// updated
PetscErrorCode BSSCR_MatStokesMVBlockDefaultBuildScaling( MatStokesBlockScaling BA, Mat A, Vec b, Vec x, PetscTruth sym )
{
Mat K,G,D,C;
Vec rG;
PetscScalar rg2, rg, ra;
PetscInt N;
Vec rA, rC;
Vec L1,L2, R1,R2;
Mat S;
VecNestGetSubVec( BA->Lz, 0, &L1 );
VecNestGetSubVec( BA->Lz, 1, &L2 );
VecNestGetSubVec( BA->Rz, 0, &R1 );
VecNestGetSubVec( BA->Rz, 1, &R2 );
rA = L1;
rC = L2;
MatNestGetSubMat( A, 0,0, &K );
MatNestGetSubMat( A, 0,1, &G );
MatNestGetSubMat( A, 1,0, &D );
MatNestGetSubMat( A, 1,1, &C );
VecDuplicate( rA, &rG );
/* Get magnitude of K */
//px_MatGetAbsRowSum( K, rA );
//MatGetRowMax( K, rA, PETSC_NULL );
MatGetDiagonal( K, rA);
VecSqrt( rA );
VecReciprocal( rA );
/* VecDot( rA,rA, &ra ); */
/* VecGetSize( rA, &N ); */
/* ra = PetscSqrtScalar( ra/N ); */
/* Get magnitude of G */
//px_MatGetAbsRowSum( G, rG );
//MatGetRowMax( G, rG, PETSC_NULL );
Mat A21_cpy;
Mat Shat;
Vec diag; /* same as rA*rA */
MatGetVecs( K, &diag, PETSC_NULL );
MatGetDiagonal( K, diag );
VecReciprocal( diag );
if( sym )
#if( PETSC_VERSION_MAJOR <= 2 )
MatTranspose( G, &A21_cpy );
#else
MatTranspose( G, MAT_INITIAL_MATRIX, &A21_cpy );
#endif
else {
int main(int argc,char **args)
{
Mat A;
Vec x;
PetscErrorCode ierr;
PetscViewer fd; /* viewer */
char file[PETSC_MAX_PATH_LEN]; /* input file name */
PetscReal norm;
PetscBool flg;
PetscInitialize(&argc,&args,(char*)0,help);
/* Determine file from which we read the matrix A */
ierr = PetscOptionsGetString(NULL,"-f",file,PETSC_MAX_PATH_LEN,&flg);CHKERRQ(ierr);
if (!flg) SETERRQ(PETSC_COMM_WORLD,1,"Must indicate binary file with the -f option");
/* Load matrix A */
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,file,FILE_MODE_READ,&fd);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
ierr = MatLoad(A,fd);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&fd);CHKERRQ(ierr);
ierr = MatCreateVecs(A,&x,NULL);CHKERRQ(ierr);
ierr = MatGetDiagonal(A,x);CHKERRQ(ierr);
ierr = VecScale(x,-1.0);CHKERRQ(ierr);
ierr = MatDiagonalSet(A,x,ADD_VALUES);CHKERRQ(ierr);
ierr = MatGetDiagonal(A,x);CHKERRQ(ierr);
ierr = VecNorm(x,NORM_2,&norm);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"Norm %g\n",(double)norm);CHKERRQ(ierr);
/* Free data structures */
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = VecDestroy(&x);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
PetscErrorCode bsscr_DGMiGtD( Mat *_K2, Mat K, Mat G, Mat M){
Mat K2;
Vec diag;
Vec Mdiag;
Mat MinvGt;
Mat Gtrans;
PetscErrorCode ierr;
PetscFunctionBegin;
MatGetVecs( K, &diag, PETSC_NULL );
MatGetDiagonal( K, diag );
VecSqrt(diag);
//VecReciprocal(diag);/* trying something different here */
MatGetVecs( M, &Mdiag, PETSC_NULL );
MatGetDiagonal( M, Mdiag );
VecReciprocal(Mdiag);
#if( PETSC_VERSION_MAJOR <= 2 )
ierr=MatTranspose(G, &Gtrans);CHKERRQ(ierr);
#else
ierr=MatTranspose(G, MAT_INITIAL_MATRIX,&Gtrans);CHKERRQ(ierr);
#endif
ierr=MatConvert(Gtrans, MATSAME, MAT_INITIAL_MATRIX, &MinvGt);CHKERRQ(ierr);/* copy Gtrans -> MinvGt */
MatDiagonalScale(MinvGt, Mdiag, PETSC_NULL);/* Minv*Gtrans */
/* MAT_INITIAL_MATRIX -> creates K2 matrix : PETSC_DEFAULT for fill ratio: run with -info to find what it should be*/
ierr=MatMatMult( G, MinvGt, MAT_INITIAL_MATRIX, PETSC_DEFAULT, &K2);CHKERRQ(ierr);/* K2 = G*Minv*Gtrans */
MatDiagonalScale(K2, diag, diag );/* K2 = D*K2*D = D*G*Minv*Gtrans*D */
Stg_MatDestroy(&Gtrans);
Stg_MatDestroy(&MinvGt);
Stg_VecDestroy(&diag);
Stg_VecDestroy(&Mdiag);
*_K2=K2;
PetscFunctionReturn(0);
}
PetscErrorCode StokesSetupApproxSchur(Stokes *s)
{
Vec diag;
PetscErrorCode ierr;
PetscFunctionBeginUser;
/* Schur complement approximation: myS = A11 - A10 diag(A00)^(-1) A01 */
/* note: A11 is zero */
/* note: in real life this matrix would be build directly, */
/* i.e. without MatMatMult */
/* inverse of diagonal of A00 */
ierr = VecCreate(PETSC_COMM_WORLD,&diag);CHKERRQ(ierr);
ierr = VecSetSizes(diag,PETSC_DECIDE,2*s->nx*s->ny);CHKERRQ(ierr);
ierr = VecSetType(diag,VECMPI);CHKERRQ(ierr);
ierr = MatGetDiagonal(s->subA[0],diag);
ierr = VecReciprocal(diag);
/* compute: - A10 diag(A00)^(-1) A01 */
ierr = MatDiagonalScale(s->subA[1],diag,NULL); /* (*warning* overwrites subA[1]) */
ierr = MatMatMult(s->subA[2],s->subA[1],MAT_INITIAL_MATRIX,PETSC_DEFAULT,&s->myS);CHKERRQ(ierr);
ierr = MatScale(s->myS,-1.0);CHKERRQ(ierr);
/* restore A10 */
ierr = MatGetDiagonal(s->subA[0],diag);
ierr = MatDiagonalScale(s->subA[1],diag,NULL);
ierr = VecDestroy(&diag);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
static PetscErrorCode PCSetUp_Eisenstat(PC pc)
{
PetscErrorCode ierr;
PetscInt M,N,m,n;
PC_Eisenstat *eis = (PC_Eisenstat*)pc->data;
PetscFunctionBegin;
if (!pc->setupcalled) {
ierr = MatGetSize(pc->mat,&M,&N);CHKERRQ(ierr);
ierr = MatGetLocalSize(pc->mat,&m,&n);CHKERRQ(ierr);
ierr = MatCreate(((PetscObject)pc)->comm,&eis->shell);CHKERRQ(ierr);
ierr = MatSetSizes(eis->shell,m,n,M,N);CHKERRQ(ierr);
ierr = MatSetType(eis->shell,MATSHELL);CHKERRQ(ierr);
ierr = MatSetUp(eis->shell);CHKERRQ(ierr);
ierr = MatShellSetContext(eis->shell,(void*)pc);CHKERRQ(ierr);
ierr = PetscLogObjectParent(pc,eis->shell);CHKERRQ(ierr);
ierr = MatShellSetOperation(eis->shell,MATOP_MULT,(void(*)(void))PCMult_Eisenstat);CHKERRQ(ierr);
}
if (!eis->usediag) PetscFunctionReturn(0);
if (!pc->setupcalled) {
ierr = MatGetVecs(pc->pmat,&eis->diag,0);CHKERRQ(ierr);
ierr = PetscLogObjectParent(pc,eis->diag);CHKERRQ(ierr);
}
ierr = MatGetDiagonal(pc->pmat,eis->diag);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
static PetscErrorCode PCSetUp_LSC(PC pc)
{
PC_LSC *lsc = (PC_LSC*)pc->data;
Mat L,Lp,B,C;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PCLSCAllocate_Private(pc);CHKERRQ(ierr);
ierr = PetscObjectQuery((PetscObject)pc->mat,"LSC_L",(PetscObject*)&L);CHKERRQ(ierr);
if (!L) {ierr = PetscObjectQuery((PetscObject)pc->pmat,"LSC_L",(PetscObject*)&L);CHKERRQ(ierr);}
ierr = PetscObjectQuery((PetscObject)pc->pmat,"LSC_Lp",(PetscObject*)&Lp);CHKERRQ(ierr);
if (!Lp) {ierr = PetscObjectQuery((PetscObject)pc->mat,"LSC_Lp",(PetscObject*)&Lp);CHKERRQ(ierr);}
if (!L) {
ierr = MatSchurComplementGetSubMatrices(pc->mat,NULL,NULL,&B,&C,NULL);CHKERRQ(ierr);
if (!lsc->L) {
ierr = MatMatMult(C,B,MAT_INITIAL_MATRIX,PETSC_DEFAULT,&lsc->L);CHKERRQ(ierr);
} else {
ierr = MatMatMult(C,B,MAT_REUSE_MATRIX,PETSC_DEFAULT,&lsc->L);CHKERRQ(ierr);
}
Lp = L = lsc->L;
}
if (lsc->scale) {
Mat Ap;
ierr = MatSchurComplementGetSubMatrices(pc->mat,NULL,&Ap,NULL,NULL,NULL);CHKERRQ(ierr);
ierr = MatGetDiagonal(Ap,lsc->scale);CHKERRQ(ierr); /* Should be the mass matrix, but we don't have plumbing for that yet */
ierr = VecReciprocal(lsc->scale);CHKERRQ(ierr);
}
ierr = KSPSetOperators(lsc->kspL,L,Lp);CHKERRQ(ierr);
ierr = KSPSetFromOptions(lsc->kspL);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
void FETI_Operations::set_jacobi_precond_vector()
{
homemade_assert_msg(m_bC_RR_MatrixSet,"Preconditioner matrix not set yet!");
// Create and set the vector
VecCreate(m_comm.get(),&m_coupling_jacobi_precond_vec);
VecSetSizes(m_coupling_jacobi_precond_vec,m_C_RR_M_local,m_C_RR_M);
VecSetFromOptions(m_coupling_jacobi_precond_vec);
// Get the diagonal
MatGetDiagonal(m_C_RR,m_coupling_jacobi_precond_vec);
// Calculate the reciprocal
VecReciprocal(m_coupling_jacobi_precond_vec);
// Export it
write_PETSC_vector(m_coupling_jacobi_precond_vec,m_scratch_folder_path + "/precond_Jacobi_vector.petscvec",m_comm.rank(),m_comm.get());
// Print MatLab debugging output? Variable defined at "carl_headers.h"
#ifdef PRINT_MATLAB_DEBUG
write_PETSC_vector_MATLAB(m_coupling_jacobi_precond_vec,m_scratch_folder_path + "/precond_Jacobi_vector.m",m_comm.get());
#endif
// Set flag
m_bCreatedPrecondJacobiVec = true;
}
void PetscSparseStorage::getDiagonal( OoqpVector& vec_in )
{
PetscVector & vec = dynamic_cast<PetscVector &>(vec_in);
int ierr;
ierr = MatGetDiagonal(M, vec.pv); assert( ierr == 0);
}
void
NRSolver :: applyConstraintsToLoadIncrement(int nite, const SparseMtrx &k, FloatArray &R,
referenceLoadInputModeType rlm, TimeStep *tStep)
{
double factor = engngModel->giveDomain(1)->giveFunction(prescribedDisplacementTF)->evaluateAtTime( tStep->giveTargetTime() );
if ( ( rlm == rlm_total ) && ( !tStep->isTheFirstStep() ) ) {
//factor -= engngModel->giveDomain(1)->giveFunction(prescribedDisplacementTF)->
// at(tStep->givePreviousStep()->giveTime()) ;
factor -= engngModel->giveDomain(1)->giveFunction(prescribedDisplacementTF)->
evaluateAtTime( tStep->giveTargetTime() - tStep->giveTimeIncrement() );
}
if ( nite == 0 ) {
#if 0
#ifdef __PETSC_MODULE
if ( solverType == ST_Petsc ) {
//Natural2LocalOrdering* n2lpm = engngModel->giveParallelContext(1)->giveN2Lmap();
//IntArray* map = n2lpm->giveN2Lmap();
for ( i = 1; i <= prescribedEqs.giveSize(); i++ ) {
eq = prescribedEqs.at(i);
R.at(eq) = prescribedDofsValues.at(i) * factor; // local eq
}
return;
}
#endif
#else
#ifdef __PETSC_MODULE
const PetscSparseMtrx *lhs = dynamic_cast< const PetscSparseMtrx * >(&k);
if ( lhs ) {
Vec diag;
PetscScalar *ptr;
lhs->createVecGlobal(& diag);
MatGetDiagonal(* ( const_cast< PetscSparseMtrx * >(lhs)->giveMtrx() ), diag);
VecGetArray(diag, & ptr);
for ( int i = 1; i <= numberOfPrescribedDofs; i++ ) {
int eq = prescribedEqs.at(i) - 1;
R.at(eq + 1) = ptr [ eq ] * prescribedDofsValues.at(i) * factor;
}
VecRestoreArray(diag, & ptr);
VecDestroy(& diag);
return;
}
#endif
#endif
for ( int i = 1; i <= numberOfPrescribedDofs; i++ ) {
int eq = prescribedEqs.at(i);
R.at(eq) = k.at(eq, eq) * prescribedDofsValues.at(i) * factor;
}
} else {
for ( int i = 1; i <= numberOfPrescribedDofs; i++ ) {
R.at( prescribedEqs.at(i) ) = 0.0;
}
}
}
PetscErrorCode MatGetDiagonal_SMF(Mat mat,Vec v)
{
PetscErrorCode ierr;
MatSubMatFreeCtx ctx;
PetscFunctionBegin;
ierr = MatShellGetContext(mat,(void **)&ctx);CHKERRQ(ierr);
ierr = MatGetDiagonal(ctx->A,v);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
static PetscErrorCode MatGetDiagonal_User(Mat A,Vec X)
{
User user;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = MatShellGetContext(A,&user);CHKERRQ(ierr);
ierr = MatGetDiagonal(user->B,X);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode PCGAMGOptProl_Classical_Jacobi(PC pc,const Mat A,Mat *P)
{
PetscErrorCode ierr;
PetscInt f,s,n,cf,cs,i,idx;
PetscInt *coarserows;
PetscInt ncols;
const PetscInt *pcols;
const PetscScalar *pvals;
Mat Pnew;
Vec diag;
PC_MG *mg = (PC_MG*)pc->data;
PC_GAMG *pc_gamg = (PC_GAMG*)mg->innerctx;
PC_GAMG_Classical *cls = (PC_GAMG_Classical*)pc_gamg->subctx;
PetscFunctionBegin;
if (cls->nsmooths == 0) {
ierr = PCGAMGTruncateProlongator_Private(pc,P);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
ierr = MatGetOwnershipRange(*P,&s,&f);CHKERRQ(ierr);
n = f-s;
ierr = MatGetOwnershipRangeColumn(*P,&cs,&cf);CHKERRQ(ierr);
ierr = PetscMalloc(sizeof(PetscInt)*n,&coarserows);CHKERRQ(ierr);
/* identify the rows corresponding to coarse unknowns */
idx = 0;
for (i=s;i<f;i++) {
ierr = MatGetRow(*P,i,&ncols,&pcols,&pvals);CHKERRQ(ierr);
/* assume, for now, that it's a coarse unknown if it has a single unit entry */
if (ncols == 1) {
if (pvals[0] == 1.) {
coarserows[idx] = i;
idx++;
}
}
ierr = MatRestoreRow(*P,i,&ncols,&pcols,&pvals);CHKERRQ(ierr);
}
ierr = MatGetVecs(A,&diag,0);CHKERRQ(ierr);
ierr = MatGetDiagonal(A,diag);CHKERRQ(ierr);
ierr = VecReciprocal(diag);CHKERRQ(ierr);
for (i=0;i<cls->nsmooths;i++) {
ierr = MatMatMult(A,*P,MAT_INITIAL_MATRIX,PETSC_DEFAULT,&Pnew);CHKERRQ(ierr);
ierr = MatZeroRows(Pnew,idx,coarserows,0.,NULL,NULL);CHKERRQ(ierr);
ierr = MatDiagonalScale(Pnew,diag,0);CHKERRQ(ierr);
ierr = MatAYPX(Pnew,-1.0,*P,DIFFERENT_NONZERO_PATTERN);CHKERRQ(ierr);
ierr = MatDestroy(P);CHKERRQ(ierr);
*P = Pnew;
Pnew = NULL;
}
ierr = VecDestroy(&diag);CHKERRQ(ierr);
ierr = PetscFree(coarserows);CHKERRQ(ierr);
ierr = PCGAMGTruncateProlongator_Private(pc,P);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode MatGetDiagonal_Composite(Mat A,Vec v)
{
Mat_Composite *shell = (Mat_Composite*)A->data;
Mat_CompositeLink next = shell->head;
PetscErrorCode ierr;
PetscFunctionBegin;
if (!next) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Must provide at least one matrix with MatCompositeAddMat()");
if (shell->right || shell->left) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Cannot get diagonal if left or right scaling");
ierr = MatGetDiagonal(next->mat,v);CHKERRQ(ierr);
if (next->next && !shell->work) {
ierr = VecDuplicate(v,&shell->work);CHKERRQ(ierr);
}
while ((next = next->next)) {
ierr = MatGetDiagonal(next->mat,shell->work);CHKERRQ(ierr);
ierr = VecAXPY(v,1.0,shell->work);CHKERRQ(ierr);
}
ierr = VecScale(v,shell->scale);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@
MatCreateSchurComplementPmat - create a preconditioning matrix for the Schur complement by assembling Sp = A11 - A10 inv(diag(A00)) A01
Collective on Mat
Input Parameters:
+ A00,A01,A10,A11 - the four parts of the original matrix A = [A00 A01; A10 A11] (A01,A10, and A11 are optional, implying zero matrices)
. ainvtype - type of approximation for inv(A00) used when forming Sp = A11 - A10 inv(A00) A01
- preuse - MAT_INITIAL_MATRIX for a new Sp, or MAT_REUSE_MATRIX to reuse an existing Sp, or MAT_IGNORE_MATRIX to put nothing in Sp
Output Parameter:
- Spmat - approximate Schur complement suitable for preconditioning S = A11 - A10 inv(diag(A00)) A01
Note:
Since the real Schur complement is usually dense, providing a good approximation to newpmat usually requires
application-specific information. The default for assembled matrices is to use the inverse of the diagonal of
the (0,0) block A00 in place of A00^{-1}. This rarely produce a scalable algorithm. Optionally, A00 can be lumped
before forming inv(diag(A00)).
Level: advanced
Concepts: matrices^submatrices
.seealso: MatCreateSchurComplement(), MatGetSchurComplement(), MatSchurComplementGetPmat(), MatSchurComplementAinvType
@*/
PetscErrorCode MatCreateSchurComplementPmat(Mat A00,Mat A01,Mat A10,Mat A11,MatSchurComplementAinvType ainvtype,MatReuse preuse,Mat *Spmat)
{
PetscErrorCode ierr;
PetscInt N00;
PetscFunctionBegin;
/* Use an appropriate approximate inverse of A00 to form A11 - A10 inv(diag(A00)) A01; a NULL A01, A10 or A11 indicates a zero matrix. */
/* TODO: Perhaps should create an appropriately-sized zero matrix of the same type as A00? */
if ((!A01 || !A10) & !A11) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Cannot assemble Spmat: A01, A10 and A11 are all NULL.");
if (preuse == MAT_IGNORE_MATRIX) PetscFunctionReturn(0);
/* A zero size A00 or empty A01 or A10 imply S = A11. */
ierr = MatGetSize(A00,&N00,NULL);CHKERRQ(ierr);
if (!A01 || !A10 || !N00) {
if (preuse == MAT_INITIAL_MATRIX) {
ierr = MatDuplicate(A11,MAT_COPY_VALUES,Spmat);CHKERRQ(ierr);
} else { /* MAT_REUSE_MATRIX */
/* TODO: when can we pass SAME_NONZERO_PATTERN? */
ierr = MatCopy(A11,*Spmat,DIFFERENT_NONZERO_PATTERN);CHKERRQ(ierr);
}
} else {
Mat AdB;
Vec diag;
ierr = MatCreateVecs(A00,&diag,NULL);CHKERRQ(ierr);
if (ainvtype == MAT_SCHUR_COMPLEMENT_AINV_LUMP) {
ierr = MatGetRowSum(A00,diag);CHKERRQ(ierr);
} else if (ainvtype == MAT_SCHUR_COMPLEMENT_AINV_DIAG) {
ierr = MatGetDiagonal(A00,diag);CHKERRQ(ierr);
} else SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Unknown MatSchurComplementAinvType: %D", ainvtype);
ierr = VecReciprocal(diag);CHKERRQ(ierr);
ierr = MatDuplicate(A01,MAT_COPY_VALUES,&AdB);CHKERRQ(ierr);
ierr = MatDiagonalScale(AdB,diag,NULL);CHKERRQ(ierr);
ierr = VecDestroy(&diag);CHKERRQ(ierr);
/* Cannot really reuse Spmat in MatMatMult() because of MatAYPX() -->
MatAXPY() --> MatHeaderReplace() --> MatDestroy_XXX_MatMatMult() */
ierr = MatDestroy(Spmat);CHKERRQ(ierr);
ierr = MatMatMult(A10,AdB,MAT_INITIAL_MATRIX,PETSC_DEFAULT,Spmat);CHKERRQ(ierr);
if (!A11) {
ierr = MatScale(*Spmat,-1.0);CHKERRQ(ierr);
} else {
/* TODO: when can we pass SAME_NONZERO_PATTERN? */
ierr = MatAYPX(*Spmat,-1,A11,DIFFERENT_NONZERO_PATTERN);CHKERRQ(ierr);
}
ierr = MatDestroy(&AdB);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
static PetscErrorCode TestMatrix(Mat A,Vec X,Vec Y,Vec Z)
{
PetscErrorCode ierr;
Vec W1,W2;
Mat E;
const char *mattypename;
PetscViewer viewer = PETSC_VIEWER_STDOUT_WORLD;
PetscFunctionBegin;
ierr = VecDuplicate(X,&W1);
CHKERRQ(ierr);
ierr = VecDuplicate(X,&W2);
CHKERRQ(ierr);
ierr = MatScale(A,31);
CHKERRQ(ierr);
ierr = MatShift(A,37);
CHKERRQ(ierr);
ierr = MatDiagonalScale(A,X,Y);
CHKERRQ(ierr);
ierr = MatScale(A,41);
CHKERRQ(ierr);
ierr = MatDiagonalScale(A,Y,Z);
CHKERRQ(ierr);
ierr = MatComputeExplicitOperator(A,&E);
CHKERRQ(ierr);
ierr = PetscObjectGetType((PetscObject)A,&mattypename);
CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"Matrix of type: %s\n",mattypename);
CHKERRQ(ierr);
ierr = MatView(E,viewer);
CHKERRQ(ierr);
ierr = MatMult(A,Z,W1);
CHKERRQ(ierr);
ierr = MatMultTranspose(A,W1,W2);
CHKERRQ(ierr);
ierr = VecView(W2,viewer);
CHKERRQ(ierr);
ierr = MatGetDiagonal(A,W2);
CHKERRQ(ierr);
ierr = VecView(W2,viewer);
CHKERRQ(ierr);
ierr = MatDestroy(&E);
CHKERRQ(ierr);
ierr = VecDestroy(&W1);
CHKERRQ(ierr);
ierr = VecDestroy(&W2);
CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*
SampleShellPCSetUp - This routine sets up a user-defined
preconditioner context.
Input Parameters:
. pc - preconditioner object
. pmat - preconditioner matrix
. x - vector
Output Parameter:
. shell - fully set up user-defined preconditioner context
Notes:
In this example, we define the shell preconditioner to be Jacobi's
method. Thus, here we create a work vector for storing the reciprocal
of the diagonal of the preconditioner matrix; this vector is then
used within the routine SampleShellPCApply().
*/
PetscErrorCode SampleShellPCSetUp(PC pc,Mat pmat,Vec x)
{
SampleShellPC *shell;
Vec diag;
PetscErrorCode ierr;
ierr = PCShellGetContext(pc,(void**)&shell);CHKERRQ(ierr);
ierr = VecDuplicate(x,&diag);CHKERRQ(ierr);
ierr = MatGetDiagonal(pmat,diag);CHKERRQ(ierr);
ierr = VecReciprocal(diag);CHKERRQ(ierr);
shell->diag = diag;
return 0;
}
/*@C
TaoMatGetSubMat - Gets a submatrix using the IS
Input Parameters:
+ M - the full matrix (n x n)
. is - the index set for the submatrix (both row and column index sets need to be the same)
. v1 - work vector of dimension n, needed for TAO_SUBSET_MASK option
- subset_type - the method TAO is using for subsetting (TAO_SUBSET_SUBVEC, TAO_SUBSET_MASK,
TAO_SUBSET_MATRIXFREE)
Output Parameters:
. Msub - the submatrix
@*/
PetscErrorCode TaoMatGetSubMat(Mat M, IS is, Vec v1, TaoSubsetType subset_type, Mat *Msub)
{
PetscErrorCode ierr;
IS iscomp;
PetscBool flg = PETSC_FALSE;
PetscFunctionBegin;
PetscValidHeaderSpecific(M,MAT_CLASSID,1);
PetscValidHeaderSpecific(is,IS_CLASSID,2);
ierr = MatDestroy(Msub);CHKERRQ(ierr);
switch (subset_type) {
case TAO_SUBSET_SUBVEC:
ierr = MatGetSubMatrix(M, is, is, MAT_INITIAL_MATRIX, Msub);CHKERRQ(ierr);
break;
case TAO_SUBSET_MASK:
/* Get Reduced Hessian
Msub[i,j] = M[i,j] if i,j in Free_Local or i==j
Msub[i,j] = 0 if i!=j and i or j not in Free_Local
*/
ierr = PetscOptionsBegin(PetscObjectComm((PetscObject)M),NULL,NULL,NULL);CHKERRQ(ierr);
ierr = PetscOptionsBool("-different_submatrix","use separate hessian matrix when computing submatrices","TaoSubsetType",flg,&flg,NULL);CHKERRQ(ierr);
ierr = PetscOptionsEnd();CHKERRQ(ierr);
if (flg) {
ierr = MatDuplicate(M, MAT_COPY_VALUES, Msub);CHKERRQ(ierr);
} else {
/* Act on hessian directly (default) */
ierr = PetscObjectReference((PetscObject)M);CHKERRQ(ierr);
*Msub = M;
}
/* Save the diagonal to temporary vector */
ierr = MatGetDiagonal(*Msub,v1);CHKERRQ(ierr);
/* Zero out rows and columns */
ierr = ISComplementVec(is,v1,&iscomp);CHKERRQ(ierr);
/* Use v1 instead of 0 here because of PETSc bug */
ierr = MatZeroRowsColumnsIS(*Msub,iscomp,1.0,v1,v1);CHKERRQ(ierr);
ierr = ISDestroy(&iscomp);CHKERRQ(ierr);
break;
case TAO_SUBSET_MATRIXFREE:
ierr = ISComplementVec(is,v1,&iscomp);CHKERRQ(ierr);
ierr = MatCreateSubMatrixFree(M,iscomp,iscomp,Msub);CHKERRQ(ierr);
ierr = ISDestroy(&iscomp);CHKERRQ(ierr);
break;
}
PetscFunctionReturn(0);
}
PetscErrorCode MatGetDiagonal_IS(Mat A, Vec v)
{
Mat_IS *is = (Mat_IS*)A->data;
PetscErrorCode ierr;
PetscFunctionBegin;
/* get diagonal of the local matrix */
ierr = MatGetDiagonal(is->A,is->y);CHKERRQ(ierr);
/* scatter diagonal back into global vector */
ierr = VecSet(v,0);CHKERRQ(ierr);
ierr = VecScatterBegin(is->rctx,is->y,v,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr);
ierr = VecScatterEnd(is->rctx,is->y,v,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
void
NRSolver :: applyConstraintsToStiffness(SparseMtrx &k)
{
if ( this->smConstraintVersion == k.giveVersion() ) {
return;
}
#ifdef __PETSC_MODULE
PetscSparseMtrx *lhs = dynamic_cast< PetscSparseMtrx * >(&k);
if ( lhs ) {
Vec diag;
PetscScalar *ptr;
int eq;
lhs->createVecGlobal(& diag);
MatGetDiagonal(* lhs->giveMtrx(), diag);
VecGetArray(diag, & ptr);
for ( int i = 1; i <= numberOfPrescribedDofs; i++ ) {
eq = prescribedEqs.at(i) - 1;
MatSetValue(* ( lhs->giveMtrx() ), eq, eq, ptr [ eq ] * 1.e6, INSERT_VALUES);
}
MatAssemblyBegin(* lhs->giveMtrx(), MAT_FINAL_ASSEMBLY);
MatAssemblyEnd(* lhs->giveMtrx(), MAT_FINAL_ASSEMBLY);
VecRestoreArray(diag, & ptr);
VecDestroy(& diag);
if ( numberOfPrescribedDofs ) {
this->smConstraintVersion = k.giveVersion();
}
return;
}
#endif // __PETSC_MODULE
for ( int i = 1; i <= numberOfPrescribedDofs; i++ ) {
k.at( prescribedEqs.at(i), prescribedEqs.at(i) ) *= 1.e6;
}
if ( numberOfPrescribedDofs ) {
this->smConstraintVersion = k.giveVersion();
}
}
void PetscMatrix<T>::get_diagonal (NumericVector<T>& dest) const
{
// Make sure the NumericVector passed in is really a PetscVector
PetscVector<T>& petsc_dest = libmesh_cast_ref<PetscVector<T>&>(dest);
// Call PETSc function.
#if PETSC_VERSION_LESS_THAN(2,3,1)
libMesh::out << "This method has been developed with PETSc 2.3.1. "
<< "No one has made it backwards compatible with older "
<< "versions of PETSc so far; however, it might work "
<< "without any change with some older version." << std::endl;
libmesh_error();
#else
// Needs a const_cast since PETSc does not work with const.
PetscErrorCode ierr =
MatGetDiagonal(const_cast<PetscMatrix<T>*>(this)->mat(),petsc_dest.vec()); LIBMESH_CHKERRABORT(ierr);
#endif
}
int Epetra_PETScAIJMatrix::ExtractDiagonalCopy(Epetra_Vector & Diagonal) const
{
//TODO optimization: only get this diagonal once
Vec petscDiag;
double *vals=0;
int length;
int ierr=VecCreate(Comm_->Comm(),&petscDiag);CHKERRQ(ierr);
VecSetSizes(petscDiag,NumMyRows_,NumGlobalRows_);
# ifdef HAVE_MPI
ierr = VecSetType(petscDiag,VECMPI);CHKERRQ(ierr);
# else //TODO untested!!
VecSetType(petscDiag,VECSEQ);
# endif
MatGetDiagonal(Amat_, petscDiag);
VecGetArray(petscDiag,&vals);
VecGetLocalSize(petscDiag,&length);
for (int i=0; i<length; i++) Diagonal[i] = vals[i];
VecRestoreArray(petscDiag,&vals);
VecDestroy(petscDiag);
return(0);
}
/* Developer Notes: This should be implemented with a MatCreate_SchurComplement() as that is the standard design for new Mat classes. */
PetscErrorCode MatGetSchurComplement_Basic(Mat mat,IS isrow0,IS iscol0,IS isrow1,IS iscol1,MatReuse mreuse,Mat *newmat,MatReuse preuse,Mat *newpmat)
{
PetscErrorCode ierr;
Mat A=0,Ap=0,B=0,C=0,D=0;
PetscFunctionBegin;
PetscValidHeaderSpecific(mat,MAT_CLASSID,1);
PetscValidHeaderSpecific(isrow0,IS_CLASSID,2);
PetscValidHeaderSpecific(iscol0,IS_CLASSID,3);
PetscValidHeaderSpecific(isrow1,IS_CLASSID,4);
PetscValidHeaderSpecific(iscol1,IS_CLASSID,5);
if (mreuse == MAT_REUSE_MATRIX) PetscValidHeaderSpecific(*newmat,MAT_CLASSID,7);
if (preuse == MAT_REUSE_MATRIX) PetscValidHeaderSpecific(*newpmat,MAT_CLASSID,9);
PetscValidType(mat,1);
if (mat->factortype) SETERRQ(((PetscObject)mat)->comm,PETSC_ERR_ARG_WRONGSTATE,"Not for factored matrix");
if (mreuse != MAT_IGNORE_MATRIX) {
/* Use MatSchurComplement */
if (mreuse == MAT_REUSE_MATRIX) {
ierr = MatSchurComplementGetSubmatrices(*newmat,&A,&Ap,&B,&C,&D);CHKERRQ(ierr);
if (!A || !Ap || !B || !C) SETERRQ(((PetscObject)mat)->comm,PETSC_ERR_ARG_WRONGSTATE,"Attempting to reuse matrix but Schur complement matrices unset");
if (A != Ap) SETERRQ(((PetscObject)mat)->comm,PETSC_ERR_ARG_WRONGSTATE,"Preconditioning matrix does not match operator");
ierr = MatDestroy(&Ap);CHKERRQ(ierr); /* get rid of extra reference */
}
ierr = MatGetSubMatrix(mat,isrow0,iscol0,mreuse,&A);CHKERRQ(ierr);
ierr = MatGetSubMatrix(mat,isrow0,iscol1,mreuse,&B);CHKERRQ(ierr);
ierr = MatGetSubMatrix(mat,isrow1,iscol0,mreuse,&C);CHKERRQ(ierr);
ierr = MatGetSubMatrix(mat,isrow1,iscol1,mreuse,&D);CHKERRQ(ierr);
switch (mreuse) {
case MAT_INITIAL_MATRIX:
ierr = MatCreateSchurComplement(A,A,B,C,D,newmat);CHKERRQ(ierr);
break;
case MAT_REUSE_MATRIX:
ierr = MatSchurComplementUpdate(*newmat,A,A,B,C,D,DIFFERENT_NONZERO_PATTERN);CHKERRQ(ierr);
break;
default:
SETERRQ(((PetscObject)mat)->comm,PETSC_ERR_SUP,"Unrecognized value of mreuse");
}
}
if (preuse != MAT_IGNORE_MATRIX) {
/* Use the diagonal part of A to form D - C inv(diag(A)) B */
Mat Ad,AdB,S;
Vec diag;
PetscInt i,m,n,mstart,mend;
PetscScalar *x;
/* We could compose these with newpmat so that the matrices can be reused. */
if (!A) {ierr = MatGetSubMatrix(mat,isrow0,iscol0,MAT_INITIAL_MATRIX,&A);CHKERRQ(ierr);}
if (!B) {ierr = MatGetSubMatrix(mat,isrow0,iscol1,MAT_INITIAL_MATRIX,&B);CHKERRQ(ierr);}
if (!C) {ierr = MatGetSubMatrix(mat,isrow1,iscol0,MAT_INITIAL_MATRIX,&C);CHKERRQ(ierr);}
if (!D) {ierr = MatGetSubMatrix(mat,isrow1,iscol1,MAT_INITIAL_MATRIX,&D);CHKERRQ(ierr);}
ierr = MatGetVecs(A,&diag,PETSC_NULL);CHKERRQ(ierr);
ierr = MatGetDiagonal(A,diag);CHKERRQ(ierr);
ierr = VecReciprocal(diag);CHKERRQ(ierr);
ierr = MatGetLocalSize(A,&m,&n);CHKERRQ(ierr);
/* We need to compute S = D - C inv(diag(A)) B. For row-oriented formats, it is easy to scale the rows of B and
* for column-oriented formats the columns of C can be scaled. Would skip creating a silly diagonal matrix. */
ierr = MatCreate(((PetscObject)A)->comm,&Ad);CHKERRQ(ierr);
ierr = MatSetSizes(Ad,m,n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr);
ierr = MatSetOptionsPrefix(Ad,((PetscObject)mat)->prefix);CHKERRQ(ierr);
ierr = MatAppendOptionsPrefix(Ad,"diag_");CHKERRQ(ierr);
ierr = MatSetFromOptions(Ad);CHKERRQ(ierr);
ierr = MatSeqAIJSetPreallocation(Ad,1,PETSC_NULL);CHKERRQ(ierr);
ierr = MatMPIAIJSetPreallocation(Ad,1,PETSC_NULL,0,PETSC_NULL);CHKERRQ(ierr);
ierr = MatGetOwnershipRange(Ad,&mstart,&mend);CHKERRQ(ierr);
ierr = VecGetArray(diag,&x);CHKERRQ(ierr);
for (i=mstart; i<mend; i++) {
ierr = MatSetValue(Ad,i,i,x[i-mstart],INSERT_VALUES);CHKERRQ(ierr);
}
ierr = VecRestoreArray(diag,&x);CHKERRQ(ierr);
ierr = MatAssemblyBegin(Ad,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(Ad,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = VecDestroy(&diag);CHKERRQ(ierr);
ierr = MatMatMult(Ad,B,MAT_INITIAL_MATRIX,1,&AdB);CHKERRQ(ierr);
S = (preuse == MAT_REUSE_MATRIX) ? *newpmat : (Mat)0;
ierr = MatMatMult(C,AdB,preuse,PETSC_DEFAULT,&S);CHKERRQ(ierr);
ierr = MatAYPX(S,-1,D,DIFFERENT_NONZERO_PATTERN);CHKERRQ(ierr);
*newpmat = S;
ierr = MatDestroy(&Ad);CHKERRQ(ierr);
ierr = MatDestroy(&AdB);CHKERRQ(ierr);
}
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = MatDestroy(&B);CHKERRQ(ierr);
ierr = MatDestroy(&C);CHKERRQ(ierr);
ierr = MatDestroy(&D);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
int main(int argc,char **args)
{
Vec x,y,u,s1,s2;
Mat A,sA,sB;
PetscRandom rctx;
PetscReal r1,r2,rnorm,tol = PETSC_SQRT_MACHINE_EPSILON;
PetscScalar one=1.0, neg_one=-1.0, value[3], four=4.0,alpha=0.1;
PetscInt n,col[3],n1,block,row,i,j,i2,j2,Ii,J,rstart,rend,bs=1,mbs=16,d_nz=3,o_nz=3,prob=2;
PetscErrorCode ierr;
PetscMPIInt size,rank;
PetscBool flg;
MatType type;
ierr = PetscInitialize(&argc,&args,(char*)0,help);
if (ierr) return ierr;
ierr = PetscOptionsGetInt(NULL,NULL,"-mbs",&mbs,NULL);
CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-bs",&bs,NULL);
CHKERRQ(ierr);
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);
CHKERRQ(ierr);
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);
CHKERRQ(ierr);
n = mbs*bs;
/* Assemble MPISBAIJ matrix sA */
ierr = MatCreate(PETSC_COMM_WORLD,&sA);
CHKERRQ(ierr);
ierr = MatSetSizes(sA,PETSC_DECIDE,PETSC_DECIDE,n,n);
CHKERRQ(ierr);
ierr = MatSetType(sA,MATSBAIJ);
CHKERRQ(ierr);
ierr = MatSetFromOptions(sA);
CHKERRQ(ierr);
ierr = MatGetType(sA,&type);
CHKERRQ(ierr);
ierr = MatMPISBAIJSetPreallocation(sA,bs,d_nz,NULL,o_nz,NULL);
CHKERRQ(ierr);
ierr = MatSeqSBAIJSetPreallocation(sA,bs,d_nz,NULL);
CHKERRQ(ierr);
ierr = MatSetOption(sA,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_FALSE);
CHKERRQ(ierr);
if (bs == 1) {
if (prob == 1) { /* tridiagonal matrix */
value[0] = -1.0;
value[1] = 2.0;
value[2] = -1.0;
for (i=1; i<n-1; i++) {
col[0] = i-1;
col[1] = i;
col[2] = i+1;
ierr = MatSetValues(sA,1,&i,3,col,value,INSERT_VALUES);
CHKERRQ(ierr);
}
i = n - 1;
col[0]=0;
col[1] = n - 2;
col[2] = n - 1;
value[0]= 0.1;
value[1]=-1;
value[2]=2;
ierr = MatSetValues(sA,1,&i,3,col,value,INSERT_VALUES);
CHKERRQ(ierr);
i = 0;
col[0] = 0;
col[1] = 1;
col[2]=n-1;
value[0] = 2.0;
value[1] = -1.0;
value[2]=0.1;
ierr = MatSetValues(sA,1,&i,3,col,value,INSERT_VALUES);
CHKERRQ(ierr);
} else if (prob ==2) { /* matrix for the five point stencil */
n1 = (int) PetscSqrtReal((PetscReal)n);
if (n1*n1 != n) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"n must be a perfect square of n1");
for (i=0; i<n1; i++) {
for (j=0; j<n1; j++) {
Ii = j + n1*i;
if (i>0) {
J = Ii - n1;
ierr = MatSetValues(sA,1,&Ii,1,&J,&neg_one,INSERT_VALUES);
CHKERRQ(ierr);
}
if (i<n1-1) {
J = Ii + n1;
ierr = MatSetValues(sA,1,&Ii,1,&J,&neg_one,INSERT_VALUES);
CHKERRQ(ierr);
}
if (j>0) {
J = Ii - 1;
ierr = MatSetValues(sA,1,&Ii,1,&J,&neg_one,INSERT_VALUES);
CHKERRQ(ierr);
}
if (j<n1-1) {
J = Ii + 1;
ierr = MatSetValues(sA,1,&Ii,1,&J,&neg_one,INSERT_VALUES);
CHKERRQ(ierr);
}
ierr = MatSetValues(sA,1,&Ii,1,&Ii,&four,INSERT_VALUES);
CHKERRQ(ierr);
}
}
}
/* end of if (bs == 1) */
} else { /* bs > 1 */
for (block=0; block<n/bs; block++) {
/* diagonal blocks */
value[0] = -1.0;
value[1] = 4.0;
value[2] = -1.0;
for (i=1+block*bs; i<bs-1+block*bs; i++) {
col[0] = i-1;
col[1] = i;
col[2] = i+1;
ierr = MatSetValues(sA,1,&i,3,col,value,INSERT_VALUES);
CHKERRQ(ierr);
}
i = bs - 1+block*bs;
col[0] = bs - 2+block*bs;
col[1] = bs - 1+block*bs;
value[0]=-1.0;
value[1]=4.0;
ierr = MatSetValues(sA,1,&i,2,col,value,INSERT_VALUES);
CHKERRQ(ierr);
i = 0+block*bs;
col[0] = 0+block*bs;
col[1] = 1+block*bs;
value[0]=4.0;
value[1] = -1.0;
ierr = MatSetValues(sA,1,&i,2,col,value,INSERT_VALUES);
CHKERRQ(ierr);
}
/* off-diagonal blocks */
value[0]=-1.0;
for (i=0; i<(n/bs-1)*bs; i++) {
col[0]=i+bs;
ierr = MatSetValues(sA,1,&i,1,col,value,INSERT_VALUES);
CHKERRQ(ierr);
col[0]=i;
row=i+bs;
ierr = MatSetValues(sA,1,&row,1,col,value,INSERT_VALUES);
CHKERRQ(ierr);
}
}
ierr = MatAssemblyBegin(sA,MAT_FINAL_ASSEMBLY);
CHKERRQ(ierr);
ierr = MatAssemblyEnd(sA,MAT_FINAL_ASSEMBLY);
CHKERRQ(ierr);
/* Test MatView() */
ierr = MatCreateBAIJ(PETSC_COMM_WORLD,bs,PETSC_DECIDE,PETSC_DECIDE,n,n,d_nz,NULL,o_nz,NULL,&A);
CHKERRQ(ierr);
ierr = MatSetOption(A,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_FALSE);
CHKERRQ(ierr);
if (bs == 1) {
if (prob == 1) { /* tridiagonal matrix */
value[0] = -1.0;
value[1] = 2.0;
value[2] = -1.0;
for (i=1; i<n-1; i++) {
col[0] = i-1;
col[1] = i;
col[2] = i+1;
ierr = MatSetValues(A,1,&i,3,col,value,INSERT_VALUES);
CHKERRQ(ierr);
}
i = n - 1;
col[0]=0;
col[1] = n - 2;
col[2] = n - 1;
value[0]= 0.1;
value[1]=-1;
value[2]=2;
ierr = MatSetValues(A,1,&i,3,col,value,INSERT_VALUES);
CHKERRQ(ierr);
i = 0;
col[0] = 0;
col[1] = 1;
col[2]=n-1;
value[0] = 2.0;
value[1] = -1.0;
value[2]=0.1;
ierr = MatSetValues(A,1,&i,3,col,value,INSERT_VALUES);
CHKERRQ(ierr);
} else if (prob ==2) { /* matrix for the five point stencil */
n1 = (int) PetscSqrtReal((PetscReal)n);
for (i=0; i<n1; i++) {
for (j=0; j<n1; j++) {
Ii = j + n1*i;
if (i>0) {
J = Ii - n1;
ierr = MatSetValues(A,1,&Ii,1,&J,&neg_one,INSERT_VALUES);
CHKERRQ(ierr);
}
if (i<n1-1) {
J = Ii + n1;
ierr = MatSetValues(A,1,&Ii,1,&J,&neg_one,INSERT_VALUES);
CHKERRQ(ierr);
}
if (j>0) {
J = Ii - 1;
ierr = MatSetValues(A,1,&Ii,1,&J,&neg_one,INSERT_VALUES);
CHKERRQ(ierr);
}
if (j<n1-1) {
J = Ii + 1;
ierr = MatSetValues(A,1,&Ii,1,&J,&neg_one,INSERT_VALUES);
CHKERRQ(ierr);
}
ierr = MatSetValues(A,1,&Ii,1,&Ii,&four,INSERT_VALUES);
CHKERRQ(ierr);
}
}
}
/* end of if (bs == 1) */
} else { /* bs > 1 */
for (block=0; block<n/bs; block++) {
/* diagonal blocks */
value[0] = -1.0;
value[1] = 4.0;
value[2] = -1.0;
for (i=1+block*bs; i<bs-1+block*bs; i++) {
col[0] = i-1;
col[1] = i;
col[2] = i+1;
ierr = MatSetValues(A,1,&i,3,col,value,INSERT_VALUES);
CHKERRQ(ierr);
}
i = bs - 1+block*bs;
col[0] = bs - 2+block*bs;
col[1] = bs - 1+block*bs;
value[0]=-1.0;
value[1]=4.0;
ierr = MatSetValues(A,1,&i,2,col,value,INSERT_VALUES);
CHKERRQ(ierr);
i = 0+block*bs;
col[0] = 0+block*bs;
col[1] = 1+block*bs;
value[0]=4.0;
value[1] = -1.0;
ierr = MatSetValues(A,1,&i,2,col,value,INSERT_VALUES);
CHKERRQ(ierr);
}
/* off-diagonal blocks */
value[0]=-1.0;
for (i=0; i<(n/bs-1)*bs; i++) {
col[0]=i+bs;
ierr = MatSetValues(A,1,&i,1,col,value,INSERT_VALUES);
CHKERRQ(ierr);
col[0]=i;
row=i+bs;
ierr = MatSetValues(A,1,&row,1,col,value,INSERT_VALUES);
CHKERRQ(ierr);
}
}
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);
CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);
CHKERRQ(ierr);
/* Test MatGetSize(), MatGetLocalSize() */
ierr = MatGetSize(sA, &i,&j);
CHKERRQ(ierr);
ierr = MatGetSize(A, &i2,&j2);
CHKERRQ(ierr);
i -= i2;
j -= j2;
if (i || j) {
ierr = PetscSynchronizedPrintf(PETSC_COMM_WORLD,"[%d], Error: MatGetSize()\n",rank);
CHKERRQ(ierr);
ierr = PetscSynchronizedFlush(PETSC_COMM_WORLD,PETSC_STDOUT);
CHKERRQ(ierr);
}
ierr = MatGetLocalSize(sA, &i,&j);
CHKERRQ(ierr);
ierr = MatGetLocalSize(A, &i2,&j2);
CHKERRQ(ierr);
i2 -= i;
j2 -= j;
if (i2 || j2) {
ierr = PetscSynchronizedPrintf(PETSC_COMM_WORLD,"[%d], Error: MatGetLocalSize()\n",rank);
CHKERRQ(ierr);
ierr = PetscSynchronizedFlush(PETSC_COMM_WORLD,PETSC_STDOUT);
CHKERRQ(ierr);
}
/* vectors */
/*--------------------*/
/* i is obtained from MatGetLocalSize() */
ierr = VecCreate(PETSC_COMM_WORLD,&x);
CHKERRQ(ierr);
ierr = VecSetSizes(x,i,PETSC_DECIDE);
CHKERRQ(ierr);
ierr = VecSetFromOptions(x);
CHKERRQ(ierr);
ierr = VecDuplicate(x,&y);
CHKERRQ(ierr);
ierr = VecDuplicate(x,&u);
CHKERRQ(ierr);
ierr = VecDuplicate(x,&s1);
CHKERRQ(ierr);
ierr = VecDuplicate(x,&s2);
CHKERRQ(ierr);
ierr = PetscRandomCreate(PETSC_COMM_WORLD,&rctx);
CHKERRQ(ierr);
ierr = PetscRandomSetFromOptions(rctx);
CHKERRQ(ierr);
ierr = VecSetRandom(x,rctx);
CHKERRQ(ierr);
ierr = VecSet(u,one);
CHKERRQ(ierr);
/* Test MatNorm() */
ierr = MatNorm(A,NORM_FROBENIUS,&r1);
CHKERRQ(ierr);
ierr = MatNorm(sA,NORM_FROBENIUS,&r2);
CHKERRQ(ierr);
rnorm = PetscAbsReal(r1-r2)/r2;
if (rnorm > tol && !rank) {
ierr = PetscPrintf(PETSC_COMM_SELF,"Error: MatNorm_FROBENIUS(), Anorm=%16.14e, sAnorm=%16.14e bs=%D\n",r1,r2,bs);
CHKERRQ(ierr);
}
ierr = MatNorm(A,NORM_INFINITY,&r1);
CHKERRQ(ierr);
ierr = MatNorm(sA,NORM_INFINITY,&r2);
CHKERRQ(ierr);
rnorm = PetscAbsReal(r1-r2)/r2;
if (rnorm > tol && !rank) {
ierr = PetscPrintf(PETSC_COMM_WORLD,"Error: MatNorm_INFINITY(), Anorm=%16.14e, sAnorm=%16.14e bs=%D\n",r1,r2,bs);
CHKERRQ(ierr);
}
ierr = MatNorm(A,NORM_1,&r1);
CHKERRQ(ierr);
ierr = MatNorm(sA,NORM_1,&r2);
CHKERRQ(ierr);
rnorm = PetscAbsReal(r1-r2)/r2;
if (rnorm > tol && !rank) {
ierr = PetscPrintf(PETSC_COMM_WORLD,"Error: MatNorm_1(), Anorm=%16.14e, sAnorm=%16.14e bs=%D\n",r1,r2,bs);
CHKERRQ(ierr);
}
/* Test MatGetOwnershipRange() */
ierr = MatGetOwnershipRange(sA,&rstart,&rend);
CHKERRQ(ierr);
ierr = MatGetOwnershipRange(A,&i2,&j2);
CHKERRQ(ierr);
i2 -= rstart;
j2 -= rend;
if (i2 || j2) {
ierr = PetscSynchronizedPrintf(PETSC_COMM_WORLD,"[%d], Error: MaGetOwnershipRange()\n",rank);
CHKERRQ(ierr);
ierr = PetscSynchronizedFlush(PETSC_COMM_WORLD,PETSC_STDOUT);
CHKERRQ(ierr);
}
/* Test MatDiagonalScale() */
ierr = MatDiagonalScale(A,x,x);
CHKERRQ(ierr);
ierr = MatDiagonalScale(sA,x,x);
CHKERRQ(ierr);
ierr = MatMultEqual(A,sA,10,&flg);
CHKERRQ(ierr);
if (!flg) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_NOTSAMETYPE,"Error in MatDiagonalScale");
/* Test MatGetDiagonal(), MatScale() */
ierr = MatGetDiagonal(A,s1);
CHKERRQ(ierr);
ierr = MatGetDiagonal(sA,s2);
CHKERRQ(ierr);
ierr = VecNorm(s1,NORM_1,&r1);
CHKERRQ(ierr);
ierr = VecNorm(s2,NORM_1,&r2);
CHKERRQ(ierr);
r1 -= r2;
if (r1<-tol || r1>tol) {
ierr = PetscSynchronizedPrintf(PETSC_COMM_WORLD,"[%d], Error: MatDiagonalScale() or MatGetDiagonal(), r1=%g \n",rank,(double)r1);
CHKERRQ(ierr);
ierr = PetscSynchronizedFlush(PETSC_COMM_WORLD,PETSC_STDOUT);
CHKERRQ(ierr);
}
ierr = MatScale(A,alpha);
CHKERRQ(ierr);
ierr = MatScale(sA,alpha);
CHKERRQ(ierr);
/* Test MatGetRowMaxAbs() */
ierr = MatGetRowMaxAbs(A,s1,NULL);
CHKERRQ(ierr);
ierr = MatGetRowMaxAbs(sA,s2,NULL);
CHKERRQ(ierr);
ierr = VecNorm(s1,NORM_1,&r1);
CHKERRQ(ierr);
ierr = VecNorm(s2,NORM_1,&r2);
CHKERRQ(ierr);
r1 -= r2;
if (r1<-tol || r1>tol) {
ierr = PetscPrintf(PETSC_COMM_SELF,"Error: MatGetRowMaxAbs() \n");
CHKERRQ(ierr);
}
/* Test MatMult(), MatMultAdd() */
ierr = MatMultEqual(A,sA,10,&flg);
CHKERRQ(ierr);
if (!flg) {
ierr = PetscSynchronizedPrintf(PETSC_COMM_WORLD,"[%d], Error: MatMult() or MatScale()\n",rank);
CHKERRQ(ierr);
ierr = PetscSynchronizedFlush(PETSC_COMM_WORLD,PETSC_STDOUT);
CHKERRQ(ierr);
}
ierr = MatMultAddEqual(A,sA,10,&flg);
CHKERRQ(ierr);
if (!flg) {
ierr = PetscSynchronizedPrintf(PETSC_COMM_WORLD,"[%d], Error: MatMultAdd()\n",rank);
CHKERRQ(ierr);
ierr = PetscSynchronizedFlush(PETSC_COMM_WORLD,PETSC_STDOUT);
CHKERRQ(ierr);
}
/* Test MatMultTranspose(), MatMultTransposeAdd() */
for (i=0; i<10; i++) {
ierr = VecSetRandom(x,rctx);
CHKERRQ(ierr);
ierr = MatMultTranspose(A,x,s1);
CHKERRQ(ierr);
ierr = MatMultTranspose(sA,x,s2);
CHKERRQ(ierr);
ierr = VecNorm(s1,NORM_1,&r1);
CHKERRQ(ierr);
ierr = VecNorm(s2,NORM_1,&r2);
CHKERRQ(ierr);
r1 -= r2;
if (r1<-tol || r1>tol) {
ierr = PetscSynchronizedPrintf(PETSC_COMM_WORLD,"[%d], Error: MatMult() or MatScale(), err=%g\n",rank,(double)r1);
CHKERRQ(ierr);
ierr = PetscSynchronizedFlush(PETSC_COMM_WORLD,PETSC_STDOUT);
CHKERRQ(ierr);
}
}
for (i=0; i<10; i++) {
ierr = VecSetRandom(x,rctx);
CHKERRQ(ierr);
ierr = VecSetRandom(y,rctx);
CHKERRQ(ierr);
ierr = MatMultTransposeAdd(A,x,y,s1);
CHKERRQ(ierr);
ierr = MatMultTransposeAdd(sA,x,y,s2);
CHKERRQ(ierr);
ierr = VecNorm(s1,NORM_1,&r1);
CHKERRQ(ierr);
ierr = VecNorm(s2,NORM_1,&r2);
CHKERRQ(ierr);
r1 -= r2;
if (r1<-tol || r1>tol) {
ierr = PetscSynchronizedPrintf(PETSC_COMM_WORLD,"[%d], Error: MatMultAdd(), err=%g \n",rank,(double)r1);
CHKERRQ(ierr);
ierr = PetscSynchronizedFlush(PETSC_COMM_WORLD,PETSC_STDOUT);
CHKERRQ(ierr);
}
}
/* Test MatDuplicate() */
ierr = MatDuplicate(sA,MAT_COPY_VALUES,&sB);
CHKERRQ(ierr);
ierr = MatEqual(sA,sB,&flg);
CHKERRQ(ierr);
if (!flg) {
ierr = PetscPrintf(PETSC_COMM_WORLD," Error in MatDuplicate(), sA != sB \n");
CHKERRQ(ierr);
CHKERRQ(ierr);
}
ierr = MatMultEqual(sA,sB,5,&flg);
CHKERRQ(ierr);
if (!flg) {
ierr = PetscSynchronizedPrintf(PETSC_COMM_WORLD,"[%d], Error: MatDuplicate() or MatMult()\n",rank);
CHKERRQ(ierr);
ierr = PetscSynchronizedFlush(PETSC_COMM_WORLD,PETSC_STDOUT);
CHKERRQ(ierr);
}
ierr = MatMultAddEqual(sA,sB,5,&flg);
CHKERRQ(ierr);
if (!flg) {
ierr = PetscSynchronizedPrintf(PETSC_COMM_WORLD,"[%d], Error: MatDuplicate() or MatMultAdd(()\n",rank);
CHKERRQ(ierr);
ierr = PetscSynchronizedFlush(PETSC_COMM_WORLD,PETSC_STDOUT);
CHKERRQ(ierr);
}
ierr = MatDestroy(&sB);
CHKERRQ(ierr);
ierr = VecDestroy(&u);
CHKERRQ(ierr);
ierr = VecDestroy(&x);
CHKERRQ(ierr);
ierr = VecDestroy(&y);
CHKERRQ(ierr);
ierr = VecDestroy(&s1);
CHKERRQ(ierr);
ierr = VecDestroy(&s2);
CHKERRQ(ierr);
ierr = MatDestroy(&sA);
CHKERRQ(ierr);
ierr = MatDestroy(&A);
CHKERRQ(ierr);
ierr = PetscRandomDestroy(&rctx);
CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
int main(int argc,char **args)
{
PetscMPIInt size;
PetscErrorCode ierr;
Vec x,y,b,s1,s2;
Mat A; /* linear system matrix */
Mat sA,sB,sC; /* symmetric part of the matrices */
PetscInt n,mbs=16,bs=1,nz=3,prob=1,i,j,k1,k2,col[3],lf,block, row,Ii,J,n1,inc;
PetscReal norm1,norm2,rnorm,tol=PETSC_SMALL;
PetscScalar neg_one = -1.0,four=4.0,value[3];
IS perm, iscol;
PetscRandom rdm;
PetscBool doIcc=PETSC_TRUE,equal;
MatInfo minfo1,minfo2;
MatFactorInfo factinfo;
MatType type;
PetscInitialize(&argc,&args,(char*)0,help);
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
if (size != 1) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_SUP,"This is a uniprocessor example only!");
ierr = PetscOptionsGetInt(NULL,"-bs",&bs,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,"-mbs",&mbs,NULL);CHKERRQ(ierr);
n = mbs*bs;
ierr = MatCreate(PETSC_COMM_SELF,&A);CHKERRQ(ierr);
ierr = MatSetSizes(A,n,n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr);
ierr = MatSetType(A,MATSEQBAIJ);CHKERRQ(ierr);
ierr = MatSetFromOptions(A);CHKERRQ(ierr);
ierr = MatSeqBAIJSetPreallocation(A,bs,nz,NULL);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_SELF,&sA);CHKERRQ(ierr);
ierr = MatSetSizes(sA,n,n,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr);
ierr = MatSetType(sA,MATSEQSBAIJ);CHKERRQ(ierr);
ierr = MatSetFromOptions(sA);CHKERRQ(ierr);
ierr = MatGetType(sA,&type);CHKERRQ(ierr);
ierr = PetscObjectTypeCompare((PetscObject)sA,MATSEQSBAIJ,&doIcc);CHKERRQ(ierr);
ierr = MatSeqSBAIJSetPreallocation(sA,bs,nz,NULL);CHKERRQ(ierr);
ierr = MatSetOption(sA,MAT_IGNORE_LOWER_TRIANGULAR,PETSC_TRUE);CHKERRQ(ierr);
/* Test MatGetOwnershipRange() */
ierr = MatGetOwnershipRange(A,&Ii,&J);CHKERRQ(ierr);
ierr = MatGetOwnershipRange(sA,&i,&j);CHKERRQ(ierr);
if (i-Ii || j-J) {
ierr = PetscPrintf(PETSC_COMM_SELF,"Error: MatGetOwnershipRange() in MatSBAIJ format\n");CHKERRQ(ierr);
}
/* Assemble matrix */
if (bs == 1) {
ierr = PetscOptionsGetInt(NULL,"-test_problem",&prob,NULL);CHKERRQ(ierr);
if (prob == 1) { /* tridiagonal matrix */
value[0] = -1.0; value[1] = 2.0; value[2] = -1.0;
for (i=1; i<n-1; i++) {
col[0] = i-1; col[1] = i; col[2] = i+1;
ierr = MatSetValues(A,1,&i,3,col,value,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatSetValues(sA,1,&i,3,col,value,INSERT_VALUES);CHKERRQ(ierr);
}
i = n - 1; col[0]=0; col[1] = n - 2; col[2] = n - 1;
value[0]= 0.1; value[1]=-1; value[2]=2;
ierr = MatSetValues(A,1,&i,3,col,value,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatSetValues(sA,1,&i,3,col,value,INSERT_VALUES);CHKERRQ(ierr);
i = 0;
col[0] = n-1; col[1] = 1; col[2] = 0;
value[0] = 0.1; value[1] = -1.0; value[2] = 2;
ierr = MatSetValues(A,1,&i,3,col,value,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatSetValues(sA,1,&i,3,col,value,INSERT_VALUES);CHKERRQ(ierr);
} else if (prob ==2) { /* matrix for the five point stencil */
n1 = (PetscInt) (PetscSqrtReal((PetscReal)n) + 0.001);
if (n1*n1 - n) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"sqrt(n) must be a positive interger!");
for (i=0; i<n1; i++) {
for (j=0; j<n1; j++) {
Ii = j + n1*i;
if (i>0) {
J = Ii - n1;
ierr = MatSetValues(A,1,&Ii,1,&J,&neg_one,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatSetValues(sA,1,&Ii,1,&J,&neg_one,INSERT_VALUES);CHKERRQ(ierr);
}
if (i<n1-1) {
J = Ii + n1;
ierr = MatSetValues(A,1,&Ii,1,&J,&neg_one,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatSetValues(sA,1,&Ii,1,&J,&neg_one,INSERT_VALUES);CHKERRQ(ierr);
}
if (j>0) {
J = Ii - 1;
ierr = MatSetValues(A,1,&Ii,1,&J,&neg_one,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatSetValues(sA,1,&Ii,1,&J,&neg_one,INSERT_VALUES);CHKERRQ(ierr);
}
if (j<n1-1) {
J = Ii + 1;
ierr = MatSetValues(A,1,&Ii,1,&J,&neg_one,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatSetValues(sA,1,&Ii,1,&J,&neg_one,INSERT_VALUES);CHKERRQ(ierr);
}
ierr = MatSetValues(A,1,&Ii,1,&Ii,&four,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatSetValues(sA,1,&Ii,1,&Ii,&four,INSERT_VALUES);CHKERRQ(ierr);
}
}
}
} else { /* bs > 1 */
for (block=0; block<n/bs; block++) {
/* diagonal blocks */
value[0] = -1.0; value[1] = 4.0; value[2] = -1.0;
for (i=1+block*bs; i<bs-1+block*bs; i++) {
col[0] = i-1; col[1] = i; col[2] = i+1;
ierr = MatSetValues(A,1,&i,3,col,value,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatSetValues(sA,1,&i,3,col,value,INSERT_VALUES);CHKERRQ(ierr);
}
i = bs - 1+block*bs; col[0] = bs - 2+block*bs; col[1] = bs - 1+block*bs;
value[0]=-1.0; value[1]=4.0;
ierr = MatSetValues(A,1,&i,2,col,value,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatSetValues(sA,1,&i,2,col,value,INSERT_VALUES);CHKERRQ(ierr);
i = 0+block*bs; col[0] = 0+block*bs; col[1] = 1+block*bs;
value[0]=4.0; value[1] = -1.0;
ierr = MatSetValues(A,1,&i,2,col,value,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatSetValues(sA,1,&i,2,col,value,INSERT_VALUES);CHKERRQ(ierr);
}
/* off-diagonal blocks */
value[0]=-1.0;
for (i=0; i<(n/bs-1)*bs; i++) {
col[0]=i+bs;
ierr = MatSetValues(A,1,&i,1,col,value,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatSetValues(sA,1,&i,1,col,value,INSERT_VALUES);CHKERRQ(ierr);
col[0]=i; row=i+bs;
ierr = MatSetValues(A,1,&row,1,col,value,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatSetValues(sA,1,&row,1,col,value,INSERT_VALUES);CHKERRQ(ierr);
}
}
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyBegin(sA,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(sA,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
/* Test MatGetInfo() of A and sA */
ierr = MatGetInfo(A,MAT_LOCAL,&minfo1);CHKERRQ(ierr);
ierr = MatGetInfo(sA,MAT_LOCAL,&minfo2);CHKERRQ(ierr);
/*
printf("A matrix nonzeros (BAIJ format) = %d, allocated nonzeros= %d\n", (int)minfo1.nz_used,(int)minfo1.nz_allocated);
printf("sA matrix nonzeros(SBAIJ format) = %d, allocated nonzeros= %d\n", (int)minfo2.nz_used,(int)minfo2.nz_allocated);
*/
i = (int) (minfo1.nz_used - minfo2.nz_used);
j = (int) (minfo1.nz_allocated - minfo2.nz_allocated);
k1 = (int) (minfo1.nz_allocated - minfo1.nz_used);
k2 = (int) (minfo2.nz_allocated - minfo2.nz_used);
if (i < 0 || j < 0 || k1 < 0 || k2 < 0) {
ierr = PetscPrintf(PETSC_COMM_SELF,"Error (compare A and sA): MatGetInfo()\n");CHKERRQ(ierr);
}
/* Test MatDuplicate() */
ierr = MatNorm(A,NORM_FROBENIUS,&norm1);CHKERRQ(ierr);
ierr = MatDuplicate(sA,MAT_COPY_VALUES,&sB);CHKERRQ(ierr);
ierr = MatEqual(sA,sB,&equal);CHKERRQ(ierr);
if (!equal) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_NOTSAMETYPE,"Error in MatDuplicate()");
/* Test MatNorm() */
ierr = MatNorm(A,NORM_FROBENIUS,&norm1);CHKERRQ(ierr);
ierr = MatNorm(sB,NORM_FROBENIUS,&norm2);CHKERRQ(ierr);
rnorm = PetscAbsReal(norm1-norm2)/norm2;
if (rnorm > tol) {
ierr = PetscPrintf(PETSC_COMM_SELF,"Error: MatNorm_FROBENIUS, NormA=%16.14e NormsB=%16.14e\n",norm1,norm2);CHKERRQ(ierr);
}
ierr = MatNorm(A,NORM_INFINITY,&norm1);CHKERRQ(ierr);
ierr = MatNorm(sB,NORM_INFINITY,&norm2);CHKERRQ(ierr);
rnorm = PetscAbsReal(norm1-norm2)/norm2;
if (rnorm > tol) {
ierr = PetscPrintf(PETSC_COMM_SELF,"Error: MatNorm_INFINITY(), NormA=%16.14e NormsB=%16.14e\n",norm1,norm2);CHKERRQ(ierr);
}
ierr = MatNorm(A,NORM_1,&norm1);CHKERRQ(ierr);
ierr = MatNorm(sB,NORM_1,&norm2);CHKERRQ(ierr);
rnorm = PetscAbsReal(norm1-norm2)/norm2;
if (rnorm > tol) {
ierr = PetscPrintf(PETSC_COMM_SELF,"Error: MatNorm_INFINITY(), NormA=%16.14e NormsB=%16.14e\n",norm1,norm2);CHKERRQ(ierr);
}
/* Test MatGetInfo(), MatGetSize(), MatGetBlockSize() */
ierr = MatGetInfo(A,MAT_LOCAL,&minfo1);CHKERRQ(ierr);
ierr = MatGetInfo(sB,MAT_LOCAL,&minfo2);CHKERRQ(ierr);
/*
printf("matrix nonzeros (BAIJ format) = %d, allocated nonzeros= %d\n", (int)minfo1.nz_used,(int)minfo1.nz_allocated);
printf("matrix nonzeros(SBAIJ format) = %d, allocated nonzeros= %d\n", (int)minfo2.nz_used,(int)minfo2.nz_allocated);
*/
i = (int) (minfo1.nz_used - minfo2.nz_used);
j = (int) (minfo1.nz_allocated - minfo2.nz_allocated);
k1 = (int) (minfo1.nz_allocated - minfo1.nz_used);
k2 = (int) (minfo2.nz_allocated - minfo2.nz_used);
if (i < 0 || j < 0 || k1 < 0 || k2 < 0) {
ierr = PetscPrintf(PETSC_COMM_SELF,"Error(compare A and sB): MatGetInfo()\n");CHKERRQ(ierr);
}
ierr = MatGetSize(A,&Ii,&J);CHKERRQ(ierr);
ierr = MatGetSize(sB,&i,&j);CHKERRQ(ierr);
if (i-Ii || j-J) {
PetscPrintf(PETSC_COMM_SELF,"Error: MatGetSize()\n");CHKERRQ(ierr);
}
ierr = MatGetBlockSize(A, &Ii);CHKERRQ(ierr);
ierr = MatGetBlockSize(sB, &i);CHKERRQ(ierr);
if (i-Ii) {
ierr = PetscPrintf(PETSC_COMM_SELF,"Error: MatGetBlockSize()\n");CHKERRQ(ierr);
}
ierr = PetscRandomCreate(PETSC_COMM_SELF,&rdm);CHKERRQ(ierr);
ierr = PetscRandomSetFromOptions(rdm);CHKERRQ(ierr);
ierr = VecCreateSeq(PETSC_COMM_SELF,n,&x);CHKERRQ(ierr);
ierr = VecDuplicate(x,&s1);CHKERRQ(ierr);
ierr = VecDuplicate(x,&s2);CHKERRQ(ierr);
ierr = VecDuplicate(x,&y);CHKERRQ(ierr);
ierr = VecDuplicate(x,&b);CHKERRQ(ierr);
ierr = VecSetRandom(x,rdm);CHKERRQ(ierr);
/* Test MatDiagonalScale(), MatGetDiagonal(), MatScale() */
#if !defined(PETSC_USE_COMPLEX)
/* Scaling matrix with complex numbers results non-spd matrix,
causing crash of MatForwardSolve() and MatBackwardSolve() */
ierr = MatDiagonalScale(A,x,x);CHKERRQ(ierr);
ierr = MatDiagonalScale(sB,x,x);CHKERRQ(ierr);
ierr = MatMultEqual(A,sB,10,&equal);CHKERRQ(ierr);
if (!equal) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_NOTSAMETYPE,"Error in MatDiagonalScale");
ierr = MatGetDiagonal(A,s1);CHKERRQ(ierr);
ierr = MatGetDiagonal(sB,s2);CHKERRQ(ierr);
ierr = VecAXPY(s2,neg_one,s1);CHKERRQ(ierr);
ierr = VecNorm(s2,NORM_1,&norm1);CHKERRQ(ierr);
if (norm1>tol) {
ierr = PetscPrintf(PETSC_COMM_SELF,"Error:MatGetDiagonal(), ||s1-s2||=%G\n",norm1);CHKERRQ(ierr);
}
{
PetscScalar alpha=0.1;
ierr = MatScale(A,alpha);CHKERRQ(ierr);
ierr = MatScale(sB,alpha);CHKERRQ(ierr);
}
#endif
/* Test MatGetRowMaxAbs() */
ierr = MatGetRowMaxAbs(A,s1,NULL);CHKERRQ(ierr);
ierr = MatGetRowMaxAbs(sB,s2,NULL);CHKERRQ(ierr);
ierr = VecNorm(s1,NORM_1,&norm1);CHKERRQ(ierr);
ierr = VecNorm(s2,NORM_1,&norm2);CHKERRQ(ierr);
norm1 -= norm2;
if (norm1<-tol || norm1>tol) {
ierr = PetscPrintf(PETSC_COMM_SELF,"Error:MatGetRowMaxAbs() \n");CHKERRQ(ierr);
}
/* Test MatMult() */
for (i=0; i<40; i++) {
ierr = VecSetRandom(x,rdm);CHKERRQ(ierr);
ierr = MatMult(A,x,s1);CHKERRQ(ierr);
ierr = MatMult(sB,x,s2);CHKERRQ(ierr);
ierr = VecNorm(s1,NORM_1,&norm1);CHKERRQ(ierr);
ierr = VecNorm(s2,NORM_1,&norm2);CHKERRQ(ierr);
norm1 -= norm2;
if (norm1<-tol || norm1>tol) {
ierr = PetscPrintf(PETSC_COMM_SELF,"Error: MatMult(), norm1-norm2: %G\n",norm1);CHKERRQ(ierr);
}
}
/* MatMultAdd() */
for (i=0; i<40; i++) {
ierr = VecSetRandom(x,rdm);CHKERRQ(ierr);
ierr = VecSetRandom(y,rdm);CHKERRQ(ierr);
ierr = MatMultAdd(A,x,y,s1);CHKERRQ(ierr);
ierr = MatMultAdd(sB,x,y,s2);CHKERRQ(ierr);
ierr = VecNorm(s1,NORM_1,&norm1);CHKERRQ(ierr);
ierr = VecNorm(s2,NORM_1,&norm2);CHKERRQ(ierr);
norm1 -= norm2;
if (norm1<-tol || norm1>tol) {
ierr = PetscPrintf(PETSC_COMM_SELF,"Error:MatMultAdd(), norm1-norm2: %G\n",norm1);CHKERRQ(ierr);
}
}
/* Test MatCholeskyFactor(), MatICCFactor() with natural ordering */
ierr = MatGetOrdering(A,MATORDERINGNATURAL,&perm,&iscol);CHKERRQ(ierr);
ierr = ISDestroy(&iscol);CHKERRQ(ierr);
norm1 = tol;
inc = bs;
/* initialize factinfo */
ierr = PetscMemzero(&factinfo,sizeof(MatFactorInfo));CHKERRQ(ierr);
for (lf=-1; lf<10; lf += inc) {
if (lf==-1) { /* Cholesky factor of sB (duplicate sA) */
factinfo.fill = 5.0;
ierr = MatGetFactor(sB,MATSOLVERPETSC,MAT_FACTOR_CHOLESKY,&sC);CHKERRQ(ierr);
ierr = MatCholeskyFactorSymbolic(sC,sB,perm,&factinfo);CHKERRQ(ierr);
} else if (!doIcc) break;
else { /* incomplete Cholesky factor */
factinfo.fill = 5.0;
factinfo.levels = lf;
ierr = MatGetFactor(sB,MATSOLVERPETSC,MAT_FACTOR_ICC,&sC);CHKERRQ(ierr);
ierr = MatICCFactorSymbolic(sC,sB,perm,&factinfo);CHKERRQ(ierr);
}
ierr = MatCholeskyFactorNumeric(sC,sB,&factinfo);CHKERRQ(ierr);
/* MatView(sC, PETSC_VIEWER_DRAW_WORLD); */
/* test MatGetDiagonal on numeric factor */
/*
if (lf == -1) {
ierr = MatGetDiagonal(sC,s1);CHKERRQ(ierr);
printf(" in ex74.c, diag: \n");
ierr = VecView(s1,PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);
}
*/
ierr = MatMult(sB,x,b);CHKERRQ(ierr);
/* test MatForwardSolve() and MatBackwardSolve() */
if (lf == -1) {
ierr = MatForwardSolve(sC,b,s1);CHKERRQ(ierr);
ierr = MatBackwardSolve(sC,s1,s2);CHKERRQ(ierr);
ierr = VecAXPY(s2,neg_one,x);CHKERRQ(ierr);
ierr = VecNorm(s2,NORM_2,&norm2);CHKERRQ(ierr);
if (10*norm1 < norm2) {
ierr = PetscPrintf(PETSC_COMM_SELF,"MatForwardSolve and BackwardSolve: Norm of error=%G, bs=%d\n",norm2,bs);CHKERRQ(ierr);
}
}
/* test MatSolve() */
ierr = MatSolve(sC,b,y);CHKERRQ(ierr);
ierr = MatDestroy(&sC);CHKERRQ(ierr);
/* Check the error */
ierr = VecAXPY(y,neg_one,x);CHKERRQ(ierr);
ierr = VecNorm(y,NORM_2,&norm2);CHKERRQ(ierr);
/* printf("lf: %d, error: %G\n", lf,norm2); */
if (10*norm1 < norm2 && lf-inc != -1) {
ierr = PetscPrintf(PETSC_COMM_SELF,"lf=%D, %D, Norm of error=%G, %G\n",lf-inc,lf,norm1,norm2);CHKERRQ(ierr);
}
norm1 = norm2;
if (norm2 < tol && lf != -1) break;
}
ierr = ISDestroy(&perm);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = MatDestroy(&sB);CHKERRQ(ierr);
ierr = MatDestroy(&sA);CHKERRQ(ierr);
ierr = VecDestroy(&x);CHKERRQ(ierr);
ierr = VecDestroy(&y);CHKERRQ(ierr);
ierr = VecDestroy(&s1);CHKERRQ(ierr);
ierr = VecDestroy(&s2);CHKERRQ(ierr);
ierr = VecDestroy(&b);CHKERRQ(ierr);
ierr = PetscRandomDestroy(&rdm);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
/*
Stokes output:
---------------------------------
Operator summary:
K
G
f,
h
u
p
---------------------------------
Solution summary:
max_u
min_u
average_u
|r_1|
|r_2|
---------------------------------
Solver summary:
name
---------------------------------
Petsc build summary:
*/
PetscErrorCode BSSCR_stokes_output( PetscViewer v, Mat stokes_A, Vec stokes_b, Vec stokes_x, KSP ksp, PetscInt monitor_index )
{
Mat K,G,D,C;
Vec f,h, u,p;
K = G = D = C = PETSC_NULL;
f = h = PETSC_NULL;
u = p = PETSC_NULL;
MatNestGetSubMat( stokes_A, 0,0, &K );
MatNestGetSubMat( stokes_A, 0,1, &G );
MatNestGetSubMat( stokes_A, 1,0, &D );
MatNestGetSubMat( stokes_A, 1,1, &C );
VecNestGetSubVec( stokes_x, 0, &u );
VecNestGetSubVec( stokes_x, 1, &p );
VecNestGetSubVec( stokes_b, 0, &f );
VecNestGetSubVec( stokes_b, 1, &h );
PetscViewerASCIIPrintf( v, "Stokes Output:\n");
PetscViewerASCIIPushTab( v );
/*--------------------------------------------------------------------------------------------*/
PetscViewerASCIIPrintf( v, "--------------------------------------------------\n");
PetscViewerASCIIPrintf( v, "Operator summary:\n");
PetscViewerASCIIPushTab( v );
if (K) {
BSSCR_MatInfoLog(v,K, "stokes_A11");
PetscViewerASCIIPrintf( v, "\n");
}
if (G) {
BSSCR_MatInfoLog(v,G, "stokes_A12");
PetscViewerASCIIPrintf( v, "\n");
}
if (D) {
BSSCR_MatInfoLog(v,D, "stokes_A21");
PetscViewerASCIIPrintf( v, "\n");
}
if (C) {
BSSCR_MatInfoLog(v,C, "stokes_A22");
PetscViewerASCIIPrintf( v, "\n");
}
if (f) {
BSSCR_VecInfoLog(v,f,"stokes_b1");
PetscViewerASCIIPrintf( v, "\n");
}
if (h) {
BSSCR_VecInfoLog(v,h,"stokes_b2");
PetscViewerASCIIPrintf( v, "\n");
}
PetscViewerASCIIPopTab( v );
/*--------------------------------------------------------------------------------------------*/
PetscViewerASCIIPrintf( v, "--------------------------------------------------\n");
PetscViewerASCIIPrintf( v, "Solution summary:\n");
PetscViewerASCIIPushTab( v );
if (u) {
BSSCR_VecInfoLog(v,u,"x1");
PetscViewerASCIIPrintf( v, "\n");
}
if (p) {
BSSCR_VecInfoLog(v,p,"x2");
PetscViewerASCIIPrintf( v, "\n");
}
{
PetscScalar s,sum;
PetscReal r,max,min;
PetscInt N, loc;
double r1,r2;
Vec K_d;
PetscInt loc_max, loc_min;
VecGetSize( u, &N );
VecMax( u, &loc, &r );
PetscViewerASCIIPrintf( v, "u_max: %1.12e [%d] \n", r, loc );
VecMin( u, &loc, &r );
PetscViewerASCIIPrintf( v, "u_min: %1.12e [%d] \n", r, loc );
VecDot( u,u, &s );
PetscViewerASCIIPrintf( v, "u_rms: %1.12e \n", sqrt( PetscRealPart(s) )/N );
VecDuplicate( u, &K_d );
MatGetDiagonal( K, K_d );
VecMax( K_d, &loc_max, &max );
VecMin( K_d, &loc_min, &min );
PetscViewerASCIIPrintf( v,"Algebraic contrast: max(K_d)=%.3e [%d] , min(K_d)=%.3e [%d] , max(K_d)/min(K_d) = %.8e \n", max,loc_max, min,loc_min, max/min );
MatGetRowMax( K, K_d, PETSC_NULL );
VecMax( K_d, &loc_max, &max );
MatGetRowMin( K, K_d, PETSC_NULL );
VecAbs( K_d );
VecMin( K_d, &loc_min, &min );
PetscViewerASCIIPrintf( v,"Algebraic contrast: max(K)=%.3e [%d] , |min(K)|=%.3e [%d] , max(K)/|min(K)| = %.8e \n", max,loc_max, min,loc_min, max/min );
Stg_VecDestroy(&K_d );
PetscViewerASCIIPrintf( v, "\n");
VecGetSize( p, &N );
VecMax( p, &loc, &r );
PetscViewerASCIIPrintf( v, "p_max: %1.12e [%d] \n", r, loc );
VecMin( p, &loc, &r );
PetscViewerASCIIPrintf( v, "p_min: %1.12e [%d] \n", r, loc );
VecDot( p,p, &s );
PetscViewerASCIIPrintf( v, "p_rms: %1.12e \n", sqrt( PetscRealPart(s) )/N );
VecSum( p, &sum );
PetscViewerASCIIPrintf( v, "sum(p): %1.12e \n", sum );
PetscViewerASCIIPrintf( v, "\n");
r1 = BSSCR_StokesMomentumResidual( K,G,f, u,p );
PetscViewerASCIIPrintf( v, "|r1| = %1.12e <momentum> \n", r1 );
r2 = BSSCR_StokesContinuityResidual( G,C,h, u,p );
PetscViewerASCIIPrintf( v, "|r2| = %1.12e <continuity> \n", r2 );
PetscViewerASCIIPrintf( v, "\n");
}
PetscViewerASCIIPopTab( v );
/*--------------------------------------------------------------------------------------------*/
if (ksp) {
PetscViewerASCIIPrintf( v, "--------------------------------------------------\n");
PetscViewerASCIIPrintf( v, "Solver summary:\n");
PetscViewerASCIIPushTab( v );
BSSCR_KSPLogSolve( v, monitor_index, ksp );
BSSCR_BSSCR_KSPLogSolveSummary( v, monitor_index, ksp );
PetscViewerASCIIPrintf( v, "\n");
PetscViewerASCIIPopTab( v );
}
/*--------------------------------------------------------------------------------------------*/
PetscViewerASCIIPrintf( v, "--------------------------------------------------\n");
PetscViewerASCIIPrintf( v, "Petsc build summary:\n");
PetscViewerASCIIPushTab( v );
BSSCR_GeneratePetscHeader_for_viewer( v );
PetscViewerASCIIPrintf( v, "\n");
PetscViewerASCIIPopTab( v );
/*--------------------------------------------------------------------------------------------*/
PetscViewerASCIIPopTab(v);
PetscFunctionReturn(0);
}
/*@C
PCGAMGFilterGraph - filter (remove zero and possibly small values from the) graph and make it symmetric if requested
Collective on Mat
Input Parameter:
+ a_Gmat - the graph
. vfilter - threshold paramter [0,1)
- symm - make the result symmetric
Level: developer
Notes:
This is called before graph coarsers are called.
.seealso: PCGAMGSetThreshold()
@*/
PetscErrorCode PCGAMGFilterGraph(Mat *a_Gmat,PetscReal vfilter,PetscBool symm)
{
PetscErrorCode ierr;
PetscInt Istart,Iend,Ii,jj,ncols,nnz0,nnz1, NN, MM, nloc;
PetscMPIInt rank;
Mat Gmat = *a_Gmat, tGmat, matTrans;
MPI_Comm comm;
const PetscScalar *vals;
const PetscInt *idx;
PetscInt *d_nnz, *o_nnz;
Vec diag;
MatType mtype;
PetscFunctionBegin;
#if defined PETSC_GAMG_USE_LOG
ierr = PetscLogEventBegin(petsc_gamg_setup_events[GRAPH],0,0,0,0);CHKERRQ(ierr);
#endif
/* scale Gmat for all values between -1 and 1 */
ierr = MatCreateVecs(Gmat, &diag, 0);CHKERRQ(ierr);
ierr = MatGetDiagonal(Gmat, diag);CHKERRQ(ierr);
ierr = VecReciprocal(diag);CHKERRQ(ierr);
ierr = VecSqrtAbs(diag);CHKERRQ(ierr);
ierr = MatDiagonalScale(Gmat, diag, diag);CHKERRQ(ierr);
ierr = VecDestroy(&diag);CHKERRQ(ierr);
if (vfilter < 0.0 && !symm) {
/* Just use the provided matrix as the graph but make all values positive */
MatInfo info;
PetscScalar *avals;
PetscBool isaij,ismpiaij;
ierr = PetscObjectBaseTypeCompare((PetscObject)Gmat,MATSEQAIJ,&isaij);CHKERRQ(ierr);
ierr = PetscObjectBaseTypeCompare((PetscObject)Gmat,MATMPIAIJ,&ismpiaij);CHKERRQ(ierr);
if (!isaij && !ismpiaij) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_USER,"Require (MPI)AIJ matrix type");
if (isaij) {
ierr = MatGetInfo(Gmat,MAT_LOCAL,&info);CHKERRQ(ierr);
ierr = MatSeqAIJGetArray(Gmat,&avals);CHKERRQ(ierr);
for (jj = 0; jj<info.nz_used; jj++) avals[jj] = PetscAbsScalar(avals[jj]);
ierr = MatSeqAIJRestoreArray(Gmat,&avals);CHKERRQ(ierr);
} else {
Mat_MPIAIJ *aij = (Mat_MPIAIJ*)Gmat->data;
ierr = MatGetInfo(aij->A,MAT_LOCAL,&info);CHKERRQ(ierr);
ierr = MatSeqAIJGetArray(aij->A,&avals);CHKERRQ(ierr);
for (jj = 0; jj<info.nz_used; jj++) avals[jj] = PetscAbsScalar(avals[jj]);
ierr = MatSeqAIJRestoreArray(aij->A,&avals);CHKERRQ(ierr);
ierr = MatGetInfo(aij->B,MAT_LOCAL,&info);CHKERRQ(ierr);
ierr = MatSeqAIJGetArray(aij->B,&avals);CHKERRQ(ierr);
for (jj = 0; jj<info.nz_used; jj++) avals[jj] = PetscAbsScalar(avals[jj]);
ierr = MatSeqAIJRestoreArray(aij->B,&avals);CHKERRQ(ierr);
}
#if defined PETSC_GAMG_USE_LOG
ierr = PetscLogEventEnd(petsc_gamg_setup_events[GRAPH],0,0,0,0);CHKERRQ(ierr);
#endif
PetscFunctionReturn(0);
}
ierr = PetscObjectGetComm((PetscObject)Gmat,&comm);CHKERRQ(ierr);
ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr);
ierr = MatGetOwnershipRange(Gmat, &Istart, &Iend);CHKERRQ(ierr);
nloc = Iend - Istart;
ierr = MatGetSize(Gmat, &MM, &NN);CHKERRQ(ierr);
if (symm) {
ierr = MatTranspose(Gmat, MAT_INITIAL_MATRIX, &matTrans);CHKERRQ(ierr);
}
/* Determine upper bound on nonzeros needed in new filtered matrix */
ierr = PetscMalloc2(nloc, &d_nnz,nloc, &o_nnz);CHKERRQ(ierr);
for (Ii = Istart, jj = 0; Ii < Iend; Ii++, jj++) {
ierr = MatGetRow(Gmat,Ii,&ncols,NULL,NULL);CHKERRQ(ierr);
d_nnz[jj] = ncols;
o_nnz[jj] = ncols;
ierr = MatRestoreRow(Gmat,Ii,&ncols,NULL,NULL);CHKERRQ(ierr);
if (symm) {
ierr = MatGetRow(matTrans,Ii,&ncols,NULL,NULL);CHKERRQ(ierr);
d_nnz[jj] += ncols;
o_nnz[jj] += ncols;
ierr = MatRestoreRow(matTrans,Ii,&ncols,NULL,NULL);CHKERRQ(ierr);
}
if (d_nnz[jj] > nloc) d_nnz[jj] = nloc;
if (o_nnz[jj] > (MM-nloc)) o_nnz[jj] = MM - nloc;
}
ierr = MatGetType(Gmat,&mtype);CHKERRQ(ierr);
ierr = MatCreate(comm, &tGmat);CHKERRQ(ierr);
ierr = MatSetSizes(tGmat,nloc,nloc,MM,MM);CHKERRQ(ierr);
ierr = MatSetBlockSizes(tGmat, 1, 1);CHKERRQ(ierr);
ierr = MatSetType(tGmat, mtype);CHKERRQ(ierr);
ierr = MatSeqAIJSetPreallocation(tGmat,0,d_nnz);CHKERRQ(ierr);
ierr = MatMPIAIJSetPreallocation(tGmat,0,d_nnz,0,o_nnz);CHKERRQ(ierr);
ierr = PetscFree2(d_nnz,o_nnz);CHKERRQ(ierr);
if (symm) {
ierr = MatDestroy(&matTrans);CHKERRQ(ierr);
} else {
/* all entries are generated locally so MatAssembly will be slightly faster for large process counts */
ierr = MatSetOption(tGmat,MAT_NO_OFF_PROC_ENTRIES,PETSC_TRUE);CHKERRQ(ierr);
}
for (Ii = Istart, nnz0 = nnz1 = 0; Ii < Iend; Ii++) {
ierr = MatGetRow(Gmat,Ii,&ncols,&idx,&vals);CHKERRQ(ierr);
for (jj=0; jj<ncols; jj++,nnz0++) {
PetscScalar sv = PetscAbs(PetscRealPart(vals[jj]));
if (PetscRealPart(sv) > vfilter) {
nnz1++;
if (symm) {
sv *= 0.5;
ierr = MatSetValues(tGmat,1,&Ii,1,&idx[jj],&sv,ADD_VALUES);CHKERRQ(ierr);
ierr = MatSetValues(tGmat,1,&idx[jj],1,&Ii,&sv,ADD_VALUES);CHKERRQ(ierr);
} else {
ierr = MatSetValues(tGmat,1,&Ii,1,&idx[jj],&sv,ADD_VALUES);CHKERRQ(ierr);
}
}
}
ierr = MatRestoreRow(Gmat,Ii,&ncols,&idx,&vals);CHKERRQ(ierr);
}
ierr = MatAssemblyBegin(tGmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(tGmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
#if defined PETSC_GAMG_USE_LOG
ierr = PetscLogEventEnd(petsc_gamg_setup_events[GRAPH],0,0,0,0);CHKERRQ(ierr);
#endif
#if defined(PETSC_USE_INFO)
{
double t1 = (!nnz0) ? 1. : 100.*(double)nnz1/(double)nnz0, t2 = (!nloc) ? 1. : (double)nnz0/(double)nloc;
ierr = PetscInfo4(*a_Gmat,"\t %g%% nnz after filtering, with threshold %g, %g nnz ave. (N=%D)\n",t1,vfilter,t2,MM);CHKERRQ(ierr);
}
#endif
ierr = MatDestroy(&Gmat);CHKERRQ(ierr);
*a_Gmat = tGmat;
PetscFunctionReturn(0);
}
int main(int argc,char **argv)
{
KSP ksp;
PC pc;
Mat A,M;
Vec X,B,D;
MPI_Comm comm;
PetscScalar v;
KSPConvergedReason reason;
PetscInt i,j,its;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscInitialize(&argc,&argv,0,help);CHKERRQ(ierr);
ierr = PetscOptionsSetValue("-options_left",PETSC_NULL);CHKERRQ(ierr);
comm = MPI_COMM_SELF;
/*
* Construct the Kershaw matrix
* and a suitable rhs / initial guess
*/
ierr = MatCreateSeqAIJ(comm,4,4,4,0,&A);CHKERRQ(ierr);
ierr = VecCreateSeq(comm,4,&B);CHKERRQ(ierr);
ierr = VecDuplicate(B,&X);CHKERRQ(ierr);
for (i=0; i<4; i++) {
v=3;
ierr = MatSetValues(A,1,&i,1,&i,&v,INSERT_VALUES);CHKERRQ(ierr);
v=1;
ierr = VecSetValues(B,1,&i,&v,INSERT_VALUES);CHKERRQ(ierr);
ierr = VecSetValues(X,1,&i,&v,INSERT_VALUES);CHKERRQ(ierr);
}
i=0; v=0;
ierr = VecSetValues(X,1,&i,&v,INSERT_VALUES);CHKERRQ(ierr);
for (i=0; i<3; i++) {
v=-2; j=i+1;
ierr = MatSetValues(A,1,&i,1,&j,&v,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatSetValues(A,1,&j,1,&i,&v,INSERT_VALUES);CHKERRQ(ierr);
}
i=0; j=3; v=2;
ierr = MatSetValues(A,1,&i,1,&j,&v,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatSetValues(A,1,&j,1,&i,&v,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = VecAssemblyBegin(B);CHKERRQ(ierr);
ierr = VecAssemblyEnd(B);CHKERRQ(ierr);
printf("\nThe Kershaw matrix:\n\n"); MatView(A,0);
/*
* A Conjugate Gradient method
* with ILU(0) preconditioning
*/
ierr = KSPCreate(comm,&ksp);CHKERRQ(ierr);
ierr = KSPSetOperators(ksp,A,A,DIFFERENT_NONZERO_PATTERN);CHKERRQ(ierr);
ierr = KSPSetType(ksp,KSPCG);CHKERRQ(ierr);
ierr = KSPSetInitialGuessNonzero(ksp,PETSC_TRUE);CHKERRQ(ierr);
/*
* ILU preconditioner;
* The iterative method will break down unless you comment in the SetShift
* line below, or use the -pc_factor_shift_positive_definite option.
* Run the code twice: once as given to see the negative pivot and the
* divergence behaviour, then comment in the Shift line, or add the
* command line option, and see that the pivots are all positive and
* the method converges.
*/
ierr = KSPGetPC(ksp,&pc);CHKERRQ(ierr);
ierr = PCSetType(pc,PCICC);CHKERRQ(ierr);
/* ierr = PCFactorSetShiftType(prec,MAT_SHIFT_POSITIVE_DEFINITE);CHKERRQ(ierr); */
ierr = KSPSetFromOptions(ksp);CHKERRQ(ierr);
ierr = KSPSetUp(ksp);CHKERRQ(ierr);
/*
* Now that the factorisation is done, show the pivots;
* note that the last one is negative. This in itself is not an error,
* but it will make the iterative method diverge.
*/
ierr = PCFactorGetMatrix(pc,&M);CHKERRQ(ierr);
ierr = VecDuplicate(B,&D);CHKERRQ(ierr);
ierr = MatGetDiagonal(M,D);CHKERRQ(ierr);
printf("\nPivots:\n\n"); VecView(D,0);
/*
* Solve the system;
* without the shift this will diverge with
* an indefinite preconditioner
*/
ierr = KSPSolve(ksp,B,X);CHKERRQ(ierr);
ierr = KSPGetConvergedReason(ksp,&reason);CHKERRQ(ierr);
if (reason==KSP_DIVERGED_INDEFINITE_PC) {
printf("\nDivergence because of indefinite preconditioner;\n");
printf("Run the executable again but with -pc_factor_shift_positive_definite option.\n");
} else if (reason<0) {
printf("\nOther kind of divergence: this should not happen.\n");
} else {
ierr = KSPGetIterationNumber(ksp,&its);CHKERRQ(ierr);
printf("\nConvergence in %d iterations.\n",(int)its);
}
printf("\n");
ierr = KSPDestroy(&ksp);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = VecDestroy(&B);CHKERRQ(ierr);
ierr = VecDestroy(&X);CHKERRQ(ierr);
ierr = VecDestroy(&D);CHKERRQ(ierr);
PetscFinalize();
PetscFunctionReturn(0);
}
PetscErrorCode PCISSetUp(PC pc)
{
PC_IS *pcis = (PC_IS*)(pc->data);
Mat_IS *matis;
PetscErrorCode ierr;
PetscBool flg,issbaij;
Vec counter;
PetscFunctionBegin;
ierr = PetscObjectTypeCompare((PetscObject)pc->pmat,MATIS,&flg);CHKERRQ(ierr);
if (!flg) SETERRQ(PetscObjectComm((PetscObject)pc),PETSC_ERR_ARG_WRONG,"Preconditioner type of Neumann Neumman requires matrix of type MATIS");
matis = (Mat_IS*)pc->pmat->data;
pcis->pure_neumann = matis->pure_neumann;
/* get info on mapping */
ierr = PetscObjectReference((PetscObject)matis->mapping);CHKERRQ(ierr);
ierr = ISLocalToGlobalMappingDestroy(&pcis->mapping);CHKERRQ(ierr);
pcis->mapping = matis->mapping;
ierr = ISLocalToGlobalMappingGetSize(pcis->mapping,&pcis->n);CHKERRQ(ierr);
ierr = ISLocalToGlobalMappingGetInfo(pcis->mapping,&(pcis->n_neigh),&(pcis->neigh),&(pcis->n_shared),&(pcis->shared));CHKERRQ(ierr);
/* Creating local and global index sets for interior and inteface nodes. */
{
PetscInt n_I;
PetscInt *idx_I_local,*idx_B_local,*idx_I_global,*idx_B_global;
PetscInt *array;
PetscInt i,j;
/* Identifying interior and interface nodes, in local numbering */
ierr = PetscMalloc1(pcis->n,&array);CHKERRQ(ierr);
ierr = PetscMemzero(array,pcis->n*sizeof(PetscInt));CHKERRQ(ierr);
for (i=0;i<pcis->n_neigh;i++)
for (j=0;j<pcis->n_shared[i];j++)
array[pcis->shared[i][j]] += 1;
ierr = PetscMalloc1(pcis->n,&idx_I_local);CHKERRQ(ierr);
ierr = PetscMalloc1(pcis->n,&idx_B_local);CHKERRQ(ierr);
for (i=0, pcis->n_B=0, n_I=0; i<pcis->n; i++) {
if (!array[i]) {
idx_I_local[n_I] = i;
n_I++;
} else {
idx_B_local[pcis->n_B] = i;
pcis->n_B++;
}
}
/* Getting the global numbering */
idx_B_global = idx_I_local + n_I; /* Just avoiding allocating extra memory, since we have vacant space */
idx_I_global = idx_B_local + pcis->n_B;
ierr = ISLocalToGlobalMappingApply(pcis->mapping,pcis->n_B,idx_B_local,idx_B_global);CHKERRQ(ierr);
ierr = ISLocalToGlobalMappingApply(pcis->mapping,n_I, idx_I_local,idx_I_global);CHKERRQ(ierr);
/* Creating the index sets. */
ierr = ISCreateGeneral(PETSC_COMM_SELF,pcis->n_B,idx_B_local,PETSC_COPY_VALUES, &pcis->is_B_local);CHKERRQ(ierr);
ierr = ISCreateGeneral(PETSC_COMM_SELF,pcis->n_B,idx_B_global,PETSC_COPY_VALUES,&pcis->is_B_global);CHKERRQ(ierr);
ierr = ISCreateGeneral(PETSC_COMM_SELF,n_I,idx_I_local,PETSC_COPY_VALUES, &pcis->is_I_local);CHKERRQ(ierr);
ierr = ISCreateGeneral(PETSC_COMM_SELF,n_I,idx_I_global,PETSC_COPY_VALUES,&pcis->is_I_global);CHKERRQ(ierr);
/* Freeing memory and restoring arrays */
ierr = PetscFree(idx_B_local);CHKERRQ(ierr);
ierr = PetscFree(idx_I_local);CHKERRQ(ierr);
ierr = PetscFree(array);CHKERRQ(ierr);
}
/*
Extracting the blocks A_II, A_BI, A_IB and A_BB from A. If the numbering
is such that interior nodes come first than the interface ones, we have
[ | ]
[ A_II | A_IB ]
A = [ | ]
[-----------+------]
[ A_BI | A_BB ]
*/
ierr = MatGetSubMatrix(matis->A,pcis->is_I_local,pcis->is_I_local,MAT_INITIAL_MATRIX,&pcis->A_II);CHKERRQ(ierr);
ierr = MatGetSubMatrix(matis->A,pcis->is_B_local,pcis->is_B_local,MAT_INITIAL_MATRIX,&pcis->A_BB);CHKERRQ(ierr);
ierr = PetscObjectTypeCompare((PetscObject)matis->A,MATSEQSBAIJ,&issbaij);CHKERRQ(ierr);
if (!issbaij) {
ierr = MatGetSubMatrix(matis->A,pcis->is_I_local,pcis->is_B_local,MAT_INITIAL_MATRIX,&pcis->A_IB);CHKERRQ(ierr);
ierr = MatGetSubMatrix(matis->A,pcis->is_B_local,pcis->is_I_local,MAT_INITIAL_MATRIX,&pcis->A_BI);CHKERRQ(ierr);
} else {
Mat newmat;
ierr = MatConvert(matis->A,MATSEQBAIJ,MAT_INITIAL_MATRIX,&newmat);CHKERRQ(ierr);
ierr = MatGetSubMatrix(newmat,pcis->is_I_local,pcis->is_B_local,MAT_INITIAL_MATRIX,&pcis->A_IB);CHKERRQ(ierr);
ierr = MatGetSubMatrix(newmat,pcis->is_B_local,pcis->is_I_local,MAT_INITIAL_MATRIX,&pcis->A_BI);CHKERRQ(ierr);
ierr = MatDestroy(&newmat);CHKERRQ(ierr);
}
/*
Creating work vectors and arrays
*/
ierr = VecDuplicate(matis->x,&pcis->vec1_N);CHKERRQ(ierr);
ierr = VecDuplicate(pcis->vec1_N,&pcis->vec2_N);CHKERRQ(ierr);
ierr = VecCreateSeq(PETSC_COMM_SELF,pcis->n-pcis->n_B,&pcis->vec1_D);CHKERRQ(ierr);
ierr = VecDuplicate(pcis->vec1_D,&pcis->vec2_D);CHKERRQ(ierr);
ierr = VecDuplicate(pcis->vec1_D,&pcis->vec3_D);CHKERRQ(ierr);
ierr = VecDuplicate(pcis->vec1_D,&pcis->vec4_D);CHKERRQ(ierr);
ierr = VecCreateSeq(PETSC_COMM_SELF,pcis->n_B,&pcis->vec1_B);CHKERRQ(ierr);
ierr = VecDuplicate(pcis->vec1_B,&pcis->vec2_B);CHKERRQ(ierr);
ierr = VecDuplicate(pcis->vec1_B,&pcis->vec3_B);CHKERRQ(ierr);
ierr = MatCreateVecs(pc->pmat,&pcis->vec1_global,0);CHKERRQ(ierr);
ierr = PetscMalloc1(pcis->n,&pcis->work_N);CHKERRQ(ierr);
/* Creating the scatter contexts */
ierr = VecScatterCreate(pcis->vec1_global,pcis->is_I_global,pcis->vec1_D,(IS)0,&pcis->global_to_D);CHKERRQ(ierr);
ierr = VecScatterCreate(pcis->vec1_N,pcis->is_B_local,pcis->vec1_B,(IS)0,&pcis->N_to_B);CHKERRQ(ierr);
ierr = VecScatterCreate(pcis->vec1_global,pcis->is_B_global,pcis->vec1_B,(IS)0,&pcis->global_to_B);CHKERRQ(ierr);
/* Creating scaling "matrix" D */
ierr = PetscOptionsGetBool(((PetscObject)pc)->prefix,"-pc_is_use_stiffness_scaling",&pcis->use_stiffness_scaling,NULL);CHKERRQ(ierr);
if (!pcis->D) {
ierr = VecDuplicate(pcis->vec1_B,&pcis->D);CHKERRQ(ierr);
if (!pcis->use_stiffness_scaling) {
ierr = VecSet(pcis->D,pcis->scaling_factor);CHKERRQ(ierr);
} else {
ierr = MatGetDiagonal(matis->A,pcis->vec1_N);CHKERRQ(ierr);
ierr = VecScatterBegin(pcis->N_to_B,pcis->vec1_N,pcis->D,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
ierr = VecScatterEnd (pcis->N_to_B,pcis->vec1_N,pcis->D,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
}
}
ierr = VecCopy(pcis->D,pcis->vec1_B);CHKERRQ(ierr);
ierr = MatCreateVecs(pc->pmat,&counter,0);CHKERRQ(ierr); /* temporary auxiliar vector */
ierr = VecSet(counter,0.0);CHKERRQ(ierr);
ierr = VecScatterBegin(pcis->global_to_B,pcis->vec1_B,counter,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr);
ierr = VecScatterEnd (pcis->global_to_B,pcis->vec1_B,counter,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr);
ierr = VecScatterBegin(pcis->global_to_B,counter,pcis->vec1_B,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
ierr = VecScatterEnd (pcis->global_to_B,counter,pcis->vec1_B,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
ierr = VecPointwiseDivide(pcis->D,pcis->D,pcis->vec1_B);CHKERRQ(ierr);
ierr = VecDestroy(&counter);CHKERRQ(ierr);
/* See historical note 01, at the bottom of this file. */
/*
Creating the KSP contexts for the local Dirichlet and Neumann problems.
*/
if (pcis->computesolvers) {
PC pc_ctx;
/* Dirichlet */
ierr = KSPCreate(PETSC_COMM_SELF,&pcis->ksp_D);CHKERRQ(ierr);
ierr = PetscObjectIncrementTabLevel((PetscObject)pcis->ksp_D,(PetscObject)pc,1);CHKERRQ(ierr);
ierr = KSPSetOperators(pcis->ksp_D,pcis->A_II,pcis->A_II);CHKERRQ(ierr);
ierr = KSPSetOptionsPrefix(pcis->ksp_D,"is_localD_");CHKERRQ(ierr);
ierr = KSPGetPC(pcis->ksp_D,&pc_ctx);CHKERRQ(ierr);
ierr = PCSetType(pc_ctx,PCLU);CHKERRQ(ierr);
ierr = KSPSetType(pcis->ksp_D,KSPPREONLY);CHKERRQ(ierr);
ierr = KSPSetFromOptions(pcis->ksp_D);CHKERRQ(ierr);
/* the vectors in the following line are dummy arguments, just telling the KSP the vector size. Values are not used */
ierr = KSPSetUp(pcis->ksp_D);CHKERRQ(ierr);
/* Neumann */
ierr = KSPCreate(PETSC_COMM_SELF,&pcis->ksp_N);CHKERRQ(ierr);
ierr = PetscObjectIncrementTabLevel((PetscObject)pcis->ksp_N,(PetscObject)pc,1);CHKERRQ(ierr);
ierr = KSPSetOperators(pcis->ksp_N,matis->A,matis->A);CHKERRQ(ierr);
ierr = KSPSetOptionsPrefix(pcis->ksp_N,"is_localN_");CHKERRQ(ierr);
ierr = KSPGetPC(pcis->ksp_N,&pc_ctx);CHKERRQ(ierr);
ierr = PCSetType(pc_ctx,PCLU);CHKERRQ(ierr);
ierr = KSPSetType(pcis->ksp_N,KSPPREONLY);CHKERRQ(ierr);
ierr = KSPSetFromOptions(pcis->ksp_N);CHKERRQ(ierr);
{
PetscBool damp_fixed = PETSC_FALSE,
remove_nullspace_fixed = PETSC_FALSE,
set_damping_factor_floating = PETSC_FALSE,
not_damp_floating = PETSC_FALSE,
not_remove_nullspace_floating = PETSC_FALSE;
PetscReal fixed_factor,
floating_factor;
ierr = PetscOptionsGetReal(((PetscObject)pc_ctx)->prefix,"-pc_is_damp_fixed",&fixed_factor,&damp_fixed);CHKERRQ(ierr);
if (!damp_fixed) fixed_factor = 0.0;
ierr = PetscOptionsGetBool(((PetscObject)pc_ctx)->prefix,"-pc_is_damp_fixed",&damp_fixed,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetBool(((PetscObject)pc_ctx)->prefix,"-pc_is_remove_nullspace_fixed",&remove_nullspace_fixed,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetReal(((PetscObject)pc_ctx)->prefix,"-pc_is_set_damping_factor_floating",
&floating_factor,&set_damping_factor_floating);CHKERRQ(ierr);
if (!set_damping_factor_floating) floating_factor = 0.0;
ierr = PetscOptionsGetBool(((PetscObject)pc_ctx)->prefix,"-pc_is_set_damping_factor_floating",&set_damping_factor_floating,NULL);CHKERRQ(ierr);
if (!set_damping_factor_floating) floating_factor = 1.e-12;
ierr = PetscOptionsGetBool(((PetscObject)pc_ctx)->prefix,"-pc_is_not_damp_floating",¬_damp_floating,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetBool(((PetscObject)pc_ctx)->prefix,"-pc_is_not_remove_nullspace_floating",¬_remove_nullspace_floating,NULL);CHKERRQ(ierr);
if (pcis->pure_neumann) { /* floating subdomain */
if (!(not_damp_floating)) {
ierr = PCFactorSetShiftType(pc_ctx,MAT_SHIFT_NONZERO);CHKERRQ(ierr);
ierr = PCFactorSetShiftAmount(pc_ctx,floating_factor);CHKERRQ(ierr);
}
if (!(not_remove_nullspace_floating)) {
MatNullSpace nullsp;
ierr = MatNullSpaceCreate(PETSC_COMM_SELF,PETSC_TRUE,0,NULL,&nullsp);CHKERRQ(ierr);
ierr = KSPSetNullSpace(pcis->ksp_N,nullsp);CHKERRQ(ierr);
ierr = MatNullSpaceDestroy(&nullsp);CHKERRQ(ierr);
}
} else { /* fixed subdomain */
if (damp_fixed) {
ierr = PCFactorSetShiftType(pc_ctx,MAT_SHIFT_NONZERO);CHKERRQ(ierr);
ierr = PCFactorSetShiftAmount(pc_ctx,floating_factor);CHKERRQ(ierr);
}
if (remove_nullspace_fixed) {
MatNullSpace nullsp;
ierr = MatNullSpaceCreate(PETSC_COMM_SELF,PETSC_TRUE,0,NULL,&nullsp);CHKERRQ(ierr);
ierr = KSPSetNullSpace(pcis->ksp_N,nullsp);CHKERRQ(ierr);
ierr = MatNullSpaceDestroy(&nullsp);CHKERRQ(ierr);
}
}
}
/* the vectors in the following line are dummy arguments, just telling the KSP the vector size. Values are not used */
ierr = KSPSetUp(pcis->ksp_N);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
PetscErrorCode PCGAMGFilterGraph(Mat *a_Gmat,const PetscReal vfilter,const PetscBool symm,const PetscInt verbose)
{
PetscErrorCode ierr;
PetscInt Istart,Iend,Ii,jj,ncols,nnz0,nnz1, NN, MM, nloc;
PetscMPIInt rank, size;
Mat Gmat = *a_Gmat, tGmat, matTrans;
MPI_Comm comm;
const PetscScalar *vals;
const PetscInt *idx;
PetscInt *d_nnz, *o_nnz;
Vec diag;
PetscFunctionBegin;
ierr = PetscObjectGetComm((PetscObject)Gmat,&comm);CHKERRQ(ierr);
ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr);
ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr);
ierr = MatGetOwnershipRange(Gmat, &Istart, &Iend);CHKERRQ(ierr);
nloc = Iend - Istart;
ierr = MatGetSize(Gmat, &MM, &NN);CHKERRQ(ierr);
#if defined PETSC_GAMG_USE_LOG
ierr = PetscLogEventBegin(petsc_gamg_setup_events[GRAPH],0,0,0,0);CHKERRQ(ierr);
#endif
/* scale Gmat so filter works */
ierr = MatGetVecs(Gmat, &diag, 0);CHKERRQ(ierr);
ierr = MatGetDiagonal(Gmat, diag);CHKERRQ(ierr);
ierr = VecReciprocal(diag);CHKERRQ(ierr);
ierr = VecSqrtAbs(diag);CHKERRQ(ierr);
ierr = MatDiagonalScale(Gmat, diag, diag);CHKERRQ(ierr);
ierr = VecDestroy(&diag);CHKERRQ(ierr);
if (symm) {
ierr = MatTranspose(Gmat, MAT_INITIAL_MATRIX, &matTrans);CHKERRQ(ierr);
}
/* filter - dup zeros out matrix */
ierr = PetscMalloc1(nloc, &d_nnz);CHKERRQ(ierr);
ierr = PetscMalloc1(nloc, &o_nnz);CHKERRQ(ierr);
for (Ii = Istart, jj = 0; Ii < Iend; Ii++, jj++) {
ierr = MatGetRow(Gmat,Ii,&ncols,NULL,NULL);CHKERRQ(ierr);
d_nnz[jj] = ncols;
o_nnz[jj] = ncols;
ierr = MatRestoreRow(Gmat,Ii,&ncols,NULL,NULL);CHKERRQ(ierr);
if (symm) {
ierr = MatGetRow(matTrans,Ii,&ncols,NULL,NULL);CHKERRQ(ierr);
d_nnz[jj] += ncols;
o_nnz[jj] += ncols;
ierr = MatRestoreRow(matTrans,Ii,&ncols,NULL,NULL);CHKERRQ(ierr);
}
if (d_nnz[jj] > nloc) d_nnz[jj] = nloc;
if (o_nnz[jj] > (MM-nloc)) o_nnz[jj] = MM - nloc;
}
ierr = MatCreateAIJ(comm, nloc, nloc, MM, MM, 0, d_nnz, 0, o_nnz, &tGmat);CHKERRQ(ierr);
ierr = PetscFree(d_nnz);CHKERRQ(ierr);
ierr = PetscFree(o_nnz);CHKERRQ(ierr);
if (symm) {
ierr = MatDestroy(&matTrans);CHKERRQ(ierr);
}
for (Ii = Istart, nnz0 = nnz1 = 0; Ii < Iend; Ii++) {
ierr = MatGetRow(Gmat,Ii,&ncols,&idx,&vals);CHKERRQ(ierr);
for (jj=0; jj<ncols; jj++,nnz0++) {
PetscScalar sv = PetscAbs(PetscRealPart(vals[jj]));
if (PetscRealPart(sv) > vfilter) {
nnz1++;
if (symm) {
sv *= 0.5;
ierr = MatSetValues(tGmat,1,&Ii,1,&idx[jj],&sv,ADD_VALUES);CHKERRQ(ierr);
ierr = MatSetValues(tGmat,1,&idx[jj],1,&Ii,&sv,ADD_VALUES);CHKERRQ(ierr);
} else {
ierr = MatSetValues(tGmat,1,&Ii,1,&idx[jj],&sv,ADD_VALUES);CHKERRQ(ierr);
}
}
}
ierr = MatRestoreRow(Gmat,Ii,&ncols,&idx,&vals);CHKERRQ(ierr);
}
ierr = MatAssemblyBegin(tGmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(tGmat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
#if defined PETSC_GAMG_USE_LOG
ierr = PetscLogEventEnd(petsc_gamg_setup_events[GRAPH],0,0,0,0);CHKERRQ(ierr);
#endif
if (verbose) {
if (verbose == 1) {
ierr = PetscPrintf(comm,"\t[%d]%s %g%% nnz after filtering, with threshold %g, %g nnz ave. (N=%d)\n",rank,__FUNCT__,
100.*(double)nnz1/(double)nnz0,vfilter,(double)nnz0/(double)nloc,MM);CHKERRQ(ierr);
} else {
PetscInt nnz[2],out[2];
nnz[0] = nnz0; nnz[1] = nnz1;
ierr = MPI_Allreduce(nnz, out, 2, MPIU_INT, MPI_SUM, comm);CHKERRQ(ierr);
ierr = PetscPrintf(comm,"\t[%d]%s %g%% nnz after filtering, with threshold %g, %g nnz ave. (N=%d)\n",rank,__FUNCT__,
100.*(double)out[1]/(double)out[0],vfilter,(double)out[0]/(double)MM,MM);CHKERRQ(ierr);
}
}
ierr = MatDestroy(&Gmat);CHKERRQ(ierr);
*a_Gmat = tGmat;
PetscFunctionReturn(0);
}
PetscErrorCode PCBDDCScalingSetUp(PC pc)
{
PC_IS* pcis=(PC_IS*)pc->data;
PC_BDDC* pcbddc=(PC_BDDC*)pc->data;
PetscErrorCode ierr;
PetscFunctionBegin;
PetscValidHeaderSpecific(pc,PC_CLASSID,1);
ierr = PetscLogEventBegin(PC_BDDC_Scaling[pcbddc->current_level],pc,0,0,0);CHKERRQ(ierr);
/* create work vector for the operator */
ierr = VecDestroy(&pcbddc->work_scaling);CHKERRQ(ierr);
ierr = VecDuplicate(pcis->vec1_B,&pcbddc->work_scaling);CHKERRQ(ierr);
/* always rebuild pcis->D */
if (pcis->use_stiffness_scaling) {
PetscScalar *a;
PetscInt i,n;
ierr = MatGetDiagonal(pcbddc->local_mat,pcis->vec1_N);CHKERRQ(ierr);
ierr = VecScatterBegin(pcis->N_to_B,pcis->vec1_N,pcis->D,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
ierr = VecScatterEnd(pcis->N_to_B,pcis->vec1_N,pcis->D,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
ierr = VecAbs(pcis->D);CHKERRQ(ierr);
ierr = VecGetLocalSize(pcis->D,&n);CHKERRQ(ierr);
ierr = VecGetArray(pcis->D,&a);CHKERRQ(ierr);
for (i=0;i<n;i++) if (PetscAbsScalar(a[i])<PETSC_SMALL) a[i] = 1.0;
ierr = VecRestoreArray(pcis->D,&a);CHKERRQ(ierr);
}
ierr = VecSet(pcis->vec1_global,0.0);CHKERRQ(ierr);
ierr = VecScatterBegin(pcis->global_to_B,pcis->D,pcis->vec1_global,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr);
ierr = VecScatterEnd(pcis->global_to_B,pcis->D,pcis->vec1_global,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr);
ierr = VecScatterBegin(pcis->global_to_B,pcis->vec1_global,pcis->vec1_B,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
ierr = VecScatterEnd(pcis->global_to_B,pcis->vec1_global,pcis->vec1_B,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
ierr = VecPointwiseDivide(pcis->D,pcis->D,pcis->vec1_B);CHKERRQ(ierr);
/* now setup */
if (pcbddc->use_deluxe_scaling) {
if (!pcbddc->deluxe_ctx) {
ierr = PCBDDCScalingCreate_Deluxe(pc);CHKERRQ(ierr);
}
ierr = PCBDDCScalingSetUp_Deluxe(pc);CHKERRQ(ierr);
ierr = PetscObjectComposeFunction((PetscObject)pc,"PCBDDCScalingRestriction_C",PCBDDCScalingRestriction_Deluxe);CHKERRQ(ierr);
ierr = PetscObjectComposeFunction((PetscObject)pc,"PCBDDCScalingExtension_C",PCBDDCScalingExtension_Deluxe);CHKERRQ(ierr);
} else {
ierr = PetscObjectComposeFunction((PetscObject)pc,"PCBDDCScalingRestriction_C",PCBDDCScalingRestriction_Basic);CHKERRQ(ierr);
ierr = PetscObjectComposeFunction((PetscObject)pc,"PCBDDCScalingExtension_C",PCBDDCScalingExtension_Basic);CHKERRQ(ierr);
}
/* test */
if (pcbddc->dbg_flag) {
Mat B0_B = NULL;
Vec B0_Bv = NULL, B0_Bv2 = NULL;
Vec vec2_global;
PetscViewer viewer = pcbddc->dbg_viewer;
PetscReal error;
/* extension -> from local to parallel */
ierr = VecSet(pcis->vec1_global,0.0);CHKERRQ(ierr);
ierr = VecSetRandom(pcis->vec1_B,NULL);CHKERRQ(ierr);
ierr = VecScatterBegin(pcis->global_to_B,pcis->vec1_B,pcis->vec1_global,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr);
ierr = VecScatterEnd(pcis->global_to_B,pcis->vec1_B,pcis->vec1_global,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr);
ierr = VecDuplicate(pcis->vec1_global,&vec2_global);CHKERRQ(ierr);
ierr = VecCopy(pcis->vec1_global,vec2_global);CHKERRQ(ierr);
ierr = VecScatterBegin(pcis->global_to_B,pcis->vec1_global,pcis->vec1_B,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
ierr = VecScatterEnd(pcis->global_to_B,pcis->vec1_global,pcis->vec1_B,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
if (pcbddc->benign_n) {
IS is_dummy;
ierr = ISCreateStride(PETSC_COMM_SELF,pcbddc->benign_n,0,1,&is_dummy);CHKERRQ(ierr);
ierr = MatCreateSubMatrix(pcbddc->benign_B0,is_dummy,pcis->is_B_local,MAT_INITIAL_MATRIX,&B0_B);CHKERRQ(ierr);
ierr = ISDestroy(&is_dummy);CHKERRQ(ierr);
ierr = MatCreateVecs(B0_B,NULL,&B0_Bv);CHKERRQ(ierr);
ierr = VecDuplicate(B0_Bv,&B0_Bv2);CHKERRQ(ierr);
ierr = MatMult(B0_B,pcis->vec1_B,B0_Bv);CHKERRQ(ierr);
}
ierr = PCBDDCScalingExtension(pc,pcis->vec1_B,pcis->vec1_global);CHKERRQ(ierr);
if (pcbddc->benign_saddle_point) {
PetscReal errorl = 0.;
ierr = VecScatterBegin(pcis->global_to_B,pcis->vec1_global,pcis->vec1_B,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
ierr = VecScatterEnd(pcis->global_to_B,pcis->vec1_global,pcis->vec1_B,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
if (pcbddc->benign_n) {
ierr = MatMult(B0_B,pcis->vec1_B,B0_Bv2);CHKERRQ(ierr);
ierr = VecAXPY(B0_Bv,-1.0,B0_Bv2);CHKERRQ(ierr);
ierr = VecNorm(B0_Bv,NORM_INFINITY,&errorl);CHKERRQ(ierr);
}
ierr = MPI_Allreduce(&errorl,&error,1,MPIU_REAL,MPI_SUM,PetscObjectComm((PetscObject)pc));CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"Error benign extension %1.14e\n",error);CHKERRQ(ierr);
}
ierr = VecAXPY(pcis->vec1_global,-1.0,vec2_global);CHKERRQ(ierr);
ierr = VecNorm(pcis->vec1_global,NORM_INFINITY,&error);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"Error scaling extension %1.14e\n",error);CHKERRQ(ierr);
ierr = VecDestroy(&vec2_global);CHKERRQ(ierr);
/* restriction -> from parallel to local */
ierr = VecSet(pcis->vec1_global,0.0);CHKERRQ(ierr);
ierr = VecSetRandom(pcis->vec1_B,NULL);CHKERRQ(ierr);
ierr = VecScatterBegin(pcis->global_to_B,pcis->vec1_B,pcis->vec1_global,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr);
ierr = VecScatterEnd(pcis->global_to_B,pcis->vec1_B,pcis->vec1_global,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr);
ierr = PCBDDCScalingRestriction(pc,pcis->vec1_global,pcis->vec1_B);CHKERRQ(ierr);
ierr = VecScale(pcis->vec1_B,-1.0);CHKERRQ(ierr);
ierr = VecScatterBegin(pcis->global_to_B,pcis->vec1_B,pcis->vec1_global,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr);
ierr = VecScatterEnd(pcis->global_to_B,pcis->vec1_B,pcis->vec1_global,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr);
ierr = VecNorm(pcis->vec1_global,NORM_INFINITY,&error);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"Error scaling restriction %1.14e\n",error);CHKERRQ(ierr);
ierr = MatDestroy(&B0_B);CHKERRQ(ierr);
ierr = VecDestroy(&B0_Bv);CHKERRQ(ierr);
ierr = VecDestroy(&B0_Bv2);CHKERRQ(ierr);
}
ierr = PetscLogEventEnd(PC_BDDC_Scaling[pcbddc->current_level],pc,0,0,0);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
