CppNoddy::SparseLinearSystem< _Type > Class Template Reference

A linear system class for vector right-hand sides. More...

#include <SparseLinearSystem.h>

Public Member Functions
	SparseLinearSystem (SparseMatrix< _Type > *Aptr, DenseVector< _Type > *Bptr, std::string which="native")
	Constructor for a sparse linear system object. More...
	~SparseLinearSystem ()
	Destructor for a linear system object. More...
void	cleanup ()
	deallocates some objects More...
void	solve ()
	Solve the sparse system. More...
void	factorise ()
	Factorise the Ax=B system. More...
void	solve_using_factorisation ()
	Resolve the same system using the same factorisation. More...
void	temp_solve ()
void	factorise ()
void	solve_using_factorisation ()
void	factorise ()
void	solve_using_factorisation ()

Detailed Description

template<typename _Type>
class CppNoddy::SparseLinearSystem< _Type >

A linear system class for vector right-hand sides.

The class is constructed for SPARSE problems of the form

.

Definition at line 20 of file SparseLinearSystem.h.

Constructor & Destructor Documentation

SparseLinearSystem()

template<typename _Type >

CppNoddy::SparseLinearSystem< _Type >::SparseLinearSystem	(	SparseMatrix< _Type > *	Aptr,
		DenseVector< _Type > *	Bptr,
		std::string	which = "native"
	)

Constructor for a sparse linear system object.

Parameters

Aptr	A pointer to the 'A matrix', an NxN double/complex sparse matrix
Bptr	A pointer to the 'B vector' a size N double/complex dense vector
which	A string that indicates which solver to use: native (default) pr petsc

Definition at line 21 of file SparseLinearSystem.cpp.

                                                                                                                    : m_factorised(false) {
    m_pA = Aptr;
    m_pB = Bptr;
    m_version = which;
    //
    if (m_version != "petsc") {
      std::string problem;
      problem = "The SparseLinearSystem has been instantiated with an unrecognised\n";
      problem += "request for a solver type. Options: 'petsc'. \n";
      throw ExceptionRuntime(problem);
    }
    //
    if(m_version == "petsc") {
#if !defined(PETSC_D) && !defined(PETSC_Z)
      std::string problem;
      problem = "The SparseLinearSystem has been instantiated for a petsc solver.\n";
      problem += "HOWEVER, CppNoddy was not compiled with PETSC_D or PETSC_Z defined.\n";
      throw ExceptionRuntime(problem);
#endif
    }
    //
#if defined(PETSC_D) || defined(PETSC_Z)
    if(m_version == "petsc") {
      int flag(0);
      MPI_Initialized(&flag);
      if(flag != 1) {
        std::string problem;
        problem = "The SparseLinearSystem has been instantiated for a petsc solver.\n";
        problem += "You must call PetscInitialize before calling the petsc solver.\n";
        throw ExceptionRuntime(problem);
      }
    }
#endif
  }

~SparseLinearSystem()

template<typename _Type >

CppNoddy::SparseLinearSystem< _Type >::~SparseLinearSystem

Destructor for a linear system object.

Definition at line 57 of file SparseLinearSystem.cpp.

                                                 {
    cleanup();
  }

Member Function Documentation

cleanup()

template<typename _Type >

void CppNoddy::SparseLinearSystem< _Type >::cleanup

deallocates some objects

Definition at line 62 of file SparseLinearSystem.cpp.

                                          {
#if defined(PETSC_D) || defined(PETSC_Z)
    // delete objects used in the factorisation?
    if(m_factorised) {
      VecDestroy(&m_petsc_x);
      VecDestroy(&m_petsc_B);
      KSPDestroy(&m_petsc_ksp);
      m_factorised = false;
    }
#endif
  }

Referenced by main().

factorise() [1/3]

template<typename _Type >

void CppNoddy::SparseLinearSystem< _Type >::factorise

(

)

Factorise the Ax=B system.

Referenced by main().

factorise() [2/3]

void CppNoddy::SparseLinearSystem< double >::factorise

(

)

Definition at line 93 of file SparseLinearSystem.cpp.

                                             {
#if !defined(PETSC_D)
    std::string problem;
    problem = "CppNoddy is linked against the COMPLEX version of PETSc\n";
    problem += "but you are trying to factorise a DOUBLE matrix. Either\n";
    problem += "redefine your matrix as complex, or recompile with $PETSC_ARCH\n";
    problem += "pointing to a DOUBLE version of the PETSc code.";
    throw ExceptionExternal(problem);
#endif
#if defined(PETSC_D)
 
    if(m_factorised) {
      // already factorised -- so delete and re-create below
      cleanup();
    }
 
    // store a boolean to indicate that we
    m_factorised = true;
    PetscInt Istart,Iend,n;
    Mat petsc_A;
 
    // size of the (assumed square) matrix
    n = m_pA -> nrows();
    /*
       Create parallel vectors B (for RHS) & x (for soln).
    */
    VecCreate(PETSC_COMM_WORLD,&m_petsc_B);
    VecSetSizes(m_petsc_B,PETSC_DECIDE,m_pA->nrows());
    // add any command line configuration
    VecSetFromOptions(m_petsc_B);
    // make a copy to define x
    VecDuplicate(m_petsc_B,&m_petsc_x);
 
    
    // configure the A matrix
    MatCreate(PETSC_COMM_WORLD,&petsc_A);
    // set A to be an nxn matrix
    MatSetSizes(petsc_A,PETSC_DECIDE,PETSC_DECIDE,n,n);
    // add any command line configuration
    MatSetFromOptions(petsc_A);
 
    // get: all_rows_nnz[i] is the number of nonzero elts in row i
    PetscInt* all_rows_nnz = new PetscInt[ n ];
    m_pA -> nelts_all_rows(all_rows_nnz);
 
    // pre-allocate memory using the number of non-zero elts
    // in each row (the 0 is ignored here)
    MatSeqAIJSetPreallocation(petsc_A, 0, all_rows_nnz);
    
    // add any command line configuration
    MatSetFromOptions(petsc_A);
    // finish the A definition
    MatSetUp(petsc_A);
    
    /*
       petsc_A is defined as Sequential above, so this is not strictly needed
    */
    MatGetOwnershipRange(petsc_A,&Istart,&Iend);
    // populate the A matrix using the CppNoddy sparse matrix data
    for(PetscInt i = Istart; i<Iend; ++i) {
      // move the matrix data into PETSc format 1 row at a time
      std::size_t nelts_in_row = all_rows_nnz[i]; 
      // row i has all_rows_nnz[i] elements that are non-zero, so we store their columns
      PetscInt* cols = new PetscInt[all_rows_nnz[i]];
      // store the non-zero elts in this row
      PetscScalar* storage = new PetscScalar[all_rows_nnz[i]];
      // get the data from the CppNoddy sparse matrix structure
      m_pA -> get_row_petsc(i, storage, cols);
      MatSetValues(petsc_A,1,&i,nelts_in_row,cols,storage,INSERT_VALUES);
      // delete temp storage made in the conversion
      delete[] cols;
      delete[] storage;
    }
    
    // MatSetValue inserted values are generally cached
    // so we need to explicitly do final assembly
    MatAssemblyBegin(petsc_A,MAT_FINAL_ASSEMBLY);
    MatAssemblyEnd(petsc_A,MAT_FINAL_ASSEMBLY);
 
    /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
                  Create the linear solver and set various options
       - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    */
    KSPCreate(PETSC_COMM_WORLD,&m_petsc_ksp);
    KSPSetOperators(m_petsc_ksp,petsc_A,petsc_A);
 
    /////////////////////////////
    // default solver is MUMPS //
    /////////////////////////////
    //KSPSetType(m_petsc_ksp,KSPPREONLY);
    KSPGetPC(m_petsc_ksp,&m_petsc_pc);
    // hardwire a DIRECT SOLVER via MUMPS
    //PCSetType(m_petsc_pc,PCLU);
    //PCFactorSetMatSolverType(m_petsc_pc,MATSOLVERMUMPS);
    //PCFactorSetUpMatSolverType(m_petsc_pc);
    /////////////////////////////
    KSPSetFromOptions(m_petsc_ksp);
    KSPSetUp(m_petsc_ksp);
 
    /* create m_petsc_F */
    PCFactorGetMatrix(m_petsc_pc,&m_petsc_F);
 
    /* increase estimate of working space by 20% */
    // MatMumpsSetIcntl(m_petsc_F,14,20.0);
 
    /* sequential ordering */
    // icntl = 7;
    // ival = 2;
    // MatMumpsSetIcntl(m_petsc_F,icntl,ival);
 
    /* threshhold for row pivot detection */
    // MatMumpsSetIcntl(m_petsc_F,24,1);
    // icntl = 3;
    // val = 1.e-6;
    // MatMumpsSetCntl(m_petsc_F,icntl,val);
 
    /* compute determinant of A */
    // MatMumpsSetIcntl(m_petsc_F,33,1);
    /* not used unless we initialise PETSc using the command line options */
    // KSPSetFromOptions(m_petsc_ksp);
    
 
    // /* determinant calculation */
    // {
    //   PetscInt  icntl,infog34;
    //   PetscReal cntl,rinfo12,rinfo13;
    //   icntl = 3;
    //   MatMumpsGetCntl(F,icntl,&cntl);
    //   // output determinant only the first proc.
    //   if (!rank)
    //   {
    //     MatMumpsGetInfog(F,34,&infog34);
    //     MatMumpsGetRinfog(F,12,&rinfo12);
    //     MatMumpsGetRinfog(F,13,&rinfo13);
    //     PetscPrintf(PETSC_COMM_SELF,"  Mumps row pivot threshhold = %g\n",cntl);
    //     PetscPrintf(PETSC_COMM_SELF,"  Mumps determinant = (%g, %g) * 2^%D \n",(double)rinfo12,(double)rinfo13,infog34);
    //   }
    // }
 
    MatDestroy(&petsc_A);
    delete[] all_rows_nnz;
    
#endif // check for PETSC_D/Z
  }

factorise() [3/3]

void CppNoddy::SparseLinearSystem< std::complex< double > >::factorise

(

)

Definition at line 301 of file SparseLinearSystem.cpp.

                                                          {
#if !defined(PETSC_Z)
    std::string problem;
    problem = "CppNoddy is linked against the DOUBLE version of PETSc\n";
    problem += "but you are trying to factorise a COMPLEX matrix.\n";
    problem += "Recompile with $PETSC_ARCH\n";
    problem += "pointing to a COMPLEX version of the PETSc code.";
    throw ExceptionExternal(problem);
#endif
 
#if defined(PETSC_Z)
    if(m_factorised) {
      // already factorised -- so delete and re-create below
      cleanup();
    }
 
    // store a boolean to indicate that we
    m_factorised = true;
    PetscInt Istart,Iend,n;
    Mat A;
 
    // size of the (assumed square) matrix
    n = m_pA -> nrows();
    /*
       Create parallel vectors.
    */
    VecCreate(PETSC_COMM_WORLD,&m_petsc_B);
    VecSetSizes(m_petsc_B,PETSC_DECIDE,m_pA->nrows());
    VecSetFromOptions(m_petsc_B);
    VecDuplicate(m_petsc_B,&m_petsc_x);
 
    // configure the A matrix
    MatCreate(PETSC_COMM_WORLD,&A);
    // set A to be an nxn matrix
    MatSetSizes(A,PETSC_DECIDE,PETSC_DECIDE,n,n);
    MatSetFromOptions(A);
 
    // get: all_rows_nnz[i] is the number of nonzero elts in row i
    PetscInt* all_rows_nnz = new PetscInt[ n ];
    m_pA -> nelts_all_rows(all_rows_nnz);
 
    // pre-allocate memory using the number of non-zero elts
    // in each row (the 0 is ignored here)
    MatSeqAIJSetPreallocation(A, 0, all_rows_nnz);
    MatSetUp(A);
 
    /*
       Currently, all PETSc parallel matrix formats are partitioned by
       contiguous chunks of rows across the processors.  Determine which
       rows of the matrix are locally owned.
    */
    MatGetOwnershipRange(A,&Istart,&Iend);
    // populate the A matrix using the CppNoddy sparse matrix data
    for(PetscInt i = Istart; i<Iend; ++i) {
      // move the matrix data into PETSc format 1 row at a time
      std::size_t nelts_in_row = all_rows_nnz[i];
      // row i has all_rows_nnz[i] elements that are non-zero, so we store their columns
      PetscInt* cols = new PetscInt[nelts_in_row];
      // store the non-zero elts in this row
      PetscScalar* storage = new PetscScalar[nelts_in_row];
      // get the data from the CppNoddy sparse matrix structure
      m_pA -> get_row_petsc(i, storage, cols);
      MatSetValues(A,1,&i,nelts_in_row,cols,storage,INSERT_VALUES);
      // delete temp storage made in the conversion
      delete[] cols;
      delete[] storage;
    }
 
    /*
       Assemble matrix, using the 2-step process:
         MatAssemblyBegin(), MatAssemblyEnd()
       Computations can be done while messages are in transition
       by placing code between these two statements.
    */
    MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);
    MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);
 
    /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
                  Create the linear solver and set various options
       - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    */
    KSPCreate(PETSC_COMM_WORLD,&m_petsc_ksp);
    KSPSetOperators(m_petsc_ksp,A,A);
 
    //KSPSetType(m_petsc_ksp,KSPPREONLY);
    KSPGetPC(m_petsc_ksp,&m_petsc_pc);
    // hardwire a DIRECT SOLVER via MUMPS
    //PCSetType(m_petsc_pc,PCLU);
    //PCFactorSetMatSolverType(m_petsc_pc,MATSOLVERSUPERLU_DIST);
    //PCFactorSetMatSolverType(m_petsc_pc,MATSOLVERMUMPS);
    //PCFactorSetMatSolverType(m_petsc_pc,MATSOLVERMKL_PARDISO);
    //PCFactorSetUpMatSolverType(m_petsc_pc);
 
    KSPSetFromOptions(m_petsc_ksp);
 
    KSPSetUp(m_petsc_ksp);
    /* call MatGetFactor() to create F */
    PCFactorGetMatrix(m_petsc_pc,&m_petsc_F);
 
    /* sequential ordering */
    //PetscInt  ival,icntl;
    //icntl = 7;
    //ival = 2;
    //MatMumpsSetIcntl(m_petsc_F,icntl,ival);
 
    /* threshhold for row pivot detection */
    //MatMumpsSetIcntl(m_petsc_F,24,1);
    //icntl = 3;
    //PetscReal val;
    //val = 1.e-6;
    //MatMumpsSetCntl(m_petsc_F,icntl,val);
 
    /* compute determinant of A */
    // MatMumpsSetIcntl(m_petsc_F,33,1);
    /* not used unless we initialise PETSc using the command line options */
    // KSPSetFromOptions(m_petsc_ksp);
 
    /* Get info from matrix factors */
 
    //KSPView(m_petsc_ksp, PETSC_VIEWER_STDOUT_WORLD);
 
    MatDestroy(&A);
    delete[] all_rows_nnz;
 
#endif // check for PETSC_D/Z
  }

solve()

template<typename _Type >

void CppNoddy::SparseLinearSystem< _Type >::solve

Solve the sparse system.

Definition at line 75 of file SparseLinearSystem.cpp.

                                        {
    if("petsc" == m_version) {
      factorise();
      solve_using_factorisation();
    } else { // we catch incorrect m_version choices in the ctor
      std::string problem;
      problem = "CppNoddy needs to be linked to PETSc to solve sparse\n";
      problem += "linear systems.";
      throw ExceptionExternal(problem);
    }
  }

Referenced by main().

solve_using_factorisation() [1/3]

template<typename _Type >

void CppNoddy::SparseLinearSystem< _Type >::solve_using_factorisation

(

)

Resolve the same system using the same factorisation.

Referenced by main().

solve_using_factorisation() [2/3]

void CppNoddy::SparseLinearSystem< double >::solve_using_factorisation

(

)

Definition at line 242 of file SparseLinearSystem.cpp.

                                                             {
#if !defined(PETSC_D)
    std::string problem;
    problem = "CppNoddy is linked against the COMPLEX version of PETSc\n";
    problem += "but you are trying to solve a DOUBLE matrix. Either\n";
    problem += "redefine your matrix as complex, or recompile with $PETSC_ARCH\n";
    problem += "pointing to a DOUBLE version of the PETSc code.";
    throw ExceptionExternal(problem);
#endif
#if defined(PETSC_D)
    // size of the (assumed square) matrix
    PetscInt n = m_pA -> nrows();
 
    // populate the RHS vector using the CppNoddy DenseVector content
    for(PetscInt i = 0; i < n; ++i) {
      VecSetValue(m_petsc_B,i,m_pB->operator[](i),INSERT_VALUES);
    }
 
    /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
                        Solve the linear system
       - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
    KSPSolve(m_petsc_ksp,m_petsc_B,m_petsc_x);
 
    /* We can now gather the parallel result back to ALL processes
      This is temporary as the SparseMatrix is stored on each processes
      and is too dumb for "proper" parallelization */
    Vec y;
    // a scatter context
    VecScatter ctx = 0;
    // map all elts of the parallel vector to a sequential copy
    VecScatterCreateToAll(m_petsc_x,&ctx,&y);
    // scatter it
    VecScatterBegin(ctx,m_petsc_x,y,INSERT_VALUES,SCATTER_FORWARD);
    VecScatterEnd(ctx,m_petsc_x,y,INSERT_VALUES,SCATTER_FORWARD);
    // clean up
    VecScatterDestroy(&ctx);
    // this array is a pointer not a copy
    PetscScalar* array;
    VecGetArray(y,&array);
    // now copy to the CppNoddy densevctor
    for(PetscInt i=0; i<n; i++) {
      m_pB -> operator[](i) = array[i];
    }
    // follow the docs and Restore after get
    VecRestoreArray(m_petsc_x,&array);
    VecDestroy(&y);
#endif
  }

solve_using_factorisation() [3/3]

void CppNoddy::SparseLinearSystem< std::complex< double > >::solve_using_factorisation

(

)

Definition at line 432 of file SparseLinearSystem.cpp.

                                                                          {
#if !defined(PETSC_Z)
    std::string problem;
    problem = "CppNoddy is linked against the DOUBLE version of PETSc\n";
    problem += "but you are trying to solve e a COMPLEX matrix.\n";
    problem += "Recompile with $PETSC_ARCH\n";
    problem += "pointing to a COMPLEX version of the PETSc code.";
    throw ExceptionExternal(problem);
#endif
#if defined(PETSC_Z)
    // size of the (assumed square) matrix
    PetscInt n = m_pA -> nrows();
 
    // populate the RHS vector using the CppNoddy DenseVector content
    for(PetscInt i = 0; i < n; ++i) {
      VecSetValue(m_petsc_B,i,m_pB->operator[](i),INSERT_VALUES);
    }
 
    /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
                        Solve the linear system
       - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
    KSPSolve(m_petsc_ksp,m_petsc_B,m_petsc_x);
 
    /* We can now gather the parallel result back to ALL processes
      This is temporary as the SparseMatrix is stored on each processes
      and is too dumb for "proper" parallelization */
    Vec y;
    // a scatter context
    VecScatter ctx = 0;
    // map all elts of the parallel vector to a sequential copy
    VecScatterCreateToAll(m_petsc_x,&ctx,&y);
    // scatter it
    VecScatterBegin(ctx,m_petsc_x,y,INSERT_VALUES,SCATTER_FORWARD);
    VecScatterEnd(ctx,m_petsc_x,y,INSERT_VALUES,SCATTER_FORWARD);
    // clean up
    VecScatterDestroy(&ctx);
    // this array is a pointer not a copy
    PetscScalar* array;
    VecGetArray(y,&array);
    // now copy to the CppNoddy densevctor
    for(PetscInt i=0; i<n; i++) {
      m_pB -> operator[](i) = array[i];
    }
    // follow the docs and Restore after get
    VecRestoreArray(m_petsc_x,&array);
    VecDestroy(&y);
#endif
  }

temp_solve()

template<typename _Type >

void CppNoddy::SparseLinearSystem< _Type >::temp_solve

(

)

---

The documentation for this class was generated from the following files:

• include/SparseLinearSystem.h
• src/SparseLinearSystem.cpp