PETSC_EXTERN PetscErrorCode MatColoringApply_Power(MatColoring mc,ISColoring *iscoloring) { PetscErrorCode ierr; Mat m = mc->mat,mp,ms; MatColoring imc; PetscInt i; const char *optionsprefix; PetscFunctionBegin; /* square the matrix repeatedly if necessary */ if (mc->dist == 1) { mp = m; } else { ierr = MatMatMult(m,m,MAT_INITIAL_MATRIX,2.0,&mp);CHKERRQ(ierr); for (i=2;i<mc->dist;i++) { ms = mp; ierr = MatMatMult(m,ms,MAT_INITIAL_MATRIX,2.0,&mp);CHKERRQ(ierr); ierr = MatDestroy(&ms);CHKERRQ(ierr); } } ierr = MatColoringCreate(mp,&imc);CHKERRQ(ierr); ierr = PetscObjectGetOptionsPrefix((PetscObject)mc,&optionsprefix);CHKERRQ(ierr); ierr = PetscObjectSetOptionsPrefix((PetscObject)imc,optionsprefix);CHKERRQ(ierr); ierr = PetscObjectAppendOptionsPrefix((PetscObject)imc,"power_");CHKERRQ(ierr); ierr = MatColoringSetType(imc,MATCOLORINGGREEDY);CHKERRQ(ierr); ierr = MatColoringSetDistance(imc,1);CHKERRQ(ierr); ierr = MatColoringSetWeightType(imc,mc->weight_type);CHKERRQ(ierr); ierr = MatColoringSetFromOptions(imc);CHKERRQ(ierr); ierr = MatColoringApply(imc,iscoloring);CHKERRQ(ierr); ierr = MatColoringDestroy(&imc);CHKERRQ(ierr); if (mp != m) {ierr = MatDestroy(&mp);CHKERRQ(ierr);} PetscFunctionReturn(0); }
PetscErrorCode SNESComputeJacobianDefaultColor(SNES snes,Vec x1,Mat J,Mat B,void *ctx) { MatFDColoring color = (MatFDColoring)ctx; PetscErrorCode ierr; DM dm; MatColoring mc; ISColoring iscoloring; PetscBool hascolor; PetscBool solvec,matcolor = PETSC_FALSE; PetscFunctionBegin; if (color) PetscValidHeaderSpecific(color,MAT_FDCOLORING_CLASSID,6); if (!color) {ierr = PetscObjectQuery((PetscObject)B,"SNESMatFDColoring",(PetscObject*)&color);CHKERRQ(ierr);} if (!color) { ierr = SNESGetDM(snes,&dm);CHKERRQ(ierr); ierr = DMHasColoring(dm,&hascolor);CHKERRQ(ierr); matcolor = PETSC_FALSE; ierr = PetscOptionsGetBool(((PetscObject)snes)->options,((PetscObject)snes)->prefix,"-snes_fd_color_use_mat",&matcolor,NULL);CHKERRQ(ierr); if (hascolor && !matcolor) { ierr = DMCreateColoring(dm,IS_COLORING_GLOBAL,&iscoloring);CHKERRQ(ierr); ierr = MatFDColoringCreate(B,iscoloring,&color);CHKERRQ(ierr); ierr = MatFDColoringSetFunction(color,(PetscErrorCode (*)(void))SNESComputeFunctionCtx,NULL);CHKERRQ(ierr); ierr = MatFDColoringSetFromOptions(color);CHKERRQ(ierr); ierr = MatFDColoringSetUp(B,iscoloring,color);CHKERRQ(ierr); ierr = ISColoringDestroy(&iscoloring);CHKERRQ(ierr); } else { ierr = MatColoringCreate(B,&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 = MatFDColoringCreate(B,iscoloring,&color);CHKERRQ(ierr); ierr = MatFDColoringSetFunction(color,(PetscErrorCode (*)(void))SNESComputeFunctionCtx,NULL);CHKERRQ(ierr); ierr = MatFDColoringSetFromOptions(color);CHKERRQ(ierr); ierr = MatFDColoringSetUp(B,iscoloring,color);CHKERRQ(ierr); ierr = ISColoringDestroy(&iscoloring);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) { Vec F; ierr = SNESGetFunction(snes,&F,NULL,NULL);CHKERRQ(ierr); ierr = MatFDColoringSetF(color,F);CHKERRQ(ierr); } ierr = MatFDColoringApply(B,color,x1,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 **argv) { PetscErrorCode ierr; PetscInt time_steps=100,iout,NOUT=1; PetscMPIInt size; Vec global; PetscReal dt,ftime,ftime_original; TS ts; PetscViewer viewfile; Mat J = 0; Vec x; Data data; PetscInt mn; PetscBool flg; MatColoring mc; ISColoring iscoloring; MatFDColoring matfdcoloring = 0; PetscBool fd_jacobian_coloring = PETSC_FALSE; SNES snes; KSP ksp; PC pc; PetscViewer viewer; char pcinfo[120],tsinfo[120]; TSType tstype; PetscBool sundials; ierr = PetscInitialize(&argc,&argv,(char*)0,help);CHKERRQ(ierr); ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr); /* set data */ data.m = 9; data.n = 9; data.a = 1.0; data.epsilon = 0.1; data.dx = 1.0/(data.m+1.0); data.dy = 1.0/(data.n+1.0); mn = (data.m)*(data.n); ierr = PetscOptionsGetInt(NULL,"-time",&time_steps,NULL);CHKERRQ(ierr); /* set initial conditions */ ierr = VecCreate(PETSC_COMM_WORLD,&global);CHKERRQ(ierr); ierr = VecSetSizes(global,PETSC_DECIDE,mn);CHKERRQ(ierr); ierr = VecSetFromOptions(global);CHKERRQ(ierr); ierr = Initial(global,&data);CHKERRQ(ierr); ierr = VecDuplicate(global,&x);CHKERRQ(ierr); /* create timestep context */ ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr); ierr = TSMonitorSet(ts,Monitor,&data,NULL);CHKERRQ(ierr); #if defined(PETSC_HAVE_SUNDIALS) ierr = TSSetType(ts,TSSUNDIALS);CHKERRQ(ierr); #else ierr = TSSetType(ts,TSEULER);CHKERRQ(ierr); #endif dt = 0.1; ftime_original = data.tfinal = 1.0; ierr = TSSetInitialTimeStep(ts,0.0,dt);CHKERRQ(ierr); ierr = TSSetDuration(ts,time_steps,ftime_original);CHKERRQ(ierr); ierr = TSSetSolution(ts,global);CHKERRQ(ierr); /* set user provided RHSFunction and RHSJacobian */ ierr = TSSetRHSFunction(ts,NULL,RHSFunction,&data);CHKERRQ(ierr); ierr = MatCreate(PETSC_COMM_WORLD,&J);CHKERRQ(ierr); ierr = MatSetSizes(J,PETSC_DECIDE,PETSC_DECIDE,mn,mn);CHKERRQ(ierr); ierr = MatSetFromOptions(J);CHKERRQ(ierr); ierr = MatSeqAIJSetPreallocation(J,5,NULL);CHKERRQ(ierr); ierr = MatMPIAIJSetPreallocation(J,5,NULL,5,NULL);CHKERRQ(ierr); ierr = PetscOptionsHasName(NULL,"-ts_fd",&flg);CHKERRQ(ierr); if (!flg) { ierr = TSSetRHSJacobian(ts,J,J,RHSJacobian,&data);CHKERRQ(ierr); } else { ierr = TSGetSNES(ts,&snes);CHKERRQ(ierr); ierr = PetscOptionsHasName(NULL,"-fd_color",&fd_jacobian_coloring);CHKERRQ(ierr); if (fd_jacobian_coloring) { /* Use finite differences with coloring */ /* Get data structure of J */ PetscBool pc_diagonal; ierr = PetscOptionsHasName(NULL,"-pc_diagonal",&pc_diagonal);CHKERRQ(ierr); if (pc_diagonal) { /* the preconditioner of J is a diagonal matrix */ PetscInt rstart,rend,i; PetscScalar zero=0.0; ierr = MatGetOwnershipRange(J,&rstart,&rend);CHKERRQ(ierr); for (i=rstart; i<rend; i++) { ierr = MatSetValues(J,1,&i,1,&i,&zero,INSERT_VALUES);CHKERRQ(ierr); } ierr = MatAssemblyBegin(J,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatAssemblyEnd(J,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); } else { /* Fill the structure using the expensive SNESComputeJacobianDefault. Temporarily set up the TS so we can call this function */ ierr = TSSetType(ts,TSBEULER);CHKERRQ(ierr); ierr = TSSetUp(ts);CHKERRQ(ierr); ierr = SNESComputeJacobianDefault(snes,x,J,J,ts);CHKERRQ(ierr); } /* create coloring context */ ierr = MatColoringCreate(J,&mc);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 = MatFDColoringCreate(J,iscoloring,&matfdcoloring);CHKERRQ(ierr); ierr = MatFDColoringSetFunction(matfdcoloring,(PetscErrorCode (*)(void))SNESTSFormFunction,ts);CHKERRQ(ierr); ierr = MatFDColoringSetFromOptions(matfdcoloring);CHKERRQ(ierr); ierr = MatFDColoringSetUp(J,iscoloring,matfdcoloring);CHKERRQ(ierr); ierr = SNESSetJacobian(snes,J,J,SNESComputeJacobianDefaultColor,matfdcoloring);CHKERRQ(ierr); ierr = ISColoringDestroy(&iscoloring);CHKERRQ(ierr); } else { /* Use finite differences (slow) */ ierr = SNESSetJacobian(snes,J,J,SNESComputeJacobianDefault,NULL);CHKERRQ(ierr); } } /* Pick up a Petsc preconditioner */ /* one can always set method or preconditioner during the run time */ ierr = TSGetSNES(ts,&snes);CHKERRQ(ierr); ierr = SNESGetKSP(snes,&ksp);CHKERRQ(ierr); ierr = KSPGetPC(ksp,&pc);CHKERRQ(ierr); ierr = PCSetType(pc,PCJACOBI);CHKERRQ(ierr); ierr = TSSetFromOptions(ts);CHKERRQ(ierr); ierr = TSSetUp(ts);CHKERRQ(ierr); /* Test TSSetPostStep() */ ierr = PetscOptionsHasName(NULL,"-test_PostStep",&flg);CHKERRQ(ierr); if (flg) { ierr = TSSetPostStep(ts,PostStep);CHKERRQ(ierr); } ierr = PetscOptionsGetInt(NULL,"-NOUT",&NOUT,NULL);CHKERRQ(ierr); for (iout=1; iout<=NOUT; iout++) { ierr = TSSetDuration(ts,time_steps,iout*ftime_original/NOUT);CHKERRQ(ierr); ierr = TSSolve(ts,global);CHKERRQ(ierr); ierr = TSGetSolveTime(ts,&ftime);CHKERRQ(ierr); ierr = TSSetInitialTimeStep(ts,ftime,dt);CHKERRQ(ierr); } /* Interpolate solution at tfinal */ ierr = TSGetSolution(ts,&global);CHKERRQ(ierr); ierr = TSInterpolate(ts,ftime_original,global);CHKERRQ(ierr); ierr = PetscOptionsHasName(NULL,"-matlab_view",&flg);CHKERRQ(ierr); if (flg) { /* print solution into a MATLAB file */ ierr = PetscViewerASCIIOpen(PETSC_COMM_WORLD,"out.m",&viewfile);CHKERRQ(ierr); ierr = PetscViewerSetFormat(viewfile,PETSC_VIEWER_ASCII_MATLAB);CHKERRQ(ierr); ierr = VecView(global,viewfile);CHKERRQ(ierr); ierr = PetscViewerDestroy(&viewfile);CHKERRQ(ierr); } /* display solver info for Sundials */ ierr = TSGetType(ts,&tstype);CHKERRQ(ierr); ierr = PetscObjectTypeCompare((PetscObject)ts,TSSUNDIALS,&sundials);CHKERRQ(ierr); if (sundials) { ierr = PetscViewerStringOpen(PETSC_COMM_WORLD,tsinfo,120,&viewer);CHKERRQ(ierr); ierr = TSView(ts,viewer);CHKERRQ(ierr); ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); ierr = PetscViewerStringOpen(PETSC_COMM_WORLD,pcinfo,120,&viewer);CHKERRQ(ierr); ierr = PCView(pc,viewer);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD,"%d Procs,%s TSType, %s Preconditioner\n",size,tsinfo,pcinfo);CHKERRQ(ierr); ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); } /* free the memories */ ierr = TSDestroy(&ts);CHKERRQ(ierr); ierr = VecDestroy(&global);CHKERRQ(ierr); ierr = VecDestroy(&x);CHKERRQ(ierr); ierr = MatDestroy(&J);CHKERRQ(ierr); if (fd_jacobian_coloring) {ierr = MatFDColoringDestroy(&matfdcoloring);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 }
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_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); }
PETSC_EXTERN PetscErrorCode SNESComputeNGSDefaultSecant(SNES snes,Vec X,Vec B,void *ctx) { PetscErrorCode ierr; SNES_NGS *gs = (SNES_NGS*)snes->data; PetscInt i,j,k,ncolors; DM dm; PetscBool flg; ISColoring coloring = gs->coloring; MatColoring mc; Vec W,G,F; PetscScalar h=gs->h; IS *coloris; PetscScalar f,g,x,w,d; PetscReal dxt,xt,ft,ft1=0; const PetscInt *idx; PetscInt size,s; PetscReal atol,rtol,stol; PetscInt its; PetscErrorCode (*func)(SNES,Vec,Vec,void*); void *fctx; PetscBool mat = gs->secant_mat,equal,isdone,alldone; PetscScalar *xa,*fa,*wa,*ga; PetscFunctionBegin; if (snes->nwork < 3) { ierr = SNESSetWorkVecs(snes,3);CHKERRQ(ierr); } W = snes->work[0]; G = snes->work[1]; F = snes->work[2]; ierr = VecGetOwnershipRange(X,&s,NULL);CHKERRQ(ierr); ierr = SNESNGSGetTolerances(snes,&atol,&rtol,&stol,&its);CHKERRQ(ierr); ierr = SNESGetDM(snes,&dm);CHKERRQ(ierr); ierr = SNESGetFunction(snes,NULL,&func,&fctx);CHKERRQ(ierr); if (!coloring) { /* create the coloring */ ierr = DMHasColoring(dm,&flg);CHKERRQ(ierr); if (flg && !mat) { ierr = DMCreateColoring(dm,IS_COLORING_GLOBAL,&coloring);CHKERRQ(ierr); } else { if (!snes->jacobian) {ierr = SNESSetUpMatrices(snes);CHKERRQ(ierr);} ierr = MatColoringCreate(snes->jacobian,&mc);CHKERRQ(ierr); ierr = MatColoringSetDistance(mc,1);CHKERRQ(ierr); ierr = MatColoringSetFromOptions(mc);CHKERRQ(ierr); ierr = MatColoringApply(mc,&coloring);CHKERRQ(ierr); ierr = MatColoringDestroy(&mc);CHKERRQ(ierr); } gs->coloring = coloring; } ierr = ISColoringGetIS(coloring,&ncolors,&coloris);CHKERRQ(ierr); ierr = VecEqual(X,snes->vec_sol,&equal);CHKERRQ(ierr); if (equal && snes->normschedule == SNES_NORM_ALWAYS) { /* assume that the function is already computed */ ierr = VecCopy(snes->vec_func,F);CHKERRQ(ierr); } else { ierr = PetscLogEventBegin(SNES_NGSFuncEval,snes,X,B,0);CHKERRQ(ierr); ierr = (*func)(snes,X,F,fctx);CHKERRQ(ierr); ierr = PetscLogEventEnd(SNES_NGSFuncEval,snes,X,B,0);CHKERRQ(ierr); if (B) {ierr = VecAXPY(F,-1.0,B);CHKERRQ(ierr);} } ierr = VecGetArray(X,&xa);CHKERRQ(ierr); ierr = VecGetArray(F,&fa);CHKERRQ(ierr); ierr = VecGetArray(G,&ga);CHKERRQ(ierr); ierr = VecGetArray(W,&wa);CHKERRQ(ierr); for (i=0;i<ncolors;i++) { ierr = ISGetIndices(coloris[i],&idx);CHKERRQ(ierr); ierr = ISGetLocalSize(coloris[i],&size);CHKERRQ(ierr); ierr = VecCopy(X,W);CHKERRQ(ierr); for (j=0;j<size;j++) { wa[idx[j]-s] += h; } ierr = PetscLogEventBegin(SNES_NGSFuncEval,snes,X,B,0);CHKERRQ(ierr); ierr = (*func)(snes,W,G,fctx);CHKERRQ(ierr); ierr = PetscLogEventEnd(SNES_NGSFuncEval,snes,X,B,0);CHKERRQ(ierr); if (B) {ierr = VecAXPY(G,-1.0,B);CHKERRQ(ierr);} for (k=0;k<its;k++) { dxt = 0.; xt = 0.; ft = 0.; for (j=0;j<size;j++) { f = fa[idx[j]-s]; x = xa[idx[j]-s]; g = ga[idx[j]-s]; w = wa[idx[j]-s]; if (PetscAbsScalar(g-f) > atol) { /* This is equivalent to d = x - (h*f) / PetscRealPart(g-f) */ d = (x*g-w*f) / PetscRealPart(g-f); } else { d = x; } dxt += PetscRealPart(PetscSqr(d-x)); xt += PetscRealPart(PetscSqr(x)); ft += PetscRealPart(PetscSqr(f)); xa[idx[j]-s] = d; } if (k == 0) ft1 = PetscSqrtReal(ft); if (k<its-1) { isdone = PETSC_FALSE; if (stol*PetscSqrtReal(xt) > PetscSqrtReal(dxt)) isdone = PETSC_TRUE; if (PetscSqrtReal(ft) < atol) isdone = PETSC_TRUE; if (rtol*ft1 > PetscSqrtReal(ft)) isdone = PETSC_TRUE; ierr = MPIU_Allreduce(&isdone,&alldone,1,MPIU_BOOL,MPI_BAND,PetscObjectComm((PetscObject)snes));CHKERRQ(ierr); if (alldone) break; } if (i < ncolors-1 || k < its-1) { ierr = PetscLogEventBegin(SNES_NGSFuncEval,snes,X,B,0);CHKERRQ(ierr); ierr = (*func)(snes,X,F,fctx);CHKERRQ(ierr); ierr = PetscLogEventEnd(SNES_NGSFuncEval,snes,X,B,0);CHKERRQ(ierr); if (B) {ierr = VecAXPY(F,-1.0,B);CHKERRQ(ierr);} } if (k<its-1) { ierr = VecSwap(X,W);CHKERRQ(ierr); ierr = VecSwap(F,G);CHKERRQ(ierr); } } } ierr = VecRestoreArray(X,&xa);CHKERRQ(ierr); ierr = VecRestoreArray(F,&fa);CHKERRQ(ierr); ierr = VecRestoreArray(G,&ga);CHKERRQ(ierr); ierr = VecRestoreArray(W,&wa);CHKERRQ(ierr); ierr = ISColoringRestoreIS(coloring,&coloris);CHKERRQ(ierr); PetscFunctionReturn(0); }