PetscErrorCode SNESComputeJacobianDefaultColor(SNES snes,Vec x1,Mat *J,Mat *B,MatStructure *flag,void *ctx) { MatFDColoring color = (MatFDColoring)ctx; PetscErrorCode ierr; DM dm; PetscErrorCode (*func)(SNES,Vec,Vec,void*); Vec F; void *funcctx; ISColoring iscoloring; PetscBool hascolor; PetscBool solvec; PetscFunctionBegin; if (color) PetscValidHeaderSpecific(color,MAT_FDCOLORING_CLASSID,6); else {ierr = PetscObjectQuery((PetscObject)*B,"SNESMatFDColoring",(PetscObject*)&color);CHKERRQ(ierr);} *flag = SAME_NONZERO_PATTERN; ierr = SNESGetFunction(snes,&F,&func,&funcctx);CHKERRQ(ierr); if (!color) { ierr = SNESGetDM(snes,&dm);CHKERRQ(ierr); ierr = DMHasColoring(dm,&hascolor);CHKERRQ(ierr); if (hascolor) { ierr = DMCreateColoring(dm,IS_COLORING_GLOBAL,&iscoloring);CHKERRQ(ierr); ierr = MatFDColoringCreate(*B,iscoloring,&color);CHKERRQ(ierr); ierr = ISColoringDestroy(&iscoloring);CHKERRQ(ierr); ierr = MatFDColoringSetFunction(color,(PetscErrorCode (*)(void))func,funcctx);CHKERRQ(ierr); ierr = MatFDColoringSetFromOptions(color);CHKERRQ(ierr); } else { ierr = MatGetColoring(*B,MATCOLORINGSL,&iscoloring);CHKERRQ(ierr); ierr = MatFDColoringCreate(*B,iscoloring,&color);CHKERRQ(ierr); ierr = ISColoringDestroy(&iscoloring);CHKERRQ(ierr); ierr = MatFDColoringSetFunction(color,(PetscErrorCode (*)(void))func,(void*)funcctx);CHKERRQ(ierr); ierr = MatFDColoringSetFromOptions(color);CHKERRQ(ierr); } ierr = PetscObjectCompose((PetscObject)*B,"SNESMatFDColoring",(PetscObject)color);CHKERRQ(ierr); ierr = PetscObjectDereference((PetscObject)color);CHKERRQ(ierr); } /* F is only usable if there is no RHS on the SNES and the full solution corresponds to x1 */ ierr = VecEqual(x1,snes->vec_sol,&solvec);CHKERRQ(ierr); if (!snes->vec_rhs && solvec) { ierr = MatFDColoringSetF(color,F);CHKERRQ(ierr); } ierr = MatFDColoringApply(*B,color,x1,flag,snes);CHKERRQ(ierr); if (*J != *B) { ierr = MatAssemblyBegin(*J,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatAssemblyEnd(*J,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); } PetscFunctionReturn(0); }
int main(int argc,char **args) { Mat A,Asp; PetscViewer fd; /* viewer */ char file[PETSC_MAX_PATH_LEN]; /* input file name */ PetscErrorCode ierr; PetscInt m,n,rstart,rend; PetscBool flg; PetscInt row,ncols,j,nrows,nnzA=0,nnzAsp=0; const PetscInt *cols; const PetscScalar *vals; PetscReal norm,percent,val,dtol=1.e-16; PetscMPIInt rank; MatInfo matinfo; PetscInt Dnnz,Onnz; PetscInitialize(&argc,&args,(char *)0,help); ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr); /* Determine files from which we read the linear systems. */ ierr = PetscOptionsGetString(PETSC_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"); /* Open binary file. Note that we use FILE_MODE_READ to indicate reading from this file. */ ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,file,FILE_MODE_READ,&fd);CHKERRQ(ierr); /* Load the matrix; then destroy the viewer. */ ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr); ierr = MatSetOptionsPrefix(A,"a_");CHKERRQ(ierr); ierr = MatSetFromOptions(A);CHKERRQ(ierr); ierr = MatLoad(A,fd);CHKERRQ(ierr); ierr = PetscViewerDestroy(&fd);CHKERRQ(ierr); ierr = MatGetSize(A,&m,&n);CHKERRQ(ierr); ierr = MatGetInfo(A,MAT_LOCAL,&matinfo);CHKERRQ(ierr); //printf("matinfo.nz_used %g\n",matinfo.nz_used); /* Get a sparse matrix Asp by dumping zero entries of A */ ierr = MatCreate(PETSC_COMM_WORLD,&Asp);CHKERRQ(ierr); ierr = MatSetSizes(Asp,m,n,PETSC_DECIDE,PETSC_DECIDE);CHKERRQ(ierr); ierr = MatSetOptionsPrefix(Asp,"asp_");CHKERRQ(ierr); ierr = MatSetFromOptions(Asp);CHKERRQ(ierr); Dnnz = (PetscInt)matinfo.nz_used/m + 1; Onnz = Dnnz/2; printf("Dnnz %d %d\n",Dnnz,Onnz); ierr = MatSeqAIJSetPreallocation(Asp,Dnnz,PETSC_NULL);CHKERRQ(ierr); ierr = MatMPIAIJSetPreallocation(Asp,Dnnz,PETSC_NULL,Onnz,PETSC_NULL);CHKERRQ(ierr); /* Check zero rows */ ierr = MatGetOwnershipRange(A,&rstart,&rend);CHKERRQ(ierr); nrows = 0; for (row=rstart; row<rend; row++){ ierr = MatGetRow(A,row,&ncols,&cols,&vals);CHKERRQ(ierr); nnzA += ncols; norm = 0.0; for (j=0; j<ncols; j++){ val = PetscAbsScalar(vals[j]); if (norm < val) norm = norm; if (val > dtol){ ierr = MatSetValues(Asp,1,&row,1,&cols[j],&vals[j],INSERT_VALUES);CHKERRQ(ierr); nnzAsp++; } } if (!norm) nrows++; ierr = MatRestoreRow(A,row,&ncols,&cols,&vals);CHKERRQ(ierr); } ierr = MatAssemblyBegin(Asp,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatAssemblyEnd(Asp,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); percent=(PetscReal)nnzA*100/(m*n); ierr = PetscPrintf(PETSC_COMM_SELF," [%d] Matrix A local size %d,%d; nnzA %d, %g percent; No. of zero rows: %d\n",rank,m,n,nnzA,percent,nrows); percent=(PetscReal)nnzAsp*100/(m*n); ierr = PetscPrintf(PETSC_COMM_SELF," [%d] Matrix Asp nnzAsp %d, %g percent\n",rank,nnzAsp,percent); /* investigate matcoloring for Asp */ PetscBool Asp_coloring = PETSC_FALSE; ierr = PetscOptionsHasName(PETSC_NULL,"-Asp_color",&Asp_coloring);CHKERRQ(ierr); if (Asp_coloring){ ISColoring iscoloring; MatFDColoring matfdcoloring; ierr = PetscPrintf(PETSC_COMM_WORLD," Create coloring of Asp...\n"); ierr = MatGetColoring(Asp,MATCOLORINGSL,&iscoloring);CHKERRQ(ierr); ierr = MatFDColoringCreate(Asp,iscoloring,&matfdcoloring);CHKERRQ(ierr); ierr = MatFDColoringSetFromOptions(matfdcoloring);CHKERRQ(ierr); //ierr = MatFDColoringView(matfdcoloring,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); ierr = ISColoringDestroy(&iscoloring);CHKERRQ(ierr); ierr = MatFDColoringDestroy(&matfdcoloring);CHKERRQ(ierr); } /* Write Asp in binary for study - see ~petsc/src/mat/examples/tests/ex124.c */ PetscBool Asp_write = PETSC_FALSE; ierr = PetscOptionsHasName(PETSC_NULL,"-Asp_write",&Asp_write);CHKERRQ(ierr); if (Asp_write){ PetscViewer viewer; ierr = PetscPrintf(PETSC_COMM_SELF,"Write Asp into file Asp.dat ...\n"); ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"Asp.dat",FILE_MODE_WRITE,&viewer);CHKERRQ(ierr); ierr = MatView(Asp,viewer);CHKERRQ(ierr); ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); } ierr = MatDestroy(&A);CHKERRQ(ierr); ierr = MatDestroy(&Asp);CHKERRQ(ierr); ierr = PetscFinalize(); return 0; }
void NonlinearSystem::setupColoringFiniteDifferencedPreconditioner() { #ifdef LIBMESH_HAVE_PETSC // Make sure that libMesh isn't going to override our preconditioner _transient_sys.nonlinear_solver->jacobian = nullptr; PetscNonlinearSolver<Number> & petsc_nonlinear_solver = dynamic_cast<PetscNonlinearSolver<Number> &>(*_transient_sys.nonlinear_solver); // Pointer to underlying PetscMatrix type PetscMatrix<Number> * petsc_mat = dynamic_cast<PetscMatrix<Number> *>(_transient_sys.matrix); #if PETSC_VERSION_LESS_THAN(3, 2, 0) // This variable is only needed for PETSC < 3.2.0 PetscVector<Number> * petsc_vec = dynamic_cast<PetscVector<Number> *>(_transient_sys.solution.get()); #endif Moose::compute_jacobian(*_transient_sys.current_local_solution, *petsc_mat, _transient_sys); if (!petsc_mat) mooseError("Could not convert to Petsc matrix."); petsc_mat->close(); PetscErrorCode ierr = 0; ISColoring iscoloring; #if PETSC_VERSION_LESS_THAN(3, 2, 0) // PETSc 3.2.x ierr = MatGetColoring(petsc_mat->mat(), MATCOLORING_LF, &iscoloring); CHKERRABORT(libMesh::COMM_WORLD, ierr); #elif PETSC_VERSION_LESS_THAN(3, 5, 0) // PETSc 3.3.x, 3.4.x ierr = MatGetColoring(petsc_mat->mat(), MATCOLORINGLF, &iscoloring); CHKERRABORT(_communicator.get(), ierr); #else // PETSc 3.5.x MatColoring matcoloring; ierr = MatColoringCreate(petsc_mat->mat(), &matcoloring); CHKERRABORT(_communicator.get(), ierr); ierr = MatColoringSetType(matcoloring, MATCOLORINGLF); CHKERRABORT(_communicator.get(), ierr); ierr = MatColoringSetFromOptions(matcoloring); CHKERRABORT(_communicator.get(), ierr); ierr = MatColoringApply(matcoloring, &iscoloring); CHKERRABORT(_communicator.get(), ierr); ierr = MatColoringDestroy(&matcoloring); CHKERRABORT(_communicator.get(), ierr); #endif MatFDColoringCreate(petsc_mat->mat(), iscoloring, &_fdcoloring); MatFDColoringSetFromOptions(_fdcoloring); MatFDColoringSetFunction(_fdcoloring, (PetscErrorCode(*)(void)) & libMesh::__libmesh_petsc_snes_fd_residual, &petsc_nonlinear_solver); #if !PETSC_RELEASE_LESS_THAN(3, 5, 0) MatFDColoringSetUp(petsc_mat->mat(), iscoloring, _fdcoloring); #endif #if PETSC_VERSION_LESS_THAN(3, 4, 0) SNESSetJacobian(petsc_nonlinear_solver.snes(), petsc_mat->mat(), petsc_mat->mat(), SNESDefaultComputeJacobianColor, _fdcoloring); #else SNESSetJacobian(petsc_nonlinear_solver.snes(), petsc_mat->mat(), petsc_mat->mat(), SNESComputeJacobianDefaultColor, _fdcoloring); #endif #if PETSC_VERSION_LESS_THAN(3, 2, 0) Mat my_mat = petsc_mat->mat(); MatStructure my_struct; SNESComputeJacobian( petsc_nonlinear_solver.snes(), petsc_vec->vec(), &my_mat, &my_mat, &my_struct); #endif #if PETSC_VERSION_LESS_THAN(3, 2, 0) ISColoringDestroy(iscoloring); #else // PETSc 3.3.0 ISColoringDestroy(&iscoloring); #endif #endif }
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); }