
-    interiorMap = iMap;
-    coarseSpaceMap = cMap;
-    subdomainLevel = sdLevel;
-    mpiCommLocal = mcLocal;
-    mpiCommGlobal = mcGlobal;
-    meshDistributor = meshDist;
-    
+    FUNCNAME("ParallelCoarseSpaceMatVec::setCoarseSpaceDofMapping()");
+
+    TEST_EXIT_DBG(coarseDofs)("Should not happen!\n");
+
+    if (component == -1) {
+      // === Set coarse space for all components. ===
+
+      coarseSpaceMap.clear();
+
+      int nComponents = coarseDofs->getNumberOfComponents();
+      for (int i = 0; i < nComponents; i++)
+	coarseSpaceMap[i] = coarseDofs;
+    } else {
+      // === Set coarse space for just one component. ===
+
+      coarseSpaceMap[component] = coarseDofs;
+    }
+  }
+
+
+  void ParallelCoarseSpaceMatVec::prepare()
+  {
+    FUNCNAME("ParallelCoarseSpaceMatVec:prepare()");
+
+    // === Create vector of unique pointers to all coarse space maps. ===
 
     uniqueCoarseMap.clear();
     if (coarseSpaceMap.size()) {
@@ -58,6 +73,9 @@ namespace AMDiS {
       }
     }
 
+
+    // === Create pointers to PETSc matrix and vector objects. ===
+
     int nCoarseMap = uniqueCoarseMap.size();
     mat.resize(nCoarseMap + 1);
     for (int i = 0; i < nCoarseMap + 1; i++)
@@ -66,6 +84,9 @@ namespace AMDiS {
     vecSol.resize(nCoarseMap + 1);
     vecRhs.resize(nCoarseMap + 1);
 
+    
+    // === Create map from component number to its coarse space map. ===
+
     componentIthCoarseMap.resize(coarseSpaceMap.size());
     for (unsigned int i = 0; i < componentIthCoarseMap.size(); i++) {
       bool found = false;
@@ -82,16 +103,30 @@ namespace AMDiS {
   }
 
 
-  void ParallelCoarseSpaceMatVec::create(Matrix<DOFMatrix*>& seqMat)
+  void ParallelCoarseSpaceMatVec::createMatVec(Matrix<DOFMatrix*>& seqMat)
   {
     FUNCNAME("ParallelCoarseSpaceMatVec::create()");
 
+    // === Prepare coarse space information and generate the correct number ===
+    // === of empty PETSc matrix and vector objects.                        ===
+
+    prepare();
+
+    
+    // === Update subdomain data (mostly required for multi-level methods) ===
+
     updateSubdomainData();
 
+
     // === If required, recompute non zero structure of the matrix. ===
 
     bool localMatrix = (coarseSpaceMap.size() && subdomainLevel == 0);
-    if (checkMeshChange(seqMat, localMatrix)) {
+    if (checkMeshChange()) {
+      // Mesh has been changed, recompute interior DOF mapping.
+      vector<const FiniteElemSpace*> feSpaces = getComponentFeSpaces(seqMat);     
+      interiorMap->setComputeMatIndex(!localMatrix);
+      interiorMap->update(feSpaces);
+
       int nMat = uniqueCoarseMap.size() + 1;
       nnz.resize(nMat);
       for (int i = 0; i < nMat; i++) {
@@ -250,8 +285,7 @@ namespace AMDiS {
   }
 
 
-  bool ParallelCoarseSpaceMatVec::checkMeshChange(Matrix<DOFMatrix*> &seqMat,
-						  bool localMatrix)
+  bool ParallelCoarseSpaceMatVec::checkMeshChange()
   {
     FUNCNAME("ParallelCoarseSpaceMatVec::checkMeshChange()");
 
@@ -261,13 +295,7 @@ namespace AMDiS {
     mpiCommGlobal.Allreduce(&sendValue, &recvAllValues, 1, MPI_INT, MPI_SUM);
 
     if (recvAllValues != 0 || alwaysCreateNnzStructure) {
-      vector<const FiniteElemSpace*> feSpaces = getComponentFeSpaces(seqMat);
-      
-      interiorMap->setComputeMatIndex(!localMatrix);
-      interiorMap->update(feSpaces);
-
       lastMeshNnz = meshDistributor->getLastMeshChangeIndex();
-
       return true;
     }
 

AMDiS/src/parallel/ParallelCoarseSpaceMatVec.h

@@ -42,149 +42,269 @@ namespace AMDiS {
    * - There are different coarse spaces for different components possible. In
    *   this case, there are as many blocks as there are different coarse spaces
    *   plus one block for the interior matrix.
+   * - This class also manages the creation of the corresponding non zero 
+   *   structure of the matrices.
    */
   class ParallelCoarseSpaceMatVec {
   public:
     ParallelCoarseSpaceMatVec();
 
-    /// Creates matrices and vectors with respect to the coarse space.
-    void init(ParallelDofMapping *interiorMap,
-	      map<int, ParallelDofMapping*> coarseSpaceMap,
-	      int subdomainLevel,
-	      MPI::Intracomm mpiCommLocal,
-	      MPI::Intracomm mpiCommGlobal,
-	      MeshDistributor *meshDistributor);
+    /// Set parallel DOF mapping for the interior DOFs.
+    void setDofMapping(ParallelDofMapping *interiorDofs)
+    {
+      interiorMap = interiorDofs;
+    }
     
-    void create(Matrix<DOFMatrix*>& seqMat);
+    /** \brief
+     * Sets the coarse space for all or a specific component.
+     * 
+     * \param[in]  coarseDofs  Coarse space DOF mapping.
+     * \param[in]  component   If the standard value -1 is used, the coarse
+     *                         space DOF mapping is set for all components
+     *                         of the equation. Otherwise, the coarse space
+     *                         DOF mapping is set only for the given one.
+     */
+    void setCoarseSpaceDofMapping(ParallelDofMapping *coarseDofs, 
+				  int component = -1);
+
+    /// Set mesh distributor object and MPI communicators.
+    void setMeshDistributor(MeshDistributor *m,
+			    MPI::Intracomm mpiComm0,
+			    MPI::Intracomm mpiComm1)
+    {
+      meshDistributor = m;
+      mpiCommGlobal = mpiComm0;
+      mpiCommLocal = mpiComm1; 
+    }
+
+    /// Set level of the interior discretization. Is only used for
+    /// multi-level methods.
+    void setLevel(int l) 
+    {
+      subdomainLevel = l;
+    }
+
+    /// Creates matrices and vectors with respect to the coarse space.
+    void createMatVec(Matrix<DOFMatrix*>& seqMat);
 
     /// Run PETSc's matrix assembly routines.
     void matAssembly();
 
-    /// Run PETSc's vector assembly routines.
+    /// Run PETSc's vector assembly routines on rhs vectors.
     void vecRhsAssembly();
 
+    /// Run PETSc's vector assembly routines on solution vectors.
     void vecSolAssembly();
 
+    /// Destroys PETSc matrix objects.
     void matDestroy();
 
+    /// Destroys PETSc vector objects.
     void vecDestroy();
 
-    bool checkMeshChange(Matrix<DOFMatrix*> &mat,
-			 bool localMatrix = false);
-
-    inline Mat& getInteriorMat()
+    /// Get interior matrix.
+    inline Mat& getMatInterior()
     {
       TEST_EXIT_DBG(mat.size() > 0)("No matrix data!\n");
       return mat[0][0];
     }
 
-    inline Mat& getCoarseMat(int coarseSpace0 = 0, int coarseSpace1 = 0)
+    /// Get coarse space matrix.
+    inline Mat& getMatCoarse(int coarseSpace0 = 0, int coarseSpace1 = 0)
     {
       TEST_EXIT_DBG(mat.size() > coarseSpace0 + 1)("No matrix data!\n");
       TEST_EXIT_DBG(mat.size() > coarseSpace1 + 1)("No matrix data!\n");
       return mat[coarseSpace0 + 1][coarseSpace1 + 1];
     }
 
-    inline Mat& getIntCoarseMat(int coarseSpace = 0)
+    /// Get coupling matrix of the interior and some coarse space.
+    inline Mat& getMatInteriorCoarse(int coarseSpace = 0)
     {
       TEST_EXIT_DBG(mat.size() > coarseSpace + 1)("No matrix data!\n");
       return mat[0][coarseSpace + 1];
     }
 
-    inline Mat& getCoarseIntMat(int coarseSpace = 0)
+    /// Get coupling of some coarse space matrix and the interior.
+    inline Mat& getMatCoarseInterior(int coarseSpace = 0)
     {
       TEST_EXIT_DBG(mat.size() > coarseSpace + 1)("No matrix data!\n");
       return mat[coarseSpace + 1][0];
     }
 
-    inline Mat& getCoarseMatComp(int comp)
+    /// Get the coarse space matrix of some system component.
+    inline Mat& getMatCoarseByComponent(int comp)
     {
       int matIndex = componentIthCoarseMap[comp] + 1;
       return mat[matIndex][matIndex];
     }
 
-    inline Mat& getIntCoarseMatComp(int comp)
+    /// Get coupling matrix of the interior and the coarse space of a 
+    /// system component.
+    inline Mat& getMatInteriorCoarseByComponent(int comp)
     {
       int matIndex = componentIthCoarseMap[comp] + 1;
       return mat[0][matIndex];
     }
 
-    inline Mat& getCoarseIntMatComp(int comp)
+    /// Get coupling matrix of the coarse space of a system component and the
+    /// interior matrix.
+    inline Mat& getMatCoarseInteriorByComponent(int comp)
     {
       int matIndex = componentIthCoarseMap[comp] + 1;
       return mat[matIndex][0];
     }
 
-    inline Vec& getInteriorVecRhs()
+    /// Get the RHS vector of the interior.
+    inline Vec& getVecRhsInterior()
     {
       return vecRhs[0];
     }
 
-    inline Vec& getCoarseVecRhs(int coarseSpace = 0)
+    /// Get the RHS vector of some coarse space.
+    inline Vec& getVecRhsCoarse(int coarseSpace = 0)
     {
       return vecRhs[coarseSpace + 1];
     }
 
-    inline Vec& getInteriorVecSol()
+    /// Get the solution vector of the interior.
+    inline Vec& getVecSolInterior()
     {
       return vecSol[0];
     }
 
-    inline Vec& getCoarseVecSol(int coarseSpace = 0)
+    /// Get the solution vector of some coarse space.
+    inline Vec& getVecSolCoarse(int coarseSpace = 0)
     {
       return vecSol[coarseSpace + 1];
     }
 
-    inline int getStartInterior() const
+    /** \brief
+     * Checks whether a given DOF index in some component is a coarse space DOF.
+     * Note (TODO): The specification of both, the component number and FE 
+     * space is not really necessary. Rewrite this!
+     *
+     * \param[in]  component  Component number of the system.
+     * \param[in]  feSpace    Finite element space of the component.
+     * \param[in]  dof        DOF index
+     *
+     * \return     True, if the dof is a coarse space DOF in the component. 
+     *             False otherwise.
+     */
+    inline bool isCoarseSpace(int component,
+			      const FiniteElemSpace *feSpace, 
+			      DegreeOfFreedom dof)
     {
-      return rStartInterior;
+      FUNCNAME("ParallelCoarseSpaceMatVec::isCoarseSpace()");
+      
+      if (coarseSpaceMap.empty())
+	return false;
+
+      TEST_EXIT_DBG(coarseSpaceMap.count(component))
+	("Component %d has no coarse space defined!\n", component);
+
+      return (*(coarseSpaceMap[component]))[feSpace].isSet(dof);
     }
 
+
   protected:
+    /// Prepare internal data structures. First, it create \ref uniqueCoarseMap
+    /// and \ref componentIthCoarseMap . Both are used to create the correct 
+    /// number of matrix and vectors in \ref mat and \ref vec.    
+    void prepare();
+    
+    /// Computes the values of \ref rStartInterior and 
+    /// \ref nGlobalOverallInterior.
     void updateSubdomainData();
 
   private:
+    /// Checks for mesh changes. Returns true if the mesh has been changed
+    /// until the last matrix creation. Is used to rebuild matrix non 
+    /// zero stricture.
+    bool checkMeshChange();
+
+  private:
+    /// Matrix of PETSc matrices. mat[0][0] is the interior discretization
+    /// matrix, mat[1][1] corresponds to the first coarse space and so on. 
+    /// mat[i][j], with i not equal to j, are the coupling between the interior
+    /// and the coarse space matrices, and between the different coarse spaces
+    /// respectively.
     vector<vector<Mat> > mat;
 
+    /// Solution and RHS vectors. vec[0] is the interior vector, vec[1] the 
+    /// first coarse space vector and so on.
     vector<Vec> vecSol, vecRhs;
 
+    /// Matrix of objects to control the matrix non zero structure of the 
+    /// corresponding PETSc matrices stored in \ref mat.
     vector<vector<MatrixNnzStructure> > nnz;
 
-    ParallelDofMapping *interiorMap;
-
-    /// Parallel DOF mapping of the (optional) coarse space. Allows to define
-    /// different coarse spaces for different components.
-    map<int, ParallelDofMapping*> coarseSpaceMap;   
-
+    /** \brief
+     * Stores for each system component (i.e. each PDE variable) the coarse
+     * space that is used for its discretization.
+     *
+     * Example: We solve the Stokes equation in 2D with a different coarse 
+     * space for the velocity unknowns (component 0 and 1) and the pressure
+     * (component 2). Than:
+     *    componentIthCoarseMap[0] = 0
+     *    componentIthCoarseMap[1] = 0
+     *    componentIthCoarseMap[2] = 1
+     * The indices can directly be used to access the correspondig parallel
+     * DOF mapping in \ref uniqueCoarseMap.
+     */
     vector<int> componentIthCoarseMap;
 
+    /// Stores a set of all coarse space DOF mapping. All entries are unique.
     vector<ParallelDofMapping*> uniqueCoarseMap;
 
+    /// Stores the mesh change index of the mesh the nnz structure was created
+    /// for. Therefore, if the mesh change index is higher than this value, we
+    /// have to create a new nnz structure for PETSc matrices, because the mesh
+    ///  has been changed and therefore also the assembled matrix structure.
+    int lastMeshNnz;
+
+    /// If this variable is set to true, the non-zero matrix structure is
+    /// created each time from scratch by calling \ref createPetscNnzStrcuture.
+    /// This can be necessary if the number of non-zeros in the matrix varies
+    /// though the mesh does not change. This may happen if there are many
+    /// operators using DOFVectors from old timestep containing many zeros due to
+    /// some phase fields.
+    bool alwaysCreateNnzStructure;
+
+  protected:
+    /// Pointer to a mesh distributor object.
     MeshDistributor *meshDistributor;
 
+    /// Level of subdomain/interior discretization. Is used for multi-level
+    /// methods only.
     int subdomainLevel;
 
+    /// MPI communicator on the subdomain level. If no multi-level is used
+    /// this is alway MPI_COMM_SELF. In the case of a multi-level method, this
+    /// is a subset of MPI_COMM_WORLD.
     MPI::Intracomm mpiCommLocal;
     
+    /// MPI communicator on the coarse space level. If no multi-level method
+    /// is used, this is always MPI_COMM_WORLD, otherwise a subset of it.
     MPI::Intracomm mpiCommGlobal;
 
+    /// Offset for the interior DOFs of the local interior with respect to the
+    /// subdomain. In the case of a one-level method, each local interior
+    /// is exactly one subdomain. In the case of a multi-level method, one
+    /// subdomain may consists of several rank domains. This value defines than
+    /// the offset ot rank's interior rows to the subdomain's interior rows.
     int rStartInterior;
 
+    /// Number of overall rows in subdomain's interior. For one-level methods,
+    /// this value is equal to the number of rows in rank's interior. See also
+    /// explenation for \ref rStarInterior.
     int nGlobalOverallInterior;
 
-    /// Stores the mesh change index of the mesh the nnz structure was created for.
-    /// Therefore, if the mesh change index is higher than this value, we have to create
-    /// a new nnz structure for PETSc matrices, because the mesh has been changed and
-    /// therefore also the assembled matrix structure.
-    int lastMeshNnz;
+    /// Parallel DOF mapping for the interior.
+    ParallelDofMapping *interiorMap;
 
-    /// If this variable is set to true, the non-zero matrix structure is
-    /// created each time from scratch by calling \ref createPetscNnzStrcuture.
-    /// This can be necessary if the number of non-zeros in the matrix varies
-    /// though the mesh does not change. This may happen if there are many
-    /// operators using DOFVectors from old timestep containing many zeros due to
-    /// some phase fields.
-    bool alwaysCreateNnzStructure;
+    /// Parallel DOF mapping of the (optional) coarse space. Allows to define
+    /// different coarse spaces for different components.
+    map<int, ParallelDofMapping*> coarseSpaceMap;   
   };
 }
 

AMDiS/src/parallel/PetscSolver.cc

@@ -21,10 +21,7 @@ namespace AMDiS {
   using namespace std;
 
   PetscSolver::PetscSolver()
-    : meshDistributor(NULL),      
-      subdomainLevel(0),
-      interiorMap(NULL),
-      mpiRank(-1),
+    : ParallelCoarseSpaceMatVec(),      
       kspPrefix(""),
       removeRhsNullspace(false),
       hasConstantNullspace(false)
@@ -41,25 +38,6 @@ namespace AMDiS {
   }
 
 
-  void PetscSolver::setCoarseSpaceDofMapping(ParallelDofMapping *coarseDofs, 
-					     int component)
-  {
-    FUNCNAME("PetscSolver::setCoarseSpaceDofMapping()");
-
-    TEST_EXIT_DBG(coarseDofs)("Should not happen!\n");
-
-    if (component == -1) {
-      coarseSpaceMap.clear();
-
-      int nComponents = coarseDofs->getNumberOfComponents();
-      for (int i = 0; i < nComponents; i++)
-	coarseSpaceMap[i] = coarseDofs;
-    } else {
-      coarseSpaceMap[component] = coarseDofs;
-    }
-  }
-
-
   void PetscSolver::solve(Vec &rhs, Vec &sol)
   {
     FUNCNAME("PetscSolver::solve()");

AMDiS/src/parallel/PetscSolver.h

@@ -42,38 +42,18 @@ namespace AMDiS {
 
   using namespace std;
 
-
-  class PetscSolver
+  /**
+   * Create an abstract interface to an arbitrary PETSc solver. This class is
+   * based on \ref ParallelCoarseSpaceMatVec to support for solvers which make
+   * use of a coarse grid problem.
+   */
+  class PetscSolver : public ParallelCoarseSpaceMatVec
   {
   public:
     PetscSolver();
 
     virtual ~PetscSolver() {}
 
-    void setMeshDistributor(MeshDistributor *m,
-			    MPI::Intracomm mpiComm0,
-			    MPI::Intracomm mpiComm1)
-    {
-      meshDistributor = m;
-      mpiCommGlobal = mpiComm0;
-      mpiCommLocal = mpiComm1; 
-      mpiRank = mpiCommGlobal.Get_rank();
-    }
-
-    void setLevel(int l) 
-    {
-      subdomainLevel = l;
-    }
-
-    /// Set parallel DOF mapping for the interior DOFs.
-    void setDofMapping(ParallelDofMapping *interiorDofs)
-    {
-      interiorMap = interiorDofs;
-    }
-    
-    void setCoarseSpaceDofMapping(ParallelDofMapping *coarseDofs, 
-				  int component = -1);
-
     /** \brief
      * Create a PETSc matrix. The given DOF matrices are used to create the nnz 
      * structure of the PETSc matrix and the values are transfered to it.
@@ -146,86 +126,6 @@ namespace AMDiS {
       constNullspaceComponent.push_back(component);
     }
 
-    inline bool isCoarseSpace(int component,
-			      const FiniteElemSpace *feSpace, 
-			      DegreeOfFreedom dof)
-    {
-      FUNCNAME("PetscSolver::isCoarseSpace()");
-      
-      if (coarseSpaceMap.empty())
-	return false;
-
-      TEST_EXIT_DBG(coarseSpaceMap.count(component))
-	("Component %d has no coarse space defined!\n", component);
-
-      return (*(coarseSpaceMap[component]))[feSpace].isSet(dof);
-    }
-
-    inline Vec& getRhsCoarseSpace()
-    {
-      FUNCNAME("PetscSolver::getRhsCoarseSpace()");
-
-      TEST_EXIT_DBG(coarseSpaceMap.size())
-	("Subdomain solver does not contain a coarse space!\n");
-
-      return petscData.getCoarseVecRhs();
-    }
-
-    inline Vec& getRhsInterior()
-    {
-      return petscData.getInteriorVecRhs();
-    }
-
-    inline Vec& getSolCoarseSpace()
-    {
-      FUNCNAME("PetscSolver::getSolCoarseSpace()");
-
-      TEST_EXIT_DBG(coarseSpaceMap.size())
-	("Subdomain solver does not contain a coarse space!\n");
-
-      return petscData.getCoarseVecSol();
-    }
-
-    inline Vec& getSolInterior()
-    {
-      return petscData.getInteriorVecSol();
-    }
-
-    inline Mat& getMatIntInt()
-    {
-      return petscData.getInteriorMat();
-    }
-
-    inline Mat& getMatCoarseCoarse()
-    {
-      FUNCNAME("PetscSolver::getMatCoarseCoarse()");
-
-      TEST_EXIT_DBG(coarseSpaceMap.size())
-	("Subdomain solver does not contain a coarse space!\n");
-
-      return petscData.getCoarseMat(0);
-    }
-
-    inline Mat& getMatIntCoarse()
-    {
-      FUNCNAME("PetscSolver::getMatIntCoarse()");
-
-      TEST_EXIT_DBG(coarseSpaceMap.size())
-	("Subdomain solver does not contain a coarse space!\n");
-
-      return petscData.getIntCoarseMat();
-    }
-
-    inline Mat& getMatCoarseInt()
-    {
-      FUNCNAME("PetscSolver::getMatCoarseInt()");
-
-      TEST_EXIT_DBG(coarseSpaceMap.size())
-	("Subdomain solver does not contain a coarse space!\n");
-      
-      return petscData.getCoarseIntMat();
-    }
-
   protected:
     /** \brief
      * Copies between to PETSc vectors by using different index sets for the
@@ -242,26 +142,6 @@ namespace AMDiS {
 		 vector<int>& originIndex, vector<int>& destIndex);
 
   protected:
-    MeshDistributor *meshDistributor;
-
-    int subdomainLevel;
-
-    ParallelDofMapping *interiorMap;
-
-    /// Parallel DOF mapping of the (optional) coarse space. Allows to define
-    /// different coarse spaces for different components.
-    map<int, ParallelDofMapping*> coarseSpaceMap;    
-
-    int mpiRank;
-