PCLDUFactorisation.cpp

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*/

#include <iostream>

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

    PetscTools::Destroy(mPCContext.A11_matrix_subblock);
    PetscTools::Destroy(mPCContext.A22_matrix_subblock);
    PetscTools::Destroy(mPCContext.B_matrix_subblock);

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

    PetscTools::Destroy(mPCContext.x1_subvector);
    PetscTools::Destroy(mPCContext.y1_subvector);
    PetscTools::Destroy(mPCContext.x2_subvector);
    PetscTools::Destroy(mPCContext.y2_subvector);
    PetscTools::Destroy(mPCContext.z);
    PetscTools::Destroy(mPCContext.temp);

    VecScatterDestroy(PETSC_DESTROY_PARAM(mPCContext.A11_scatter_ctx));
    VecScatterDestroy(PETSC_DESTROY_PARAM(mPCContext.A22_scatter_ctx));
}

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

    Mat system_matrix, dummy;
#if ( PETSC_VERSION_MAJOR==3 && PETSC_VERSION_MINOR>=5 )
    KSPGetOperators(rKspObject, &system_matrix, &dummy);
#else
    MatStructure flag;
    KSPGetOperators(rKspObject, &system_matrix, &dummy, &flag);
#endif

    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);

        PetscTools::Destroy(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 or later
        MatGetSubMatrix(system_matrix, A11_local_rows, A11_local_rows,
            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(PETSC_DESTROY_PARAM(A11_local_rows));
        ISDestroy(PETSC_DESTROY_PARAM(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 or later
        MatGetSubMatrix(system_matrix, A22_local_rows, A22_local_rows,
            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(PETSC_DESTROY_PARAM(A22_local_rows));
        ISDestroy(PETSC_DESTROY_PARAM(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);

#if (PETSC_VERSION_MAJOR == 3 && PETSC_VERSION_MINOR >= 1) //PETSc 3.1 or later
        ISCreateStride(PETSC_COMM_WORLD, high-low, 2*low+1, 2, &B_columns);
        MatGetSubMatrix(system_matrix, B_local_rows, B_columns,
            MAT_INITIAL_MATRIX, &mPCContext.B_matrix_subblock);
#else
    ISCreateStride(PETSC_COMM_WORLD, global_size, 1, 2, &B_columns);
        MatGetSubMatrix(system_matrix, B_local_rows, B_columns, PETSC_DECIDE,
            MAT_INITIAL_MATRIX, &mPCContext.B_matrix_subblock);
#endif

        ISDestroy(PETSC_DESTROY_PARAM(B_local_rows));
        ISDestroy(PETSC_DESTROY_PARAM(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));
#if ( PETSC_VERSION_MAJOR==3 && PETSC_VERSION_MINOR>=5 )
    // Attempt to emulate SAME_PRECONDITIONER below
    PCSetReusePreconditioner(mPCContext.PC_amg_A11, PETSC_TRUE);
    PCSetOperators(mPCContext.PC_amg_A11, mPCContext.A11_matrix_subblock, mPCContext.A11_matrix_subblock);
#else
    PCSetOperators(mPCContext.PC_amg_A11, mPCContext.A11_matrix_subblock, mPCContext.A11_matrix_subblock, SAME_PRECONDITIONER);
#endif

    // 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);

    // We are expecting an error from PETSC on systems that don't have the hypre library, so suppress it
    // in case it aborts
    PetscPushErrorHandler(PetscIgnoreErrorHandler, NULL);
    PetscErrorCode pc_set_error = PCSetType(mPCContext.PC_amg_A11, PCHYPRE);
    if (pc_set_error != 0)
    {
        WARNING("PETSc hypre preconditioning library is not installed");
    }
    // Stop supressing error
    PetscPopErrorHandler();

    //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));
#if ( PETSC_VERSION_MAJOR==3 && PETSC_VERSION_MINOR>=5 )
    // Attempt to emulate SAME_PRECONDITIONER below
    PCSetReusePreconditioner(mPCContext.PC_amg_A22, PETSC_TRUE);
    PCSetOperators(mPCContext.PC_amg_A22, mPCContext.A22_matrix_subblock, mPCContext.A22_matrix_subblock);
#else
    PCSetOperators(mPCContext.PC_amg_A22, mPCContext.A22_matrix_subblock, mPCContext.A22_matrix_subblock, SAME_PRECONDITIONER);
#endif

    // Choose between the two following blocks in order to approximate inv(A11) with one AMG cycle
    // or with an CG solve with high tolerance
    // We are expecting an error from PETSC on systems that don't have the hypre library, so suppress it
    // in case it aborts
    PetscPushErrorHandler(PetscIgnoreErrorHandler, NULL);
    PCSetType(mPCContext.PC_amg_A22, PCHYPRE);
    // Stop supressing error
    PetscPopErrorHandler();

    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 or later
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
    Timer::Reset();
#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 += Timer::GetElapsedTime();
#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
    Timer::Reset();
#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 += Timer::GetElapsedTime();
#endif

    //y2 = inv(A22)*(x2 - B*z)
#ifdef TRACE_KSP
    Timer::Reset();
#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 += Timer::GetElapsedTime();
#endif


#ifdef TRACE_KSP
    Timer::Reset();
#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 += Timer::GetElapsedTime();
#endif

    // y1 = z - inv(A11)(B*y2)
#ifdef TRACE_KSP
    Timer::Reset();
#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 += Timer::GetElapsedTime();
#endif
#ifdef TRACE_KSP
    Timer::Reset();
#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 += Timer::GetElapsedTime();
#endif

#ifdef TRACE_KSP
    Timer::Reset();
#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 += Timer::GetElapsedTime();
#endif

    /*
     * Gather vectors y1 and y2. y = [y1 y2]'
     */
#ifdef TRACE_KSP
    Timer::Reset();
#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 += Timer::GetElapsedTime();
#endif

    return 0;
}