#include <deal.II/lac/petsc_vector.h>

Inheritance diagram for PETScWrappers::MPI::Vector:

Public Types
using	size_type = types::global_dof_index

Public Types inherited from PETScWrappers::VectorBase
using	value_type = PetscScalar

Public Member Functions
	Vector ()

	Vector (const MPI_Comm &communicator, const size_type n, const size_type local_size)

template<typename Number >
	Vector (const MPI_Comm &communicator, const ::Vector< Number > &v, const size_type local_size)

	Vector (const MPI_Comm &communicator, const VectorBase &v, const size_type local_size)

	Vector (const IndexSet &local, const IndexSet &ghost, const MPI_Comm &communicator)

	Vector (const IndexSet &local, const MPI_Comm &communicator)

virtual void	clear () override

Vector &	operator= (const Vector &v)

Vector &	operator= (const PetscScalar s)

template<typename number >
Vector &	operator= (const ::Vector< number > &v)

void	reinit (const MPI_Comm &communicator, const size_type N, const size_type local_size, const bool omit_zeroing_entries=false)

void	reinit (const Vector &v, const bool omit_zeroing_entries=false)

void	reinit (const IndexSet &local, const IndexSet &ghost, const MPI_Comm &communicator)

void	reinit (const IndexSet &local, const MPI_Comm &communicator)

const MPI_Comm &	get_mpi_communicator () const override

void	print (std::ostream &out, const unsigned int precision=3, const bool scientific=true, const bool across=true) const

bool	all_zero () const

Public Member Functions inherited from PETScWrappers::VectorBase
	VectorBase ()

	VectorBase (const VectorBase &v)

	VectorBase (const Vec &v)

virtual	~VectorBase () override

void	compress (const VectorOperation::values operation)

VectorBase &	operator= (const PetscScalar s)

bool	operator== (const VectorBase &v) const

bool	operator!= (const VectorBase &v) const

size_type	size () const

size_type	local_size () const

std::pair< size_type, size_type >	local_range () const

bool	in_local_range (const size_type index) const

IndexSet	locally_owned_elements () const

bool	has_ghost_elements () const

void	update_ghost_values () const

reference	operator() (const size_type index)

PetscScalar	operator() (const size_type index) const

reference	operator[] (const size_type index)

PetscScalar	operator[] (const size_type index) const

void	set (const std::vector< size_type > &indices, const std::vector< PetscScalar > &values)

void	extract_subvector_to (const std::vector< size_type > &indices, std::vector< PetscScalar > &values) const

template<typename ForwardIterator , typename OutputIterator >
void	extract_subvector_to (const ForwardIterator indices_begin, const ForwardIterator indices_end, OutputIterator values_begin) const

void	add (const std::vector< size_type > &indices, const std::vector< PetscScalar > &values)

void	add (const std::vector< size_type > &indices, const ::Vector< PetscScalar > &values)

void	add (const size_type n_elements, const size_type indices, const PetscScalar values)

PetscScalar	operator* (const VectorBase &vec) const

real_type	norm_sqr () const

PetscScalar	mean_value () const

real_type	l1_norm () const

real_type	l2_norm () const

real_type	lp_norm (const real_type p) const

real_type	linfty_norm () const

PetscScalar	add_and_dot (const PetscScalar a, const VectorBase &V, const VectorBase &W)

real_type	min () const

real_type	max () const

bool	all_zero () const

bool	is_non_negative () const

VectorBase &	operator*= (const PetscScalar factor)

VectorBase &	operator/= (const PetscScalar factor)

VectorBase &	operator+= (const VectorBase &V)

VectorBase &	operator-= (const VectorBase &V)

void	add (const PetscScalar s)

void	add (const PetscScalar a, const VectorBase &V)

void	add (const PetscScalar a, const VectorBase &V, const PetscScalar b, const VectorBase &W)

void	sadd (const PetscScalar s, const VectorBase &V)

void	sadd (const PetscScalar s, const PetscScalar a, const VectorBase &V)

void	scale (const VectorBase &scaling_factors)

void	equ (const PetscScalar a, const VectorBase &V)

void	ratio (const VectorBase &a, const VectorBase &b)

void	write_ascii (const PetscViewerFormat format=PETSC_VIEWER_DEFAULT)

void	print (std::ostream &out, const unsigned int precision=3, const bool scientific=true, const bool across=true) const

void	swap (VectorBase &v)

	operator const Vec & () const

std::size_t	memory_consumption () const

Public Member Functions inherited from Subscriptor
	Subscriptor ()

	Subscriptor (const Subscriptor &)

	Subscriptor (Subscriptor &&) noexcept

virtual	~Subscriptor ()

Subscriptor &	operator= (const Subscriptor &)

Subscriptor &	operator= (Subscriptor &&) noexcept

void	subscribe (const char *identifier=nullptr) const

void	unsubscribe (const char *identifier=nullptr) const

unsigned int	n_subscriptions () const

template<typename StreamType >
void	list_subscribers (StreamType &stream) const

void	list_subscribers () const

template<class Archive >
void	serialize (Archive &ar, const unsigned int version)

Protected Member Functions
virtual void	create_vector (const size_type n, const size_type local_size)

virtual void	create_vector (const size_type n, const size_type local_size, const IndexSet &ghostnodes)

Protected Member Functions inherited from PETScWrappers::VectorBase
void	do_set_add_operation (const size_type n_elements, const size_type indices, const PetscScalar values, const bool add_values)

Private Attributes
MPI_Comm	communicator

Related Functions
(Note that these are not member functions.)
void	swap (Vector &u, Vector &v)

Related Functions inherited from PETScWrappers::VectorBase
void	swap (VectorBase &u, VectorBase &v)

Additional Inherited Members
Static Public Member Functions inherited from Subscriptor
static::ExceptionBase &	ExcInUse (int arg1, std::string arg2, std::string arg3)

static::ExceptionBase &	ExcNoSubscriber (std::string arg1, std::string arg2)

Protected Attributes inherited from PETScWrappers::VectorBase
Vec	vector

bool	ghosted

IndexSet	ghost_indices

VectorOperation::values	last_action

bool	obtained_ownership

Detailed Description

Implementation of a parallel vector class based on PETSC and using MPI communication to synchronize distributed operations. All the functionality is actually in the base class, except for the calls to generate a parallel vector. This is possible since PETSc only works on an abstract vector type and internally distributes to functions that do the actual work depending on the actual vector type (much like using virtual functions). Only the functions creating a vector of specific type differ, and are implemented in this particular class.

Parallel communication model

The parallel functionality of PETSc is built on top of the Message Passing Interface (MPI). MPI's communication model is built on collective communications: if one process wants something from another, that other process has to be willing to accept this communication. A process cannot query data from another process by calling a remote function, without that other process expecting such a transaction. The consequence is that most of the operations in the base class of this class have to be called collectively. For example, if you want to compute the l2 norm of a parallel vector, all processes across which this vector is shared have to call the l2_norm function. If you don't do this, but instead only call the l2_norm function on one process, then the following happens: This one process will call one of the collective MPI functions and wait for all the other processes to join in on this. Since the other processes don't call this function, you will either get a time-out on the first process, or, worse, by the time the next a call to a PETSc function generates an MPI message on the other processes, you will get a cryptic message that only a subset of processes attempted a communication. These bugs can be very hard to figure out, unless you are well-acquainted with the communication model of MPI, and know which functions may generate MPI messages.

One particular case, where an MPI message may be generated unexpectedly is discussed below.

Accessing individual elements of a vector

PETSc does allow read access to individual elements of a vector, but in the distributed case only to elements that are stored locally. We implement this through calls like d=vec(i). However, if you access an element outside the locally stored range, an exception is generated.

In contrast to read access, PETSc (and the respective deal.II wrapper classes) allow to write (or add) to individual elements of vectors, even if they are stored on a different process. You can do this writing, for example, vec(i)=d or vec(i)+=d, or similar operations. There is one catch, however, that may lead to very confusing error messages: PETSc requires application programs to call the compress() function when they switch from adding, to elements to writing to elements. The reasoning is that all processes might accumulate addition operations to elements, even if multiple processes write to the same elements. By the time we call compress() the next time, all these additions are executed. However, if one process adds to an element, and another overwrites to it, the order of execution would yield non-deterministic behavior if we don't make sure that a synchronization with compress() happens in between.

In order to make sure these calls to compress() happen at the appropriate time, the deal.II wrappers keep a state variable that store which is the presently allowed operation: additions or writes. If it encounters an operation of the opposite kind, it calls compress() and flips the state. This can sometimes lead to very confusing behavior, in code that may for example look like this:

PETScWrappers::MPI::Vector vector;
...
// do some write operations on the vector
for (unsigned int i=0; i<vector.size(); ++i)
  vector(i) = i;
// do some additions to vector elements, but only for some elements
for (unsigned int i=0; i<vector.size(); ++i)
  if (some_condition(i) == true)
    vector(i) += 1;
// do another collective operation
const double norm = vector.l2_norm();

This code can run into trouble: by the time we see the first addition operation, we need to flush the overwrite buffers for the vector, and the deal.II library will do so by calling compress(). However, it will only do so for all processes that actually do an addition – if the condition is never true for one of the processes, then this one will not get to the actual compress() call, whereas all the other ones do. This gets us into trouble, since all the other processes hang in the call to flush the write buffers, while the one other process advances to the call to compute the l2 norm. At this time, you will get an error that some operation was attempted by only a subset of processes. This behavior may seem surprising, unless you know that write/addition operations on single elements may trigger this behavior.

The problem described here may be avoided by placing additional calls to compress(), or making sure that all processes do the same type of operations at the same time, for example by placing zero additions if necessary.

See also: vectors with ghost elements

Author: Wolfgang Bangerth, 2004

Definition at line 158 of file petsc_vector.h.

Member Typedef Documentation

using PETScWrappers::MPI::Vector::size_type = types::global_dof_index

Declare type for container size.

Definition at line 164 of file petsc_vector.h.

Constructor & Destructor Documentation

Vector< Number >::Vector ( )

Default constructor. Initialize the vector as empty.

Definition at line 31 of file petsc_parallel_vector.cc.

Vector< Number >::Vector	(	const MPI_Comm &	communicator,
		const size_type	n,
		const size_type	local_size
	)

explicit

Constructor. Set dimension to n and initialize all elements with zero.

local_size denotes the size of the chunk that shall be stored on the present process.

communicator denotes the MPI communicator over which the different parts of the vector shall communicate

The constructor is made explicit to avoid accidents like this: v=0;. Presumably, the user wants to set every element of the vector to zero, but instead, what happens is this call: v=Vector<number>(0);, i.e. the vector is replaced by one of length zero.

Definition at line 42 of file petsc_parallel_vector.cc.

template<typename Number >

PETScWrappers::MPI::Vector::Vector	(	const MPI_Comm &	communicator,
		const ::Vector< Number > &	v,
		const size_type	local_size
	)

explicit

Copy-constructor from deal.II vectors. Sets the dimension to that of the given vector, and copies all elements.

local_size denotes the size of the chunk that shall be stored on the present process.

communicator denotes the MPI communicator over which the different parts of the vector shall communicate

Vector< Number >::Vector	(	const MPI_Comm &	communicator,
		const VectorBase &	v,
		const size_type	local_size
	)

explicit

Copy-constructor the values from a PETSc wrapper vector class.

local_size denotes the size of the chunk that shall be stored on the present process.

communicator denotes the MPI communicator over which the different parts of the vector shall communicate

Deprecated:: The use of objects that are explicitly of type VectorBase is deprecated: use PETScWrappers::MPI::Vector instead.

Definition at line 52 of file petsc_parallel_vector.cc.

Vector< Number >::Vector	(	const IndexSet &	local,
		const IndexSet &	ghost,
		const MPI_Comm &	communicator
	)

Construct a new parallel ghosted PETSc vector from IndexSets.

Note that local must be ascending and 1:1, see IndexSet::is_ascending_and_one_to_one(). In particular, the DoFs in local need to be contiguous, meaning you can only create vectors from a DoFHandler with several finite element components if they are not reordered by component (use a PETScWrappers::BlockVector otherwise). The global size of the vector is determined by local.size(). The global indices in ghost are supplied as ghost indices so that they can be read locally.

Note that the ghost IndexSet may be empty and that any indices already contained in local are ignored during construction. That way, the ghost parameter can equal the set of locally relevant degrees of freedom, see step-32.

Note: This operation always creates a ghosted vector, which is considered read-only.

See also: vectors with ghost elements

Definition at line 72 of file petsc_parallel_vector.cc.

Vector< Number >::Vector	(	const IndexSet &	local,
		const MPI_Comm &	communicator
	)

explicit

Construct a new parallel PETSc vector without ghost elements from an IndexSet.

Note that local must be ascending and 1:1, see IndexSet::is_ascending_and_one_to_one(). In particular, the DoFs in local need to be contiguous, meaning you can only create vectors from a DoFHandler with several finite element components if they are not reordered by component (use a PETScWrappers::BlockVector otherwise).

Definition at line 88 of file petsc_parallel_vector.cc.

Member Function Documentation

void Vector< Number >::clear ( )

overridevirtual

Release all memory and return to a state just like after having called the default constructor.

Reimplemented from PETScWrappers::VectorBase.

Definition at line 136 of file petsc_parallel_vector.cc.

Vector & Vector< Number >::operator= ( const Vector & v )

Copy the given vector. Resize the present vector if necessary. Also take over the MPI communicator of v.

Definition at line 99 of file petsc_parallel_vector.cc.

Vector& PETScWrappers::MPI::Vector::operator= ( const PetscScalar s )

Set all components of the vector to the given number s. Simply pass this down to the base class, but we still need to declare this function to make the example given in the discussion about making the constructor explicit work.

template<typename number >

Vector& PETScWrappers::MPI::Vector::operator= ( const ::Vector< number > & v )

Copy the values of a deal.II vector (as opposed to those of the PETSc vector wrapper class) into this object.

Contrary to the case of sequential vectors, this operators requires that the present vector already has the correct size, since we need to have a partition and a communicator present which we otherwise can't get from the source vector.

void Vector< Number >::reinit	(	const MPI_Comm &	communicator,
		const size_type	N,
		const size_type	local_size,
		const bool	omit_zeroing_entries = `false`
	)

Change the dimension of the vector to N. It is unspecified how resizing the vector affects the memory allocation of this object; i.e., it is not guaranteed that resizing it to a smaller size actually also reduces memory consumption, or if for efficiency the same amount of memory is used

local_size denotes how many of the N values shall be stored locally on the present process. for less data.

communicator denotes the MPI communicator henceforth to be used for this vector.

If omit_zeroing_entries is false, the vector is filled by zeros. Otherwise, the elements are left an unspecified state.

Definition at line 147 of file petsc_parallel_vector.cc.

void Vector< Number >::reinit	(	const Vector &	v,
		const bool	omit_zeroing_entries = `false`
	)

Change the dimension to that of the vector v, and also take over the partitioning into local sizes as well as the MPI communicator. The same applies as for the other reinit function.

The elements of v are not copied, i.e. this function is the same as calling reinit(v.size(), v.local_size(), omit_zeroing_entries).

Definition at line 190 of file petsc_parallel_vector.cc.

void Vector< Number >::reinit	(	const IndexSet &	local,
		const IndexSet &	ghost,
		const MPI_Comm &	communicator
	)

Reinit as a vector with ghost elements. See the constructor with same signature for more details.

See also: vectors with ghost elements

Definition at line 208 of file petsc_parallel_vector.cc.

void Vector< Number >::reinit	(	const IndexSet &	local,
		const MPI_Comm &	communicator
	)

Reinit as a vector without ghost elements. See constructor with same signature for more details.

See also: vectors with ghost elements

Definition at line 226 of file petsc_parallel_vector.cc.

const MPI_Comm& PETScWrappers::MPI::Vector::get_mpi_communicator ( ) const

overridevirtual

Return a reference to the MPI communicator object in use with this vector.

Reimplemented from PETScWrappers::VectorBase.

void Vector< Number >::print	(	std::ostream &	out,
		const unsigned int	precision = `3`,
		const bool	scientific = `true`,
		const bool	across = `true`
	)		const

Print to a stream. precision denotes the desired precision with which values shall be printed, scientific whether scientific notation shall be used. If across is true then the vector is printed in a line, while if false then the elements are printed on a separate line each.

Note: This function overloads the one in the base class to ensure that the right thing happens for parallel vectors that are distributed across processors.

Definition at line 339 of file petsc_parallel_vector.cc.

bool Vector< Number >::all_zero ( ) const

Return whether the vector contains only elements with value zero. This is a collective operation. This function is expensive, because potentially all elements have to be checked.

Note: This function overloads the one in the base class to make this a collective operation.

Definition at line 324 of file petsc_parallel_vector.cc.

void Vector< Number >::create_vector	(	const size_type	n,
		const size_type	local_size
	)

protectedvirtual

Create a vector of length n. For this class, we create a parallel vector. n denotes the total size of the vector to be created. local_size denotes how many of these elements shall be stored locally.

Definition at line 240 of file petsc_parallel_vector.cc.

void Vector< Number >::create_vector	(	const size_type	n,
		const size_type	local_size,
		const IndexSet &	ghostnodes
	)

protectedvirtual

Create a vector of global length n, local size local_size and with the specified ghost indices. Note that you need to call update_ghost_values() before accessing those.

Definition at line 256 of file petsc_parallel_vector.cc.

Friends And Related Function Documentation

void swap	(	Vector &	u,
		Vector &	v
	)

Author: Wolfgang Bangerth, 2004

Definition at line 433 of file petsc_vector.h.

Member Data Documentation

MPI_Comm PETScWrappers::MPI::Vector::communicator

private

Copy of the communicator object to be used for this parallel vector.

Definition at line 417 of file petsc_vector.h.

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

deal.II/lac/petsc_vector.h
/mnt/data/darndt/Sources/dealii-clang-6.0.0/source/lac/petsc_parallel_vector.cc

Public Types

Public Member Functions

Protected Member Functions

Private Attributes

Related Functions

Additional Inherited Members

Detailed Description

Parallel communication model

Accessing individual elements of a vector

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation