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mfem/examples/petsc/ex5p.cpp
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// MFEM Example 5 - Parallel Version
// PETSc Modification
//
// Compile with: make ex5p
//
// Sample runs:
// mpirun -np 4 ex5p -m ../../data/beam-tet.mesh --petscopts rc_ex5p_fieldsplit
// mpirun -np 4 ex5p -m ../../data/star.mesh --petscopts rc_ex5p_bddc --nonoverlapping
//
// Description: This example code solves a simple 2D/3D mixed Darcy problem
// corresponding to the saddle point system
// k*u + grad p = f
// - div u = g
// with natural boundary condition -p = <given pressure>.
// Here, we use a given exact solution (u,p) and compute the
// corresponding r.h.s. (f,g). We discretize with Raviart-Thomas
// finite elements (velocity u) and piecewise discontinuous
// polynomials (pressure p).
//
// The example demonstrates the use of the BlockMatrix class, as
// well as the collective saving of several grid functions in a
// VisIt (visit.llnl.gov) visualization format.
//
// Two types of PETSc solvers can be used: BDDC or fieldsplit.
// When using BDDC, the nonoverlapping assembly feature should be
// used. This specific example needs PETSc compiled with support
// for SuiteSparse and/or MUMPS for using BDDC.
//
// We recommend viewing examples 1-4 before viewing this example.
#include "mfem.hpp"
#include <fstream>
#include <iostream>
#ifndef MFEM_USE_PETSC
#error This example requires that MFEM is built with MFEM_USE_PETSC=YES
#endif
using namespace std;
using namespace mfem;
// Define the analytical solution and forcing terms / boundary conditions
void uFun_ex(const Vector & x, Vector & u);
double pFun_ex(const Vector & x);
void fFun(const Vector & x, Vector & f);
double gFun(const Vector & x);
double f_natural(const Vector & x);
int main(int argc, char *argv[])
{
StopWatch chrono;
// 1. Initialize MPI and HYPRE.
Mpi::Init(argc, argv);
int num_procs = Mpi::WorldSize();
int myid = Mpi::WorldRank();
Hypre::Init();
bool verbose = (myid == 0);
// 2. Parse command-line options.
const char *mesh_file = "../../data/star.mesh";
int order = 1;
bool par_format = false;
bool visualization = 1;
bool use_petsc = true;
bool use_nonoverlapping = false;
bool local_bdr_spec = false;
const char *petscrc_file = "";
OptionsParser args(argc, argv);
args.AddOption(&mesh_file, "-m", "--mesh",
"Mesh file to use.");
args.AddOption(&order, "-o", "--order",
"Finite element order (polynomial degree).");
args.AddOption(&par_format, "-pf", "--parallel-format", "-sf",
"--serial-format",
"Format to use when saving the results for VisIt.");
args.AddOption(&visualization, "-vis", "--visualization", "-no-vis",
"--no-visualization",
"Enable or disable GLVis visualization.");
args.AddOption(&use_petsc, "-usepetsc", "--usepetsc", "-no-petsc",
"--no-petsc",
"Use or not PETSc to solve the linear system.");
args.AddOption(&petscrc_file, "-petscopts", "--petscopts",
"PetscOptions file to use.");
args.AddOption(&use_nonoverlapping, "-nonoverlapping", "--nonoverlapping",
"-no-nonoverlapping", "--no-nonoverlapping",
"Use or not the block diagonal PETSc's matrix format "
"for non-overlapping domain decomposition.");
args.AddOption(&local_bdr_spec, "-local-bdr", "--local-bdr", "-no-local-bdr",
"--no-local-bdr",
"Specify boundary dofs in local (Vdofs) ordering.");
args.Parse();
if (!args.Good())
{
if (verbose)
{
args.PrintUsage(cout);
}
return 1;
}
if (verbose)
{
args.PrintOptions(cout);
}
// 2b. We initialize PETSc
if (use_petsc) { MFEMInitializePetsc(NULL,NULL,petscrc_file,NULL); }
// 3. Read the (serial) mesh from the given mesh file on all processors. We
// can handle triangular, quadrilateral, tetrahedral, hexahedral, surface
// and volume meshes with the same code.
Mesh *mesh = new Mesh(mesh_file, 1, 1);
int dim = mesh->Dimension();
// 4. Refine the serial mesh on all processors to increase the resolution. In
// this example we do 'ref_levels' of uniform refinement. We choose
// 'ref_levels' to be the largest number that gives a final mesh with no
// more than 10,000 elements.
{
int ref_levels =
(int)floor(log(10000./mesh->GetNE())/log(2.)/dim);
for (int l = 0; l < ref_levels; l++)
{
mesh->UniformRefinement();
}
}
// 5. Define a parallel mesh by a partitioning of the serial mesh. Refine
// this mesh further in parallel to increase the resolution. Once the
// parallel mesh is defined, the serial mesh can be deleted.
ParMesh *pmesh = new ParMesh(MPI_COMM_WORLD, *mesh);
delete mesh;
{
int par_ref_levels = 2;
for (int l = 0; l < par_ref_levels; l++)
{
pmesh->UniformRefinement();
}
}
// 6. Define a parallel finite element space on the parallel mesh. Here we
// use the Raviart-Thomas finite elements of the specified order.
FiniteElementCollection *hdiv_coll(new RT_FECollection(order, dim));
FiniteElementCollection *l2_coll(new L2_FECollection(order, dim));
ParFiniteElementSpace *R_space = new ParFiniteElementSpace(pmesh, hdiv_coll);
ParFiniteElementSpace *W_space = new ParFiniteElementSpace(pmesh, l2_coll);
HYPRE_BigInt dimR = R_space->GlobalTrueVSize();
HYPRE_BigInt dimW = W_space->GlobalTrueVSize();
if (verbose)
{
std::cout << "***********************************************************\n";
std::cout << "dim(R) = " << dimR << "\n";
std::cout << "dim(W) = " << dimW << "\n";
std::cout << "dim(R+W) = " << dimR + dimW << "\n";
std::cout << "***********************************************************\n";
}
// 7. Define the two BlockStructure of the problem. block_offsets is used
// for Vector based on dof (like ParGridFunction or ParLinearForm),
// block_trueOffstes is used for Vector based on trueDof (HypreParVector
// for the rhs and solution of the linear system). The offsets computed
// here are local to the processor.
Array<int> block_offsets(3); // number of variables + 1
block_offsets[0] = 0;
block_offsets[1] = R_space->GetVSize();
block_offsets[2] = W_space->GetVSize();
block_offsets.PartialSum();
Array<int> block_trueOffsets(3); // number of variables + 1
block_trueOffsets[0] = 0;
block_trueOffsets[1] = R_space->TrueVSize();
block_trueOffsets[2] = W_space->TrueVSize();
block_trueOffsets.PartialSum();
// 8. Define the coefficients, analytical solution, and rhs of the PDE.
ConstantCoefficient k(1.0);
VectorFunctionCoefficient fcoeff(dim, fFun);
FunctionCoefficient fnatcoeff(f_natural);
FunctionCoefficient gcoeff(gFun);
VectorFunctionCoefficient ucoeff(dim, uFun_ex);
FunctionCoefficient pcoeff(pFun_ex);
// 9. Define the parallel grid function and parallel linear forms, solution
// vector and rhs.
BlockVector x(block_offsets), rhs(block_offsets);
BlockVector trueX(block_trueOffsets), trueRhs(block_trueOffsets);
ParLinearForm *fform(new ParLinearForm);
fform->Update(R_space, rhs.GetBlock(0), 0);
fform->AddDomainIntegrator(new VectorFEDomainLFIntegrator(fcoeff));
fform->AddBoundaryIntegrator(new VectorFEBoundaryFluxLFIntegrator(fnatcoeff));
fform->Assemble();
fform->ParallelAssemble(trueRhs.GetBlock(0));
ParLinearForm *gform(new ParLinearForm);
gform->Update(W_space, rhs.GetBlock(1), 0);
gform->AddDomainIntegrator(new DomainLFIntegrator(gcoeff));
gform->Assemble();
gform->ParallelAssemble(trueRhs.GetBlock(1));
// 10. Assemble the finite element matrices for the Darcy operator
//
// D = [ M B^T ]
// [ B 0 ]
// where:
//
// M = \int_\Omega k u_h \cdot v_h d\Omega u_h, v_h \in R_h
// B = -\int_\Omega \div u_h q_h d\Omega u_h \in R_h, q_h \in W_h
ParBilinearForm *mVarf(new ParBilinearForm(R_space));
ParMixedBilinearForm *bVarf(new ParMixedBilinearForm(R_space, W_space));
PetscParMatrix *pM = NULL, *pB = NULL, *pBT = NULL;
HypreParMatrix *M = NULL, *B = NULL, *BT = NULL;
Operator::Type tid =
!use_petsc ? Operator::Hypre_ParCSR :
(use_nonoverlapping ? Operator::PETSC_MATIS : Operator::PETSC_MATAIJ);
OperatorHandle Mh(tid), Bh(tid);
mVarf->AddDomainIntegrator(new VectorFEMassIntegrator(k));
mVarf->Assemble();
mVarf->Finalize();
mVarf->ParallelAssemble(Mh);
if (!use_petsc) { Mh.Get(M); }
else { Mh.Get(pM); }
Mh.SetOperatorOwner(false);
bVarf->AddDomainIntegrator(new VectorFEDivergenceIntegrator);
bVarf->Assemble();
bVarf->Finalize();
if (!use_petsc)
{
B = bVarf->ParallelAssemble();
(*B) *= -1;
}
else
{
bVarf->ParallelAssemble(Bh);
Bh.Get(pB);
Bh.SetOperatorOwner(false);
(*pB) *= -1;
}
if (!use_petsc) { BT = B->Transpose(); }
else { pBT = pB->Transpose(); };
Operator *darcyOp = NULL;
if (!use_petsc)
{
BlockOperator *tdarcyOp = new BlockOperator(block_trueOffsets);
tdarcyOp->SetBlock(0,0,M);
tdarcyOp->SetBlock(0,1,BT);
tdarcyOp->SetBlock(1,0,B);
darcyOp = tdarcyOp;
}
else
{
// We construct the BlockOperator and we then convert it to a
// PetscParMatrix to avoid any conversion in the construction of the
// preconditioners.
BlockOperator *tdarcyOp = new BlockOperator(block_trueOffsets);
tdarcyOp->SetBlock(0,0,pM);
tdarcyOp->SetBlock(0,1,pBT);
tdarcyOp->SetBlock(1,0,pB);
darcyOp = new PetscParMatrix(pM->GetComm(),tdarcyOp,
use_nonoverlapping ? Operator::PETSC_MATIS :
Operator::PETSC_MATAIJ);
delete tdarcyOp;
}
// 11. Construct the operators for preconditioner
//
// P = [ diag(M) 0 ]
// [ 0 B diag(M)^-1 B^T ]
//
// Here we use Symmetric Gauss-Seidel to approximate the inverse of the
// pressure Schur Complement.
PetscPreconditioner *pdarcyPr = NULL;
BlockDiagonalPreconditioner *darcyPr = NULL;
HypreSolver *invM = NULL, *invS = NULL;
HypreParMatrix *S = NULL;
HypreParMatrix *MinvBt = NULL;
HypreParVector *Md = NULL;
if (!use_petsc)
{
MinvBt = B->Transpose();
Md = new HypreParVector(MPI_COMM_WORLD, M->GetGlobalNumRows(),
M->GetRowStarts());
M->GetDiag(*Md);
MinvBt->InvScaleRows(*Md);
S = ParMult(B, MinvBt);
invM = new HypreDiagScale(*M);
invS = new HypreBoomerAMG(*S);
invM->iterative_mode = false;
invS->iterative_mode = false;
darcyPr = new BlockDiagonalPreconditioner(block_trueOffsets);
darcyPr->SetDiagonalBlock(0, invM);
darcyPr->SetDiagonalBlock(1, invS);
}
else
{
if (use_nonoverlapping)
{
PetscBDDCSolverParams opts;
// For saddle point problems, we need to provide BDDC the list of
// boundary dofs either essential or natural.
// Since R_space is the only space that may have boundary dofs and it
// is ordered first then W_space, we don't need any local offset when
// specifying the dofs.
Array<int> bdr_tdof_list;
if (pmesh->bdr_attributes.Size())
{
Array<int> bdr(pmesh->bdr_attributes.Max());
bdr = 1;
if (!local_bdr_spec)
{
// Essential dofs in global ordering
R_space->GetEssentialTrueDofs(bdr, bdr_tdof_list);
}
else
{
// Alternatively, you can also provide the list of dofs in local
// ordering
R_space->GetEssentialVDofs(bdr, bdr_tdof_list);
bdr_tdof_list.SetSize(R_space->GetVSize()+W_space->GetVSize(),0);
}
opts.SetNatBdrDofs(&bdr_tdof_list,local_bdr_spec);
}
else
{
MFEM_WARNING("Missing boundary dofs. This may cause solver failures.");
}
// See also command line options rc_ex5p_bddc
pdarcyPr = new PetscBDDCSolver(MPI_COMM_WORLD,*darcyOp,opts,"prec_");
}
else
{
// With PETSc, we can construct the (same) block-diagonal solver with
// command line options (see rc_ex5p_fieldsplit)
pdarcyPr = new PetscFieldSplitSolver(MPI_COMM_WORLD,*darcyOp,"prec_");
}
}
// 12. Solve the linear system with MINRES.
// Check the norm of the unpreconditioned residual.
int maxIter(500);
double rtol(1.e-6);
double atol(1.e-10);
chrono.Clear();
chrono.Start();
trueX = 0.0;
if (!use_petsc)
{
MINRESSolver solver(MPI_COMM_WORLD);
solver.SetAbsTol(atol);
solver.SetRelTol(rtol);
solver.SetMaxIter(maxIter);
solver.SetOperator(*darcyOp);
solver.SetPreconditioner(*darcyPr);
solver.SetPrintLevel(1);
solver.Mult(trueRhs, trueX);
if (verbose)
{
if (solver.GetConverged())
{
std::cout << "MINRES converged in " << solver.GetNumIterations()
<< " iterations with a residual norm of "
<< solver.GetFinalNorm() << ".\n";
}
else
{
std::cout << "MINRES did not converge in "
<< solver.GetNumIterations()
<< " iterations. Residual norm is "
<< solver.GetFinalNorm() << ".\n";
}
std::cout << "MINRES solver took " << chrono.RealTime() << "s. \n";
}
}
else
{
std::string solvertype;
PetscLinearSolver *solver;
if (use_nonoverlapping)
{
// We can use conjugate gradients to solve the problem
solver = new PetscPCGSolver(MPI_COMM_WORLD);
solvertype = "PCG";
}
else
{
solver = new PetscLinearSolver(MPI_COMM_WORLD);
solvertype = "MINRES";
}
solver->SetOperator(*darcyOp);
solver->SetPreconditioner(*pdarcyPr);
solver->SetAbsTol(atol);
solver->SetRelTol(rtol);
solver->SetMaxIter(maxIter);
solver->SetPrintLevel(2);
solver->Mult(trueRhs, trueX);
if (verbose)
{
if (solver->GetConverged())
{
std::cout << solvertype << " converged in "
<< solver->GetNumIterations()
<< " iterations with a residual norm of "
<< solver->GetFinalNorm() << ".\n";
}
else
{
std::cout << solvertype << " did not converge in "
<< solver->GetNumIterations()
<< " iterations. Residual norm is "
<< solver->GetFinalNorm() << ".\n";
}
std::cout << solvertype << " solver took "
<< chrono.RealTime() << "s. \n";
}
delete solver;
}
chrono.Stop();
// 13. Extract the parallel grid function corresponding to the finite element
// approximation X. This is the local solution on each processor. Compute
// L2 error norms.
ParGridFunction *u(new ParGridFunction);
ParGridFunction *p(new ParGridFunction);
u->MakeRef(R_space, x.GetBlock(0), 0);
p->MakeRef(W_space, x.GetBlock(1), 0);
u->Distribute(&(trueX.GetBlock(0)));
p->Distribute(&(trueX.GetBlock(1)));
int order_quad = max(2, 2*order+1);
const IntegrationRule *irs[Geometry::NumGeom];
for (int i=0; i < Geometry::NumGeom; ++i)
{
irs[i] = &(IntRules.Get(i, order_quad));
}
double err_u = u->ComputeL2Error(ucoeff, irs);
double norm_u = ComputeGlobalLpNorm(2, ucoeff, *pmesh, irs);
double err_p = p->ComputeL2Error(pcoeff, irs);
double norm_p = ComputeGlobalLpNorm(2, pcoeff, *pmesh, irs);
if (verbose)
{
std::cout << "|| u_h - u_ex || / || u_ex || = " << err_u / norm_u << "\n";
std::cout << "|| p_h - p_ex || / || p_ex || = " << err_p / norm_p << "\n";
}
// 14. Save the refined mesh and the solution in parallel. This output can be
// viewed later using GLVis: "glvis -np <np> -m mesh -g sol_*".
{
ostringstream mesh_name, u_name, p_name;
mesh_name << "mesh." << setfill('0') << setw(6) << myid;
u_name << "sol_u." << setfill('0') << setw(6) << myid;
p_name << "sol_p." << setfill('0') << setw(6) << myid;
ofstream mesh_ofs(mesh_name.str().c_str());
mesh_ofs.precision(8);
pmesh->Print(mesh_ofs);
ofstream u_ofs(u_name.str().c_str());
u_ofs.precision(8);
u->Save(u_ofs);
ofstream p_ofs(p_name.str().c_str());
p_ofs.precision(8);
p->Save(p_ofs);
}
// 15. Save data in the VisIt format
VisItDataCollection visit_dc("Example5-Parallel", pmesh);
visit_dc.RegisterField("velocity", u);
visit_dc.RegisterField("pressure", p);
visit_dc.SetFormat(!par_format ?
DataCollection::SERIAL_FORMAT :
DataCollection::PARALLEL_FORMAT);
visit_dc.Save();
// 16. Send the solution by socket to a GLVis server.
if (visualization)
{
char vishost[] = "localhost";
int visport = 19916;
socketstream u_sock(vishost, visport);
u_sock << "parallel " << num_procs << " " << myid << "\n";
u_sock.precision(8);
u_sock << "solution\n" << *pmesh << *u << "window_title 'Velocity'"
<< endl;
// Make sure all ranks have sent their 'u' solution before initiating
// another set of GLVis connections (one from each rank):
MPI_Barrier(pmesh->GetComm());
socketstream p_sock(vishost, visport);
p_sock << "parallel " << num_procs << " " << myid << "\n";
p_sock.precision(8);
p_sock << "solution\n" << *pmesh << *p << "window_title 'Pressure'"
<< endl;
}
// 17. Free the used memory.
delete fform;
delete gform;
delete u;
delete p;
delete darcyOp;
delete darcyPr;
delete pdarcyPr;
delete invM;
delete invS;
delete S;
delete BT;
delete B;
delete M;
delete pBT;
delete pB;
delete pM;
delete MinvBt;
delete Md;
delete mVarf;
delete bVarf;
delete W_space;
delete R_space;
delete l2_coll;
delete hdiv_coll;
delete pmesh;
// We finalize PETSc
if (use_petsc) { MFEMFinalizePetsc(); }
return 0;
}
void uFun_ex(const Vector & x, Vector & u)
{
double xi(x(0));
double yi(x(1));
double zi(0.0);
if (x.Size() == 3)
{
zi = x(2);
}
u(0) = - exp(xi)*sin(yi)*cos(zi);
u(1) = - exp(xi)*cos(yi)*cos(zi);
if (x.Size() == 3)
{
u(2) = exp(xi)*sin(yi)*sin(zi);
}
}
// Change if needed
double pFun_ex(const Vector & x)
{
double xi(x(0));
double yi(x(1));
double zi(0.0);
if (x.Size() == 3)
{
zi = x(2);
}
return exp(xi)*sin(yi)*cos(zi);
}
void fFun(const Vector & x, Vector & f)
{
f = 0.0;
}
double gFun(const Vector & x)
{
if (x.Size() == 3)
{
return -pFun_ex(x);
}
else
{
return 0;
}
}
double f_natural(const Vector & x)
{
return (-pFun_ex(x));
}
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