libMesh::PetscPreconditioner< T > Class Template Reference

#include <petsc_preconditioner.h>

Inheritance diagram for libMesh::PetscPreconditioner< T >:

[legend]

List of all members.

Public Member Functions
	PetscPreconditioner ()
virtual	~PetscPreconditioner ()
virtual void	apply (const NumericVector< T > &x, NumericVector< T > &y)
virtual void	clear ()
virtual void	init ()
PC	pc ()
bool	initialized () const
virtual void	setup ()
void	set_matrix (SparseMatrix< Number > &mat)
PreconditionerType	type () const
void	set_type (const PreconditionerType pct)
Static Public Member Functions
static void	set_petsc_preconditioner_type (const PreconditionerType &preconditioner_type, PC &pc)
static Preconditioner< T > *	build (const SolverPackage solver_package=libMesh::default_solver_package())
static std::string	get_info ()
static void	print_info (std::ostream &out=libMesh::out)
static unsigned int	n_objects ()
static void	enable_print_counter_info ()
static void	disable_print_counter_info ()
Protected Types
typedef std::map< std::string, std::pair< unsigned int, unsigned int > >	Counts
Protected Member Functions
void	increment_constructor_count (const std::string &name)
void	increment_destructor_count (const std::string &name)
Protected Attributes
PC	_pc
Mat	_mat
SparseMatrix< T > *	_matrix
PreconditionerType	_preconditioner_type
bool	_is_initialized
Static Protected Attributes
static Counts	_counts
static Threads::atomic < unsigned int >	_n_objects
static Threads::spin_mutex	_mutex
static bool	_enable_print_counter = true
Static Private Member Functions
static void	set_petsc_subpreconditioner_type (PCType type, PC &pc)
static void	set_petsc_subpreconditioner_type (const PCType type, PC &pc)

---

Detailed Description

template<typename T>
class libMesh::PetscPreconditioner< T >

This class provides an interface to the suite of preconditioners available from Petsc.

Author:

Derek Gaston, 2009

Definition at line 60 of file petsc_preconditioner.h.

---

Member Typedef Documentation

typedef std::map<std::string, std::pair<unsigned int, unsigned int> > libMesh::ReferenceCounter::Counts [protected, inherited]

Data structure to log the information. The log is identified by the class name.

Definition at line 113 of file reference_counter.h.

---

Constructor & Destructor Documentation

template<typename T >

libMesh::PetscPreconditioner< T >::PetscPreconditioner

(

)

[inline]

Constructor. Initializes PetscPreconditioner data structures

Definition at line 137 of file petsc_preconditioner.h.

                                             :
  Preconditioner<T>(),
  _pc(PETSC_NULL)
{
}

template<typename T >

libMesh::PetscPreconditioner< T >::~PetscPreconditioner

(

)

[inline, virtual]

Destructor.

Definition at line 147 of file petsc_preconditioner.h.

References libMesh::PetscPreconditioner< T >::clear().

{
  this->clear ();
}

---

Member Function Documentation

template<typename T >

void libMesh::PetscPreconditioner< T >::apply	(	const NumericVector< T > &	x,
		NumericVector< T > &	y
	)			[inline, virtual]

Computes the preconditioned vector "y" based on input "x". Usually by solving Py=x to get the action of P^-1 x.

Implements libMesh::Preconditioner< T >.

Definition at line 44 of file petsc_preconditioner.C.

References libMesh::PetscPreconditioner< T >::_pc, libMesh::COMM_WORLD, and libMesh::PetscVector< T >::vec().

{
  PetscVector<T> & x_pvec = libmesh_cast_ref<PetscVector<T>&>(const_cast<NumericVector<T>&>(x));
  PetscVector<T> & y_pvec = libmesh_cast_ref<PetscVector<T>&>(const_cast<NumericVector<T>&>(y));

  Vec x_vec = x_pvec.vec();
  Vec y_vec = y_pvec.vec();

  int ierr = PCApply(_pc,x_vec,y_vec);
  CHKERRABORT(libMesh::COMM_WORLD,ierr);
}

template<typename T >

Preconditioner< T > * libMesh::Preconditioner< T >::build

(

const SolverPackage

solver_package = libMesh::default_solver_package()

)

[inline, static, inherited]

Builds a Preconditioner using the linear solver package specified by solver_package

Definition at line 35 of file preconditioner.C.

References libMesh::err, libMeshEnums::PETSC_SOLVERS, and libMesh::TRILINOS_SOLVERS.

{
  // Build the appropriate solver
  switch (solver_package)
    {

/*
#ifdef LIBMESH_HAVE_LASPACK
    case LASPACK_SOLVERS:
      {
        AutoPtr<Preconditioner<T> > ap(new LaspackPreconditioner<T>);
        return ap;
      }
#endif
*/

#ifdef LIBMESH_HAVE_PETSC
    case PETSC_SOLVERS:
      {
        return new PetscPreconditioner<T>();
      }
#endif

#ifdef LIBMESH_HAVE_TRILINOS
    case TRILINOS_SOLVERS:
      return new TrilinosPreconditioner<T>();
#endif

    default:
      libMesh::err << "ERROR:  Unrecognized solver package: "
                    << solver_package
                    << std::endl;
      libmesh_error();
    }

  return NULL;
}

template<typename T >

virtual void libMesh::PetscPreconditioner< T >::clear

(

)

[inline, virtual]

Release all memory and clear data structures.

Reimplemented from libMesh::Preconditioner< T >.

Definition at line 83 of file petsc_preconditioner.h.

Referenced by libMesh::PetscPreconditioner< T >::~PetscPreconditioner().

{}

void libMesh::ReferenceCounter::disable_print_counter_info

(

)

[static, inherited]

Definition at line 106 of file reference_counter.C.

References libMesh::ReferenceCounter::_enable_print_counter.

{
  _enable_print_counter = false;
  return;
}

void libMesh::ReferenceCounter::enable_print_counter_info

(

)

[static, inherited]

Methods to enable/disable the reference counter output from print_info()

Definition at line 100 of file reference_counter.C.

References libMesh::ReferenceCounter::_enable_print_counter.

{
  _enable_print_counter = true;
  return;
}

std::string libMesh::ReferenceCounter::get_info

(

)

[static, inherited]

Gets a string containing the reference information.

Definition at line 47 of file reference_counter.C.

References libMesh::ReferenceCounter::_counts, and libMesh::Quality::name().

Referenced by libMesh::ReferenceCounter::print_info().

{
#if defined(LIBMESH_ENABLE_REFERENCE_COUNTING) && defined(DEBUG)

  std::ostringstream oss;

  oss << '\n'
      << " ---------------------------------------------------------------------------- \n"
      << "| Reference count information                                                |\n"
      << " ---------------------------------------------------------------------------- \n";

  for (Counts::iterator it = _counts.begin();
       it != _counts.end(); ++it)
    {
      const std::string name(it->first);
      const unsigned int creations    = it->second.first;
      const unsigned int destructions = it->second.second;

      oss << "| " << name << " reference count information:\n"
          << "|  Creations:    " << creations    << '\n'
          << "|  Destructions: " << destructions << '\n';
    }

  oss << " ---------------------------------------------------------------------------- \n";

  return oss.str();

#else

  return "";

#endif
}

void libMesh::ReferenceCounter::increment_constructor_count

(

const std::string &

name

)

[inline, protected, inherited]

Increments the construction counter. Should be called in the constructor of any derived class that will be reference counted.

Definition at line 163 of file reference_counter.h.

References libMesh::ReferenceCounter::_counts, and libMesh::Threads::spin_mtx.

Referenced by libMesh::ReferenceCountedObject< RBParametrized >::ReferenceCountedObject().

{
  Threads::spin_mutex::scoped_lock lock(Threads::spin_mtx);
  std::pair<unsigned int, unsigned int>& p = _counts[name];

  p.first++;
}

void libMesh::ReferenceCounter::increment_destructor_count

(

const std::string &

name

)

[inline, protected, inherited]

Increments the destruction counter. Should be called in the destructor of any derived class that will be reference counted.

Definition at line 176 of file reference_counter.h.

References libMesh::ReferenceCounter::_counts, and libMesh::Threads::spin_mtx.

Referenced by libMesh::ReferenceCountedObject< RBParametrized >::~ReferenceCountedObject().

{
  Threads::spin_mutex::scoped_lock lock(Threads::spin_mtx);
  std::pair<unsigned int, unsigned int>& p = _counts[name];

  p.second++;
}

template<typename T >

void libMesh::PetscPreconditioner< T >::init

(

)

[inline, virtual]

Initialize data structures if not done so already.

Reimplemented from libMesh::Preconditioner< T >.

Definition at line 60 of file petsc_preconditioner.C.

References libMesh::Preconditioner< T >::_is_initialized, libMesh::PetscPreconditioner< T >::_mat, libMesh::Preconditioner< T >::_matrix, libMesh::PetscPreconditioner< T >::_pc, libMesh::Preconditioner< T >::_preconditioner_type, libMesh::COMM_WORLD, libMesh::err, libMesh::PetscMatrix< T >::mat(), and libMesh::PetscPreconditioner< T >::set_petsc_preconditioner_type().

{
  if(!this->_matrix)
  {
    libMesh::err << "ERROR: No matrix set for PetscPreconditioner, but init() called" << std::endl;
    libmesh_error();
  }

  // Clear the preconditioner in case it has been created in the past
  if (!this->_is_initialized)
  {
    // Should probably use PCReset(), but it's not working at the moment so we'll destroy instead
    if (_pc)
    {
      int ierr = LibMeshPCDestroy(&_pc);
      CHKERRABORT(libMesh::COMM_WORLD,ierr);
    }

    int ierr = PCCreate(libMesh::COMM_WORLD,&_pc);
    CHKERRABORT(libMesh::COMM_WORLD,ierr);

    PetscMatrix<T> * pmatrix = libmesh_cast_ptr<PetscMatrix<T>*, SparseMatrix<T> >(this->_matrix);

    _mat = pmatrix->mat();
  }

  int ierr = PCSetOperators(_pc,_mat,_mat,SAME_NONZERO_PATTERN);
  CHKERRABORT(libMesh::COMM_WORLD,ierr);

  // Set the PCType.  Note: this used to be done *before* the call to
  // PCSetOperators(), and only when !_is_initialized, but
  // 1.) Some preconditioners (those employing sub-preconditioners,
  // for example) have to call PCSetUp(), and can only do this after
  // the operators have been set.
  // 2.) It should be safe to call set_petsc_preconditioner_type()
  // multiple times.
  set_petsc_preconditioner_type(this->_preconditioner_type, _pc);

  this->_is_initialized = true;
}

template<typename T>

bool libMesh::Preconditioner< T >::initialized

(

)

const [inline, inherited]

Returns:

true if the data structures are initialized, false otherwise.

Definition at line 86 of file preconditioner.h.

{ return _is_initialized; }

static unsigned int libMesh::ReferenceCounter::n_objects

(

)

[inline, static, inherited]

Prints the number of outstanding (created, but not yet destroyed) objects.

Definition at line 79 of file reference_counter.h.

References libMesh::ReferenceCounter::_n_objects.

  { return _n_objects; }

template<typename T >

PC libMesh::PetscPreconditioner< T >::pc

(

)

[inline]

Returns the actual Petsc PC struct. Useful for more advanced purposes

Definition at line 94 of file petsc_preconditioner.h.

References libMesh::PetscPreconditioner< T >::_pc.

{ return _pc; }

void libMesh::ReferenceCounter::print_info

(

std::ostream &

out = libMesh::out

)

[static, inherited]

Prints the reference information, by default to libMesh::out.

Definition at line 88 of file reference_counter.C.

References libMesh::ReferenceCounter::_enable_print_counter, and libMesh::ReferenceCounter::get_info().

{
  if( _enable_print_counter ) out_stream << ReferenceCounter::get_info();
}

template<typename T >

void libMesh::Preconditioner< T >::set_matrix

(

SparseMatrix< Number > &

mat

)

[inline, inherited]

Sets the matrix P to be preconditioned.

Definition at line 172 of file preconditioner.h.

References libMesh::Preconditioner< T >::_is_initialized, and libMesh::Preconditioner< T >::_matrix.

{
  //If the matrix is changing then we (probably) need to reinitialize.
  _is_initialized = false;
  _matrix = &mat;
}

template<typename T >

void libMesh::PetscPreconditioner< T >::set_petsc_preconditioner_type	(	const PreconditionerType &	preconditioner_type,
		PC &	pc
	)			[inline, static]

Tells PETSC to use the user-specified preconditioner

Definition at line 105 of file petsc_preconditioner.C.

References libMeshEnums::AMG_PRECOND, libMeshEnums::ASM_PRECOND, libMeshEnums::BLOCK_JACOBI_PRECOND, libMeshEnums::CHOLESKY_PRECOND, libMesh::COMM_WORLD, libMeshEnums::EISENSTAT_PRECOND, libMesh::err, libMeshEnums::ICC_PRECOND, libMeshEnums::IDENTITY_PRECOND, libMeshEnums::ILU_PRECOND, libMeshEnums::JACOBI_PRECOND, libMeshEnums::LU_PRECOND, libMesh::n_processors(), libMesh::PetscPreconditioner< T >::set_petsc_subpreconditioner_type(), libMeshEnums::SHELL_PRECOND, libMeshEnums::SOR_PRECOND, and libMeshEnums::USER_PRECOND.

Referenced by libMesh::PetscPreconditioner< T >::init().

{
  int ierr = 0;

  switch (preconditioner_type)
  {
  case IDENTITY_PRECOND:
    ierr = PCSetType (pc, (char*) PCNONE);      CHKERRABORT(libMesh::COMM_WORLD,ierr); break;

  case CHOLESKY_PRECOND:
    ierr = PCSetType (pc, (char*) PCCHOLESKY);  CHKERRABORT(libMesh::COMM_WORLD,ierr); break;

  case ICC_PRECOND:
    ierr = PCSetType (pc, (char*) PCICC);       CHKERRABORT(libMesh::COMM_WORLD,ierr); break;

  case ILU_PRECOND:
    {
      // In serial, just set the ILU preconditioner type
      if (libMesh::n_processors() == 1)
        {
          ierr = PCSetType (pc, (char*) PCILU);
          CHKERRABORT(libMesh::COMM_WORLD,ierr);
        }
      else
        {
          // But PETSc has no truly parallel ILU, instead you have to set
          // an actual parallel preconditioner (e.g. block Jacobi) and then
          // assign ILU sub-preconditioners.
          ierr = PCSetType (pc, (char*) PCBJACOBI);
          CHKERRABORT(libMesh::COMM_WORLD,ierr);

          // Set ILU as the sub preconditioner type
          set_petsc_subpreconditioner_type(PCILU, pc);
        }
      break;
    }

  case LU_PRECOND:
    {
      // In serial, just set the LU preconditioner type
      if (libMesh::n_processors() == 1)
        {
          ierr = PCSetType (pc, (char*) PCLU);
          CHKERRABORT(libMesh::COMM_WORLD,ierr);
        }
      else
        {
          // But PETSc has no truly parallel LU, instead you have to set
          // an actual parallel preconditioner (e.g. block Jacobi) and then
          // assign LU sub-preconditioners.
          ierr = PCSetType (pc, (char*) PCBJACOBI);
          CHKERRABORT(libMesh::COMM_WORLD,ierr);

          // Set ILU as the sub preconditioner type
          set_petsc_subpreconditioner_type(PCLU, pc);
        }
      break;
    }

  case ASM_PRECOND:
    {
      // In parallel, I think ASM uses ILU by default as the sub-preconditioner...
      // I tried setting a different sub-preconditioner here, but apparently the matrix
      // is not in the correct state (at this point) to call PCSetUp().
      ierr = PCSetType (pc, (char*) PCASM);
      CHKERRABORT(libMesh::COMM_WORLD,ierr);
      break;
    }

  case JACOBI_PRECOND:
    ierr = PCSetType (pc, (char*) PCJACOBI);    CHKERRABORT(libMesh::COMM_WORLD,ierr); break;

  case BLOCK_JACOBI_PRECOND:
    ierr = PCSetType (pc, (char*) PCBJACOBI);   CHKERRABORT(libMesh::COMM_WORLD,ierr); break;

  case SOR_PRECOND:
    ierr = PCSetType (pc, (char*) PCSOR);       CHKERRABORT(libMesh::COMM_WORLD,ierr); break;

  case EISENSTAT_PRECOND:
    ierr = PCSetType (pc, (char*) PCEISENSTAT); CHKERRABORT(libMesh::COMM_WORLD,ierr); break;

  case AMG_PRECOND:
    ierr = PCSetType (pc, (char*) PCHYPRE);     CHKERRABORT(libMesh::COMM_WORLD,ierr); break;

#if !(PETSC_VERSION_LESS_THAN(2,1,2))
    // Only available for PETSC >= 2.1.2
  case USER_PRECOND:
    ierr = PCSetType (pc, (char*) PCMAT);       CHKERRABORT(libMesh::COMM_WORLD,ierr); break;
#endif

  case SHELL_PRECOND:
    ierr = PCSetType (pc, (char*) PCSHELL);     CHKERRABORT(libMesh::COMM_WORLD,ierr); break;

  default:
    libMesh::err << "ERROR:  Unsupported PETSC Preconditioner: "
                  << preconditioner_type       << std::endl
                  << "Continuing with PETSC defaults" << std::endl;
  }

  // Set additional options if we are doing AMG and
  // HYPRE is available
#ifdef LIBMESH_HAVE_PETSC_HYPRE
  if (preconditioner_type == AMG_PRECOND)
    {
      ierr = PCHYPRESetType(pc, "boomeramg");
      CHKERRABORT(libMesh::COMM_WORLD,ierr);
    }
#endif

  // Let the commandline override stuff
  // FIXME: Unless we are doing AMG???
  if (preconditioner_type != AMG_PRECOND)
    {
      ierr = PCSetFromOptions(pc);
      CHKERRABORT(libMesh::COMM_WORLD,ierr);
    }
}

template<typename T >

static void libMesh::PetscPreconditioner< T >::set_petsc_subpreconditioner_type	(	const PCType	type,
		PC &	pc
	)			[static, private]

template<typename T >

void libMesh::PetscPreconditioner< T >::set_petsc_subpreconditioner_type	(	PCType	type,
		PC &	pc
	)			[inline, static, private]

Some PETSc preconditioners (ILU, LU) don't work in parallel. This function is called from set_petsc_preconditioner_type() to set additional options for those so-called sub-preconditioners. This method ends up being static so that it can be called from set_petsc_preconditioner_type(). Not sure why set_petsc_preconditioner_type() needs to be static though...

Definition at line 227 of file petsc_preconditioner.C.

References libMesh::COMM_WORLD.

Referenced by libMesh::PetscPreconditioner< T >::set_petsc_preconditioner_type().

{
  // For catching PETSc error return codes
  int ierr = 0;

  // All docs say must call KSPSetUp or PCSetUp before calling PCBJacobiGetSubKSP.
  // You must call PCSetUp after the preconditioner operators have been set, otherwise you get the:
  //
  // "Object is in wrong state!"
  // "Matrix must be set first."
  //
  // error messages...
  ierr = PCSetUp(pc);
  CHKERRABORT(libMesh::COMM_WORLD,ierr);

  // To store array of local KSP contexts on this processor
  KSP* subksps;

  // the number of blocks on this processor
  int n_local;

  // The global number of the first block on this processor.
  // This is not used, so we just pass PETSC_NULL instead.
  // int first_local;

  // Fill array of local KSP contexts
  ierr = PCBJacobiGetSubKSP(pc, &n_local, PETSC_NULL, &subksps);
  CHKERRABORT(libMesh::COMM_WORLD,ierr);

  // Loop over sub-ksp objects, set ILU preconditioner
  for (int i=0; i<n_local; ++i)
    {
      // Get pointer to sub KSP object's PC
      PC subpc;
      ierr = KSPGetPC(subksps[i], &subpc);
      CHKERRABORT(libMesh::COMM_WORLD,ierr);

      // Set requested type on the sub PC
      ierr = PCSetType(subpc, type);
      CHKERRABORT(libMesh::COMM_WORLD,ierr);
    }

}

template<typename T >

void libMesh::Preconditioner< T >::set_type

(

const PreconditionerType

pct

)

[inline, inherited]

Sets the type of preconditioner to use.

Definition at line 181 of file preconditioner.h.

References libMesh::Preconditioner< T >::_is_initialized, and libMesh::Preconditioner< T >::_preconditioner_type.

{
  //If the preconditioner type changes we (probably) need to reinitialize.
  _is_initialized = false;
  _preconditioner_type = pct;
}

template<typename T>

virtual void libMesh::Preconditioner< T >::setup

(

)

[inline, virtual, inherited]

This is called every time the "operator might have changed".

This is essentially where you need to fill in your preconditioning matrix.

Definition at line 111 of file preconditioner.h.

{}

template<typename T>

PreconditionerType libMesh::Preconditioner< T >::type

(

)

const [inline, inherited]

Returns the type of preconditioner to use.

Definition at line 121 of file preconditioner.h.

  { return _preconditioner_type; }

---

Member Data Documentation

ReferenceCounter::Counts libMesh::ReferenceCounter::_counts [static, protected, inherited]

Actually holds the data.

Definition at line 118 of file reference_counter.h.

Referenced by libMesh::ReferenceCounter::get_info(), libMesh::ReferenceCounter::increment_constructor_count(), and libMesh::ReferenceCounter::increment_destructor_count().

bool libMesh::ReferenceCounter::_enable_print_counter = true [static, protected, inherited]

Flag to control whether reference count information is printed when print_info is called.

Definition at line 137 of file reference_counter.h.

Referenced by libMesh::ReferenceCounter::disable_print_counter_info(), libMesh::ReferenceCounter::enable_print_counter_info(), and libMesh::ReferenceCounter::print_info().

template<typename T>

bool libMesh::Preconditioner< T >::_is_initialized [protected, inherited]

Flag indicating if the data structures have been initialized.

Definition at line 145 of file preconditioner.h.

Referenced by libMesh::TrilinosPreconditioner< T >::init(), libMesh::PetscPreconditioner< T >::init(), libMesh::Preconditioner< Number >::initialized(), libMesh::Preconditioner< T >::set_matrix(), and libMesh::Preconditioner< T >::set_type().

template<typename T >

Mat libMesh::PetscPreconditioner< T >::_mat [protected]

Petsc Matrix that's been pulled out of the _matrix object. This happens during init...

Definition at line 112 of file petsc_preconditioner.h.

Referenced by libMesh::PetscPreconditioner< T >::init().

template<typename T>

SparseMatrix<T>* libMesh::Preconditioner< T >::_matrix [protected, inherited]

The matrix P... ie the matrix to be preconditioned. This is often the actual system matrix of a linear sytem.

Definition at line 135 of file preconditioner.h.

Referenced by libMesh::TrilinosPreconditioner< T >::init(), libMesh::PetscPreconditioner< T >::init(), and libMesh::Preconditioner< T >::set_matrix().

Threads::spin_mutex libMesh::ReferenceCounter::_mutex [static, protected, inherited]

Mutual exclusion object to enable thread-safe reference counting.

Definition at line 131 of file reference_counter.h.

Threads::atomic< unsigned int > libMesh::ReferenceCounter::_n_objects [static, protected, inherited]

The number of objects. Print the reference count information when the number returns to 0.

Definition at line 126 of file reference_counter.h.

Referenced by libMesh::ReferenceCounter::n_objects(), libMesh::ReferenceCounter::ReferenceCounter(), and libMesh::ReferenceCounter::~ReferenceCounter().

template<typename T >

PC libMesh::PetscPreconditioner< T >::_pc [protected]

Preconditioner context

Definition at line 106 of file petsc_preconditioner.h.

Referenced by libMesh::PetscPreconditioner< T >::apply(), libMesh::PetscPreconditioner< T >::init(), and libMesh::PetscPreconditioner< T >::pc().

template<typename T>

PreconditionerType libMesh::Preconditioner< T >::_preconditioner_type [protected, inherited]

Enum statitng with type of preconditioner to use.

Definition at line 140 of file preconditioner.h.

Referenced by libMesh::TrilinosPreconditioner< T >::compute(), libMesh::TrilinosPreconditioner< T >::init(), libMesh::PetscPreconditioner< T >::init(), libMesh::Preconditioner< T >::set_type(), and libMesh::Preconditioner< Number >::type().

---

The documentation for this class was generated from the following files:

• petsc_preconditioner.h
• petsc_preconditioner.C