PetscErrorCode MatRARtSymbolic_SeqAIJ_SeqAIJ_colorrart(Mat A,Mat R,PetscReal fill,Mat *C) { PetscErrorCode ierr; Mat P; PetscInt *rti,*rtj; Mat_RARt *rart; MatColoring coloring; MatTransposeColoring matcoloring; ISColoring iscoloring; Mat Rt_dense,RARt_dense; Mat_SeqAIJ *c; PetscFunctionBegin; /* create symbolic P=Rt */ ierr = MatGetSymbolicTranspose_SeqAIJ(R,&rti,&rtj);CHKERRQ(ierr); ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,R->cmap->n,R->rmap->n,rti,rtj,NULL,&P);CHKERRQ(ierr); /* get symbolic C=Pt*A*P */ ierr = MatPtAPSymbolic_SeqAIJ_SeqAIJ_SparseAxpy(A,P,fill,C);CHKERRQ(ierr); ierr = MatSetBlockSizes(*C,PetscAbs(R->rmap->bs),PetscAbs(R->rmap->bs));CHKERRQ(ierr); (*C)->ops->rartnumeric = MatRARtNumeric_SeqAIJ_SeqAIJ_colorrart; /* create a supporting struct */ ierr = PetscNew(&rart);CHKERRQ(ierr); c = (Mat_SeqAIJ*)(*C)->data; c->rart = rart; /* ------ Use coloring ---------- */ /* inode causes memory problem, don't know why */ if (c->inode.use) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"MAT_USE_INODES is not supported. Use '-mat_no_inode'"); /* Create MatTransposeColoring from symbolic C=R*A*R^T */ ierr = MatColoringCreate(*C,&coloring);CHKERRQ(ierr); ierr = MatColoringSetDistance(coloring,2);CHKERRQ(ierr); ierr = MatColoringSetType(coloring,MATCOLORINGSL);CHKERRQ(ierr); ierr = MatColoringSetFromOptions(coloring);CHKERRQ(ierr); ierr = MatColoringApply(coloring,&iscoloring);CHKERRQ(ierr); ierr = MatColoringDestroy(&coloring);CHKERRQ(ierr); ierr = MatTransposeColoringCreate(*C,iscoloring,&matcoloring);CHKERRQ(ierr); rart->matcoloring = matcoloring; ierr = ISColoringDestroy(&iscoloring);CHKERRQ(ierr); /* Create Rt_dense */ ierr = MatCreate(PETSC_COMM_SELF,&Rt_dense);CHKERRQ(ierr); ierr = MatSetSizes(Rt_dense,A->cmap->n,matcoloring->ncolors,A->cmap->n,matcoloring->ncolors);CHKERRQ(ierr); ierr = MatSetType(Rt_dense,MATSEQDENSE);CHKERRQ(ierr); ierr = MatSeqDenseSetPreallocation(Rt_dense,NULL);CHKERRQ(ierr); Rt_dense->assembled = PETSC_TRUE; rart->Rt = Rt_dense; /* Create RARt_dense = R*A*Rt_dense */ ierr = MatCreate(PETSC_COMM_SELF,&RARt_dense);CHKERRQ(ierr); ierr = MatSetSizes(RARt_dense,(*C)->rmap->n,matcoloring->ncolors,(*C)->rmap->n,matcoloring->ncolors);CHKERRQ(ierr); ierr = MatSetType(RARt_dense,MATSEQDENSE);CHKERRQ(ierr); ierr = MatSeqDenseSetPreallocation(RARt_dense,NULL);CHKERRQ(ierr); rart->RARt = RARt_dense; /* Allocate work array to store columns of A*R^T used in MatMatMatMultNumeric_SeqAIJ_SeqAIJ_SeqDense() */ ierr = PetscMalloc1(A->rmap->n*4,&rart->work);CHKERRQ(ierr); rart->destroy = (*C)->ops->destroy; (*C)->ops->destroy = MatDestroy_SeqAIJ_RARt; /* clean up */ ierr = MatRestoreSymbolicTranspose_SeqAIJ(R,&rti,&rtj);CHKERRQ(ierr); ierr = MatDestroy(&P);CHKERRQ(ierr); #if defined(PETSC_USE_INFO) { PetscReal density= (PetscReal)(c->nz)/(RARt_dense->rmap->n*RARt_dense->cmap->n); ierr = PetscInfo(*C,"C=R*(A*Rt) via coloring C - use sparse-dense inner products\n");CHKERRQ(ierr); ierr = PetscInfo6(*C,"RARt_den %D %D; Rt %D %D (RARt->nz %D)/(m*ncolors)=%g\n",RARt_dense->rmap->n,RARt_dense->cmap->n,R->cmap->n,R->rmap->n,c->nz,density);CHKERRQ(ierr); } #endif PetscFunctionReturn(0); }
int main(int argc,char **argv) { Mat A,R,C,C_dense,C_sparse,Rt_dense,P,PtAP; PetscInt row,col,m,n; PetscErrorCode ierr; MatScalar one =1.0,val; MatColoring mc; MatTransposeColoring matcoloring = 0; ISColoring iscoloring; PetscBool equal; PetscMPIInt size; ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr; 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!"); /* Create seqaij A */ ierr = MatCreate(PETSC_COMM_SELF,&A);CHKERRQ(ierr); ierr = MatSetSizes(A,4,4,4,4);CHKERRQ(ierr); ierr = MatSetType(A,MATSEQAIJ);CHKERRQ(ierr); ierr = MatSetFromOptions(A);CHKERRQ(ierr); ierr = MatSetUp(A);CHKERRQ(ierr); row = 0; col=0; val=1.0; ierr = MatSetValues(A,1,&row,1,&col,&val,ADD_VALUES);CHKERRQ(ierr); row = 1; col=3; val=2.0; ierr = MatSetValues(A,1,&row,1,&col,&val,ADD_VALUES);CHKERRQ(ierr); row = 2; col=2; val=3.0; ierr = MatSetValues(A,1,&row,1,&col,&val,ADD_VALUES);CHKERRQ(ierr); row = 3; col=0; val=4.0; ierr = MatSetValues(A,1,&row,1,&col,&val,ADD_VALUES);CHKERRQ(ierr); ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatSetOptionsPrefix(A,"A_");CHKERRQ(ierr); ierr = MatView(A,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_SELF,"\n");CHKERRQ(ierr); /* Create seqaij R */ ierr = MatCreate(PETSC_COMM_SELF,&R);CHKERRQ(ierr); ierr = MatSetSizes(R,2,4,2,4);CHKERRQ(ierr); ierr = MatSetType(R,MATSEQAIJ);CHKERRQ(ierr); ierr = MatSetFromOptions(R);CHKERRQ(ierr); ierr = MatSetUp(R);CHKERRQ(ierr); row = 0; col=0; ierr = MatSetValues(R,1,&row,1,&col,&one,ADD_VALUES);CHKERRQ(ierr); row = 0; col=1; ierr = MatSetValues(R,1,&row,1,&col,&one,ADD_VALUES);CHKERRQ(ierr); row = 1; col=1; ierr = MatSetValues(R,1,&row,1,&col,&one,ADD_VALUES);CHKERRQ(ierr); row = 1; col=2; ierr = MatSetValues(R,1,&row,1,&col,&one,ADD_VALUES);CHKERRQ(ierr); row = 1; col=3; ierr = MatSetValues(R,1,&row,1,&col,&one,ADD_VALUES);CHKERRQ(ierr); ierr = MatAssemblyBegin(R,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatAssemblyEnd(R,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatSetOptionsPrefix(R,"R_");CHKERRQ(ierr); ierr = MatView(R,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_SELF,"\n");CHKERRQ(ierr); /* C = A*R^T */ ierr = MatMatTransposeMult(A,R,MAT_INITIAL_MATRIX,2.0,&C);CHKERRQ(ierr); ierr = MatSetOptionsPrefix(C,"ARt_");CHKERRQ(ierr); ierr = MatView(C,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_SELF,"\n");CHKERRQ(ierr); /* Create MatTransposeColoring from symbolic C=A*R^T */ ierr = MatColoringCreate(C,&mc);CHKERRQ(ierr); ierr = MatColoringSetDistance(mc,2);CHKERRQ(ierr); /* ierr = MatColoringSetType(mc,MATCOLORINGSL);CHKERRQ(ierr); */ ierr = MatColoringSetFromOptions(mc);CHKERRQ(ierr); ierr = MatColoringApply(mc,&iscoloring);CHKERRQ(ierr); ierr = MatColoringDestroy(&mc);CHKERRQ(ierr); ierr = MatTransposeColoringCreate(C,iscoloring,&matcoloring);CHKERRQ(ierr); ierr = ISColoringDestroy(&iscoloring);CHKERRQ(ierr); /* Create Rt_dense */ ierr = MatCreate(PETSC_COMM_WORLD,&Rt_dense);CHKERRQ(ierr); ierr = MatSetSizes(Rt_dense,4,matcoloring->ncolors,PETSC_DECIDE,PETSC_DECIDE);CHKERRQ(ierr); ierr = MatSetType(Rt_dense,MATDENSE);CHKERRQ(ierr); ierr = MatSeqDenseSetPreallocation(Rt_dense,NULL);CHKERRQ(ierr); ierr = MatAssemblyBegin(Rt_dense,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatAssemblyEnd(Rt_dense,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatGetLocalSize(Rt_dense,&m,&n);CHKERRQ(ierr); printf("Rt_dense: %d,%d\n",(int)m,(int)n); /* Get Rt_dense by Apply MatTransposeColoring to R */ ierr = MatTransColoringApplySpToDen(matcoloring,R,Rt_dense);CHKERRQ(ierr); /* C_dense = A*Rt_dense */ ierr = MatMatMult(A,Rt_dense,MAT_INITIAL_MATRIX,2.0,&C_dense);CHKERRQ(ierr); ierr = MatSetOptionsPrefix(C_dense,"ARt_dense_");CHKERRQ(ierr); /*ierr = MatView(C_dense,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); */ /*ierr = PetscPrintf(PETSC_COMM_SELF,"\n");CHKERRQ(ierr); */ /* Recover C from C_dense */ ierr = MatDuplicate(C,MAT_DO_NOT_COPY_VALUES,&C_sparse);CHKERRQ(ierr); ierr = MatTransColoringApplyDenToSp(matcoloring,C_dense,C_sparse);CHKERRQ(ierr); ierr = MatSetOptionsPrefix(C_sparse,"ARt_color_");CHKERRQ(ierr); ierr = MatView(C_sparse,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_SELF,"\n");CHKERRQ(ierr); ierr = MatDestroy(&C_dense);CHKERRQ(ierr); ierr = MatDestroy(&C_sparse);CHKERRQ(ierr); ierr = MatDestroy(&Rt_dense);CHKERRQ(ierr); ierr = MatTransposeColoringDestroy(&matcoloring);CHKERRQ(ierr); ierr = MatDestroy(&C);CHKERRQ(ierr); /* Test PtAP = P^T*A*P, P = R^T */ ierr = MatTranspose(R,MAT_INITIAL_MATRIX,&P);CHKERRQ(ierr); ierr = MatPtAP(A,P,MAT_INITIAL_MATRIX,2.0,&PtAP);CHKERRQ(ierr); ierr = MatSetOptionsPrefix(PtAP,"PtAP_");CHKERRQ(ierr); ierr = MatView(PtAP,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); ierr = MatDestroy(&P);CHKERRQ(ierr); /* Test C = RARt */ ierr = MatRARt(A,R,MAT_INITIAL_MATRIX,2.0,&C);CHKERRQ(ierr); ierr = MatRARt(A,R,MAT_REUSE_MATRIX,2.0,&C);CHKERRQ(ierr); ierr = MatEqual(C,PtAP,&equal);CHKERRQ(ierr); if (!equal) { ierr = PetscPrintf(PETSC_COMM_SELF,"Error: PtAP != RARt");CHKERRQ(ierr); } /* Free spaces */ ierr = MatDestroy(&C);CHKERRQ(ierr); ierr = MatDestroy(&A);CHKERRQ(ierr); ierr = MatDestroy(&R);CHKERRQ(ierr); ierr = MatDestroy(&PtAP);CHKERRQ(ierr); ierr = PetscFinalize(); return ierr; }
PetscErrorCode MatRARtSymbolic_SeqAIJ_SeqAIJ(Mat A,Mat R,PetscReal fill,Mat *C) { PetscErrorCode ierr; Mat P; PetscInt *rti,*rtj; Mat_RARt *rart; PetscContainer container; MatTransposeColoring matcoloring; ISColoring iscoloring; Mat Rt_dense,RARt_dense; PetscLogDouble GColor=0.0,MCCreate=0.0,MDenCreate=0.0,t0,tf,etime=0.0; Mat_SeqAIJ *c; PetscFunctionBegin; ierr = PetscGetTime(&t0);CHKERRQ(ierr); /* create symbolic P=Rt */ ierr = MatGetSymbolicTranspose_SeqAIJ(R,&rti,&rtj);CHKERRQ(ierr); ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,R->cmap->n,R->rmap->n,rti,rtj,PETSC_NULL,&P);CHKERRQ(ierr); /* get symbolic C=Pt*A*P */ ierr = MatPtAPSymbolic_SeqAIJ_SeqAIJ(A,P,fill,C);CHKERRQ(ierr); (*C)->rmap->bs = R->rmap->bs; (*C)->cmap->bs = R->rmap->bs; /* create a supporting struct */ ierr = PetscNew(Mat_RARt,&rart);CHKERRQ(ierr); /* attach the supporting struct to C */ ierr = PetscContainerCreate(PETSC_COMM_SELF,&container);CHKERRQ(ierr); ierr = PetscContainerSetPointer(container,rart);CHKERRQ(ierr); ierr = PetscContainerSetUserDestroy(container,PetscContainerDestroy_Mat_RARt);CHKERRQ(ierr); ierr = PetscObjectCompose((PetscObject)(*C),"Mat_RARt",(PetscObject)container);CHKERRQ(ierr); ierr = PetscContainerDestroy(&container);CHKERRQ(ierr); ierr = PetscGetTime(&tf);CHKERRQ(ierr); etime += tf - t0; /* Create MatTransposeColoring from symbolic C=R*A*R^T */ c=(Mat_SeqAIJ*)(*C)->data; ierr = PetscGetTime(&t0);CHKERRQ(ierr); ierr = MatGetColoring(*C,MATCOLORINGLF,&iscoloring);CHKERRQ(ierr); ierr = PetscGetTime(&tf);CHKERRQ(ierr); GColor += tf - t0; ierr = PetscGetTime(&t0);CHKERRQ(ierr); ierr = MatTransposeColoringCreate(*C,iscoloring,&matcoloring);CHKERRQ(ierr); rart->matcoloring = matcoloring; ierr = ISColoringDestroy(&iscoloring);CHKERRQ(ierr); ierr = PetscGetTime(&tf);CHKERRQ(ierr); MCCreate += tf - t0; ierr = PetscGetTime(&t0);CHKERRQ(ierr); /* Create Rt_dense */ ierr = MatCreate(PETSC_COMM_SELF,&Rt_dense);CHKERRQ(ierr); ierr = MatSetSizes(Rt_dense,A->cmap->n,matcoloring->ncolors,A->cmap->n,matcoloring->ncolors);CHKERRQ(ierr); ierr = MatSetType(Rt_dense,MATSEQDENSE);CHKERRQ(ierr); ierr = MatSeqDenseSetPreallocation(Rt_dense,PETSC_NULL);CHKERRQ(ierr); Rt_dense->assembled = PETSC_TRUE; rart->Rt = Rt_dense; /* Create RARt_dense = R*A*Rt_dense */ ierr = MatCreate(PETSC_COMM_SELF,&RARt_dense);CHKERRQ(ierr); ierr = MatSetSizes(RARt_dense,(*C)->rmap->n,matcoloring->ncolors,(*C)->rmap->n,matcoloring->ncolors);CHKERRQ(ierr); ierr = MatSetType(RARt_dense,MATSEQDENSE);CHKERRQ(ierr); ierr = MatSeqDenseSetPreallocation(RARt_dense,PETSC_NULL);CHKERRQ(ierr); rart->RARt = RARt_dense; /* Allocate work array to store columns of A*R^T used in MatMatMatMultNumeric_SeqAIJ_SeqAIJ_SeqDense() */ ierr = PetscMalloc(A->rmap->n*4*sizeof(PetscScalar),&rart->work);CHKERRQ(ierr); ierr = PetscGetTime(&tf);CHKERRQ(ierr); MDenCreate += tf - t0; rart->destroy = (*C)->ops->destroy; (*C)->ops->destroy = MatDestroy_SeqAIJ_RARt; /* clean up */ ierr = MatRestoreSymbolicTranspose_SeqAIJ(R,&rti,&rtj);CHKERRQ(ierr); ierr = MatDestroy(&P);CHKERRQ(ierr); #if defined(PETSC_USE_INFO) { PetscReal density= (PetscReal)(c->nz)/(RARt_dense->rmap->n*RARt_dense->cmap->n); ierr = PetscInfo6(*C,"RARt_den %D %D; Rt_den %D %D, (RARt->nz %D)/(m*ncolors)=%g\n",RARt_dense->rmap->n,RARt_dense->cmap->n,Rt_dense->rmap->n,Rt_dense->cmap->n,c->nz,density);CHKERRQ(ierr); ierr = PetscInfo5(*C,"Sym = GetColor %g + MColorCreate %g + MDenCreate %g + other %g = %g\n",GColor,MCCreate,MDenCreate,etime,GColor+MCCreate+MDenCreate+etime);CHKERRQ(ierr); } #endif PetscFunctionReturn(0); }