Reference documentation for deal.II version Git 41fd616 20181115 11:08:04 0500

#include <deal.II/lac/petsc_vector.h>
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 (std::atomic< bool > *const validity, const char *identifier=nullptr) const 
void  unsubscribe (std::atomic< bool > *const validity, 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 
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.
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 timeout 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 wellacquainted 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.
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 nondeterministic 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:
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.
Definition at line 158 of file petsc_vector.h.
Declare type for container size.
Definition at line 164 of file petsc_vector.h.
Default constructor. Initialize the vector as empty.
Definition at line 31 of file petsc_parallel_vector.cc.

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

explicit 
Copyconstructor from deal.II vectors. Sets the dimension to that of the given vector, and copies all elements.

explicit 
Copyconstructor the values from a PETSc wrapper vector class.
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 step32.
Definition at line 72 of file petsc_parallel_vector.cc.
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.

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.
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.
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.
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.
Definition at line 208 of file petsc_parallel_vector.cc.
Reinit as a vector without ghost elements. See constructor with same signature for more details.
Definition at line 226 of file petsc_parallel_vector.cc.

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.
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.
Definition at line 324 of file petsc_parallel_vector.cc.

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.

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.
Global function swap
which overloads the default implementation of the C++ standard library which uses a temporary object. The function simply exchanges the data of the two vectors.
Definition at line 433 of file petsc_vector.h.

private 
Copy of the communicator object to be used for this parallel vector.
Definition at line 417 of file petsc_vector.h.