PCLDUFactorisation.cpp

/*

Copyright (C) University of Oxford, 2005-2011

University of Oxford means the Chancellor, Masters and Scholars of the
University of Oxford, having an administrative office at Wellington
Square, Oxford OX1 2JD, UK.

This file is part of Chaste.

Chaste is free software: you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License as published
by the Free Software Foundation, either version 2.1 of the License, or
(at your option) any later version.

Chaste is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public
License for more details. The offer of Chaste under the terms of the
License is subject to the License being interpreted in accordance with
English Law and subject to any action against the University of Oxford
being under the jurisdiction of the English Courts.

You should have received a copy of the GNU Lesser General Public License
along with Chaste. If not, see <http://www.gnu.org/licenses/>.

*/

#include <iostream>

#include "PetscVecTools.hpp" // Includes Ublas so must come first
#include "PCLDUFactorisation.hpp"
#include "Exception.hpp"

PCLDUFactorisation::PCLDUFactorisation(KSP& rKspObject)
{
#ifdef TRACE_KSP
    mPCContext.mScatterTime = 0.0;
    mPCContext.mA1PreconditionerTime = 0.0;;
    mPCContext.mA2PreconditionerTime = 0.0;;
    mPCContext.mGatherTime = 0.0;;
#endif

    PCLDUFactorisationCreate(rKspObject);
    PCLDUFactorisationSetUp();
}

PCLDUFactorisation::~PCLDUFactorisation()
{
#ifdef TRACE_KSP
    if (PetscTools::AmMaster())
    {
        std::cout << " -- LDU factorisation preconditioner profile information: " << std::endl;
        std::cout << "\t mScatterTime: " << mPCContext.mScatterTime << std::endl;
        std::cout << "\t mA1PreconditionerTime: " << mPCContext.mA1PreconditionerTime << std::endl;
        std::cout << "\t mA2PreconditionerTime: " << mPCContext.mA2PreconditionerTime << std::endl;
        std::cout << "\t mExtraLAOperations: " << mPCContext.mExtraLAOperations << std::endl;
        std::cout << "\t mGatherTime: " << mPCContext.mGatherTime << std::endl;
    }
#endif

    MatDestroy(mPCContext.A11_matrix_subblock);
    MatDestroy(mPCContext.A22_matrix_subblock);
    MatDestroy(mPCContext.B_matrix_subblock);

    PCDestroy(mPCContext.PC_amg_A11);
    PCDestroy(mPCContext.PC_amg_A22);

    VecDestroy(mPCContext.x1_subvector);
    VecDestroy(mPCContext.y1_subvector);
    VecDestroy(mPCContext.x2_subvector);
    VecDestroy(mPCContext.y2_subvector);
    VecDestroy(mPCContext.z);
    VecDestroy(mPCContext.temp);
    
    VecScatterDestroy(mPCContext.A11_scatter_ctx);
    VecScatterDestroy(mPCContext.A22_scatter_ctx);        
}

void PCLDUFactorisation::PCLDUFactorisationCreate(KSP& rKspObject)
{
    KSPGetPC(rKspObject, &mPetscPCObject);

    Mat system_matrix, dummy;
    MatStructure flag;
    KSPGetOperators(rKspObject, &system_matrix, &dummy, &flag);

    PetscInt num_rows, num_columns;
    MatGetSize(system_matrix, &num_rows, &num_columns);

    PetscInt num_local_rows, num_local_columns;
    MatGetLocalSize(system_matrix, &num_local_rows, &num_local_columns);

    // odd number of rows: impossible in Bidomain.
    // odd number of local rows: impossible if V_m and phi_e for each node are stored in the same processor.
    if ((num_rows%2 != 0) || (num_local_rows%2 != 0))
    {
        TERMINATE("Wrong matrix parallel layout detected in PCLDUFactorisation.");
    }

    // Allocate memory     
    unsigned subvector_num_rows = num_rows/2;    
    unsigned subvector_local_rows = num_local_rows/2;
    mPCContext.x1_subvector = PetscTools::CreateVec(subvector_num_rows, subvector_local_rows);
    mPCContext.x2_subvector = PetscTools::CreateVec(subvector_num_rows, subvector_local_rows);
    mPCContext.y1_subvector = PetscTools::CreateVec(subvector_num_rows, subvector_local_rows);
    mPCContext.y2_subvector = PetscTools::CreateVec(subvector_num_rows, subvector_local_rows);
    mPCContext.z = PetscTools::CreateVec(subvector_num_rows, subvector_local_rows);
    mPCContext.temp = PetscTools::CreateVec(subvector_num_rows, subvector_local_rows);

    // Create scatter contexts
    {
        // Needed by VecScatterCreate in order to find out parallel layout.
        Vec dummy_vec = PetscTools::CreateVec(num_rows, num_local_rows);

        PetscVecTools::SetupInterleavedVectorScatterGather(dummy_vec, mPCContext.A11_scatter_ctx, mPCContext.A22_scatter_ctx);

        VecDestroy(dummy_vec);
    }


    // Get matrix sublock A11        
    {
        // Work out local row range for subblock A11 (same as x1 or y1) 
        PetscInt low, high, global_size;
        VecGetOwnershipRange(mPCContext.x1_subvector, &low, &high);
        VecGetSize(mPCContext.x1_subvector, &global_size);        
        assert(global_size == num_rows/2);       
        
        IS A11_local_rows;
        IS A11_columns;
        ISCreateStride(PETSC_COMM_WORLD, high-low, 2*low, 2, &A11_local_rows);
        ISCreateStride(PETSC_COMM_WORLD, global_size, 0, 2, &A11_columns);
    
#if (PETSC_VERSION_MAJOR == 3 && PETSC_VERSION_MINOR == 1) //PETSc 3.1
        MatGetSubMatrix(system_matrix, A11_local_rows, A11_columns,
            MAT_INITIAL_MATRIX, &mPCContext.A11_matrix_subblock);
#else
        MatGetSubMatrix(system_matrix, A11_local_rows, A11_columns, PETSC_DECIDE,
            MAT_INITIAL_MATRIX, &mPCContext.A11_matrix_subblock);
#endif    
        ISDestroy(A11_local_rows);
        ISDestroy(A11_columns);
    }

    // Get matrix sublock A22
    {
        // Work out local row range for subblock A22 (same as x2 or y2) 
        PetscInt low, high, global_size;
        VecGetOwnershipRange(mPCContext.x2_subvector, &low, &high);
        VecGetSize(mPCContext.x2_subvector, &global_size);        
        assert(global_size == num_rows/2);       
        
        IS A22_local_rows;
        IS A22_columns;
        ISCreateStride(PETSC_COMM_WORLD, high-low, 2*low+1, 2, &A22_local_rows);
        ISCreateStride(PETSC_COMM_WORLD, global_size, 1, 2, &A22_columns);

#if (PETSC_VERSION_MAJOR == 3 && PETSC_VERSION_MINOR == 1) //PETSc 3.1
        MatGetSubMatrix(system_matrix, A22_local_rows, A22_columns,
            MAT_INITIAL_MATRIX, &mPCContext.A22_matrix_subblock);
#else
        MatGetSubMatrix(system_matrix, A22_local_rows, A22_columns, PETSC_DECIDE, 
            MAT_INITIAL_MATRIX, &mPCContext.A22_matrix_subblock);
#endif
    
        ISDestroy(A22_local_rows);
        ISDestroy(A22_columns);
    }

    // Get matrix sublock B (the upper triangular one)
    {
        // Work out local row range for subblock B (same as A11, x1 or y1) 
        PetscInt low, high, global_size;
        VecGetOwnershipRange(mPCContext.x1_subvector, &low, &high);
        VecGetSize(mPCContext.x1_subvector, &global_size);        
        assert(global_size == num_rows/2);        
        
        IS B_local_rows;
        IS B_columns;
        ISCreateStride(PETSC_COMM_WORLD, high-low, 2*low, 2, &B_local_rows);
        ISCreateStride(PETSC_COMM_WORLD, global_size, 1, 2, &B_columns);
    
#if (PETSC_VERSION_MAJOR == 3 && PETSC_VERSION_MINOR == 1) //PETSc 3.1
        MatGetSubMatrix(system_matrix, B_local_rows, B_columns,
            MAT_INITIAL_MATRIX, &mPCContext.B_matrix_subblock);        
#else
        MatGetSubMatrix(system_matrix, B_local_rows, B_columns, PETSC_DECIDE, 
            MAT_INITIAL_MATRIX, &mPCContext.B_matrix_subblock);
#endif
    
        ISDestroy(B_local_rows);
        ISDestroy(B_columns);
    }
    
    /*
     * Experimental (#1082): in PP removing the mass matrix from the A22 block seems to work better.
     *                       This is equivalent to do A22 = A22 + B in this implementation. 
     */
// #if (PETSC_VERSION_MAJOR == 2 && PETSC_VERSION_MINOR == 2) //PETSc 2.2
//     PetscScalar petsc_one = 1.0;
//     MatAXPY(&petsc_one, mPCContext.B_matrix_subblock, mPCContext.A22_matrix_subblock, DIFFERENT_NONZERO_PATTERN);
// #else
//     MatAXPY(mPCContext.A22_matrix_subblock, 1.0, mPCContext.B_matrix_subblock, DIFFERENT_NONZERO_PATTERN);
// #endif    
    
//     // Shift the block
// #if (PETSC_VERSION_MAJOR == 2 && PETSC_VERSION_MINOR == 2) //PETSc 2.2
//     PetscScalar shift = -1e-8;
//     MatShift(&shift, mPCContext.A22_matrix_subblock);
// #else
//     PetscScalar shift = -1e-8;
//     MatShift(mPCContext.A22_matrix_subblock, shift);
// #endif    



    PCSetType(mPetscPCObject, PCSHELL);
#if (PETSC_VERSION_MAJOR == 2 && PETSC_VERSION_MINOR == 2) //PETSc 2.2
    // Register PC context and call-back function
    PCShellSetApply(mPetscPCObject, PCLDUFactorisationApply, (void*) &mPCContext);
#else
    // Register PC context so it gets passed to PCBlockDiagonalApply
    PCShellSetContext(mPetscPCObject, &mPCContext);
    // Register call-back function
    PCShellSetApply(mPetscPCObject, PCLDUFactorisationApply);
#endif

}

void PCLDUFactorisation::PCLDUFactorisationSetUp()
{
    // These options will get read by PCSetFromOptions
//     PetscOptionsSetValue("-pc_hypre_boomeramg_max_iter", "1");
//     PetscOptionsSetValue("-pc_hypre_boomeramg_strong_threshold", "0.0");
//     PetscOptionsSetValue("-pc_hypre_type", "boomeramg");

    /*
     *  Set up preconditioner for block A11
     */
    PCCreate(PETSC_COMM_WORLD, &(mPCContext.PC_amg_A11));
    PCSetOperators(mPCContext.PC_amg_A11, mPCContext.A11_matrix_subblock, mPCContext.A11_matrix_subblock, SAME_PRECONDITIONER);

    // Choose between the two following blocks in order to approximate inv(A11) with one AMG cycle
    // or with an CG solve with high tolerance
//    PCSetType(mPCContext.PC_amg_A11, PCBJACOBI);

    PCSetType(mPCContext.PC_amg_A11, PCHYPRE);
    //PCHYPRESetType(mPCContext.PC_amg_A11, "euclid");
    PetscOptionsSetValue("-pc_hypre_type", "euclid");
    PetscOptionsSetValue("-pc_hypre_euclid_levels", "0");
    
//     PCSetType(mPCContext.PC_amg_A11, PCHYPRE);
//     PetscOptionsSetValue("-pc_hypre_type", "boomeramg");
//     PetscOptionsSetValue("-pc_hypre_boomeramg_max_iter", "1");
//     PetscOptionsSetValue("-pc_hypre_boomeramg_strong_threshold", "0.0");
//     PetscOptionsSetValue("-pc_hypre_boomeramg_coarsen_type", "HMIS");

//    PCSetType(mPCContext.PC_amg_A11, PCKSP);
//    KSP ksp1;
//    PCKSPGetKSP(mPCContext.PC_amg_A11,&ksp1);
//    KSPSetType(ksp1, KSPCG);
//    KSPSetTolerances(ksp1, 0.1, PETSC_DEFAULT, PETSC_DEFAULT, PETSC_DEFAULT);
//
//    PC prec1;
//    KSPGetPC(ksp1, &prec1);
//    PCSetType(prec1, PCBJACOBI);
//    PCSetFromOptions(prec1);
//    PCSetOperators(prec1, mPCContext.A11_matrix_subblock, mPCContext.A11_matrix_subblock, DIFFERENT_NONZERO_PATTERN);//   SAME_PRECONDITIONER);
//    PCSetUp(prec1);
//
//    KSPSetFromOptions(ksp1);
//    KSPSetUp(ksp1);

    PCSetFromOptions(mPCContext.PC_amg_A11);
    PCSetUp(mPCContext.PC_amg_A11);


    /*
     *  Set up amg preconditioner for block A22
     */
    PCCreate(PETSC_COMM_WORLD, &(mPCContext.PC_amg_A22));
    PCSetOperators(mPCContext.PC_amg_A22, mPCContext.A22_matrix_subblock, mPCContext.A22_matrix_subblock, SAME_PRECONDITIONER);

    // Choose between the two following blocks in order to approximate inv(A11) with one AMG cycle
    // or with an CG solve with high tolerance
    PCSetType(mPCContext.PC_amg_A22, PCHYPRE);
    PetscOptionsSetValue("-pc_hypre_type", "boomeramg");
    PetscOptionsSetValue("-pc_hypre_boomeramg_max_iter", "1");
    PetscOptionsSetValue("-pc_hypre_boomeramg_strong_threshold", "0.0");
    PetscOptionsSetValue("-pc_hypre_boomeramg_coarsen_type", "HMIS");
    //    PetscOptionsSetValue("-pc_hypre_boomeramg_interp_type","ext+i");

//    PCSetType(mPCContext.PC_amg_A22, PCKSP);
//    KSP ksp2;
//    PCKSPGetKSP(mPCContext.PC_amg_A22,&ksp2);
//    KSPSetType(ksp2, KSPCG);
//    KSPSetTolerances(ksp2, 0.1, PETSC_DEFAULT, PETSC_DEFAULT, PETSC_DEFAULT);
//
//    PC prec2;
//    KSPGetPC(ksp2, &prec2);
//    PCSetType(prec2, PCBJACOBI);
//    PCSetFromOptions(prec2);
//    PCSetOperators(prec2, mPCContext.A22_matrix_subblock, mPCContext.A22_matrix_subblock, DIFFERENT_NONZERO_PATTERN);//   SAME_PRECONDITIONER);
//    PCSetUp(prec2);
//
//    KSPSetFromOptions(ksp2);
//    KSPSetUp(ksp2);

    PCSetFromOptions(mPCContext.PC_amg_A22);
    PCSetUp(mPCContext.PC_amg_A22);
}
#if (PETSC_VERSION_MAJOR == 3 && PETSC_VERSION_MINOR == 1) //PETSc 3.1
PetscErrorCode PCLDUFactorisationApply(PC pc_object, Vec x, Vec y)
{
  void* pc_context;

  PCShellGetContext(pc_object, &pc_context);   
#else
PetscErrorCode PCLDUFactorisationApply(void* pc_context, Vec x, Vec y)
{
#endif

    // Cast the pointer to a PC context to our defined type
    PCLDUFactorisation::PCLDUFactorisationContext* block_diag_context = (PCLDUFactorisation::PCLDUFactorisationContext*) pc_context;
    assert(block_diag_context!=NULL);

    /*
     *  Split vector x into two. x = [x1 x2]'
     */
#ifdef TRACE_KSP
    double init_time = MPI_Wtime();
#endif

    PetscVecTools::DoInterleavedVecScatter(x, block_diag_context->A11_scatter_ctx, block_diag_context->x1_subvector, block_diag_context->A22_scatter_ctx, block_diag_context->x2_subvector);

#ifdef TRACE_KSP
    block_diag_context->mScatterTime += MPI_Wtime() - init_time;
#endif

    /*
     *  Apply preconditioner: [y1 y2]' = inv(P)[x1 x2]' 
     *
     *     z  = inv(A11)*x1
     *     y2 = inv(A22)*(x2 - B*z)
     *     y1 = z - inv(A11)(B*y2)
     */
#ifdef TRACE_KSP
    init_time = MPI_Wtime();
#endif
    //z  = inv(A11)*x1
    PCApply(block_diag_context->PC_amg_A11, block_diag_context->x1_subvector, block_diag_context->z);
#ifdef TRACE_KSP
    block_diag_context->mA1PreconditionerTime += MPI_Wtime() - init_time;
#endif

    //y2 = inv(A22)*(x2 - B*z)
#ifdef TRACE_KSP
    init_time = MPI_Wtime();
#endif
    MatMult(block_diag_context->B_matrix_subblock,block_diag_context->z,block_diag_context->temp); //temp = B*z
    double minus_one = -1.0;
#if (PETSC_VERSION_MAJOR == 2 && PETSC_VERSION_MINOR == 2) //PETSc 2.2
    VecAYPX(&minus_one, block_diag_context->x2_subvector, block_diag_context->temp); // temp <-- x2 - temp
#else
    VecAYPX(block_diag_context->temp, minus_one, block_diag_context->x2_subvector); // temp <-- x2 - temp
#endif
#ifdef TRACE_KSP
    block_diag_context->mExtraLAOperations += MPI_Wtime() - init_time;
#endif


#ifdef TRACE_KSP
    init_time = MPI_Wtime();
#endif
    PCApply(block_diag_context->PC_amg_A22, block_diag_context->temp, block_diag_context->y2_subvector); // y2 = inv(A22)*temp
#ifdef TRACE_KSP
    block_diag_context->mA2PreconditionerTime += MPI_Wtime() - init_time;
#endif


    //y1 = z - inv(A11)(B*y2)
#ifdef TRACE_KSP
    init_time = MPI_Wtime();
#endif
    MatMult(block_diag_context->B_matrix_subblock,block_diag_context->y2_subvector,block_diag_context->temp); //temp = B*y2
#ifdef TRACE_KSP
    block_diag_context->mExtraLAOperations += MPI_Wtime() - init_time;
#endif
#ifdef TRACE_KSP
    init_time = MPI_Wtime();
#endif
    PCApply(block_diag_context->PC_amg_A11, block_diag_context->temp, block_diag_context->y1_subvector); // y1 = inv(A11)*temp
#ifdef TRACE_KSP
    block_diag_context->mA1PreconditionerTime += MPI_Wtime() - init_time;
#endif

#ifdef TRACE_KSP
    init_time = MPI_Wtime();
#endif
#if (PETSC_VERSION_MAJOR == 2 && PETSC_VERSION_MINOR == 2) //PETSc 2.2
    VecAYPX(&minus_one, block_diag_context->z, block_diag_context->y1_subvector); // y1 <-- z - y1
#else
    VecAYPX(block_diag_context->y1_subvector, minus_one, block_diag_context->z); // y1 <-- z - y1
#endif
#ifdef TRACE_KSP
    block_diag_context->mExtraLAOperations += MPI_Wtime() - init_time;
#endif


    /*
     *  Gather vectors y1 and y2. y = [y1 y2]'
     */
#ifdef TRACE_KSP
    init_time = MPI_Wtime();
#endif

    PetscVecTools::DoInterleavedVecGather(y, block_diag_context->A11_scatter_ctx, block_diag_context->y1_subvector, block_diag_context->A22_scatter_ctx, block_diag_context->y2_subvector);

#ifdef TRACE_KSP
    block_diag_context->mGatherTime += MPI_Wtime() - init_time;
#endif

    return 0;
}

---