PetscErrorCode SolveInit(FEMInf fem, int L, PetscScalar *e0, Vec *x) {
PetscErrorCode ierr;
Mat H, S;
ierr = CalcMat(fem, L, &H, &S); CHKERRQ(ierr);
EPS eps;
ierr = PrintTimeStamp(fem->comm, "EPS", NULL); CHKERRQ(ierr);
ierr = EPSCreate(fem->comm, &eps); CHKERRQ(ierr);
ierr = EPSSetTarget(eps, -0.6); CHKERRQ(ierr);
ierr = EPSSetWhichEigenpairs(eps, EPS_TARGET_MAGNITUDE); CHKERRQ(ierr);
ierr = EPSSetOperators(eps, H, S); CHKERRQ(ierr);
if(S == NULL) {
ierr = EPSSetProblemType(eps, EPS_NHEP); CHKERRQ(ierr);
} else {
ierr = EPSSetProblemType(eps, EPS_GNHEP); CHKERRQ(ierr);
}
Vec x0[1]; MatCreateVecs(H, &x0[0], NULL);
int num; FEMInfGetSize(fem, &num);
for(int i = 0; i < num; i++) {
VecSetValue(x0[0], i, 0.5, INSERT_VALUES);
}
VecAssemblyBegin(x0[0]); VecAssemblyEnd(x0[0]);
EPSSetInitialSpace(eps, 1, x0);
ierr = EPSSetFromOptions(eps); CHKERRQ(ierr);
ierr = EPSSolve(eps); CHKERRQ(ierr);
PetscInt nconv;
EPSGetConverged(eps, &nconv);
if(nconv == 0)
SETERRQ(fem->comm, 1, "Failed to digonalize in init state\n");
Vec x_ans;
MatCreateVecs(H, &x_ans, NULL);
EPSGetEigenpair(eps, 0, e0, NULL, x_ans, NULL);
EPSDestroy(&eps);
PetscScalar v[1]; PetscInt idx[1] = {1};
VecGetValues(x_ans, 1, idx, v);
PetscScalar scale_factor = v[0] / cabs(v[0]);
VecScale( x_ans, 1.0/scale_factor);
PetscScalar norm0;
Vec Sx; MatCreateVecs(S, &Sx, NULL);
MatMult(S, x_ans, Sx); VecDot(x_ans, Sx, &norm0);
VecScale(x_ans, 1.0/sqrt(norm0));
*x = x_ans;
return 0;
}
static void ApplyPCPrecPETSCGen(void *x, PRIMME_INT *ldx, void *y,
PRIMME_INT *ldy, int *blockSize, int trans, PC *pc, MPI_Comm comm) {
int i;
Vec xvec, yvec;
Mat matrix;
PetscErrorCode ierr;
PetscInt mLocal, nLocal;
ierr = PCGetOperators(pc[0],&matrix,NULL); CHKERRABORT(comm, ierr);
assert(sizeof(PetscScalar) == sizeof(SCALAR));
ierr = MatGetLocalSize(matrix, &mLocal, &nLocal); CHKERRABORT(comm, ierr);
assert(mLocal == nLocal && nLocal <= *ldx && mLocal <= *ldy);
#if PETSC_VERSION_LT(3,6,0)
ierr = MatGetVecs(matrix, &xvec, &yvec); CHKERRABORT(comm, ierr);
#else
ierr = MatCreateVecs(matrix, &xvec, &yvec); CHKERRABORT(comm, ierr);
#endif
for (i=0; i<*blockSize; i++) {
ierr = VecPlaceArray(xvec, ((SCALAR*)x) + (*ldx)*i); CHKERRABORT(comm, ierr);
ierr = VecPlaceArray(yvec, ((SCALAR*)y) + (*ldy)*i); CHKERRABORT(comm, ierr);
if (trans == 0) {
ierr = PCApply(*pc, xvec, yvec); CHKERRABORT(comm, ierr);
} else if (pc[1]) {
ierr = PCApply(pc[1], xvec, yvec); CHKERRABORT(comm, ierr);
} else {
ierr = PCApplyTranspose(pc[0], xvec, yvec);
}
ierr = VecResetArray(xvec); CHKERRABORT(comm, ierr);
ierr = VecResetArray(yvec); CHKERRABORT(comm, ierr);
}
ierr = VecDestroy(&xvec); CHKERRABORT(comm, ierr);
ierr = VecDestroy(&yvec); CHKERRABORT(comm, ierr);
}
PetscErrorCode MatSetLocalToGlobalMapping_IS(Mat A,ISLocalToGlobalMapping rmapping,ISLocalToGlobalMapping cmapping)
{
PetscErrorCode ierr;
PetscInt n,bs;
Mat_IS *is = (Mat_IS*)A->data;
IS from,to;
Vec global;
PetscFunctionBegin;
PetscCheckSameComm(A,1,rmapping,2);
if (rmapping != cmapping) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_ARG_INCOMP,"MATIS requires the row and column mappings to be identical");
if (is->mapping) { /* Currenly destroys the objects that will be created by this routine. Is there anything else that should be checked? */
ierr = ISLocalToGlobalMappingDestroy(&is->mapping);CHKERRQ(ierr);
ierr = VecDestroy(&is->x);CHKERRQ(ierr);
ierr = VecDestroy(&is->y);CHKERRQ(ierr);
ierr = VecScatterDestroy(&is->ctx);CHKERRQ(ierr);
ierr = MatDestroy(&is->A);CHKERRQ(ierr);
}
ierr = PetscObjectReference((PetscObject)rmapping);CHKERRQ(ierr);
ierr = ISLocalToGlobalMappingDestroy(&is->mapping);CHKERRQ(ierr);
is->mapping = rmapping;
/*
ierr = PetscLayoutSetISLocalToGlobalMapping(A->rmap,rmapping);CHKERRQ(ierr);
ierr = PetscLayoutSetISLocalToGlobalMapping(A->cmap,cmapping);CHKERRQ(ierr);
*/
/* Create the local matrix A */
ierr = ISLocalToGlobalMappingGetSize(rmapping,&n);CHKERRQ(ierr);
ierr = ISLocalToGlobalMappingGetBlockSize(rmapping,&bs);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_SELF,&is->A);CHKERRQ(ierr);
if (bs > 1) {
ierr = MatSetType(is->A,MATSEQBAIJ);CHKERRQ(ierr);
} else {
ierr = MatSetType(is->A,MATSEQAIJ);CHKERRQ(ierr);
}
ierr = MatSetSizes(is->A,n,n,n,n);CHKERRQ(ierr);
ierr = MatSetBlockSize(is->A,bs);CHKERRQ(ierr);
ierr = MatSetOptionsPrefix(is->A,((PetscObject)A)->prefix);CHKERRQ(ierr);
ierr = MatAppendOptionsPrefix(is->A,"is_");CHKERRQ(ierr);
ierr = MatSetFromOptions(is->A);CHKERRQ(ierr);
/* Create the local work vectors */
ierr = VecCreate(PETSC_COMM_SELF,&is->x);CHKERRQ(ierr);
ierr = VecSetBlockSize(is->x,bs);CHKERRQ(ierr);
ierr = VecSetSizes(is->x,n,n);CHKERRQ(ierr);
ierr = VecSetOptionsPrefix(is->x,((PetscObject)A)->prefix);CHKERRQ(ierr);
ierr = VecAppendOptionsPrefix(is->x,"is_");CHKERRQ(ierr);
ierr = VecSetFromOptions(is->x);CHKERRQ(ierr);
ierr = VecDuplicate(is->x,&is->y);CHKERRQ(ierr);
/* setup the global to local scatter */
ierr = ISCreateStride(PETSC_COMM_SELF,n,0,1,&to);CHKERRQ(ierr);
ierr = ISLocalToGlobalMappingApplyIS(rmapping,to,&from);CHKERRQ(ierr);
ierr = MatCreateVecs(A,&global,NULL);CHKERRQ(ierr);
ierr = VecScatterCreate(global,from,is->x,to,&is->ctx);CHKERRQ(ierr);
ierr = VecDestroy(&global);CHKERRQ(ierr);
ierr = ISDestroy(&to);CHKERRQ(ierr);
ierr = ISDestroy(&from);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
static PetscErrorCode KSPSetUp_TSIRM(KSP ksp)
{
PetscErrorCode ierr;
KSP_TSIRM *tsirm = (KSP_TSIRM*)ksp->data;
PetscFunctionBegin;
/* Initialization */
tsirm->tol_ls = 1e-40;
tsirm->size_ls = 12;
tsirm->maxiter_ls = 15;
tsirm->cgls = 0;
/* Matrix of the system */
ierr = KSPGetOperators(ksp,&tsirm->A,NULL);
CHKERRQ(ierr); /* Matrix of the system */
ierr = MatGetSize(tsirm->A,&tsirm->size,NULL);
CHKERRQ(ierr); /* Size of the system */
ierr = MatGetOwnershipRange(tsirm->A,&tsirm->Istart,&tsirm->Iend);
CHKERRQ(ierr);
/* Matrix S of residuals */
ierr = MatCreate(PETSC_COMM_WORLD,&tsirm->S);
CHKERRQ(ierr);
ierr = MatSetSizes(tsirm->S,tsirm->Iend-tsirm->Istart,PETSC_DECIDE,tsirm->size,tsirm->size_ls);
CHKERRQ(ierr);
ierr = MatSetType(tsirm->S,MATDENSE);
CHKERRQ(ierr);
ierr = MatSetUp(tsirm->S);
CHKERRQ(ierr);
/* Residual and vector Alpha computed in the minimization step */
ierr = MatCreateVecs(tsirm->S,&tsirm->Alpha,&tsirm->r);
CHKERRQ(ierr);
PetscFunctionReturn(0);
}
int main(int argc, char **argv)
{
MPI_Comm comm;
Mat A; /* A graph */
Vec c; /* A vector giving the component of each vertex */
Vec cold; /* The vector c from the last iteration */
PetscScalar *carray;
PetscInt testnum = 0;
PetscInt V, vStart, vEnd, v, n;
PetscMPIInt size;
PetscErrorCode ierr;
ierr = PetscInitialize(&argc, &argv, NULL,help);if (ierr) return ierr;
comm = PETSC_COMM_WORLD;
ierr = MPI_Comm_size(comm, &size);CHKERRQ(ierr);
/* Use matrix to encode a graph */
ierr = PetscOptionsGetInt(NULL,NULL, "-testnum", &testnum, NULL);CHKERRQ(ierr);
ierr = CreateGraph(comm, testnum, &A);CHKERRQ(ierr);
ierr = MatGetSize(A, &V, NULL);CHKERRQ(ierr);
/* Replace matrix-vector multiplication with one that calculates the minimum rather than the sum */
if (size == 1) {
ierr = MatShellSetOperation(A, MATOP_MULT, (void (*)) MatMultMax_SeqAIJ);CHKERRQ(ierr);
} else {
Mat_MPIAIJ *a = (Mat_MPIAIJ *) A->data;
ierr = MatShellSetOperation(a->A, MATOP_MULT, (void (*)) MatMultMax_SeqAIJ);CHKERRQ(ierr);
ierr = MatShellSetOperation(a->B, MATOP_MULT, (void (*)) MatMultMax_SeqAIJ);CHKERRQ(ierr);
ierr = MatShellSetOperation(a->B, MATOP_MULT_ADD, (void (*)) MatMultAddMax_SeqAIJ);CHKERRQ(ierr);
}
/* Initialize each vertex as a separate component */
ierr = MatCreateVecs(A, &c, NULL);CHKERRQ(ierr);
ierr = MatGetOwnershipRange(A, &vStart, &vEnd);CHKERRQ(ierr);
ierr = VecGetArray(c, &carray);CHKERRQ(ierr);
for (v = vStart; v < vEnd; ++v) {
carray[v-vStart] = v;
}
ierr = VecRestoreArray(c, &carray);CHKERRQ(ierr);
/* Preprocess in parallel to find local components */
/* Multiply until c does not change */
ierr = VecDuplicate(c, &cold);CHKERRQ(ierr);
for (v = 0; v < V; ++v) {
Vec cnew = cold;
PetscBool stop;
ierr = MatMult(A, c, cnew);CHKERRQ(ierr);
ierr = VecEqual(c, cnew, &stop);CHKERRQ(ierr);
if (stop) break;
cold = c;
c = cnew;
}
/* Report */
ierr = VecUniqueEntries(c, &n, NULL);CHKERRQ(ierr);
ierr = PetscPrintf(comm, "Components: %d Iterations: %d\n", n, v);CHKERRQ(ierr);
ierr = VecView(c, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
/* Cleanup */
ierr = VecDestroy(&c);CHKERRQ(ierr);
ierr = VecDestroy(&cold);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
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;
}
/*@
PCMGGetRScale - Gets the pointwise scaling for the restriction operator from level l to l-1.
Collective on PC
Input Parameters:
+ pc - the multigrid context
. rscale - the scaling
- l - the level (0 is coarsest) to supply [Do not supply 0]
Level: advanced
Notes:
When evaluating a function on a coarse level one does not want to do F(R * x) one does F(rscale * R * x) where rscale is 1 over the row sums of R.
.keywords: MG, set, multigrid, restriction, level
.seealso: PCMGSetInterpolation(), PCMGGetRestriction()
@*/
PetscErrorCode PCMGGetRScale(PC pc,PetscInt l,Vec *rscale)
{
PetscErrorCode ierr;
PC_MG *mg = (PC_MG*)pc->data;
PC_MG_Levels **mglevels = mg->levels;
PetscFunctionBegin;
PetscValidHeaderSpecific(pc,PC_CLASSID,1);
if (!mglevels) SETERRQ(PetscObjectComm((PetscObject)pc),PETSC_ERR_ARG_WRONGSTATE,"Must set MG levels before calling");
if (l <= 0 || mg->nlevels <= l) SETERRQ2(PetscObjectComm((PetscObject)pc),PETSC_ERR_ARG_OUTOFRANGE,"Level %D must be in range {1,...,%D}",l,mg->nlevels-1);
if (!mglevels[l]->rscale) {
Mat R;
Vec X,Y,coarse,fine;
PetscInt M,N;
ierr = PCMGGetRestriction(pc,l,&R);CHKERRQ(ierr);
ierr = MatCreateVecs(R,&X,&Y);CHKERRQ(ierr);
ierr = MatGetSize(R,&M,&N);CHKERRQ(ierr);
if (M < N) {
fine = X;
coarse = Y;
} else if (N < M) {
fine = Y; coarse = X;
} else SETERRQ(PetscObjectComm((PetscObject)R),PETSC_ERR_SUP,"Restriction matrix is square, cannot determine which Vec is coarser");
ierr = VecSet(fine,1.);CHKERRQ(ierr);
ierr = MatRestrict(R,fine,coarse);CHKERRQ(ierr);
ierr = VecDestroy(&fine);CHKERRQ(ierr);
ierr = VecReciprocal(coarse);CHKERRQ(ierr);
mglevels[l]->rscale = coarse;
}
*rscale = mglevels[l]->rscale;
PetscFunctionReturn(0);
}
PETSC_EXTERN PetscErrorCode MatMFFDSetBase_MFFD(Mat J,Vec U,Vec F)
{
PetscErrorCode ierr;
MatMFFD ctx = (MatMFFD)J->data;
PetscFunctionBegin;
ierr = MatMFFDResetHHistory(J);CHKERRQ(ierr);
if (!ctx->current_u) {
ierr = VecDuplicate(U,&ctx->current_u);CHKERRQ(ierr);
ierr = VecLockReadPush(ctx->current_u);CHKERRQ(ierr);
}
ierr = VecLockReadPop(ctx->current_u);CHKERRQ(ierr);
ierr = VecCopy(U,ctx->current_u);CHKERRQ(ierr);
ierr = VecLockReadPush(ctx->current_u);CHKERRQ(ierr);
if (F) {
if (ctx->current_f_allocated) {ierr = VecDestroy(&ctx->current_f);CHKERRQ(ierr);}
ctx->current_f = F;
ctx->current_f_allocated = PETSC_FALSE;
} else if (!ctx->current_f_allocated) {
ierr = MatCreateVecs(J,NULL,&ctx->current_f);CHKERRQ(ierr);
ctx->current_f_allocated = PETSC_TRUE;
}
if (!ctx->w) {
ierr = VecDuplicate(ctx->current_u,&ctx->w);CHKERRQ(ierr);
}
J->assembled = PETSC_TRUE;
PetscFunctionReturn(0);
}
PetscErrorCode MatMultTranspose_Composite_Multiplicative(Mat A,Vec x,Vec y)
{
Mat_Composite *shell = (Mat_Composite*)A->data;
Mat_CompositeLink tail = shell->tail;
PetscErrorCode ierr;
Vec in,out;
PetscFunctionBegin;
if (!tail) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Must provide at least one matrix with MatCompositeAddMat()");
in = x;
if (shell->left) {
if (!shell->leftwork) {
ierr = VecDuplicate(shell->left,&shell->leftwork);CHKERRQ(ierr);
}
ierr = VecPointwiseMult(shell->leftwork,shell->left,in);CHKERRQ(ierr);
in = shell->leftwork;
}
while (tail->prev) {
if (!tail->prev->work) { /* should reuse previous work if the same size */
ierr = MatCreateVecs(tail->mat,NULL,&tail->prev->work);CHKERRQ(ierr);
}
out = tail->prev->work;
ierr = MatMultTranspose(tail->mat,in,out);CHKERRQ(ierr);
in = out;
tail = tail->prev;
}
ierr = MatMultTranspose(tail->mat,in,y);CHKERRQ(ierr);
if (shell->right) {
ierr = VecPointwiseMult(y,shell->right,y);CHKERRQ(ierr);
}
ierr = VecScale(y,shell->scale);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
int main(int argc,char **args)
{
const PetscInt inds[] = {0,1};
PetscScalar avals[] = {2,3,5,7};
Mat S;
User user;
PetscErrorCode ierr;
Vec base;
ierr = PetscInitialize(&argc,&args,(char*)0,help);if (ierr) return ierr;
ierr = PetscNew(&user);CHKERRQ(ierr);
ierr = MatCreateSeqAIJ(PETSC_COMM_WORLD,2,2,2,NULL,&user->B);CHKERRQ(ierr);
ierr = MatSetUp(user->B);CHKERRQ(ierr);
ierr = MatSetValues(user->B,2,inds,2,inds,avals,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatAssemblyBegin(user->B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(user->B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatCreateVecs(user->B,&base,NULL);CHKERRQ(ierr);
ierr = MatCreateShell(PETSC_COMM_WORLD,2,2,2,2,user,&S);CHKERRQ(ierr);
ierr = MatSetUp(S);CHKERRQ(ierr);
ierr = MatShellSetOperation(S,MATOP_MULT,(void (*)(void))MatMult_User);CHKERRQ(ierr);
ierr = MatShellSetOperation(S,MATOP_MULT_TRANSPOSE,(void (*)(void))MatMultTranspose_User);CHKERRQ(ierr);
ierr = MatShellTestMult(S,MyFunction,base,user,NULL);CHKERRQ(ierr);
ierr = MatShellTestMultTranspose(S,MyFunction,base,user,NULL);CHKERRQ(ierr);
ierr = VecDestroy(&base);CHKERRQ(ierr);
ierr = MatDestroy(&user->B);CHKERRQ(ierr);
ierr = MatDestroy(&S);CHKERRQ(ierr);
ierr = PetscFree(user);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
static void PETScMatvecGenNoBlock(void *x, PRIMME_INT ldx, void *y, PRIMME_INT ldy,
int blockSize, int trans, Mat matrix, MPI_Comm comm) {
int i;
Vec xvec, yvec;
PetscInt m, n, mLocal, nLocal;
PetscErrorCode ierr;
assert(sizeof(PetscScalar) == sizeof(SCALAR));
ierr = MatGetSize(matrix, &m, &n); CHKERRABORT(comm, ierr);
ierr = MatGetLocalSize(matrix, &mLocal, &nLocal); CHKERRABORT(comm, ierr);
#if PETSC_VERSION_LT(3,6,0)
ierr = MatGetVecs(matrix, &xvec, &yvec); CHKERRABORT(comm, ierr);
#else
ierr = MatCreateVecs(matrix, &xvec, &yvec); CHKERRABORT(comm, ierr);
#endif
if (trans == 1) {
Vec aux = xvec; xvec = yvec; yvec = aux;
}
for (i=0; i<blockSize; i++) {
ierr = VecPlaceArray(xvec, ((SCALAR*)x) + ldx*i); CHKERRABORT(comm, ierr);
ierr = VecPlaceArray(yvec, ((SCALAR*)y) + ldy*i); CHKERRABORT(comm, ierr);
if (trans == 0) {
ierr = MatMult(matrix, xvec, yvec); CHKERRABORT(comm, ierr);
} else {
ierr = MatMultHermitianTranspose(matrix, xvec, yvec); CHKERRABORT(comm, ierr);
}
ierr = VecResetArray(xvec); CHKERRABORT(comm, ierr);
ierr = VecResetArray(yvec); CHKERRABORT(comm, ierr);
}
ierr = VecDestroy(&xvec); CHKERRABORT(comm, ierr);
ierr = VecDestroy(&yvec); CHKERRABORT(comm, ierr);
}
static PetscErrorCode PCBDDCScalingSetUp_Deluxe_Private(PC pc)
{
PC_BDDC *pcbddc=(PC_BDDC*)pc->data;
PCBDDCDeluxeScaling deluxe_ctx=pcbddc->deluxe_ctx;
PCBDDCSubSchurs sub_schurs = pcbddc->sub_schurs;
PetscErrorCode ierr;
PetscFunctionBegin;
if (!sub_schurs->n_subs) {
PetscFunctionReturn(0);
}
/* Create work vectors for sequential part of deluxe */
ierr = MatCreateVecs(sub_schurs->S_Ej_all,&deluxe_ctx->seq_work1,&deluxe_ctx->seq_work2);CHKERRQ(ierr);
/* Compute deluxe sequential scatter */
if (sub_schurs->reuse_mumps && !sub_schurs->is_dir) {
PCBDDCReuseMumps reuse_mumps = sub_schurs->reuse_mumps;
ierr = PetscObjectReference((PetscObject)reuse_mumps->correction_scatter_B);CHKERRQ(ierr);
deluxe_ctx->seq_scctx = reuse_mumps->correction_scatter_B;
} else {
ierr = VecScatterCreate(pcbddc->work_scaling,sub_schurs->is_Ej_all,deluxe_ctx->seq_work1,NULL,&deluxe_ctx->seq_scctx);CHKERRQ(ierr);
}
/* Create Mat object for deluxe scaling */
ierr = PetscObjectReference((PetscObject)sub_schurs->S_Ej_all);CHKERRQ(ierr);
deluxe_ctx->seq_mat = sub_schurs->S_Ej_all;
if (sub_schurs->sum_S_Ej_all) { /* if this matrix is present, then we need to create the KSP object to invert it */
PC pc_temp;
MatSolverPackage solver=NULL;
char ksp_prefix[256];
size_t len;
ierr = KSPCreate(PETSC_COMM_SELF,&deluxe_ctx->seq_ksp);CHKERRQ(ierr);
ierr = KSPSetOperators(deluxe_ctx->seq_ksp,sub_schurs->sum_S_Ej_all,sub_schurs->sum_S_Ej_all);CHKERRQ(ierr);
ierr = KSPSetType(deluxe_ctx->seq_ksp,KSPPREONLY);CHKERRQ(ierr);
ierr = KSPGetPC(deluxe_ctx->seq_ksp,&pc_temp);CHKERRQ(ierr);
ierr = PCSetType(pc_temp,PCLU);CHKERRQ(ierr);
ierr = KSPGetPC(pcbddc->ksp_D,&pc_temp);CHKERRQ(ierr);
ierr = PCFactorGetMatSolverPackage(pc_temp,(const MatSolverPackage*)&solver);CHKERRQ(ierr);
if (solver) {
PC new_pc;
PCType type;
ierr = PCGetType(pc_temp,&type);CHKERRQ(ierr);
ierr = KSPGetPC(deluxe_ctx->seq_ksp,&new_pc);CHKERRQ(ierr);
ierr = PCSetType(new_pc,type);CHKERRQ(ierr);
ierr = PCFactorSetMatSolverPackage(new_pc,solver);CHKERRQ(ierr);
}
ierr = PetscStrlen(((PetscObject)(pcbddc->ksp_D))->prefix,&len);CHKERRQ(ierr);
len -= 10; /* remove "dirichlet_" */
ierr = PetscStrncpy(ksp_prefix,((PetscObject)(pcbddc->ksp_D))->prefix,len+1);CHKERRQ(ierr);
ierr = PetscStrcat(ksp_prefix,"deluxe_");CHKERRQ(ierr);
ierr = KSPSetOptionsPrefix(deluxe_ctx->seq_ksp,ksp_prefix);CHKERRQ(ierr);
ierr = KSPSetFromOptions(deluxe_ctx->seq_ksp);CHKERRQ(ierr);
ierr = KSPSetUp(deluxe_ctx->seq_ksp);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
PetscErrorCode MatMult_SchurComplement(Mat N,Vec x,Vec y)
{
Mat_SchurComplement *Na = (Mat_SchurComplement*)N->data;
PetscErrorCode ierr;
PetscFunctionBegin;
if (!Na->work1) {ierr = MatCreateVecs(Na->A,&Na->work1,NULL);CHKERRQ(ierr);}
if (!Na->work2) {ierr = MatCreateVecs(Na->A,&Na->work2,NULL);CHKERRQ(ierr);}
ierr = MatMult(Na->B,x,Na->work1);CHKERRQ(ierr);
ierr = KSPSolve(Na->ksp,Na->work1,Na->work2);CHKERRQ(ierr);
ierr = MatMult(Na->C,Na->work2,y);CHKERRQ(ierr);
ierr = VecScale(y,-1.0);CHKERRQ(ierr);
if (Na->D) {
ierr = MatMultAdd(Na->D,x,y,y);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
PetscErrorCode MatCreateVecs_SchurComplement(Mat N,Vec *right,Vec *left)
{
Mat_SchurComplement *Na = (Mat_SchurComplement*)N->data;
PetscErrorCode ierr;
PetscFunctionBegin;
if (Na->D) {
ierr = MatCreateVecs(Na->D,right,left);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
if (right) {
ierr = MatCreateVecs(Na->B,right,NULL);CHKERRQ(ierr);
}
if (left) {
ierr = MatCreateVecs(Na->C,NULL,left);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
PetscErrorCode MatCreateVecs_Transpose(Mat A,Vec *r, Vec *l)
{
Mat_Transpose *Aa = (Mat_Transpose*)A->data;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = MatCreateVecs(Aa->A,l,r);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode MatCreateVecs_HT(Mat N,Vec *r, Vec *l)
{
Mat_HT *Na = (Mat_HT*)N->data;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = MatCreateVecs(Na->A,l,r);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode SolveFinal(FEMInf fem, int L1, PetscScalar energy,
Vec x0, Vec *x1, PetscScalar *alpha) {
PetscErrorCode ierr;
Mat S, L, D;
CalcMat(fem, L1, &L, &S);
MatAXPY(L, -energy, S, DIFFERENT_NONZERO_PATTERN);
MatDestroy(&S);
PetscScalar mat_ele_cos;
// <Y_10 | P_q(cos theta) | Y_00>
mat_ele_cos = Y1ElePq(1, 1, 0,
0, 0);
if(getenv("SHOW_DEBUG"))
printf("mat_ele_cos = %f\n", PetscRealPart(mat_ele_cos));
PF dp_length; PotCreate(PETSC_COMM_SELF, &dp_length);
ierr = PotSetPower(dp_length, mat_ele_cos, 1); CHKERRQ(ierr);
ierr =FEMInfCreateMat(fem, 1, &D);
ierr = FEMInfPotR1Mat(fem, dp_length, D); CHKERRQ(ierr);
Vec driv;
MatCreateVecs(L, &driv, NULL);
ierr = MatMult(D, x0, driv); CHKERRQ(ierr);
ierr = MatDestroy(&D); CHKERRQ(ierr);
KSP ksp;
ierr = KSPCreate(fem->comm, &ksp); CHKERRQ(ierr);
ierr = KSPSetOperators(ksp, L, L); CHKERRQ(ierr);
ierr = KSPSetFromOptions(ksp); CHKERRQ(ierr);
ierr = MatCreateVecs(L, x1, NULL);
ierr = KSPSolve(ksp, driv, *x1); CHKERRQ(ierr);
ierr = VecDot(*x1, driv, alpha); CHKERRQ(ierr);
// KSPView(ksp, PETSC_VIEWER_STDOUT_SELF);
KSPDestroy(&ksp);
MatDestroy(&L);
VecDestroy(&driv);
return 0;
}
/*@
MatComputeExplicitOperatorTranspose - Computes the explicit matrix representation of
a give matrix that can apply MatMultTranspose()
Collective on Mat
Input Parameter:
. inmat - the matrix
Output Parameter:
. mat - the explict operator transposed
Notes:
This computation is done by applying the transpose of the operator to columns of the
identity matrix.
Currently, this routine uses a dense matrix format when 1 processor
is used and a sparse format otherwise. This routine is costly in general,
and is recommended for use only with relatively small systems.
Level: advanced
.keywords: Mat, compute, explicit, operator
@*/
PetscErrorCode MatComputeExplicitOperatorTranspose(Mat inmat,Mat *mat)
{
Vec in,out;
PetscErrorCode ierr;
PetscInt i,m,n,M,N,*rows,start,end;
MPI_Comm comm;
PetscScalar *array,zero = 0.0,one = 1.0;
PetscMPIInt size;
PetscFunctionBegin;
PetscValidHeaderSpecific(inmat,MAT_CLASSID,1);
PetscValidPointer(mat,2);
ierr = PetscObjectGetComm((PetscObject)inmat,&comm);CHKERRQ(ierr);
ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr);
ierr = MatGetLocalSize(inmat,&m,&n);CHKERRQ(ierr);
ierr = MatGetSize(inmat,&M,&N);CHKERRQ(ierr);
ierr = MatCreateVecs(inmat,&in,&out);CHKERRQ(ierr);
ierr = VecSetOption(in,VEC_IGNORE_OFF_PROC_ENTRIES,PETSC_TRUE);CHKERRQ(ierr);
ierr = VecGetOwnershipRange(out,&start,&end);CHKERRQ(ierr);
ierr = PetscMalloc1(m,&rows);CHKERRQ(ierr);
for (i=0; i<m; i++) rows[i] = start + i;
ierr = MatCreate(comm,mat);CHKERRQ(ierr);
ierr = MatSetSizes(*mat,m,n,M,N);CHKERRQ(ierr);
if (size == 1) {
ierr = MatSetType(*mat,MATSEQDENSE);CHKERRQ(ierr);
ierr = MatSeqDenseSetPreallocation(*mat,NULL);CHKERRQ(ierr);
} else {
ierr = MatSetType(*mat,MATMPIAIJ);CHKERRQ(ierr);
ierr = MatMPIAIJSetPreallocation(*mat,n,NULL,N-n,NULL);CHKERRQ(ierr);
}
for (i=0; i<N; i++) {
ierr = VecSet(in,zero);CHKERRQ(ierr);
ierr = VecSetValues(in,1,&i,&one,INSERT_VALUES);CHKERRQ(ierr);
ierr = VecAssemblyBegin(in);CHKERRQ(ierr);
ierr = VecAssemblyEnd(in);CHKERRQ(ierr);
ierr = MatMultTranspose(inmat,in,out);CHKERRQ(ierr);
ierr = VecGetArray(out,&array);CHKERRQ(ierr);
ierr = MatSetValues(*mat,m,rows,1,&i,array,INSERT_VALUES);CHKERRQ(ierr);
ierr = VecRestoreArray(out,&array);CHKERRQ(ierr);
}
ierr = PetscFree(rows);CHKERRQ(ierr);
ierr = VecDestroy(&out);CHKERRQ(ierr);
ierr = VecDestroy(&in);CHKERRQ(ierr);
ierr = MatAssemblyBegin(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(*mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
static PetscErrorCode PCSetUp_Jacobi_NonSymmetric(PC pc)
{
PetscErrorCode ierr;
PC_Jacobi *jac = (PC_Jacobi*)pc->data;
PetscFunctionBegin;
ierr = MatCreateVecs(pc->pmat,&jac->diag,0);CHKERRQ(ierr);
ierr = PetscLogObjectParent((PetscObject)pc,(PetscObject)jac->diag);CHKERRQ(ierr);
ierr = PCSetUp_Jacobi(pc);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@
SNESFASCreateCoarseVec - create Vec corresponding to a state vector on one level coarser than current level
Collective
Input Arguments:
. snes - SNESFAS
Output Arguments:
. Xcoarse - vector on level one coarser than snes
Level: developer
.seealso: SNESFASSetRestriction(), SNESFASRestrict()
@*/
PetscErrorCode SNESFASCreateCoarseVec(SNES snes,Vec *Xcoarse)
{
PetscErrorCode ierr;
SNES_FAS *fas = (SNES_FAS*)snes->data;
PetscFunctionBegin;
if (fas->rscale) {
ierr = VecDuplicate(fas->rscale,Xcoarse);CHKERRQ(ierr);
} else if (fas->inject) {
ierr = MatCreateVecs(fas->inject,Xcoarse,NULL);CHKERRQ(ierr);
} else SETERRQ(PetscObjectComm((PetscObject)snes),PETSC_ERR_ARG_WRONGSTATE,"Must set restriction or injection");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 PCLSCAllocate_Private(PC pc)
{
PC_LSC *lsc = (PC_LSC*)pc->data;
Mat A;
PetscErrorCode ierr;
PetscFunctionBegin;
if (lsc->allocated) PetscFunctionReturn(0);
ierr = KSPCreate(PetscObjectComm((PetscObject)pc),&lsc->kspL);CHKERRQ(ierr);
ierr = KSPSetErrorIfNotConverged(lsc->kspL,pc->erroriffailure);CHKERRQ(ierr);
ierr = PetscObjectIncrementTabLevel((PetscObject)lsc->kspL,(PetscObject)pc,1);CHKERRQ(ierr);
ierr = KSPSetType(lsc->kspL,KSPPREONLY);CHKERRQ(ierr);
ierr = KSPSetOptionsPrefix(lsc->kspL,((PetscObject)pc)->prefix);CHKERRQ(ierr);
ierr = KSPAppendOptionsPrefix(lsc->kspL,"lsc_");CHKERRQ(ierr);
ierr = MatSchurComplementGetSubMatrices(pc->mat,&A,NULL,NULL,NULL,NULL);CHKERRQ(ierr);
ierr = MatCreateVecs(A,&lsc->x0,&lsc->y0);CHKERRQ(ierr);
ierr = MatCreateVecs(pc->pmat,&lsc->x1,NULL);CHKERRQ(ierr);
if (lsc->scalediag) {
ierr = VecDuplicate(lsc->x0,&lsc->scale);CHKERRQ(ierr);
}
lsc->allocated = PETSC_TRUE;
PetscFunctionReturn(0);
}
int main(int argc,char **args)
{
KSP ksp; /* linear solver context */
Mat A; /* linear system matrix */
Vec x,b; /* approx solution, RHS */
PetscInt Ii,Istart,Iend;
PetscErrorCode ierr;
PetscScalar v[3] = {-1./2., 1., -1./2.};
PetscInt j[3];
PetscInt k=15;
PetscInt M,m=420;
ierr = PetscInitialize(&argc,&args,(char*)0,help);if (ierr) return ierr;
ierr = PetscOptionsGetInt(NULL,NULL,"-k",&k,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-m",&m,NULL);CHKERRQ(ierr);
ierr = KSPCreate(PETSC_COMM_WORLD,&ksp);CHKERRQ(ierr);
ierr = KSPSetFromOptions(ksp);CHKERRQ(ierr);
ierr = KSPGetOperators(ksp,&A,NULL);CHKERRQ(ierr);
ierr = MatSetSizes(A,m,m,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr);
ierr = MatSetFromOptions(A);CHKERRQ(ierr);
ierr = MatSetUp(A);CHKERRQ(ierr);
ierr = MatGetOwnershipRange(A,&Istart,&Iend);CHKERRQ(ierr);
ierr = MatGetSize(A,&M,NULL);CHKERRQ(ierr);
for (Ii=Istart; Ii<Iend; Ii++) {
j[0] = Ii - k;
j[1] = Ii;
j[2] = (Ii + k) < M ? (Ii + k) : -1;
ierr = MatSetValues(A,1,&Ii,3,j,v,INSERT_VALUES);CHKERRQ(ierr);
}
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatCreateVecs(A,&x,&b);CHKERRQ(ierr);
ierr = VecSetFromOptions(b);CHKERRQ(ierr);
ierr = VecSet(b,1.0);CHKERRQ(ierr);
ierr = VecSetFromOptions(x);CHKERRQ(ierr);
ierr = VecSet(x,2.0);CHKERRQ(ierr);
ierr = KSPSolve(ksp,b,x);CHKERRQ(ierr);
ierr = VecDestroy(&b);CHKERRQ(ierr);
ierr = VecDestroy(&x);CHKERRQ(ierr);
ierr = KSPDestroy(&ksp);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
int main(int argc, char **argv)
{
PetscErrorCode ierr;
Mat A;
KSP ksp;
PC pc;
IS zero, one;
MatNullSpace nullsp;
Vec x, b;
MPI_Comm comm;
PetscInitialize(&argc, &argv, NULL, NULL);
comm = PETSC_COMM_WORLD;
ierr = MatCreate(comm, &A);CHKERRQ(ierr);
ierr = MatSetSizes(A, 4, 4, PETSC_DECIDE, PETSC_DECIDE);CHKERRQ(ierr);
ierr = MatSetUp(A);CHKERRQ(ierr);
ierr = MatSetFromOptions(A);CHKERRQ(ierr);
ierr = MatCreateVecs(A, &x, &b);CHKERRQ(ierr);
ierr = VecSet(x, 2.0);CHKERRQ(ierr);
ierr = VecSet(b, 12.0);CHKERRQ(ierr);
ierr = MatDiagonalSet(A, x, INSERT_VALUES);CHKERRQ(ierr);
ierr = MatAssemblyBegin(A, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = ISCreateStride(comm, 2, 0, 1, &zero);CHKERRQ(ierr);
ierr = ISCreateStride(comm, 2, 2, 1, &one);CHKERRQ(ierr);
ierr = MatNullSpaceCreate(comm, PETSC_TRUE, 0, NULL, &nullsp);CHKERRQ(ierr);
ierr = PetscObjectCompose((PetscObject)zero, "nullspace",(PetscObject)nullsp);CHKERRQ(ierr);
ierr = KSPCreate(comm, &ksp);CHKERRQ(ierr);
ierr = KSPSetOperators(ksp, A, A);CHKERRQ(ierr);
ierr = KSPSetUp(ksp);CHKERRQ(ierr);
ierr = KSPGetPC(ksp, &pc);CHKERRQ(ierr);
ierr = KSPSetFromOptions(ksp);CHKERRQ(ierr);
ierr = PCFieldSplitSetIS(pc, "0", zero);
ierr = PCFieldSplitSetIS(pc, "1", one);
ierr = KSPSolve(ksp, b, x);CHKERRQ(ierr);
ierr = KSPDestroy(&ksp);CHKERRQ(ierr);
ierr = MatNullSpaceDestroy(&nullsp);CHKERRQ(ierr);
ierr = ISDestroy(&zero);CHKERRQ(ierr);
ierr = ISDestroy(&one);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = VecDestroy(&x);CHKERRQ(ierr);
ierr = VecDestroy(&b);CHKERRQ(ierr);
PetscFinalize();
return 0;
}
int main(int argc,char **args)
{
KSP ksp;
Mat A;
Vec x,b;
PetscViewer fd;
char file[PETSC_MAX_PATH_LEN];
PetscErrorCode ierr;
PetscBool flg,preload = PETSC_TRUE;
PetscInitialize(&argc,&args,(char*)0,help);
ierr = PetscLogDefaultBegin();CHKERRQ(ierr);
ierr = PetscOptionsGetString(NULL,NULL,"-f",file,PETSC_MAX_PATH_LEN,&flg);CHKERRQ(ierr);
PetscPreLoadBegin(preload,"Load system");
/*
Load the matrix and vector; then destroy the viewer.
*/
ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
ierr = MatSetFromOptions(A);CHKERRQ(ierr);
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,file,FILE_MODE_READ,&fd);CHKERRQ(ierr);
ierr = MatLoad(A,fd);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&fd);CHKERRQ(ierr);
ierr = MatCreateVecs(A,&x,&b);CHKERRQ(ierr);
ierr = VecSetFromOptions(b);CHKERRQ(ierr);
ierr = VecSet(b,1.0);CHKERRQ(ierr);
ierr = KSPCreate(PETSC_COMM_WORLD,&ksp);CHKERRQ(ierr);
ierr = KSPSetFromOptions(ksp);CHKERRQ(ierr);
ierr = KSPSetOperators(ksp,A,A);CHKERRQ(ierr);
ierr = KSPSetUp(ksp);CHKERRQ(ierr);
ierr = KSPSetUpOnBlocks(ksp);CHKERRQ(ierr);
PetscPreLoadStage("KSPSolve");
ierr = KSPSolve(ksp,b,x);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = VecDestroy(&b);CHKERRQ(ierr);
ierr = VecDestroy(&x);CHKERRQ(ierr);
ierr = KSPDestroy(&ksp);CHKERRQ(ierr);
PetscPreLoadEnd();
ierr = PetscLogView_VecScatter(PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
static PetscErrorCode PCSetUp_CP(PC pc)
{
PC_CP *cp = (PC_CP*)pc->data;
PetscInt i,j,*colcnt;
PetscErrorCode ierr;
PetscBool flg;
Mat_SeqAIJ *aij = (Mat_SeqAIJ*)pc->pmat->data;
PetscFunctionBegin;
ierr = PetscObjectTypeCompare((PetscObject)pc->pmat,MATSEQAIJ,&flg);CHKERRQ(ierr);
if (!flg) SETERRQ(PetscObjectComm((PetscObject)pc),PETSC_ERR_SUP,"Currently only handles SeqAIJ matrices");
ierr = MatGetLocalSize(pc->pmat,&cp->m,&cp->n);CHKERRQ(ierr);
if (cp->m != cp->n) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Currently only for square matrices");
if (!cp->work) {ierr = MatCreateVecs(pc->pmat,&cp->work,NULL);CHKERRQ(ierr);}
if (!cp->d) {ierr = PetscMalloc1(cp->n,&cp->d);CHKERRQ(ierr);}
if (cp->a && pc->flag != SAME_NONZERO_PATTERN) {
ierr = PetscFree3(cp->a,cp->i,cp->j);CHKERRQ(ierr);
cp->a = 0;
}
/* convert to column format */
if (!cp->a) {
ierr = PetscMalloc3(aij->nz,&cp->a,cp->n+1,&cp->i,aij->nz,&cp->j);CHKERRQ(ierr);
}
ierr = PetscCalloc1(cp->n,&colcnt);CHKERRQ(ierr);
for (i=0; i<aij->nz; i++) colcnt[aij->j[i]]++;
cp->i[0] = 0;
for (i=0; i<cp->n; i++) cp->i[i+1] = cp->i[i] + colcnt[i];
ierr = PetscMemzero(colcnt,cp->n*sizeof(PetscInt));CHKERRQ(ierr);
for (i=0; i<cp->m; i++) { /* over rows */
for (j=aij->i[i]; j<aij->i[i+1]; j++) { /* over columns in row */
cp->j[cp->i[aij->j[j]]+colcnt[aij->j[j]]] = i;
cp->a[cp->i[aij->j[j]]+colcnt[aij->j[j]]++] = aij->a[j];
}
}
ierr = PetscFree(colcnt);CHKERRQ(ierr);
/* compute sum of squares of each column d[] */
for (i=0; i<cp->n; i++) { /* over columns */
cp->d[i] = 0.;
for (j=cp->i[i]; j<cp->i[i+1]; j++) cp->d[i] += cp->a[j]*cp->a[j]; /* over rows in column */
cp->d[i] = 1.0/cp->d[i];
}
PetscFunctionReturn(0);
}
static PetscErrorCode PCSetUp_Composite(PC pc)
{
PetscErrorCode ierr;
PC_Composite *jac = (PC_Composite*)pc->data;
PC_CompositeLink next = jac->head;
PetscFunctionBegin;
if (!jac->work1) {
ierr = MatCreateVecs(pc->pmat,&jac->work1,0);CHKERRQ(ierr);
}
while (next) {
ierr = PCSetOperators(next->pc,pc->mat,pc->pmat);CHKERRQ(ierr);
next = next->next;
}
PetscFunctionReturn(0);
}
// Test Mat BNHat up to N=10 when Op is a diagonal Mat
TEST(operatorsCreateBnHeadTest, testBNHatDiagonalOp)
{
Mat Op; // operator (e.g., Laplacian)
PetscReal dt = 2.3, // time-step size
c = 0.5, // time-scheme coefficient of the implicit diffusive term
val = 2.0 / dt; // value set on the diagonal of the operator
PetscInt nx = 10, // number of points in the x-direction
ny = 12; // number of points in the y-direction
PetscReal ans = nx * ny * dt; // expected sum of all elements of B1Hat
// Create and assemble operator
MatCreate(PETSC_COMM_WORLD, &Op);
MatSetSizes(Op, PETSC_DECIDE, PETSC_DECIDE, nx * ny, nx * ny);
MatSetType(Op, MATAIJ);
MatSetUp(Op);
for (PetscInt i = 0; i < nx * ny; i++)
MatSetValues(Op, 1, &i, 1, &i, &val, INSERT_VALUES);
MatAssemblyBegin(Op, MAT_FINAL_ASSEMBLY);
MatAssemblyEnd(Op, MAT_FINAL_ASSEMBLY);
for (PetscInt N = 1; N <= 10; N++)
{
Mat BNHat; // Nth-order approximation of the inverse of (I/dt - c*Op)
// Call function to test
petibm::operators::createBnHead(Op, dt, c, N, BNHat);
// Check size of Mat BNHat
{
PetscInt nrows, ncols;
MatGetSize(BNHat, &nrows, &ncols);
ASSERT_EQ(nx * ny, nrows);
ASSERT_EQ(nx * ny, ncols);
}
// Check sum of elements of BNHat is the expected value
if (N > 1) ans += dt * nx * ny * std::pow(c * dt * val, N - 1);
{
PetscReal sum;
Vec v;
MatCreateVecs(Op, &v, nullptr);
MatGetRowSum(BNHat, v);
VecSum(v, &sum);
ASSERT_TRUE(std::abs(sum - ans) <= 1.0E-11);
VecDestroy(&v);
}
MatDestroy(&BNHat);
}
MatDestroy(&Op);
}
static PetscErrorCode KSPSetUp_GCR(KSP ksp)
{
KSP_GCR *ctx = (KSP_GCR*)ksp->data;
PetscErrorCode ierr;
Mat A;
PetscBool diagonalscale;
PetscFunctionBegin;
ierr = PCGetDiagonalScale(ksp->pc,&diagonalscale);CHKERRQ(ierr);
if (diagonalscale) SETERRQ1(PetscObjectComm((PetscObject)ksp),PETSC_ERR_SUP,"Krylov method %s does not support diagonal scaling",((PetscObject)ksp)->type_name);
ierr = KSPGetOperators(ksp, &A, NULL);CHKERRQ(ierr);
ierr = MatCreateVecs(A, &ctx->R, NULL);CHKERRQ(ierr);
ierr = VecDuplicateVecs(ctx->R, ctx->restart, &ctx->VV);CHKERRQ(ierr);
ierr = VecDuplicateVecs(ctx->R, ctx->restart, &ctx->SS);CHKERRQ(ierr);
ierr = PetscMalloc1(ctx->restart, &ctx->val);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*
PCGAMGGetDataWithGhosts - hacks into Mat MPIAIJ so this must have size > 1
Input Parameter:
. Gmat - MPIAIJ matrix for scattters
. data_sz - number of data terms per node (# cols in output)
. data_in[nloc*data_sz] - column oriented data
Output Parameter:
. a_stride - numbrt of rows of output
. a_data_out[stride*data_sz] - output data with ghosts
*/
PetscErrorCode PCGAMGGetDataWithGhosts(Mat Gmat,PetscInt data_sz,PetscReal data_in[],PetscInt *a_stride,PetscReal **a_data_out)
{
PetscErrorCode ierr;
Vec tmp_crds;
Mat_MPIAIJ *mpimat = (Mat_MPIAIJ*)Gmat->data;
PetscInt nnodes,num_ghosts,dir,kk,jj,my0,Iend,nloc;
PetscScalar *data_arr;
PetscReal *datas;
PetscBool isMPIAIJ;
PetscFunctionBegin;
ierr = PetscObjectBaseTypeCompare((PetscObject)Gmat, MATMPIAIJ, &isMPIAIJ);CHKERRQ(ierr);
ierr = MatGetOwnershipRange(Gmat, &my0, &Iend);CHKERRQ(ierr);
nloc = Iend - my0;
ierr = VecGetLocalSize(mpimat->lvec, &num_ghosts);CHKERRQ(ierr);
nnodes = num_ghosts + nloc;
*a_stride = nnodes;
ierr = MatCreateVecs(Gmat, &tmp_crds, 0);CHKERRQ(ierr);
ierr = PetscMalloc1(data_sz*nnodes, &datas);CHKERRQ(ierr);
for (dir=0; dir<data_sz; dir++) {
/* set local, and global */
for (kk=0; kk<nloc; kk++) {
PetscInt gid = my0 + kk;
PetscScalar crd = (PetscScalar)data_in[dir*nloc + kk]; /* col oriented */
datas[dir*nnodes + kk] = PetscRealPart(crd);
ierr = VecSetValues(tmp_crds, 1, &gid, &crd, INSERT_VALUES);CHKERRQ(ierr);
}
ierr = VecAssemblyBegin(tmp_crds);CHKERRQ(ierr);
ierr = VecAssemblyEnd(tmp_crds);CHKERRQ(ierr);
/* get ghost datas */
ierr = VecScatterBegin(mpimat->Mvctx,tmp_crds,mpimat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
ierr = VecScatterEnd(mpimat->Mvctx,tmp_crds,mpimat->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
ierr = VecGetArray(mpimat->lvec, &data_arr);CHKERRQ(ierr);
for (kk=nloc,jj=0;jj<num_ghosts;kk++,jj++) datas[dir*nnodes + kk] = PetscRealPart(data_arr[jj]);
ierr = VecRestoreArray(mpimat->lvec, &data_arr);CHKERRQ(ierr);
}
ierr = VecDestroy(&tmp_crds);CHKERRQ(ierr);
*a_data_out = datas;
PetscFunctionReturn(0);
}
