libMesh
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libMesh::PetscMatrix< T > Class Template Referencefinal

This class provides a nice interface to the PETSc C-based AIJ data structures for parallel, sparse matrices. More...

#include <petsc_matrix.h>

Inheritance diagram for libMesh::PetscMatrix< T >:
[legend]

Public Member Functions

 PetscMatrix (const Parallel::Communicator &comm_in)
 Constructor; initializes the matrix to be empty, without any structure, i.e. More...
 
 PetscMatrix (Mat m, const Parallel::Communicator &comm_in, bool destroy_on_exit=false)
 Constructor. More...
 
 PetscMatrix (const Parallel::Communicator &comm_in, const numeric_index_type m, const numeric_index_type n, const numeric_index_type m_l, const numeric_index_type n_l, const numeric_index_type n_nz=30, const numeric_index_type n_oz=10, const numeric_index_type blocksize=1)
 Constructor. More...
 
 PetscMatrix (PetscMatrix &&)=delete
 This class manages a C-style struct (Mat) manually, so we don't want to allow any automatic copy/move functions to be generated, and we can't default the destructor. More...
 
 PetscMatrix (const PetscMatrix &)=delete
 
PetscMatrixoperator= (PetscMatrix &&)=delete
 
virtual ~PetscMatrix ()
 
PetscMatrixoperator= (const PetscMatrix &)
 
virtual SparseMatrix< T > & operator= (const SparseMatrix< T > &v) override
 This looks like a copy assignment operator, but note that, unlike normal copy assignment operators, it is pure virtual. More...
 
virtual void init (const numeric_index_type m, const numeric_index_type n, const numeric_index_type m_l, const numeric_index_type n_l, const numeric_index_type n_nz=30, const numeric_index_type n_oz=10, const numeric_index_type blocksize=1) override
 Initialize a PETSc matrix. More...
 
void init (const numeric_index_type m, const numeric_index_type n, const numeric_index_type m_l, const numeric_index_type n_l, const std::vector< numeric_index_type > &n_nz, const std::vector< numeric_index_type > &n_oz, const numeric_index_type blocksize=1)
 Initialize a PETSc matrix. More...
 
virtual void init (ParallelType=PARALLEL) override
 Initialize this matrix using the sparsity structure computed by dof_map. More...
 
void update_preallocation_and_zero ()
 Update the sparsity pattern based on dof_map, and set the matrix to zero. More...
 
void reset_preallocation ()
 Reset matrix to use the original nonzero pattern provided by users. More...
 
virtual void zero () override
 Set all entries to 0. More...
 
virtual std::unique_ptr< SparseMatrix< T > > zero_clone () const override
 
virtual std::unique_ptr< SparseMatrix< T > > clone () const override
 
virtual void zero_rows (std::vector< numeric_index_type > &rows, T diag_value=0.0) override
 Sets all row entries to 0 then puts diag_value in the diagonal entry. More...
 
virtual void flush () override
 For PETSc matrix , this function is similar to close but without shrinking memory. More...
 
virtual void set (const numeric_index_type i, const numeric_index_type j, const T value) override
 Set the element (i,j) to value. More...
 
virtual void add (const numeric_index_type i, const numeric_index_type j, const T value) override
 Add value to the element (i,j). More...
 
virtual void add_matrix (const DenseMatrix< T > &dm, const std::vector< numeric_index_type > &rows, const std::vector< numeric_index_type > &cols) override
 Add the full matrix dm to the SparseMatrix. More...
 
virtual void add_matrix (const DenseMatrix< T > &dm, const std::vector< numeric_index_type > &dof_indices) override
 Same as add_matrix, but assumes the row and column maps are the same. More...
 
virtual void add_block_matrix (const DenseMatrix< T > &dm, const std::vector< numeric_index_type > &brows, const std::vector< numeric_index_type > &bcols) override
 Add the full matrix dm to the SparseMatrix. More...
 
virtual void add_block_matrix (const DenseMatrix< T > &dm, const std::vector< numeric_index_type > &dof_indices) override
 Same as add_block_matrix(), but assumes the row and column maps are the same. More...
 
virtual void add (const T a, const SparseMatrix< T > &X) override
 Compute A += a*X for scalar a, matrix X. More...
 
virtual void matrix_matrix_mult (SparseMatrix< T > &X, SparseMatrix< T > &Y, bool reuse=false) override
 Compute Y = A*X for matrix X. More...
 
virtual void add_sparse_matrix (const SparseMatrix< T > &spm, const std::map< numeric_index_type, numeric_index_type > &row_ltog, const std::map< numeric_index_type, numeric_index_type > &col_ltog, const T scalar) override
 Add scalar* spm to the rows and cols of this matrix (A): A(rows[i], cols[j]) += scalar * spm(i,j) More...
 
virtual T operator() (const numeric_index_type i, const numeric_index_type j) const override
 
virtual Real l1_norm () const override
 
virtual Real frobenius_norm () const
 
virtual Real linfty_norm () const override
 
virtual void print_personal (std::ostream &os=libMesh::out) const override
 Print the contents of the matrix to the screen with the PETSc viewer. More...
 
virtual void print_matlab (const std::string &name="") const override
 Print the contents of the matrix in Matlab's sparse matrix format. More...
 
virtual void print_petsc_binary (const std::string &filename) override
 Write the contents of the matrix to a file in PETSc's binary sparse matrix format. More...
 
virtual void print_petsc_hdf5 (const std::string &filename) override
 Write the contents of the matrix to a file in PETSc's HDF5 sparse matrix format. More...
 
virtual void read_petsc_binary (const std::string &filename) override
 Read the contents of the matrix from a file in PETSc's binary sparse matrix format. More...
 
virtual void read_petsc_hdf5 (const std::string &filename) override
 Read the contents of the matrix from a file in PETSc's HDF5 sparse matrix format. More...
 
virtual void get_diagonal (NumericVector< T > &dest) const override
 Copies the diagonal part of the matrix into dest. More...
 
virtual void get_transpose (SparseMatrix< T > &dest) const override
 Copies the transpose of the matrix into dest, which may be *this. More...
 
virtual void get_row (numeric_index_type i, std::vector< numeric_index_type > &indices, std::vector< T > &values) const override
 Get a row from the matrix. More...
 
virtual void create_submatrix_nosort (SparseMatrix< T > &submatrix, const std::vector< numeric_index_type > &rows, const std::vector< numeric_index_type > &cols) const override
 Similar to the create_submatrix function, this function creates a submatrix which is defined by the indices given in the rows and cols vectors. More...
 
virtual void scale (const T scale) override
 Scales all elements of this matrix by scale. More...
 
std::unique_ptr< PetscMatrix< T > > copy_from_hash ()
 Creates a copy of the current hash table matrix and then performs assembly. More...
 
virtual bool supports_hash_table () const override
 
virtual void restore_original_nonzero_pattern () override
 Reset the memory storage of the matrix. More...
 
virtual SolverPackage solver_package () override
 
Mat mat ()
 
Mat mat () const
 
virtual void clear () noexcept override
 clear() is called from the destructor, so it should not throw. More...
 
void set_destroy_mat_on_exit (bool destroy=true)
 If set to false, we don't delete the Mat on destruction and allow instead for PETSc to manage it. More...
 
void swap (PetscMatrixBase< T > &)
 Swaps the internal data pointers of two PetscMatrices, no actual values are swapped. More...
 
void set_context ()
 Set the context (ourself) for _mat. More...
 
virtual numeric_index_type m () const override
 
virtual numeric_index_type local_m () const final
 Get the number of rows owned by this process. More...
 
virtual numeric_index_type n () const override
 
virtual numeric_index_type local_n () const final
 Get the number of columns owned by this process. More...
 
virtual numeric_index_type row_start () const override
 
virtual numeric_index_type row_stop () const override
 
virtual numeric_index_type col_start () const override
 
virtual numeric_index_type col_stop () const override
 
virtual void close () override
 Calls the SparseMatrix's internal assembly routines, ensuring that the values are consistent across processors. More...
 
virtual bool closed () const override
 
virtual bool initialized () const
 
void attach_dof_map (const DofMap &dof_map)
 Set a pointer to the DofMap to use. More...
 
void attach_sparsity_pattern (const SparsityPattern::Build &sp)
 Set a pointer to a sparsity pattern to use. More...
 
virtual bool need_full_sparsity_pattern () const
 
virtual bool require_sparsity_pattern () const
 
virtual void update_sparsity_pattern (const SparsityPattern::Graph &)
 Updates the matrix sparsity pattern. More...
 
Real l1_norm_diff (const SparseMatrix< T > &other_mat) const
 
virtual std::size_t n_nonzeros () const
 
void print (std::ostream &os=libMesh::out, const bool sparse=false) const
 Print the contents of the matrix to the screen in a uniform style, regardless of matrix/solver package being used. More...
 
template<>
void print (std::ostream &os, const bool sparse) const
 
virtual void read (const std::string &filename)
 Read the contents of the matrix from a file, with the file format inferred from the extension of filename. More...
 
virtual void read_coreform_hdf5 (const std::string &filename, const std::string &groupname="extraction")
 Read the contents of the matrix from a file, with the HDF5 sparse matrix format used by CoreForm, expecing sparse matrix data in the group given by groupname. More...
 
virtual void read_matlab (const std::string &filename)
 Read the contents of the matrix from the Matlab-script sparse matrix format used by PETSc. More...
 
virtual void create_submatrix (SparseMatrix< T > &submatrix, const std::vector< numeric_index_type > &rows, const std::vector< numeric_index_type > &cols) const
 This function creates a matrix called "submatrix" which is defined by the row and column indices given in the "rows" and "cols" entries. More...
 
virtual void reinit_submatrix (SparseMatrix< T > &submatrix, const std::vector< numeric_index_type > &rows, const std::vector< numeric_index_type > &cols) const
 This function is similar to the one above, but it allows you to reuse the existing sparsity pattern of "submatrix" instead of reallocating it again. More...
 
void vector_mult (NumericVector< T > &dest, const NumericVector< T > &arg) const
 Multiplies the matrix by the NumericVector arg and stores the result in NumericVector dest. More...
 
void vector_mult_add (NumericVector< T > &dest, const NumericVector< T > &arg) const
 Multiplies the matrix by the NumericVector arg and adds the result to the NumericVector dest. More...
 
void use_hash_table (bool use_hash)
 Sets whether to use hash table assembly. More...
 
bool use_hash_table () const
 
const Parallel::Communicatorcomm () const
 
processor_id_type n_processors () const
 
processor_id_type processor_id () const
 

Static Public Member Functions

static PetscMatrixBase< T > * get_context (Mat mat, const TIMPI::Communicator &comm)
 
static std::unique_ptr< SparseMatrix< T > > build (const Parallel::Communicator &comm, const SolverPackage solver_package=libMesh::default_solver_package(), const MatrixBuildType matrix_build_type=MatrixBuildType::AUTOMATIC)
 Builds a SparseMatrix<T> using the linear solver package specified by solver_package. More...
 
static std::string get_info ()
 Gets a string containing the reference information. More...
 
static void print_info (std::ostream &out_stream=libMesh::out)
 Prints the reference information, by default to libMesh::out. More...
 
static unsigned int n_objects ()
 Prints the number of outstanding (created, but not yet destroyed) objects. More...
 
static void enable_print_counter_info ()
 Methods to enable/disable the reference counter output from print_info() More...
 
static void disable_print_counter_info ()
 

Protected Types

typedef std::map< std::string, std::pair< unsigned int, unsigned int > > Counts
 Data structure to log the information. More...
 

Protected Member Functions

void init_without_preallocation (numeric_index_type m, numeric_index_type n, numeric_index_type m_l, numeric_index_type n_l, numeric_index_type blocksize)
 Perform matrix initialization steps sans preallocation. More...
 
void preallocate (numeric_index_type m_l, const std::vector< numeric_index_type > &n_nz, const std::vector< numeric_index_type > &n_oz, numeric_index_type blocksize)
 
void finish_initialization ()
 Finish up the initialization process. More...
 
virtual void _get_submatrix (SparseMatrix< T > &submatrix, const std::vector< numeric_index_type > &rows, const std::vector< numeric_index_type > &cols, const bool reuse_submatrix) const override
 This function either creates or re-initializes a matrix called submatrix which is defined by the indices given in the rows and cols vectors. More...
 
void _petsc_viewer (const std::string &filename, PetscViewerType viewertype, PetscFileMode filemode)
 
void increment_constructor_count (const std::string &name) noexcept
 Increments the construction counter. More...
 
void increment_destructor_count (const std::string &name) noexcept
 Increments the destruction counter. More...
 

Protected Attributes

PetscMatrixType _mat_type
 
Mat _mat
 PETSc matrix datatype to store values. More...
 
bool _destroy_mat_on_exit
 This boolean value should only be set to false for the constructor which takes a PETSc Mat object. More...
 
DofMap const * _dof_map
 The DofMap object associated with this object. More...
 
SparsityPattern::Build const * _sp
 The sparsity pattern associated with this object. More...
 
bool _is_initialized
 Flag indicating whether or not the matrix has been initialized. More...
 
bool _use_hash_table
 Flag indicating whether the matrix is assembled using a hash table. More...
 
const Parallel::Communicator_communicator
 

Static Protected Attributes

static Counts _counts
 Actually holds the data. More...
 
static Threads::atomic< unsigned int_n_objects
 The number of objects. More...
 
static Threads::spin_mutex _mutex
 Mutual exclusion object to enable thread-safe reference counting. More...
 
static bool _enable_print_counter = true
 Flag to control whether reference count information is printed when print_info is called. More...
 

Private Member Functions

template<NormType N>
Real norm () const
 

Private Attributes

std::mutex _petsc_matrix_mutex
 
Threads::spin_mutex _petsc_matrix_mutex
 

Friends

class ::PetscMatrixTest
 

Detailed Description

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

This class provides a nice interface to the PETSc C-based AIJ data structures for parallel, sparse matrices.

All overridden virtual functions are documented in sparse_matrix.h.

Author
Benjamin S. Kirk
Date
2002 SparseMatrix interface to PETSc Mat.

Definition at line 61 of file petsc_matrix.h.

Member Typedef Documentation

◆ Counts

typedef std::map<std::string, std::pair<unsigned int, unsigned int> > libMesh::ReferenceCounter::Counts
protectedinherited

Data structure to log the information.

The log is identified by the class name.

Definition at line 119 of file reference_counter.h.

Constructor & Destructor Documentation

◆ PetscMatrix() [1/5]

template<typename T >
libMesh::PetscMatrix< T >::PetscMatrix ( const Parallel::Communicator comm_in)
explicit

Constructor; initializes the matrix to be empty, without any structure, i.e.

the matrix is not usable at all. This constructor is therefore only useful for matrices which are members of a class. All other matrices should be created at a point in the data flow where all necessary information is available.

You have to initialize the matrix before usage with init(...).

Definition at line 86 of file petsc_matrix.C.

86  :
88 {
89 }
This class provides a nice interface to the PETSc C-based data structures for parallel, sparse matrices.
PetscMatrixType _mat_type
Definition: petsc_matrix.h:349

◆ PetscMatrix() [2/5]

template<typename T >
libMesh::PetscMatrix< T >::PetscMatrix ( Mat  m,
const Parallel::Communicator comm_in,
bool  destroy_on_exit = false 
)
explicit

Constructor.

Creates a PetscMatrix assuming you already have a valid Mat object. In this case, m may not be destroyed by the PetscMatrix destructor when this object goes out of scope. This allows ownership of m to remain with the original creator, and to simply provide additional functionality with the PetscMatrix.

Definition at line 96 of file petsc_matrix.C.

References libMesh::PetscMatrix< T >::_mat_type, libMesh::AIJ, and libMesh::HYPRE.

98  :
99  PetscMatrixBase<T>(mat_in, comm_in, destroy_on_exit)
100 {
101  MatType mat_type;
102  LibmeshPetscCall(MatGetType(mat_in, &mat_type));
103  PetscBool is_hypre;
104  LibmeshPetscCall(PetscStrcmp(mat_type, MATHYPRE, &is_hypre));
105  if (is_hypre == PETSC_TRUE)
106  _mat_type = HYPRE;
107  else
108  _mat_type = AIJ;
109 }
This class provides a nice interface to the PETSc C-based data structures for parallel, sparse matrices.
PetscMatrixType _mat_type
Definition: petsc_matrix.h:349

◆ PetscMatrix() [3/5]

template<typename T >
libMesh::PetscMatrix< T >::PetscMatrix ( const Parallel::Communicator comm_in,
const numeric_index_type  m,
const numeric_index_type  n,
const numeric_index_type  m_l,
const numeric_index_type  n_l,
const numeric_index_type  n_nz = 30,
const numeric_index_type  n_oz = 10,
const numeric_index_type  blocksize = 1 
)
explicit

Constructor.

Creates and initializes a PetscMatrix with the given structure. See init(...) for a description of the parameters.

Definition at line 115 of file petsc_matrix.C.

References libMesh::PetscMatrix< T >::init().

122  :
123  PetscMatrixBase<T>(comm_in), _mat_type(AIJ)
124 {
125  this->init(m_in, n_in, m_l, n_l, n_nz, n_oz, blocksize_in);
126 }
This class provides a nice interface to the PETSc C-based data structures for parallel, sparse matrices.
PetscMatrixType _mat_type
Definition: petsc_matrix.h:349
virtual void init(const numeric_index_type m, const numeric_index_type n, const numeric_index_type m_l, const numeric_index_type n_l, const numeric_index_type n_nz=30, const numeric_index_type n_oz=10, const numeric_index_type blocksize=1) override
Initialize a PETSc matrix.
Definition: petsc_matrix.C:214

◆ PetscMatrix() [4/5]

template<typename T>
libMesh::PetscMatrix< T >::PetscMatrix ( PetscMatrix< T > &&  )
delete

This class manages a C-style struct (Mat) manually, so we don't want to allow any automatic copy/move functions to be generated, and we can't default the destructor.

◆ PetscMatrix() [5/5]

template<typename T>
libMesh::PetscMatrix< T >::PetscMatrix ( const PetscMatrix< T > &  )
delete

◆ ~PetscMatrix()

template<typename T >
libMesh::PetscMatrix< T >::~PetscMatrix ( )
virtualdefault

Member Function Documentation

◆ _get_submatrix()

template<typename T >
void libMesh::PetscMatrix< T >::_get_submatrix ( SparseMatrix< T > &  submatrix,
const std::vector< numeric_index_type > &  rows,
const std::vector< numeric_index_type > &  cols,
const bool  reuse_submatrix 
) const
overrideprotectedvirtual

This function either creates or re-initializes a matrix called submatrix which is defined by the indices given in the rows and cols vectors.

This function is implemented in terms of MatGetSubMatrix(). The reuse_submatrix parameter determines whether or not PETSc will treat submatrix as one which has already been used (had memory allocated) or as a new matrix.

Reimplemented from libMesh::SparseMatrix< T >.

Definition at line 798 of file petsc_matrix.C.

References libMesh::SparseMatrix< T >::_is_initialized, libMesh::PetscMatrixBase< T >::_mat, libMesh::SparseMatrix< T >::clear(), libMesh::PetscMatrixBase< T >::close(), libMesh::closed(), libMesh::WrappedPetsc< T >::get(), libMesh::SparseMatrix< T >::initialized(), and libMesh::numeric_petsc_cast().

802 {
803  if (!this->closed())
804  {
805  libmesh_deprecated();
806  libmesh_warning("The matrix must be assembled before calling PetscMatrix::create_submatrix().\n"
807  "Please update your code, as this warning will become an error in a future release.");
808  const_cast<PetscMatrix<T> *>(this)->close();
809  }
810 
811  semiparallel_only();
812 
813  // Make sure the SparseMatrix passed in is really a PetscMatrix
814  PetscMatrix<T> * petsc_submatrix = cast_ptr<PetscMatrix<T> *>(&submatrix);
815 
816  // If we're not reusing submatrix and submatrix is already initialized
817  // then we need to clear it, otherwise we get a memory leak.
818  if (!reuse_submatrix && submatrix.initialized())
819  submatrix.clear();
820 
821  // Construct row and column index sets.
822  WrappedPetsc<IS> isrow;
823  LibmeshPetscCall(ISCreateGeneral(this->comm().get(),
824  cast_int<PetscInt>(rows.size()),
825  numeric_petsc_cast(rows.data()),
826  PETSC_USE_POINTER,
827  isrow.get()));
828 
829  WrappedPetsc<IS> iscol;
830  LibmeshPetscCall(ISCreateGeneral(this->comm().get(),
831  cast_int<PetscInt>(cols.size()),
832  numeric_petsc_cast(cols.data()),
833  PETSC_USE_POINTER,
834  iscol.get()));
835 
836  // Extract submatrix
837  LibmeshPetscCall(LibMeshCreateSubMatrix(this->_mat,
838  isrow,
839  iscol,
840  (reuse_submatrix ? MAT_REUSE_MATRIX : MAT_INITIAL_MATRIX),
841  (&petsc_submatrix->_mat)));
842 
843  // Specify that the new submatrix is initialized and close it.
844  petsc_submatrix->_is_initialized = true;
845  petsc_submatrix->close();
846 }
virtual bool initialized() const
const Parallel::Communicator & comm() const
virtual void clear()=0
Restores the SparseMatrix<T> to a pristine state.
PetscInt * numeric_petsc_cast(const numeric_index_type *p)
bool _is_initialized
Flag indicating whether or not the matrix has been initialized.
virtual void close() override
Calls the SparseMatrix&#39;s internal assembly routines, ensuring that the values are consistent across p...
Mat _mat
PETSc matrix datatype to store values.
virtual bool closed() const override
This class provides a nice interface to the PETSc C-based AIJ data structures for parallel...
Definition: petsc_matrix.h:61

◆ _petsc_viewer()

template<typename T >
void libMesh::PetscMatrix< T >::_petsc_viewer ( const std::string &  filename,
PetscViewerType  viewertype,
PetscFileMode  filemode 
)
protected

Definition at line 661 of file petsc_matrix.C.

References libMesh::libMeshPrivateData::_is_initialized, and libMesh::initialized().

664 {
665  parallel_object_only();
666 
667  // We'll get matrix sizes from the file, but we need to at least
668  // have a Mat object
669  if (!this->initialized())
670  {
671  LibmeshPetscCall(MatCreate(this->comm().get(), &this->_mat));
672  this->_is_initialized = true;
673  }
674 
675  PetscViewer viewer;
676  LibmeshPetscCall(PetscViewerCreate(this->comm().get(), &viewer));
677  LibmeshPetscCall(PetscViewerSetType(viewer, viewertype));
678  LibmeshPetscCall(PetscViewerSetFromOptions(viewer));
679  LibmeshPetscCall(PetscViewerFileSetMode(viewer, filemode));
680  LibmeshPetscCall(PetscViewerFileSetName(viewer, filename.c_str()));
681  if (filemode == FILE_MODE_READ)
682  LibmeshPetscCall(MatLoad(this->_mat, viewer));
683  else
684  LibmeshPetscCall(MatView(this->_mat, viewer));
685  LibmeshPetscCall(PetscViewerDestroy(&viewer));
686 }
virtual bool initialized() const
const Parallel::Communicator & comm() const
bool _is_initialized
Flag indicating whether or not the matrix has been initialized.
Mat _mat
PETSc matrix datatype to store values.

◆ add() [1/2]

template<typename T >
void libMesh::PetscMatrix< T >::add ( const numeric_index_type  i,
const numeric_index_type  j,
const T  value 
)
overridevirtual

Add value to the element (i,j).

Throws an error if the entry does not exist. Zero values can be "added" to non-existent entries.

Implements libMesh::SparseMatrix< T >.

Definition at line 985 of file petsc_matrix.C.

References libMesh::initialized(), libMesh::libmesh_assert(), and value.

Referenced by PetscMatrixTest::testPetscCopyFromHash().

988 {
989  libmesh_assert (this->initialized());
990 
991  PetscInt i_val=i, j_val=j;
992 
993  PetscScalar petsc_value = static_cast<PetscScalar>(value);
994  std::scoped_lock lock(this->_petsc_matrix_mutex);
995  LibmeshPetscCall(MatSetValues(this->_mat, 1, &i_val, 1, &j_val,
996  &petsc_value, ADD_VALUES));
997 }
virtual bool initialized() const
std::mutex _petsc_matrix_mutex
Definition: petsc_matrix.h:353
libmesh_assert(ctx)
Mat _mat
PETSc matrix datatype to store values.
static const bool value
Definition: xdr_io.C:55

◆ add() [2/2]

template<typename T >
void libMesh::PetscMatrix< T >::add ( const T  a,
const SparseMatrix< T > &  X 
)
overridevirtual

Compute A += a*X for scalar a, matrix X.

Note
The matrices A and X need to have the same nonzero pattern, otherwise PETSc will crash!
It is advisable to not only allocate appropriate memory with init(), but also explicitly zero the terms of this whenever you add a non-zero value to X.
X will be closed, if not already done, before performing any work.

Implements libMesh::SparseMatrix< T >.

Definition at line 1015 of file petsc_matrix.C.

References libMesh::PetscMatrixBase< T >::_mat, libMesh::PetscMatrixBase< T >::closed(), libMesh::initialized(), libMesh::libmesh_assert(), libMesh::SparseMatrix< T >::m(), and libMesh::SparseMatrix< T >::n().

1016 {
1017  libmesh_assert (this->initialized());
1018 
1019  // sanity check. but this cannot avoid
1020  // crash due to incompatible sparsity structure...
1021  libmesh_assert_equal_to (this->m(), X_in.m());
1022  libmesh_assert_equal_to (this->n(), X_in.n());
1023 
1024  PetscScalar a = static_cast<PetscScalar> (a_in);
1025  const PetscMatrix<T> * X = cast_ptr<const PetscMatrix<T> *> (&X_in);
1026 
1027  libmesh_assert (X);
1028 
1029  // the matrix from which we copy the values has to be assembled/closed
1030  libmesh_assert(X->closed());
1031 
1032  semiparallel_only();
1033 
1034  LibmeshPetscCall(MatAXPY(this->_mat, a, X->_mat, DIFFERENT_NONZERO_PATTERN));
1035 }
virtual numeric_index_type n() const override
virtual bool initialized() const
virtual numeric_index_type m() const override
libmesh_assert(ctx)
Mat _mat
PETSc matrix datatype to store values.
virtual bool closed() const override
This class provides a nice interface to the PETSc C-based AIJ data structures for parallel...
Definition: petsc_matrix.h:61

◆ add_block_matrix() [1/2]

template<typename T >
void libMesh::PetscMatrix< T >::add_block_matrix ( const DenseMatrix< T > &  dm,
const std::vector< numeric_index_type > &  brows,
const std::vector< numeric_index_type > &  bcols 
)
overridevirtual

Add the full matrix dm to the SparseMatrix.

This is useful for adding an element matrix at assembly time. The matrix is assumed blocked, and brow, bcol correspond to the block row and column indices.

Reimplemented from libMesh::SparseMatrix< T >.

Definition at line 757 of file petsc_matrix.C.

References libMesh::DenseMatrix< T >::get_values(), libMesh::initialized(), libMesh::libmesh_assert(), libMesh::DenseMatrixBase< T >::m(), libMesh::DenseMatrixBase< T >::n(), libMesh::numeric_petsc_cast(), and libMesh::pPS().

Referenced by libMesh::PetscMatrix< T >::add_block_matrix().

760 {
761  libmesh_assert (this->initialized());
762 
763  const numeric_index_type n_brows =
764  cast_int<numeric_index_type>(brows.size());
765  const numeric_index_type n_bcols =
766  cast_int<numeric_index_type>(bcols.size());
767 
768 #ifndef NDEBUG
769  const numeric_index_type n_rows =
770  cast_int<numeric_index_type>(dm.m());
771  const numeric_index_type n_cols =
772  cast_int<numeric_index_type>(dm.n());
773  const numeric_index_type blocksize = n_rows / n_brows;
774 
775  libmesh_assert_equal_to (n_cols / n_bcols, blocksize);
776  libmesh_assert_equal_to (blocksize*n_brows, n_rows);
777  libmesh_assert_equal_to (blocksize*n_bcols, n_cols);
778 
779  PetscInt petsc_blocksize;
780  LibmeshPetscCall(MatGetBlockSize(this->_mat, &petsc_blocksize));
781  libmesh_assert_equal_to (blocksize, static_cast<numeric_index_type>(petsc_blocksize));
782 #endif
783 
784  std::scoped_lock lock(this->_petsc_matrix_mutex);
785  // These casts are required for PETSc <= 2.1.5
786  LibmeshPetscCall(MatSetValuesBlocked(this->_mat,
787  n_brows, numeric_petsc_cast(brows.data()),
788  n_bcols, numeric_petsc_cast(bcols.data()),
789  pPS(const_cast<T*>(dm.get_values().data())),
790  ADD_VALUES));
791 }
virtual bool initialized() const
unsigned int m() const
PetscScalar * pPS(T *ptr)
Definition: petsc_macro.h:174
PetscInt * numeric_petsc_cast(const numeric_index_type *p)
std::mutex _petsc_matrix_mutex
Definition: petsc_matrix.h:353
dof_id_type numeric_index_type
Definition: id_types.h:99
libmesh_assert(ctx)
std::vector< T > & get_values()
Definition: dense_matrix.h:382
Mat _mat
PETSc matrix datatype to store values.
unsigned int n() const

◆ add_block_matrix() [2/2]

template<typename T>
virtual void libMesh::PetscMatrix< T >::add_block_matrix ( const DenseMatrix< T > &  dm,
const std::vector< numeric_index_type > &  dof_indices 
)
inlineoverridevirtual

Same as add_block_matrix(), but assumes the row and column maps are the same.

Thus the matrix dm must be square.

Reimplemented from libMesh::SparseMatrix< T >.

Definition at line 197 of file petsc_matrix.h.

References libMesh::PetscMatrix< T >::add_block_matrix().

199  { this->add_block_matrix (dm, dof_indices, dof_indices); }
virtual void add_block_matrix(const DenseMatrix< T > &dm, const std::vector< numeric_index_type > &brows, const std::vector< numeric_index_type > &bcols) override
Add the full matrix dm to the SparseMatrix.
Definition: petsc_matrix.C:757

◆ add_matrix() [1/2]

template<typename T >
void libMesh::PetscMatrix< T >::add_matrix ( const DenseMatrix< T > &  dm,
const std::vector< numeric_index_type > &  rows,
const std::vector< numeric_index_type > &  cols 
)
overridevirtual

Add the full matrix dm to the SparseMatrix.

This is useful for adding an element matrix at assembly time.

Implements libMesh::SparseMatrix< T >.

Definition at line 731 of file petsc_matrix.C.

References libMesh::DenseMatrix< T >::get_values(), libMesh::initialized(), libMesh::libmesh_assert(), libMesh::DenseMatrixBase< T >::m(), libMesh::DenseMatrixBase< T >::n(), libMesh::numeric_petsc_cast(), and libMesh::pPS().

734 {
735  libmesh_assert (this->initialized());
736 
737  const numeric_index_type n_rows = dm.m();
738  const numeric_index_type n_cols = dm.n();
739 
740  libmesh_assert_equal_to (rows.size(), n_rows);
741  libmesh_assert_equal_to (cols.size(), n_cols);
742 
743  std::scoped_lock lock(this->_petsc_matrix_mutex);
744  LibmeshPetscCall(MatSetValues(this->_mat,
745  n_rows, numeric_petsc_cast(rows.data()),
746  n_cols, numeric_petsc_cast(cols.data()),
747  pPS(const_cast<T*>(dm.get_values().data())),
748  ADD_VALUES));
749 }
virtual bool initialized() const
unsigned int m() const
PetscScalar * pPS(T *ptr)
Definition: petsc_macro.h:174
PetscInt * numeric_petsc_cast(const numeric_index_type *p)
std::mutex _petsc_matrix_mutex
Definition: petsc_matrix.h:353
dof_id_type numeric_index_type
Definition: id_types.h:99
libmesh_assert(ctx)
std::vector< T > & get_values()
Definition: dense_matrix.h:382
Mat _mat
PETSc matrix datatype to store values.
unsigned int n() const

◆ add_matrix() [2/2]

template<typename T >
void libMesh::PetscMatrix< T >::add_matrix ( const DenseMatrix< T > &  dm,
const std::vector< numeric_index_type > &  dof_indices 
)
overridevirtual

Same as add_matrix, but assumes the row and column maps are the same.

Thus the matrix dm must be square.

Implements libMesh::SparseMatrix< T >.

Definition at line 1002 of file petsc_matrix.C.

1004 {
1005  this->add_matrix (dm, dof_indices, dof_indices);
1006 }
virtual void add_matrix(const DenseMatrix< T > &dm, const std::vector< numeric_index_type > &rows, const std::vector< numeric_index_type > &cols) override
Add the full matrix dm to the SparseMatrix.
Definition: petsc_matrix.C:731

◆ add_sparse_matrix()

template<typename T >
void libMesh::PetscMatrix< T >::add_sparse_matrix ( const SparseMatrix< T > &  spm,
const std::map< numeric_index_type, numeric_index_type > &  row_ltog,
const std::map< numeric_index_type, numeric_index_type > &  col_ltog,
const T  scalar 
)
overridevirtual

Add scalar* spm to the rows and cols of this matrix (A): A(rows[i], cols[j]) += scalar * spm(i,j)

Reimplemented from libMesh::SparseMatrix< T >.

Definition at line 1069 of file petsc_matrix.C.

References libMesh::closed(), libMesh::index_range(), libMesh::SparseMatrix< T >::m(), libMesh::SparseMatrix< T >::n(), and libMesh::PS().

1073 {
1074  // size of spm is usually greater than row_ltog and col_ltog in parallel as the indices are owned by the processor
1075  // also, we should allow adding certain parts of spm to _mat
1076  libmesh_assert_greater_equal(spm.m(), row_ltog.size());
1077  libmesh_assert_greater_equal(spm.n(), col_ltog.size());
1078 
1079  // make sure matrix has larger size than spm
1080  libmesh_assert_greater_equal(this->m(), spm.m());
1081  libmesh_assert_greater_equal(this->n(), spm.n());
1082 
1083  if (!this->closed())
1084  this->close();
1085 
1086  auto pscm = cast_ptr<const PetscMatrix<T> *>(&spm);
1087 
1088  PetscInt ncols = 0;
1089 
1090  const PetscInt * lcols;
1091  const PetscScalar * vals;
1092 
1093  std::vector<PetscInt> gcols;
1094  std::vector<PetscScalar> values;
1095 
1096  for (auto ltog : row_ltog)
1097  {
1098  PetscInt grow[] = {static_cast<PetscInt>(ltog.second)}; // global row index
1099 
1100  LibmeshPetscCall(MatGetRow(pscm->_mat, static_cast<PetscInt>(ltog.first), &ncols, &lcols, &vals));
1101 
1102  // get global indices (gcols) from lcols, increment values = vals*scalar
1103  gcols.resize(ncols);
1104  values.resize(ncols);
1105  for (auto i : index_range(gcols))
1106  {
1107  gcols[i] = libmesh_map_find(col_ltog, lcols[i]);
1108  values[i] = PS(scalar) * vals[i];
1109  }
1110 
1111  LibmeshPetscCall(MatSetValues(this->_mat, 1, grow, ncols, gcols.data(), values.data(), ADD_VALUES));
1112  LibmeshPetscCall(MatRestoreRow(pscm->_mat, static_cast<PetscInt>(ltog.first), &ncols, &lcols, &vals));
1113  }
1114  // Note: We are not closing the matrix because it is expensive to do so when adding multiple sparse matrices.
1115  // Remember to manually close the matrix once all changes to the matrix have been made.
1116 }
virtual numeric_index_type n() const override
virtual numeric_index_type m() const override
PetscScalar PS(T val)
Definition: petsc_macro.h:168
virtual numeric_index_type m() const =0
virtual void close() override
Calls the SparseMatrix&#39;s internal assembly routines, ensuring that the values are consistent across p...
Mat _mat
PETSc matrix datatype to store values.
virtual bool closed() const override
auto index_range(const T &sizable)
Helper function that returns an IntRange<std::size_t> representing all the indices of the passed-in v...
Definition: int_range.h:117
virtual numeric_index_type n() const =0

◆ attach_dof_map()

template<typename T >
void libMesh::SparseMatrix< T >::attach_dof_map ( const DofMap dof_map)
inherited

Set a pointer to the DofMap to use.

If a separate sparsity pattern is not being used, use the one from the DofMap.

The lifetime of dof_map must exceed the lifetime of this.

Definition at line 77 of file sparse_matrix.C.

Referenced by libMesh::__libmesh_tao_hessian(), DMlibMeshJacobian(), libMesh::libmesh_petsc_snes_jacobian(), and libMesh::DofMap::update_sparsity_pattern().

78 {
79  _dof_map = &dof_map;
80  if (!_sp)
81  _sp = dof_map.get_sparsity_pattern();
82 }
SparsityPattern::Build const * _sp
The sparsity pattern associated with this object.
const SparsityPattern::Graph & get_sparsity_pattern() const
Rows of sparse matrix indices, indexed by the offset from the first DoF on this processor.
DofMap const * _dof_map
The DofMap object associated with this object.

◆ attach_sparsity_pattern()

template<typename T >
void libMesh::SparseMatrix< T >::attach_sparsity_pattern ( const SparsityPattern::Build sp)
inherited

Set a pointer to a sparsity pattern to use.

Useful in cases where a matrix requires a wider (or for efficiency narrower) pattern than most matrices in the system, or in cases where no system sparsity pattern is being calculated by the DofMap.

The lifetime of sp must exceed the lifetime of this.

Definition at line 87 of file sparse_matrix.C.

Referenced by libMesh::DofMap::update_sparsity_pattern().

88 {
89  _sp = &sp;
90 }
SparsityPattern::Build const * _sp
The sparsity pattern associated with this object.

◆ build()

template<typename T >
std::unique_ptr< SparseMatrix< T > > libMesh::SparseMatrix< T >::build ( const Parallel::Communicator comm,
const SolverPackage  solver_package = libMesh::default_solver_package(),
const MatrixBuildType  matrix_build_type = MatrixBuildType::AUTOMATIC 
)
staticinherited

Builds a SparseMatrix<T> using the linear solver package specified by solver_package.

Definition at line 170 of file sparse_matrix.C.

Referenced by libMesh::CondensedEigenSystem::add_matrices(), libMesh::System::add_matrix(), libMesh::TransientRBConstruction::allocate_data_structures(), libMesh::RBConstruction::allocate_data_structures(), libMesh::CondensedEigenSystem::copy_super_to_sub(), libMesh::StaticCondensation::init(), main(), libMesh::DofMap::process_mesh_constraint_rows(), ConstraintOperatorTest::test1DCoarseningNewNodes(), ConstraintOperatorTest::test1DCoarseningOperator(), ConstraintOperatorTest::testCoreform(), ConnectedComponentsTest::testEdge(), SystemsTest::testProjectMatrix1D(), SystemsTest::testProjectMatrix2D(), and SystemsTest::testProjectMatrix3D().

173 {
174  // Avoid unused parameter warnings when no solver packages are enabled.
176 
177  if (matrix_build_type == MatrixBuildType::DIAGONAL)
178  return std::make_unique<DiagonalMatrix<T>>(comm);
179 
180  // Build the appropriate vector
181  switch (solver_package)
182  {
183 
184 #ifdef LIBMESH_HAVE_LASPACK
185  case LASPACK_SOLVERS:
186  return std::make_unique<LaspackMatrix<T>>(comm);
187 #endif
188 
189 
190 #ifdef LIBMESH_HAVE_PETSC
191  case PETSC_SOLVERS:
192  return std::make_unique<PetscMatrix<T>>(comm);
193 #endif
194 
195 
196 #ifdef LIBMESH_TRILINOS_HAVE_EPETRA
197  case TRILINOS_SOLVERS:
198  return std::make_unique<EpetraMatrix<T>>(comm);
199 #endif
200 
201 
202 #ifdef LIBMESH_HAVE_EIGEN
203  case EIGEN_SOLVERS:
204  return std::make_unique<EigenSparseMatrix<T>>(comm);
205 #endif
206 
207  default:
208  libmesh_error_msg("ERROR: Unrecognized solver package: " << solver_package);
209  }
210 }
const Parallel::Communicator & comm() const
void libmesh_ignore(const Args &...)
virtual SolverPackage solver_package()=0

◆ clear()

template<typename T >
void libMesh::PetscMatrixBase< T >::clear ( )
overridevirtualnoexceptinherited

clear() is called from the destructor, so it should not throw.

Implements libMesh::SparseMatrix< T >.

Reimplemented in libMesh::StaticCondensation, and libMesh::StaticCondensation.

Definition at line 74 of file petsc_matrix_base.C.

Referenced by libMesh::StaticCondensation::clear().

75 {
76  if ((this->initialized()) && (this->_destroy_mat_on_exit))
77  {
78  exceptionless_semiparallel_only();
79 
80  // If we encounter an error here, print a warning but otherwise
81  // keep going since we may be recovering from an exception.
82  PetscErrorCode ierr = MatDestroy (&_mat);
83  if (ierr)
84  libmesh_warning("Warning: MatDestroy returned a non-zero error code which we ignored.");
85 
86  this->_is_initialized = false;
87  }
88 }
virtual bool initialized() const
bool _destroy_mat_on_exit
This boolean value should only be set to false for the constructor which takes a PETSc Mat object...
bool _is_initialized
Flag indicating whether or not the matrix has been initialized.
Mat _mat
PETSc matrix datatype to store values.

◆ clone()

template<typename T >
std::unique_ptr< SparseMatrix< T > > libMesh::PetscMatrix< T >::clone ( ) const
overridevirtual
Returns
A smart pointer to a copy of this matrix.
Note
This must be overridden in the derived classes.

Implements libMesh::SparseMatrix< T >.

Definition at line 454 of file petsc_matrix.C.

References libMesh::closed().

455 {
456  libmesh_error_msg_if(!this->closed(), "Matrix must be closed before it can be cloned!");
457 
458  // Copy the nonzero pattern and numerical values
459  Mat copy;
460  LibmeshPetscCall(MatDuplicate(this->_mat, MAT_COPY_VALUES, &copy));
461 
462  // Call wrapping PetscMatrix constructor, have it take over
463  // ownership.
464  auto ret = std::make_unique<PetscMatrix<T>>(copy, this->comm());
465  ret->set_destroy_mat_on_exit(true);
466 
467  return ret;
468 }
const Parallel::Communicator & comm() const
Mat _mat
PETSc matrix datatype to store values.
virtual bool closed() const override

◆ close()

template<typename T >
void libMesh::PetscMatrixBase< T >::close ( )
overridevirtualinherited

Calls the SparseMatrix's internal assembly routines, ensuring that the values are consistent across processors.

Implements libMesh::SparseMatrix< T >.

Reimplemented in libMesh::StaticCondensation, and libMesh::StaticCondensation.

Definition at line 226 of file petsc_matrix_base.C.

Referenced by libMesh::PetscMatrix< T >::_get_submatrix(), libMesh::PetscMatrix< T >::create_submatrix_nosort(), DMlibMeshJacobian(), libMesh::PetscMatrix< T >::get_transpose(), libMesh::libmesh_petsc_snes_jacobian(), and libMesh::PetscLinearSolver< Number >::solve_common().

227 {
228  semiparallel_only();
229 
230  // BSK - 1/19/2004
231  // strictly this check should be OK, but it seems to
232  // fail on matrix-free matrices. Do they falsely
233  // state they are assembled? Check with the developers...
234  // if (this->closed())
235  // return;
236 
237  MatAssemblyBeginEnd(this->comm(), this->_mat, MAT_FINAL_ASSEMBLY);
238 }
const Parallel::Communicator & comm() const
Mat _mat
PETSc matrix datatype to store values.

◆ closed()

template<typename T >
bool libMesh::PetscMatrixBase< T >::closed ( ) const
overridevirtualinherited
Returns
true if the matrix has been assembled.

Implements libMesh::SparseMatrix< T >.

Reimplemented in libMesh::StaticCondensation, and libMesh::StaticCondensation.

Definition at line 241 of file petsc_matrix_base.C.

Referenced by libMesh::PetscMatrix< T >::add().

242 {
243  libmesh_assert (this->initialized());
244 
245  PetscBool assembled;
246 
247  LibmeshPetscCall(MatAssembled(this->_mat, &assembled));
248 
249  return (assembled == PETSC_TRUE);
250 }
virtual bool initialized() const
libmesh_assert(ctx)
Mat _mat
PETSc matrix datatype to store values.

◆ col_start()

template<typename T >
numeric_index_type libMesh::PetscMatrixBase< T >::col_start ( ) const
overridevirtualinherited
Returns
The index of the first matrix column owned by this processor.

Implements libMesh::SparseMatrix< T >.

Reimplemented in libMesh::StaticCondensation, and libMesh::StaticCondensation.

Definition at line 202 of file petsc_matrix_base.C.

203 {
204  libmesh_assert (this->initialized());
205 
206  PetscInt start=0, stop=0;
207 
208  LibmeshPetscCall(MatGetOwnershipRangeColumn(this->_mat, &start, &stop));
209 
210  return static_cast<numeric_index_type>(start);
211 }
virtual bool initialized() const
dof_id_type numeric_index_type
Definition: id_types.h:99
libmesh_assert(ctx)
void stop(const char *file, int line, const char *date, const char *time)
Mat _mat
PETSc matrix datatype to store values.

◆ col_stop()

template<typename T >
numeric_index_type libMesh::PetscMatrixBase< T >::col_stop ( ) const
overridevirtualinherited
Returns
The index of the last matrix column (+1) owned by this processor.

Implements libMesh::SparseMatrix< T >.

Reimplemented in libMesh::StaticCondensation, and libMesh::StaticCondensation.

Definition at line 214 of file petsc_matrix_base.C.

215 {
216  libmesh_assert (this->initialized());
217 
218  PetscInt start=0, stop=0;
219 
220  LibmeshPetscCall(MatGetOwnershipRangeColumn(this->_mat, &start, &stop));
221 
222  return static_cast<numeric_index_type>(stop);
223 }
virtual bool initialized() const
dof_id_type numeric_index_type
Definition: id_types.h:99
libmesh_assert(ctx)
void stop(const char *file, int line, const char *date, const char *time)
Mat _mat
PETSc matrix datatype to store values.

◆ comm()

const Parallel::Communicator& libMesh::ParallelObject::comm ( ) const
inlineinherited
Returns
A reference to the Parallel::Communicator object used by this mesh.

Definition at line 97 of file parallel_object.h.

References libMesh::ParallelObject::_communicator.

Referenced by libMesh::__libmesh_petsc_diff_solver_jacobian(), libMesh::__libmesh_petsc_diff_solver_monitor(), libMesh::__libmesh_petsc_diff_solver_residual(), libMesh::__libmesh_tao_equality_constraints(), libMesh::__libmesh_tao_equality_constraints_jacobian(), libMesh::__libmesh_tao_gradient(), libMesh::__libmesh_tao_hessian(), libMesh::__libmesh_tao_inequality_constraints(), libMesh::__libmesh_tao_inequality_constraints_jacobian(), libMesh::__libmesh_tao_objective(), libMesh::MeshRefinement::_coarsen_elements(), libMesh::ExactSolution::_compute_error(), libMesh::UniformRefinementEstimator::_estimate_error(), libMesh::Partitioner::_find_global_index_by_pid_map(), libMesh::BoundaryInfo::_find_id_maps(), libMesh::PetscLinearSolver< Number >::_petsc_shell_matrix_get_diagonal(), libMesh::SlepcEigenSolver< libMesh::Number >::_petsc_shell_matrix_get_diagonal(), libMesh::PetscLinearSolver< Number >::_petsc_shell_matrix_mult(), libMesh::SlepcEigenSolver< libMesh::Number >::_petsc_shell_matrix_mult(), libMesh::PetscLinearSolver< Number >::_petsc_shell_matrix_mult_add(), libMesh::MeshRefinement::_refine_elements(), libMesh::MeshRefinement::_smooth_flags(), libMesh::DofMap::add_constraints_to_send_list(), add_cube_convex_hull_to_mesh(), libMesh::PetscDMWrapper::add_dofs_helper(), libMesh::PetscDMWrapper::add_dofs_to_section(), libMesh::TransientRBConstruction::add_IC_to_RB_space(), libMesh::RBEIMEvaluation::add_interpolation_data(), libMesh::CondensedEigenSystem::add_matrices(), libMesh::EigenSystem::add_matrices(), libMesh::System::add_matrix(), libMesh::RBConstruction::add_scaled_matrix_and_vector(), libMesh::System::add_variable(), libMesh::System::add_variables(), libMesh::System::add_vector(), libMesh::MeshTools::Modification::all_tri(), libMesh::LaplaceMeshSmoother::allgather_graph(), libMesh::DofMap::allgather_recursive_constraints(), libMesh::TransientRBConstruction::allocate_data_structures(), libMesh::RBConstruction::allocate_data_structures(), libMesh::TransientRBConstruction::assemble_affine_expansion(), libMesh::AdvectionSystem::assemble_claw_rhs(), libMesh::FEMSystem::assemble_qoi(), libMesh::Nemesis_IO::assert_symmetric_cmaps(), libMesh::MeshCommunication::assign_global_indices(), libMesh::Partitioner::assign_partitioning(), libMesh::MeshTools::Generation::build_extrusion(), libMesh::Partitioner::build_graph(), libMesh::BoundaryInfo::build_node_list_from_side_list(), libMesh::EquationSystems::build_parallel_elemental_solution_vector(), libMesh::EquationSystems::build_parallel_solution_vector(), libMesh::PetscDMWrapper::build_section(), libMesh::PetscDMWrapper::build_sf(), libMesh::MeshBase::cache_elem_data(), libMesh::System::calculate_norm(), libMesh::DofMap::check_dirichlet_bcid_consistency(), libMesh::RBConstruction::compute_Fq_representor_innerprods(), libMesh::RBConstruction::compute_max_error_bound(), libMesh::Nemesis_IO_Helper::compute_num_global_elem_blocks(), libMesh::Nemesis_IO_Helper::compute_num_global_nodesets(), libMesh::Nemesis_IO_Helper::compute_num_global_sidesets(), libMesh::RBConstruction::compute_output_dual_innerprods(), libMesh::RBConstruction::compute_residual_dual_norm_slow(), libMesh::RBSCMConstruction::compute_SCM_bounds_on_training_set(), libMesh::DofMap::computed_sparsity_already(), libMesh::Problem_Interface::computeF(), libMesh::Problem_Interface::computeJacobian(), libMesh::Problem_Interface::computePreconditioner(), libMesh::ContinuationSystem::ContinuationSystem(), libMesh::MeshBase::copy_constraint_rows(), libMesh::ExodusII_IO::copy_elemental_solution(), libMesh::ExodusII_IO::copy_nodal_solution(), libMesh::ExodusII_IO::copy_scalar_solution(), libMesh::CondensedEigenSystem::copy_super_to_sub(), libMesh::MeshTools::correct_node_proc_ids(), libMesh::MeshTools::create_bounding_box(), libMesh::DofMap::create_dof_constraints(), libMesh::MeshTools::create_nodal_bounding_box(), libMesh::MeshRefinement::create_parent_error_vector(), libMesh::MeshTools::create_processor_bounding_box(), libMesh::MeshTools::create_subdomain_bounding_box(), libMesh::PetscMatrix< T >::create_submatrix_nosort(), create_wrapped_function(), libMesh::MeshCommunication::delete_remote_elements(), libMesh::RBEIMEvaluation::distribute_bfs(), DMlibMeshFunction(), DMlibMeshJacobian(), DMlibMeshSetSystem_libMesh(), DMVariableBounds_libMesh(), libMesh::DTKSolutionTransfer::DTKSolutionTransfer(), libMesh::MeshRefinement::eliminate_unrefined_patches(), libMesh::RBEIMConstruction::enrich_eim_approximation_on_interiors(), libMesh::RBEIMConstruction::enrich_eim_approximation_on_nodes(), libMesh::RBEIMConstruction::enrich_eim_approximation_on_sides(), libMesh::TransientRBConstruction::enrich_RB_space(), libMesh::EpetraVector< T >::EpetraVector(), AssembleOptimization::equality_constraints(), libMesh::PatchRecoveryErrorEstimator::estimate_error(), libMesh::WeightedPatchRecoveryErrorEstimator::estimate_error(), libMesh::AdjointRefinementEstimator::estimate_error(), libMesh::ExactErrorEstimator::estimate_error(), libMesh::SmoothnessEstimator::estimate_smoothness(), libMesh::MeshRefinement::flag_elements_by_elem_fraction(), libMesh::MeshRefinement::flag_elements_by_error_fraction(), libMesh::MeshRefinement::flag_elements_by_error_tolerance(), libMesh::MeshRefinement::flag_elements_by_mean_stddev(), libMesh::MeshRefinement::flag_elements_by_nelem_target(), libMesh::RBEIMEvaluation::gather_bfs(), libMesh::DofMap::gather_constraints(), libMesh::MeshfreeInterpolation::gather_remote_data(), libMesh::CondensedEigenSystem::get_eigenpair(), libMesh::RBEIMEvaluation::get_eim_basis_function_node_value(), libMesh::RBEIMEvaluation::get_eim_basis_function_side_value(), libMesh::RBEIMEvaluation::get_eim_basis_function_value(), libMesh::MeshBase::get_info(), libMesh::System::get_info(), libMesh::DofMap::get_info(), libMesh::RBEIMEvaluation::get_interior_basis_functions_as_vecs(), libMesh::ImplicitSystem::get_linear_solver(), libMesh::RBEIMConstruction::get_max_abs_value(), libMesh::RBEIMConstruction::get_node_max_abs_value(), libMesh::RBEIMEvaluation::get_parametrized_function_node_value(), libMesh::RBEIMEvaluation::get_parametrized_function_side_value(), libMesh::RBEIMEvaluation::get_parametrized_function_value(), libMesh::RBEIMConstruction::get_random_point(), AssembleOptimization::inequality_constraints(), AssembleOptimization::inequality_constraints_jacobian(), libMesh::LocationMap< T >::init(), libMesh::TimeSolver::init(), libMesh::StaticCondensation::init(), libMesh::SystemSubsetBySubdomain::init(), libMesh::PetscDMWrapper::init_and_attach_petscdm(), libMesh::AdvectionSystem::init_data(), libMesh::ClawSystem::init_data(), libMesh::PetscDMWrapper::init_petscdm(), libMesh::ExodusII_IO_Helper::initialize(), libMesh::OptimizationSystem::initialize_equality_constraints_storage(), libMesh::OptimizationSystem::initialize_inequality_constraints_storage(), libMesh::RBEIMConstruction::initialize_parametrized_functions_in_training_set(), libMesh::RBEIMConstruction::inner_product(), integrate_function(), libMesh::MeshTools::libmesh_assert_consistent_distributed(), libMesh::MeshTools::libmesh_assert_consistent_distributed_nodes(), libMesh::MeshTools::libmesh_assert_contiguous_dof_ids(), libMesh::MeshTools::libmesh_assert_equal_connectivity(), libMesh::MeshTools::libmesh_assert_equal_points(), libMesh::MeshTools::libmesh_assert_parallel_consistent_new_node_procids(), libMesh::MeshTools::libmesh_assert_parallel_consistent_procids< Elem >(), libMesh::MeshTools::libmesh_assert_parallel_consistent_procids< Node >(), libMesh::MeshTools::libmesh_assert_topology_consistent_procids< Node >(), libMesh::MeshTools::libmesh_assert_valid_boundary_ids(), libMesh::MeshTools::libmesh_assert_valid_constraint_rows(), libMesh::MeshTools::libmesh_assert_valid_dof_ids(), libMesh::MeshTools::libmesh_assert_valid_neighbors(), libMesh::DistributedMesh::libmesh_assert_valid_parallel_flags(), libMesh::DistributedMesh::libmesh_assert_valid_parallel_object_ids(), libMesh::DistributedMesh::libmesh_assert_valid_parallel_p_levels(), libMesh::MeshTools::libmesh_assert_valid_refinement_flags(), libMesh::MeshTools::libmesh_assert_valid_unique_ids(), libMesh::libmesh_petsc_linesearch_shellfunc(), libMesh::libmesh_petsc_preconditioner_apply(), libMesh::libmesh_petsc_recalculate_monitor(), libMesh::libmesh_petsc_snes_fd_residual(), libMesh::libmesh_petsc_snes_jacobian(), libMesh::libmesh_petsc_snes_mffd_interface(), libMesh::libmesh_petsc_snes_mffd_residual(), libMesh::libmesh_petsc_snes_postcheck(), libMesh::libmesh_petsc_snes_precheck(), libMesh::libmesh_petsc_snes_residual(), libMesh::libmesh_petsc_snes_residual_helper(), libMesh::MeshRefinement::limit_level_mismatch_at_edge(), libMesh::MeshRefinement::limit_level_mismatch_at_node(), libMesh::MeshRefinement::limit_overrefined_boundary(), libMesh::MeshRefinement::limit_underrefined_boundary(), libMesh::LinearImplicitSystem::LinearImplicitSystem(), main(), libMesh::MeshRefinement::make_coarsening_compatible(), libMesh::MeshCommunication::make_elems_parallel_consistent(), libMesh::MeshRefinement::make_flags_parallel_consistent(), libMesh::MeshCommunication::make_new_node_proc_ids_parallel_consistent(), libMesh::MeshCommunication::make_new_nodes_parallel_consistent(), libMesh::MeshCommunication::make_node_bcids_parallel_consistent(), libMesh::MeshCommunication::make_node_ids_parallel_consistent(), libMesh::MeshCommunication::make_node_proc_ids_parallel_consistent(), libMesh::MeshCommunication::make_node_unique_ids_parallel_consistent(), libMesh::MeshCommunication::make_nodes_parallel_consistent(), libMesh::MeshCommunication::make_p_levels_parallel_consistent(), libMesh::MeshRefinement::make_refinement_compatible(), libMesh::TransientRBConstruction::mass_matrix_scaled_matvec(), libMesh::FEMSystem::mesh_position_set(), libMesh::TriangulatorInterface::MeshedHole::MeshedHole(), LinearElasticityWithContact::move_mesh(), libMesh::DistributedMesh::n_active_elem(), libMesh::MeshTools::n_active_levels(), libMesh::BoundaryInfo::n_boundary_conds(), libMesh::MeshTools::n_connected_components(), libMesh::DofMap::n_constrained_dofs(), libMesh::MeshBase::n_constraint_rows(), libMesh::DofMap::n_dofs(), libMesh::DofMap::n_dofs_per_processor(), libMesh::BoundaryInfo::n_edge_conds(), libMesh::CondensedEigenSystem::n_global_non_condensed_dofs(), libMesh::MeshTools::n_levels(), MixedOrderTest::n_neighbor_links(), libMesh::BoundaryInfo::n_nodeset_conds(), libMesh::SparsityPattern::Build::n_nonzeros(), libMesh::MeshTools::n_p_levels(), libMesh::BoundaryInfo::n_shellface_conds(), libMesh::RBEIMEvaluation::node_distribute_bfs(), libMesh::RBEIMEvaluation::node_gather_bfs(), libMesh::RBEIMConstruction::node_inner_product(), libMesh::MeshBase::operator==(), libMesh::DistributedMesh::parallel_max_elem_id(), libMesh::DistributedMesh::parallel_max_node_id(), libMesh::ReplicatedMesh::parallel_max_unique_id(), libMesh::DistributedMesh::parallel_max_unique_id(), libMesh::DistributedMesh::parallel_n_elem(), libMesh::DistributedMesh::parallel_n_nodes(), libMesh::SparsityPattern::Build::parallel_sync(), libMesh::BoundaryInfo::parallel_sync_node_ids(), libMesh::BoundaryInfo::parallel_sync_side_ids(), libMesh::MeshTools::paranoid_n_levels(), libMesh::Partitioner::partition(), libMesh::Partitioner::partition_unpartitioned_elements(), libMesh::petsc_auto_fieldsplit(), libMesh::System::point_gradient(), libMesh::System::point_hessian(), libMesh::System::point_value(), libMesh::MeshBase::prepare_for_use(), libMesh::MeshBase::print_constraint_rows(), libMesh::DofMap::print_dof_constraints(), libMesh::DofMap::process_mesh_constraint_rows(), libMesh::Partitioner::processor_pairs_to_interface_nodes(), libMesh::InterMeshProjection::project_system_vectors(), FEMParameters::read(), libMesh::Nemesis_IO::read(), libMesh::XdrIO::read(), libMesh::EquationSystems::read(), libMesh::ExodusII_IO::read_header(), libMesh::CheckpointIO::read_header(), libMesh::XdrIO::read_header(), libMesh::System::read_header(), libMesh::RBEIMEvaluation::read_in_interior_basis_functions(), libMesh::RBEIMEvaluation::read_in_node_basis_functions(), libMesh::RBEIMEvaluation::read_in_side_basis_functions(), libMesh::RBEvaluation::read_in_vectors_from_multiple_files(), libMesh::System::read_legacy_data(), libMesh::TransientRBConstruction::read_riesz_representors_from_files(), libMesh::RBConstruction::read_riesz_representors_from_files(), libMesh::System::read_SCALAR_dofs(), libMesh::XdrIO::read_serialized_bc_names(), libMesh::XdrIO::read_serialized_bcs_helper(), libMesh::System::read_serialized_blocked_dof_objects(), libMesh::XdrIO::read_serialized_connectivity(), libMesh::XdrIO::read_serialized_nodes(), libMesh::XdrIO::read_serialized_nodesets(), libMesh::XdrIO::read_serialized_subdomain_names(), libMesh::System::read_serialized_vector(), libMesh::Nemesis_IO_Helper::read_var_names_impl(), MeshFunctionTest::read_variable_info_from_output_data(), libMesh::MeshBase::recalculate_n_partitions(), libMesh::MeshRefinement::refine_and_coarsen_elements(), libMesh::SimplexRefiner::refine_via_edges(), libMesh::StaticCondensationDofMap::reinit(), libMesh::DistributedMesh::renumber_dof_objects(), libMesh::DistributedMesh::renumber_nodes_and_elements(), LinearElasticityWithContact::residual_and_jacobian(), OverlappingAlgebraicGhostingTest::run_ghosting_test(), OverlappingCouplingGhostingTest::run_sparsity_pattern_test(), scale_mesh_and_plot(), libMesh::DofMap::scatter_constraints(), libMesh::CheckpointIO::select_split_config(), libMesh::GenericProjector< FFunctor, GFunctor, FValue, ProjectionAction >::send_and_insert_dof_values(), libMesh::TransientRBConstruction::set_error_temporal_data(), libMesh::Partitioner::set_interface_node_processor_ids_BFS(), libMesh::Partitioner::set_interface_node_processor_ids_linear(), libMesh::Partitioner::set_interface_node_processor_ids_petscpartitioner(), libMesh::Partitioner::set_node_processor_ids(), libMesh::DofMap::set_nonlocal_dof_objects(), libMesh::Partitioner::set_parent_processor_ids(), libMesh::PetscDMWrapper::set_point_range_in_section(), libMesh::PetscDiffSolver::setup_petsc_data(), libMesh::RBEIMEvaluation::side_distribute_bfs(), libMesh::RBEIMEvaluation::side_gather_bfs(), libMesh::RBEIMConstruction::side_inner_product(), libMesh::Partitioner::single_partition(), libMesh::LaplaceMeshSmoother::smooth(), libMesh::VariationalMeshSmoother::smooth(), libMesh::ClawSystem::solve_conservation_law(), libMesh::split_mesh(), libMesh::RBEIMConstruction::store_eim_solutions_for_training_set(), libMesh::MeshBase::subdomain_ids(), libMesh::BoundaryInfo::sync(), ConstraintOperatorTest::test1DCoarseningNewNodes(), ConstraintOperatorTest::test1DCoarseningOperator(), libMesh::MeshRefinement::test_level_one(), MeshfunctionDFEM::test_mesh_function_dfem(), MeshfunctionDFEM::test_mesh_function_dfem_grad(), MeshFunctionTest::test_p_level(), libMesh::MeshRefinement::test_unflagged(), DofMapTest::testBadElemFECombo(), SystemsTest::testBlockRestrictedVarNDofs(), BoundaryInfoTest::testBoundaryOnChildrenErrors(), VolumeTest::testC0PolygonMethods(), VolumeTest::testC0PolyhedronMethods(), ConstraintOperatorTest::testCoreform(), ConnectedComponentsTest::testEdge(), MeshInputTest::testExodusIGASidesets(), MeshTriangulationTest::testFoundCenters(), PointLocatorTest::testLocator(), BoundaryInfoTest::testMesh(), PointLocatorTest::testPlanar(), MeshTriangulationTest::testPoly2TriRefinementBase(), SystemsTest::testProjectCubeWithMeshFunction(), BoundaryInfoTest::testRenumber(), CheckpointIOTest::testSplitter(), MeshInputTest::testTetgenIO(), MeshTriangulationTest::testTriangulatorInterp(), MeshTriangulationTest::testTriangulatorMeshedHoles(), MeshTriangulationTest::testTriangulatorRoundHole(), MeshSmootherTest::testVariationalSmoother(), libMesh::MeshTools::total_weight(), libMesh::RBConstruction::train_reduced_basis_with_POD(), libMesh::MeshFunctionSolutionTransfer::transfer(), libMesh::MeshfreeSolutionTransfer::transfer(), libMesh::Poly2TriTriangulator::triangulate(), libMesh::TransientRBConstruction::truth_assembly(), libMesh::RBConstruction::truth_assembly(), libMesh::MeshRefinement::uniformly_coarsen(), update_current_local_solution(), libMesh::TransientRBConstruction::update_RB_initial_condition_all_N(), libMesh::TransientRBConstruction::update_RB_system_matrices(), libMesh::RBConstruction::update_RB_system_matrices(), libMesh::TransientRBConstruction::update_residual_terms(), libMesh::RBConstruction::update_residual_terms(), libMesh::MeshTools::volume(), libMesh::STLIO::write(), libMesh::NameBasedIO::write(), libMesh::XdrIO::write(), libMesh::VTKIO::write_nodal_data(), libMesh::RBEIMEvaluation::write_out_interior_basis_functions(), libMesh::RBEIMEvaluation::write_out_node_basis_functions(), libMesh::RBEIMEvaluation::write_out_side_basis_functions(), libMesh::RBEvaluation::write_out_vectors(), libMesh::TransientRBConstruction::write_riesz_representors_to_files(), libMesh::RBConstruction::write_riesz_representors_to_files(), libMesh::System::write_SCALAR_dofs(), libMesh::XdrIO::write_serialized_bcs_helper(), libMesh::System::write_serialized_blocked_dof_objects(), libMesh::XdrIO::write_serialized_connectivity(), libMesh::XdrIO::write_serialized_nodes(), libMesh::XdrIO::write_serialized_nodesets(), libMesh::RBDataSerialization::RBEvaluationSerialization::write_to_file(), libMesh::RBDataSerialization::TransientRBEvaluationSerialization::write_to_file(), libMesh::RBDataSerialization::RBEIMEvaluationSerialization::write_to_file(), and libMesh::RBDataSerialization::RBSCMEvaluationSerialization::write_to_file().

98  { return _communicator; }
const Parallel::Communicator & _communicator

◆ copy_from_hash()

template<typename T >
std::unique_ptr< PetscMatrix< T > > libMesh::PetscMatrix< T >::copy_from_hash ( )

Creates a copy of the current hash table matrix and then performs assembly.

This is very useful in cases where you are not done filling this matrix but want to be able to read the current state of it

Definition at line 1250 of file petsc_matrix.C.

References libMesh::closed(), libMesh::initialized(), and libMesh::libmesh_assert().

Referenced by PetscMatrixTest::testPetscCopyFromHash().

1251 {
1252  Mat xaij;
1253  libmesh_assert(this->initialized());
1254  libmesh_assert(!this->closed());
1255  LibmeshPetscCall(MatDuplicate(this->_mat, MAT_DO_NOT_COPY_VALUES, &xaij));
1256  LibmeshPetscCall(MatCopyHashToXAIJ(this->_mat, xaij));
1257  return std::make_unique<PetscMatrix<T>>(xaij, this->comm(), /*destroy_on_exit=*/true);
1258 }
virtual bool initialized() const
const Parallel::Communicator & comm() const
libmesh_assert(ctx)
Mat _mat
PETSc matrix datatype to store values.
virtual bool closed() const override

◆ create_submatrix()

template<typename T>
virtual void libMesh::SparseMatrix< T >::create_submatrix ( SparseMatrix< T > &  submatrix,
const std::vector< numeric_index_type > &  rows,
const std::vector< numeric_index_type > &  cols 
) const
inlinevirtualinherited

This function creates a matrix called "submatrix" which is defined by the row and column indices given in the "rows" and "cols" entries.

Currently this operation is only defined for the PetscMatrixBase subclasses. Note: The rows and cols vectors need to be sorted; Use the nosort version below if rows and cols vectors are not sorted; The rows and cols only contain indices that are owned by this processor.

Definition at line 520 of file sparse_matrix.h.

Referenced by libMesh::CondensedEigenSystem::copy_super_to_sub(), libMesh::libmesh_petsc_DMCreateInterpolation(), and libMesh::CondensedEigenSystem::solve().

523  {
524  this->_get_submatrix(submatrix,
525  rows,
526  cols,
527  false); // false means DO NOT REUSE submatrix
528  }
virtual void _get_submatrix(SparseMatrix< T > &, const std::vector< numeric_index_type > &, const std::vector< numeric_index_type > &, const bool) const
Protected implementation of the create_submatrix and reinit_submatrix routines.

◆ create_submatrix_nosort()

template<typename T >
void libMesh::PetscMatrix< T >::create_submatrix_nosort ( SparseMatrix< T > &  submatrix,
const std::vector< numeric_index_type > &  rows,
const std::vector< numeric_index_type > &  cols 
) const
overridevirtual

Similar to the create_submatrix function, this function creates a submatrix which is defined by the indices given in the rows and cols vectors.

Note: Both rows and cols can be unsorted; Use the above function for better efficiency if your indices are sorted; rows and cols can contain indices that are owned by other processors.

Reimplemented from libMesh::SparseMatrix< T >.

Definition at line 849 of file petsc_matrix.C.

References libMesh::SparseMatrix< T >::_is_initialized, libMesh::PetscMatrixBase< T >::_mat, libMesh::PetscMatrixBase< T >::close(), libMesh::closed(), libMesh::ParallelObject::comm(), libMesh::MeshTools::Generation::Private::idx(), and libMesh::index_range().

852 {
853  if (!this->closed())
854  {
855  libmesh_deprecated();
856  libmesh_warning("The matrix must be assembled before calling PetscMatrix::create_submatrix_nosort().\n"
857  "Please update your code, as this warning will become an error in a future release.");
858  const_cast<PetscMatrix<T> *>(this)->close();
859  }
860 
861  // Make sure the SparseMatrix passed in is really a PetscMatrix
862  PetscMatrix<T> * petsc_submatrix = cast_ptr<PetscMatrix<T> *>(&submatrix);
863 
864  LibmeshPetscCall(MatZeroEntries(petsc_submatrix->_mat));
865 
866  PetscInt pc_ncols = 0;
867  const PetscInt * pc_cols;
868  const PetscScalar * pc_vals;
869 
870  // // data for creating the submatrix
871  std::vector<PetscInt> sub_cols;
872  std::vector<PetscScalar> sub_vals;
873 
874  for (auto i : index_range(rows))
875  {
876  PetscInt sub_rid[] = {static_cast<PetscInt>(i)};
877  PetscInt rid = static_cast<PetscInt>(rows[i]);
878  // only get value from local rows, and set values to the corresponding columns in the submatrix
879  if (rows[i]>= this->row_start() && rows[i]< this->row_stop())
880  {
881  // get one row of data from the original matrix
882  LibmeshPetscCall(MatGetRow(this->_mat, rid, &pc_ncols, &pc_cols, &pc_vals));
883  // extract data from certain cols, save the indices and entries sub_cols and sub_vals
884  for (auto j : index_range(cols))
885  {
886  for (unsigned int idx = 0; idx< static_cast<unsigned int>(pc_ncols); idx++)
887  {
888  if (pc_cols[idx] == static_cast<PetscInt>(cols[j]))
889  {
890  sub_cols.push_back(static_cast<PetscInt>(j));
891  sub_vals.push_back(pc_vals[idx]);
892  }
893  }
894  }
895  // set values
896  LibmeshPetscCall(MatSetValues(petsc_submatrix->_mat,
897  1,
898  sub_rid,
899  static_cast<PetscInt>(sub_vals.size()),
900  sub_cols.data(),
901  sub_vals.data(),
902  INSERT_VALUES));
903  LibmeshPetscCall(MatRestoreRow(this->_mat, rid, &pc_ncols, &pc_cols, &pc_vals));
904  // clear data for this row
905  sub_cols.clear();
906  sub_vals.clear();
907  }
908  }
909  MatAssemblyBeginEnd(petsc_submatrix->comm(), petsc_submatrix->_mat, MAT_FINAL_ASSEMBLY);
910  // Specify that the new submatrix is initialized and close it.
911  petsc_submatrix->_is_initialized = true;
912  petsc_submatrix->close();
913 }
virtual numeric_index_type row_stop() const override
const Parallel::Communicator & comm() const
bool _is_initialized
Flag indicating whether or not the matrix has been initialized.
virtual void close() override
Calls the SparseMatrix&#39;s internal assembly routines, ensuring that the values are consistent across p...
Mat _mat
PETSc matrix datatype to store values.
virtual bool closed() const override
virtual numeric_index_type row_start() const override
This class provides a nice interface to the PETSc C-based AIJ data structures for parallel...
Definition: petsc_matrix.h:61
auto index_range(const T &sizable)
Helper function that returns an IntRange<std::size_t> representing all the indices of the passed-in v...
Definition: int_range.h:117
unsigned int idx(const ElemType type, const unsigned int nx, const unsigned int i, const unsigned int j)
A useful inline function which replaces the macros used previously.

◆ disable_print_counter_info()

void libMesh::ReferenceCounter::disable_print_counter_info ( )
staticinherited

Definition at line 100 of file reference_counter.C.

References libMesh::ReferenceCounter::_enable_print_counter.

101 {
102  _enable_print_counter = false;
103  return;
104 }
static bool _enable_print_counter
Flag to control whether reference count information is printed when print_info is called...

◆ enable_print_counter_info()

void libMesh::ReferenceCounter::enable_print_counter_info ( )
staticinherited

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

Definition at line 94 of file reference_counter.C.

References libMesh::ReferenceCounter::_enable_print_counter.

95 {
96  _enable_print_counter = true;
97  return;
98 }
static bool _enable_print_counter
Flag to control whether reference count information is printed when print_info is called...

◆ finish_initialization()

template<typename T >
void libMesh::PetscMatrix< T >::finish_initialization ( )
protected

Finish up the initialization process.

This method does a few things which include

  • Setting the option to make new nonzeroes an error (otherwise users will just have a silent (often huge) performance penalty
  • Marking the matrix as initialized

Definition at line 329 of file petsc_matrix.C.

References libMesh::libMeshPrivateData::_is_initialized.

Referenced by PetscMatrixTest::testPetscCopyFromHash().

330 {
331  // Make it an error for PETSc to allocate new nonzero entries during assembly. For old PETSc
332  // versions this option must be set after preallocation for MPIAIJ matrices
333  LibmeshPetscCall(MatSetOption(this->_mat, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_TRUE));
334  this->_is_initialized = true;
335 }
bool _is_initialized
Flag indicating whether or not the matrix has been initialized.
Mat _mat
PETSc matrix datatype to store values.

◆ flush()

template<typename T >
void libMesh::PetscMatrix< T >::flush ( )
overridevirtual

For PETSc matrix , this function is similar to close but without shrinking memory.

This is useful when we want to switch between ADD_VALUES and INSERT_VALUES. close should be called before using the matrix.

Reimplemented from libMesh::SparseMatrix< T >.

Definition at line 958 of file petsc_matrix.C.

959 {
960  semiparallel_only();
961 
962  MatAssemblyBeginEnd(this->comm(), this->_mat, MAT_FLUSH_ASSEMBLY);
963 }
const Parallel::Communicator & comm() const
Mat _mat
PETSc matrix datatype to store values.

◆ frobenius_norm()

template<typename T >
Real libMesh::PetscMatrix< T >::frobenius_norm ( ) const
virtual

Definition at line 497 of file petsc_matrix.C.

498 {
499  return PetscMatrix<T>::norm<NORM_FROBENIUS>();
500 }
This class provides a nice interface to the PETSc C-based AIJ data structures for parallel...
Definition: petsc_matrix.h:61

◆ get_context()

template<typename T >
PetscMatrixBase< T > * libMesh::PetscMatrixBase< T >::get_context ( Mat  mat,
const TIMPI::Communicator comm 
)
staticinherited
Returns
The context for mat if it exists, else a nullptr

Definition at line 116 of file petsc_matrix_base.C.

Referenced by DMlibMeshJacobian(), form_matrixA(), and libMesh::libmesh_petsc_snes_jacobian().

117 {
118  void * ctx;
119  PetscContainer container;
120  LibmeshPetscCall2(comm, PetscObjectQuery((PetscObject)mat, "PetscMatrixCtx", (PetscObject *)&container));
121  if (!container)
122  return nullptr;
123 
124  LibmeshPetscCall2(comm, PetscContainerGetPointer(container, &ctx));
126  return static_cast<PetscMatrixBase<T> *>(ctx);
127 }
const Parallel::Communicator & comm() const
libmesh_assert(ctx)
void * ctx

◆ get_diagonal()

template<typename T >
void libMesh::PetscMatrix< T >::get_diagonal ( NumericVector< T > &  dest) const
overridevirtual

Copies the diagonal part of the matrix into dest.

Implements libMesh::SparseMatrix< T >.

Definition at line 917 of file petsc_matrix.C.

References libMesh::PetscVector< T >::vec().

918 {
919  // Make sure the NumericVector passed in is really a PetscVector
920  PetscVector<T> & petsc_dest = cast_ref<PetscVector<T> &>(dest);
921 
922  // Needs a const_cast since PETSc does not work with const.
923  LibmeshPetscCall(MatGetDiagonal(const_cast<PetscMatrix<T> *>(this)->mat(),petsc_dest.vec()));
924 }
This class provides a nice interface to PETSc&#39;s Vec object.
Definition: petsc_vector.h:73
This class provides a nice interface to the PETSc C-based AIJ data structures for parallel...
Definition: petsc_matrix.h:61

◆ get_info()

std::string libMesh::ReferenceCounter::get_info ( )
staticinherited

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().

48 {
49 #if defined(LIBMESH_ENABLE_REFERENCE_COUNTING) && defined(DEBUG)
50 
51  std::ostringstream oss;
52 
53  oss << '\n'
54  << " ---------------------------------------------------------------------------- \n"
55  << "| Reference count information |\n"
56  << " ---------------------------------------------------------------------------- \n";
57 
58  for (const auto & [name, cd] : _counts)
59  oss << "| " << name << " reference count information:\n"
60  << "| Creations: " << cd.first << '\n'
61  << "| Destructions: " << cd.second << '\n';
62 
63  oss << " ---------------------------------------------------------------------------- \n";
64 
65  return oss.str();
66 
67 #else
68 
69  return "";
70 
71 #endif
72 }
std::string name(const ElemQuality q)
This function returns a string containing some name for q.
Definition: elem_quality.C:42
static Counts _counts
Actually holds the data.

◆ get_row()

template<typename T >
void libMesh::PetscMatrix< T >::get_row ( numeric_index_type  i,
std::vector< numeric_index_type > &  indices,
std::vector< T > &  values 
) const
overridevirtual

Get a row from the matrix.

Parameters
iThe matrix row to get
indicesA container that will be filled with the column indices corresponding to (possibly) non-zero values
valuesA container holding the column values

Implements libMesh::SparseMatrix< T >.

Definition at line 1144 of file petsc_matrix.C.

References libMesh::closed(), libMesh::index_range(), libMesh::initialized(), and libMesh::libmesh_assert().

1147 {
1148  libmesh_assert (this->initialized());
1149 
1150  const PetscScalar * petsc_row;
1151  const PetscInt * petsc_cols;
1152 
1153  PetscInt
1154  ncols=0,
1155  i_val = static_cast<PetscInt>(i_in);
1156 
1157  // the matrix needs to be closed for this to work
1158  // this->close();
1159  // but closing it is a semiparallel operation; we want operator()
1160  // to run on one processor.
1161  libmesh_assert(this->closed());
1162 
1163  // PETSc makes no effort at being thread safe. Helgrind complains about
1164  // possible data races even just in PetscFunctionBegin (due to things
1165  // like stack counter incrementing). Perhaps we could ignore
1166  // this, but there are legitimate data races for Mat data members like
1167  // mat->getrowactive between MatGetRow and MatRestoreRow. Moreover,
1168  // there could be a write into mat->rowvalues during MatGetRow from
1169  // one thread while we are attempting to read from mat->rowvalues
1170  // (through petsc_cols) during data copy in another thread. So
1171  // the safe thing to do is to lock the whole method
1172 
1173  std::lock_guard<std::mutex> lock(_petsc_matrix_mutex);
1174 
1175  LibmeshPetscCall(MatGetRow(this->_mat, i_val, &ncols, &petsc_cols, &petsc_row));
1176 
1177  // Copy the data
1178  indices.resize(static_cast<std::size_t>(ncols));
1179  values.resize(static_cast<std::size_t>(ncols));
1180 
1181  for (auto i : index_range(indices))
1182  {
1183  indices[i] = static_cast<numeric_index_type>(petsc_cols[i]);
1184  values[i] = static_cast<T>(petsc_row[i]);
1185  }
1186 
1187  LibmeshPetscCall(MatRestoreRow(this->_mat, i_val,
1188  &ncols, &petsc_cols, &petsc_row));
1189 }
virtual bool initialized() const
std::mutex _petsc_matrix_mutex
Definition: petsc_matrix.h:353
dof_id_type numeric_index_type
Definition: id_types.h:99
libmesh_assert(ctx)
Mat _mat
PETSc matrix datatype to store values.
virtual bool closed() const override
auto index_range(const T &sizable)
Helper function that returns an IntRange<std::size_t> representing all the indices of the passed-in v...
Definition: int_range.h:117

◆ get_transpose()

template<typename T >
void libMesh::PetscMatrix< T >::get_transpose ( SparseMatrix< T > &  dest) const
overridevirtual

Copies the transpose of the matrix into dest, which may be *this.

Implements libMesh::SparseMatrix< T >.

Definition at line 929 of file petsc_matrix.C.

References libMesh::SparseMatrix< T >::_is_initialized, libMesh::PetscMatrixBase< T >::_mat, libMesh::SparseMatrix< T >::clear(), and libMesh::PetscMatrixBase< T >::close().

930 {
931  // Make sure the SparseMatrix passed in is really a PetscMatrix
932  PetscMatrix<T> & petsc_dest = cast_ref<PetscMatrix<T> &>(dest);
933 
934  // If we aren't reusing the matrix then need to clear dest,
935  // otherwise we get a memory leak
936  if (&petsc_dest != this)
937  dest.clear();
938 
939  if (&petsc_dest == this)
940  // The MAT_REUSE_MATRIX flag was replaced by MAT_INPLACE_MATRIX
941  // in PETSc 3.7.0
942 #if PETSC_VERSION_LESS_THAN(3,7,0)
943  LibmeshPetscCall(MatTranspose(this->_mat,MAT_REUSE_MATRIX, &petsc_dest._mat));
944 #else
945  LibmeshPetscCall(MatTranspose(this->_mat, MAT_INPLACE_MATRIX, &petsc_dest._mat));
946 #endif
947  else
948  LibmeshPetscCall(MatTranspose(this->_mat,MAT_INITIAL_MATRIX, &petsc_dest._mat));
949 
950  // Specify that the transposed matrix is initialized and close it.
951  petsc_dest._is_initialized = true;
952  petsc_dest.close();
953 }
virtual void clear()=0
Restores the SparseMatrix<T> to a pristine state.
bool _is_initialized
Flag indicating whether or not the matrix has been initialized.
virtual void close() override
Calls the SparseMatrix&#39;s internal assembly routines, ensuring that the values are consistent across p...
Mat _mat
PETSc matrix datatype to store values.
This class provides a nice interface to the PETSc C-based AIJ data structures for parallel...
Definition: petsc_matrix.h:61

◆ increment_constructor_count()

void libMesh::ReferenceCounter::increment_constructor_count ( const std::string &  name)
inlineprotectednoexceptinherited

Increments the construction counter.

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

Definition at line 183 of file reference_counter.h.

References libMesh::err, libMesh::BasicOStreamProxy< charT, traits >::get(), libMesh::Quality::name(), and libMesh::Threads::spin_mtx.

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

184 {
185  libmesh_try
186  {
187  Threads::spin_mutex::scoped_lock lock(Threads::spin_mtx);
188  std::pair<unsigned int, unsigned int> & p = _counts[name];
189  p.first++;
190  }
191  libmesh_catch (...)
192  {
193  auto stream = libMesh::err.get();
194  stream->exceptions(stream->goodbit); // stream must not throw
195  libMesh::err << "Encountered unrecoverable error while calling "
196  << "ReferenceCounter::increment_constructor_count() "
197  << "for a(n) " << name << " object." << std::endl;
198  std::terminate();
199  }
200 }
std::string name(const ElemQuality q)
This function returns a string containing some name for q.
Definition: elem_quality.C:42
OStreamProxy err
static Counts _counts
Actually holds the data.
streamT * get()
Rather than implement every ostream/ios/ios_base function, we&#39;ll be lazy and make esoteric uses go th...
spin_mutex spin_mtx
A convenient spin mutex object which can be used for obtaining locks.
Definition: threads.C:30

◆ increment_destructor_count()

void libMesh::ReferenceCounter::increment_destructor_count ( const std::string &  name)
inlineprotectednoexceptinherited

Increments the destruction counter.

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

Definition at line 207 of file reference_counter.h.

References libMesh::err, libMesh::BasicOStreamProxy< charT, traits >::get(), libMesh::Quality::name(), and libMesh::Threads::spin_mtx.

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

208 {
209  libmesh_try
210  {
211  Threads::spin_mutex::scoped_lock lock(Threads::spin_mtx);
212  std::pair<unsigned int, unsigned int> & p = _counts[name];
213  p.second++;
214  }
215  libmesh_catch (...)
216  {
217  auto stream = libMesh::err.get();
218  stream->exceptions(stream->goodbit); // stream must not throw
219  libMesh::err << "Encountered unrecoverable error while calling "
220  << "ReferenceCounter::increment_destructor_count() "
221  << "for a(n) " << name << " object." << std::endl;
222  std::terminate();
223  }
224 }
std::string name(const ElemQuality q)
This function returns a string containing some name for q.
Definition: elem_quality.C:42
OStreamProxy err
static Counts _counts
Actually holds the data.
streamT * get()
Rather than implement every ostream/ios/ios_base function, we&#39;ll be lazy and make esoteric uses go th...
spin_mutex spin_mtx
A convenient spin mutex object which can be used for obtaining locks.
Definition: threads.C:30

◆ init() [1/3]

template<typename T >
void libMesh::PetscMatrix< T >::init ( const numeric_index_type  m,
const numeric_index_type  n,
const numeric_index_type  m_l,
const numeric_index_type  n_l,
const numeric_index_type  n_nz = 30,
const numeric_index_type  n_oz = 10,
const numeric_index_type  blocksize = 1 
)
overridevirtual

Initialize a PETSc matrix.

Parameters
mThe global number of rows.
nThe global number of columns.
m_lThe local number of rows.
n_lThe local number of columns.
n_nzThe number of nonzeros in each row of the DIAGONAL portion of the local submatrix.
n_ozThe number of nonzeros in each row of the OFF-DIAGONAL portion of the local submatrix.
blocksizeOptional value indicating dense coupled blocks for systems with multiple variables all of the same type.

Implements libMesh::SparseMatrix< T >.

Definition at line 214 of file petsc_matrix.C.

References libMesh::AIJ, finish_initialization(), and libMesh::HYPRE.

Referenced by libMesh::PetscMatrix< T >::PetscMatrix().

221 {
222  this->init_without_preallocation(m_in, n_in, m_l, n_l, blocksize_in);
223 
224  PetscInt n_nz = static_cast<PetscInt>(nnz);
225  PetscInt n_oz = static_cast<PetscInt>(noz);
226 
227 #ifdef LIBMESH_ENABLE_BLOCKED_STORAGE
228  if (blocksize > 1)
229  {
230  LibmeshPetscCall(MatSeqBAIJSetPreallocation(this->_mat, blocksize, n_nz/blocksize, NULL));
231  LibmeshPetscCall(MatMPIBAIJSetPreallocation(this->_mat, blocksize,
232  n_nz/blocksize, NULL,
233  n_oz/blocksize, NULL));
234  }
235  else
236 #endif
237  {
238  switch (this->_mat_type) {
239  case AIJ:
240  LibmeshPetscCall(MatSeqAIJSetPreallocation(this->_mat, n_nz, NULL));
241  LibmeshPetscCall(MatMPIAIJSetPreallocation(this->_mat, n_nz, NULL, n_oz, NULL));
242  break;
243 
244  case HYPRE:
245 #if !PETSC_VERSION_LESS_THAN(3,9,4) && LIBMESH_HAVE_PETSC_HYPRE
246  LibmeshPetscCall(MatHYPRESetPreallocation(this->_mat, n_nz, NULL, n_oz, NULL));
247 #else
248  libmesh_error_msg("PETSc 3.9.4 or higher with hypre is required for MatHypre");
249 #endif
250  break;
251 
252  default: libmesh_error_msg("Unsupported petsc matrix type");
253  }
254  }
255 
256  this->finish_initialization();
257 }
void init_without_preallocation(numeric_index_type m, numeric_index_type n, numeric_index_type m_l, numeric_index_type n_l, numeric_index_type blocksize)
Perform matrix initialization steps sans preallocation.
Definition: petsc_matrix.C:135
Mat _mat
PETSc matrix datatype to store values.
PetscMatrixType _mat_type
Definition: petsc_matrix.h:349
void finish_initialization()
Finish up the initialization process.
Definition: petsc_matrix.C:329

◆ init() [2/3]

template<typename T >
void libMesh::PetscMatrix< T >::init ( const numeric_index_type  m,
const numeric_index_type  n,
const numeric_index_type  m_l,
const numeric_index_type  n_l,
const std::vector< numeric_index_type > &  n_nz,
const std::vector< numeric_index_type > &  n_oz,
const numeric_index_type  blocksize = 1 
)

Initialize a PETSc matrix.

Parameters
mThe global number of rows.
nThe global number of columns.
m_lThe local number of rows.
n_lThe local number of columns.
n_nzarray containing the number of nonzeros in each row of the DIAGONAL portion of the local submatrix.
n_ozArray containing the number of nonzeros in each row of the OFF-DIAGONAL portion of the local submatrix.
blocksizeOptional value indicating dense coupled blocks for systems with multiple variables all of the same type.

Definition at line 338 of file petsc_matrix.C.

References finish_initialization().

345 {
346  this->init_without_preallocation(m_in, n_in, m_l, n_l, blocksize_in);
347  this->preallocate(m_l, n_nz, n_oz, blocksize_in);
348 
349  this->finish_initialization();
350 }
void init_without_preallocation(numeric_index_type m, numeric_index_type n, numeric_index_type m_l, numeric_index_type n_l, numeric_index_type blocksize)
Perform matrix initialization steps sans preallocation.
Definition: petsc_matrix.C:135
void preallocate(numeric_index_type m_l, const std::vector< numeric_index_type > &n_nz, const std::vector< numeric_index_type > &n_oz, numeric_index_type blocksize)
Definition: petsc_matrix.C:260
void finish_initialization()
Finish up the initialization process.
Definition: petsc_matrix.C:329

◆ init() [3/3]

template<typename T>
virtual void libMesh::PetscMatrix< T >::init ( ParallelType  type = PARALLEL)
overridevirtual

Initialize this matrix using the sparsity structure computed by dof_map.

Parameters
typeThe serial/parallel/ghosted type of the matrix

Implements libMesh::SparseMatrix< T >.

◆ init_without_preallocation()

template<typename T >
void libMesh::PetscMatrix< T >::init_without_preallocation ( numeric_index_type  m,
numeric_index_type  n,
numeric_index_type  m_l,
numeric_index_type  n_l,
numeric_index_type  blocksize 
)
protected

Perform matrix initialization steps sans preallocation.

Parameters
mThe global number of rows
nThe global number of columns
m_lThe local number of rows
n_lThe local number of columns
blocksizeThe matrix block size

Definition at line 135 of file petsc_matrix.C.

References libMesh::AIJ, libMesh::HYPRE, libMesh::initialized(), and libMesh::libmesh_ignore().

Referenced by PetscMatrixTest::testPetscCopyFromHash().

140 {
141  // So compilers don't warn when !LIBMESH_ENABLE_BLOCKED_STORAGE
142  libmesh_ignore(blocksize_in);
143 
144  // Clear initialized matrices
145  if (this->initialized())
146  this->clear();
147 
148  PetscInt m_global = static_cast<PetscInt>(m_in);
149  PetscInt n_global = static_cast<PetscInt>(n_in);
150  PetscInt m_local = static_cast<PetscInt>(m_l);
151  PetscInt n_local = static_cast<PetscInt>(n_l);
152 
153  LibmeshPetscCall(MatCreate(this->comm().get(), &this->_mat));
154  LibmeshPetscCall(MatSetSizes(this->_mat, m_local, n_local, m_global, n_global));
155  PetscInt blocksize = static_cast<PetscInt>(blocksize_in);
156  LibmeshPetscCall(MatSetBlockSize(this->_mat,blocksize));
157  LibmeshPetscCall(MatSetOptionsPrefix(this->_mat, ""));
158 
159 #ifdef LIBMESH_ENABLE_BLOCKED_STORAGE
160  if (blocksize > 1)
161  {
162  // specified blocksize, bs>1.
163  // double check sizes.
164  libmesh_assert_equal_to (m_local % blocksize, 0);
165  libmesh_assert_equal_to (n_local % blocksize, 0);
166  libmesh_assert_equal_to (m_global % blocksize, 0);
167  libmesh_assert_equal_to (n_global % blocksize, 0);
168  libmesh_assert_equal_to (n_nz % blocksize, 0);
169  libmesh_assert_equal_to (n_oz % blocksize, 0);
170 
171  LibmeshPetscCall(MatSetType(this->_mat, MATBAIJ)); // Automatically chooses seqbaij or mpibaij
172 
173  // MatSetFromOptions needs to happen before Preallocation routines
174  // since MatSetFromOptions can change matrix type and remove incompatible
175  // preallocation
176  LibmeshPetscCall(MatSetFromOptions(this->_mat));
177  }
178  else
179 #endif
180  {
181  switch (this->_mat_type) {
182  case AIJ:
183  LibmeshPetscCall(MatSetType(this->_mat, MATAIJ)); // Automatically chooses seqaij or mpiaij
184 
185  // MatSetFromOptions needs to happen before Preallocation routines
186  // since MatSetFromOptions can change matrix type and remove incompatible
187  // preallocation
188  LibmeshPetscCall(MatSetFromOptions(this->_mat));
189  break;
190 
191  case HYPRE:
192 #if !PETSC_VERSION_LESS_THAN(3,9,4) && LIBMESH_HAVE_PETSC_HYPRE
193  LibmeshPetscCall(MatSetType(this->_mat, MATHYPRE));
194 
195  // MatSetFromOptions needs to happen before Preallocation routines
196  // since MatSetFromOptions can change matrix type and remove incompatible
197  // preallocation
198  LibmeshPetscCall(MatSetFromOptions(this->_mat));
199 #else
200  libmesh_error_msg("PETSc 3.9.4 or higher with hypre is required for MatHypre");
201 #endif
202  break;
203 
204  default: libmesh_error_msg("Unsupported petsc matrix type");
205  }
206  }
207 
208  this->set_context ();
209 }
virtual bool initialized() const
virtual void clear() noexcept override
clear() is called from the destructor, so it should not throw.
const Parallel::Communicator & comm() const
void set_context()
Set the context (ourself) for _mat.
void libmesh_ignore(const Args &...)
Mat _mat
PETSc matrix datatype to store values.
PetscMatrixType _mat_type
Definition: petsc_matrix.h:349

◆ initialized()

template<typename T>
virtual bool libMesh::SparseMatrix< T >::initialized ( ) const
inlinevirtualinherited
Returns
true if the matrix has been initialized, false otherwise.

Reimplemented in libMesh::StaticCondensation.

Definition at line 133 of file sparse_matrix.h.

Referenced by libMesh::PetscMatrix< T >::_get_submatrix(), libMesh::ImplicitSystem::assemble(), libMesh::System::init_matrices(), and libMesh::StaticCondensation::initialized().

133 { return _is_initialized; }
bool _is_initialized
Flag indicating whether or not the matrix has been initialized.

◆ l1_norm()

template<typename T >
Real libMesh::PetscMatrix< T >::l1_norm ( ) const
overridevirtual
Returns
The \( \ell_1 \)-norm of the matrix, that is the max column sum: \( |M|_1 = \max_{j} \sum_{i} |M_{ij}| \)

This is the natural matrix norm that is compatible with the \( \ell_1 \)-norm for vectors, i.e. \( |Mv|_1 \leq |M|_1 |v|_1 \). (cf. Haemmerlin-Hoffmann : Numerische Mathematik)

Implements libMesh::SparseMatrix< T >.

Definition at line 492 of file petsc_matrix.C.

493 {
494  return PetscMatrix<T>::norm<NORM_1>();
495 }
This class provides a nice interface to the PETSc C-based AIJ data structures for parallel...
Definition: petsc_matrix.h:61

◆ l1_norm_diff()

template<typename T>
Real libMesh::SparseMatrix< T >::l1_norm_diff ( const SparseMatrix< T > &  other_mat) const
inherited
Returns
The l1_norm() of the difference of this and other_mat

Definition at line 1124 of file sparse_matrix.C.

1125 {
1126  auto diff_mat = this->clone();
1127  diff_mat->add(-1.0, other_mat);
1128  return diff_mat->l1_norm();
1129 }
virtual std::unique_ptr< SparseMatrix< T > > clone() const =0

◆ linfty_norm()

template<typename T >
Real libMesh::PetscMatrix< T >::linfty_norm ( ) const
overridevirtual
Returns
The \( \ell_{\infty} \)-norm of the matrix, that is the max row sum:

\( |M|_{\infty} = \max_{i} \sum_{j} |M_{ij}| \)

This is the natural matrix norm that is compatible to the \( \ell_{\infty} \)-norm of vectors, i.e. \( |Mv|_{\infty} \leq |M|_{\infty} |v|_{\infty} \). (cf. Haemmerlin-Hoffmann : Numerische Mathematik)

Implements libMesh::SparseMatrix< T >.

Definition at line 502 of file petsc_matrix.C.

503 {
504  return PetscMatrix<T>::norm<NORM_INFINITY>();
505 }
This class provides a nice interface to the PETSc C-based AIJ data structures for parallel...
Definition: petsc_matrix.h:61

◆ local_m()

template<typename T >
numeric_index_type libMesh::PetscMatrixBase< T >::local_m ( ) const
finalvirtualinherited

Get the number of rows owned by this process.

Reimplemented from libMesh::SparseMatrix< T >.

Definition at line 142 of file petsc_matrix_base.C.

143 {
144  libmesh_assert (this->initialized());
145 
146  PetscInt m = 0;
147 
148  LibmeshPetscCall(MatGetLocalSize (this->_mat, &m, NULL));
149 
150  return static_cast<numeric_index_type>(m);
151 }
virtual bool initialized() const
virtual numeric_index_type m() const override
dof_id_type numeric_index_type
Definition: id_types.h:99
libmesh_assert(ctx)
Mat _mat
PETSc matrix datatype to store values.

◆ local_n()

template<typename T >
numeric_index_type libMesh::PetscMatrixBase< T >::local_n ( ) const
finalvirtualinherited

Get the number of columns owned by this process.

Reimplemented from libMesh::SparseMatrix< T >.

Definition at line 166 of file petsc_matrix_base.C.

167 {
168  libmesh_assert (this->initialized());
169 
170  PetscInt n = 0;
171 
172  LibmeshPetscCall(MatGetLocalSize (this->_mat, NULL, &n));
173 
174  return static_cast<numeric_index_type>(n);
175 }
virtual numeric_index_type n() const override
virtual bool initialized() const
dof_id_type numeric_index_type
Definition: id_types.h:99
libmesh_assert(ctx)
Mat _mat
PETSc matrix datatype to store values.

◆ m()

template<typename T >
numeric_index_type libMesh::PetscMatrixBase< T >::m ( ) const
overridevirtualinherited
Returns
The row-dimension of the matrix.

Implements libMesh::SparseMatrix< T >.

Reimplemented in libMesh::StaticCondensation, and libMesh::StaticCondensation.

Definition at line 130 of file petsc_matrix_base.C.

131 {
132  libmesh_assert (this->initialized());
133 
134  PetscInt petsc_m=0, petsc_n=0;
135 
136  LibmeshPetscCall(MatGetSize (this->_mat, &petsc_m, &petsc_n));
137 
138  return static_cast<numeric_index_type>(petsc_m);
139 }
virtual bool initialized() const
dof_id_type numeric_index_type
Definition: id_types.h:99
libmesh_assert(ctx)
Mat _mat
PETSc matrix datatype to store values.

◆ mat() [1/2]

template<typename T>
Mat libMesh::PetscMatrixBase< T >::mat ( )
inlineinherited
Returns
The raw PETSc matrix pointer.
Note
This is generally not required in user-level code.
Don't do anything crazy like calling MatDestroy() on it, or very bad things will likely happen!

Definition at line 120 of file petsc_matrix_base.h.

Referenced by libMesh::StaticCondensation::add_matrix(), libMesh::PetscLinearSolver< Number >::init(), libMesh::libmesh_petsc_DMCreateInterpolation(), libMesh::libmesh_petsc_DMCreateRestriction(), libMesh::PetscDiffSolver::solve(), libMesh::TaoOptimizationSolver< T >::solve(), libMesh::PetscNonlinearSolver< Number >::solve(), and libMesh::PetscLinearSolver< Number >::solve_common().

120 { libmesh_assert (_mat); return _mat; }
libmesh_assert(ctx)
Mat _mat
PETSc matrix datatype to store values.

◆ mat() [2/2]

template<typename T>
Mat libMesh::PetscMatrixBase< T >::mat ( ) const
inlineinherited

Definition at line 121 of file petsc_matrix_base.h.

121 { libmesh_assert(_mat); return _mat; }
libmesh_assert(ctx)
Mat _mat
PETSc matrix datatype to store values.

◆ matrix_matrix_mult()

template<typename T >
void libMesh::PetscMatrix< T >::matrix_matrix_mult ( SparseMatrix< T > &  X,
SparseMatrix< T > &  Y,
bool  reuse = false 
)
overridevirtual

Compute Y = A*X for matrix X.

Set reuse = true if this->_mat and X have the same nonzero pattern as before, and Y is obtained from a previous call to this function with reuse = false

Reimplemented from libMesh::SparseMatrix< T >.

Definition at line 1039 of file petsc_matrix.C.

References libMesh::initialized(), libMesh::libmesh_assert(), and libMesh::SparseMatrix< T >::m().

1040 {
1041  libmesh_assert (this->initialized());
1042 
1043  // sanity check
1044  // we do not check the Y_out size here as we will initialize & close it at the end
1045  libmesh_assert_equal_to (this->n(), X_in.m());
1046 
1047  const PetscMatrix<T> * X = cast_ptr<const PetscMatrix<T> *> (&X_in);
1048  PetscMatrix<T> * Y = cast_ptr<PetscMatrix<T> *> (&Y_out);
1049 
1050  // the matrix from which we copy the values has to be assembled/closed
1051  libmesh_assert(X->closed());
1052 
1053  semiparallel_only();
1054 
1055  if (reuse)
1056  LibmeshPetscCall(MatMatMult(this->_mat, X->_mat, MAT_REUSE_MATRIX, PETSC_DEFAULT, &Y->_mat));
1057  else
1058  {
1059  Y->clear();
1060  LibmeshPetscCall(MatMatMult(this->_mat, X->_mat, MAT_INITIAL_MATRIX, PETSC_DEFAULT, &Y->_mat));
1061  }
1062  // Specify that the new matrix is initialized
1063  // We do not close it here as `MatMatMult` ensures Y being closed
1064  Y->_is_initialized = true;
1065 }
virtual numeric_index_type n() const override
virtual bool initialized() const
libmesh_assert(ctx)
Mat _mat
PETSc matrix datatype to store values.
This class provides a nice interface to the PETSc C-based AIJ data structures for parallel...
Definition: petsc_matrix.h:61

◆ n()

template<typename T >
numeric_index_type libMesh::PetscMatrixBase< T >::n ( ) const
overridevirtualinherited
Returns
The column-dimension of the matrix.

Implements libMesh::SparseMatrix< T >.

Reimplemented in libMesh::StaticCondensation, and libMesh::StaticCondensation.

Definition at line 154 of file petsc_matrix_base.C.

155 {
156  libmesh_assert (this->initialized());
157 
158  PetscInt petsc_m=0, petsc_n=0;
159 
160  LibmeshPetscCall(MatGetSize (this->_mat, &petsc_m, &petsc_n));
161 
162  return static_cast<numeric_index_type>(petsc_n);
163 }
virtual bool initialized() const
dof_id_type numeric_index_type
Definition: id_types.h:99
libmesh_assert(ctx)
Mat _mat
PETSc matrix datatype to store values.

◆ n_nonzeros()

template<typename T >
std::size_t libMesh::SparseMatrix< T >::n_nonzeros ( ) const
virtualinherited
Returns
the global number of non-zero entries in the matrix sparsity pattern

Definition at line 243 of file sparse_matrix.C.

Referenced by libMesh::SparseMatrix< ValOut >::n_nonzeros().

244 {
245  if (!_sp)
246  return 0;
247  return _sp->n_nonzeros();
248 }
std::size_t n_nonzeros() const
The total number of nonzeros in the global matrix.
SparsityPattern::Build const * _sp
The sparsity pattern associated with this object.

◆ n_objects()

static unsigned int libMesh::ReferenceCounter::n_objects ( )
inlinestaticinherited

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

Definition at line 85 of file reference_counter.h.

References libMesh::ReferenceCounter::_n_objects.

Referenced by libMesh::LibMeshInit::~LibMeshInit().

86  { return _n_objects; }
static Threads::atomic< unsigned int > _n_objects
The number of objects.

◆ n_processors()

processor_id_type libMesh::ParallelObject::n_processors ( ) const
inlineinherited
Returns
The number of processors in the group.

Definition at line 103 of file parallel_object.h.

References libMesh::ParallelObject::_communicator, libMesh::libmesh_assert(), and TIMPI::Communicator::size().

Referenced by libMesh::Partitioner::_find_global_index_by_pid_map(), libMesh::BoundaryInfo::_find_id_maps(), libMesh::DofMap::add_constraints_to_send_list(), libMesh::PetscDMWrapper::add_dofs_to_section(), libMesh::DistributedMesh::add_elem(), libMesh::DofMap::add_neighbors_to_send_list(), libMesh::DistributedMesh::add_node(), libMesh::System::add_vector(), libMesh::LaplaceMeshSmoother::allgather_graph(), libMesh::DofMap::allgather_recursive_constraints(), libMesh::FEMSystem::assembly(), libMesh::Nemesis_IO::assert_symmetric_cmaps(), libMesh::Partitioner::assign_partitioning(), libMesh::AztecLinearSolver< T >::AztecLinearSolver(), libMesh::Partitioner::build_graph(), libMesh::EquationSystems::build_parallel_elemental_solution_vector(), libMesh::DistributedMesh::clear(), libMesh::DistributedMesh::clear_elems(), libMesh::Nemesis_IO_Helper::compute_border_node_ids(), libMesh::Nemesis_IO_Helper::construct_nemesis_filename(), libMesh::UnstructuredMesh::copy_nodes_and_elements(), libMesh::ExodusII_IO::copy_scalar_solution(), libMesh::Nemesis_IO::copy_scalar_solution(), libMesh::UnstructuredMesh::create_pid_mesh(), libMesh::MeshTools::create_processor_bounding_box(), libMesh::DofMap::distribute_dofs(), libMesh::DofMap::distribute_scalar_dofs(), libMesh::DistributedMesh::DistributedMesh(), libMesh::EnsightIO::EnsightIO(), libMesh::RBEIMEvaluation::gather_bfs(), libMesh::MeshBase::get_info(), libMesh::StaticCondensation::init(), libMesh::SystemSubsetBySubdomain::init(), libMesh::PetscDMWrapper::init_petscdm(), libMesh::Nemesis_IO_Helper::initialize(), libMesh::ExodusII_IO_Helper::initialize(), libMesh::DistributedMesh::insert_elem(), libMesh::MeshTools::libmesh_assert_contiguous_dof_ids(), libMesh::MeshTools::libmesh_assert_parallel_consistent_new_node_procids(), libMesh::MeshTools::libmesh_assert_parallel_consistent_procids< Elem >(), libMesh::MeshTools::libmesh_assert_parallel_consistent_procids< Node >(), libMesh::MeshTools::libmesh_assert_topology_consistent_procids< Node >(), libMesh::MeshTools::libmesh_assert_valid_boundary_ids(), libMesh::MeshTools::libmesh_assert_valid_dof_ids(), libMesh::MeshTools::libmesh_assert_valid_neighbors(), libMesh::MeshTools::libmesh_assert_valid_refinement_flags(), libMesh::DofMap::local_variable_indices(), libMesh::MeshRefinement::make_coarsening_compatible(), libMesh::MeshBase::n_active_elem_on_proc(), libMesh::DofMap::n_dofs_per_processor(), libMesh::MeshBase::n_elem_on_proc(), libMesh::MeshBase::n_nodes_on_proc(), libMesh::RBEIMEvaluation::node_gather_bfs(), libMesh::Partitioner::partition(), libMesh::MeshBase::partition(), libMesh::Partitioner::partition_unpartitioned_elements(), libMesh::System::point_gradient(), libMesh::System::point_hessian(), libMesh::System::point_value(), libMesh::DofMap::prepare_send_list(), libMesh::MeshBase::print_constraint_rows(), libMesh::DofMap::print_dof_constraints(), libMesh::NameBasedIO::read(), libMesh::Nemesis_IO::read(), libMesh::CheckpointIO::read(), libMesh::CheckpointIO::read_connectivity(), libMesh::XdrIO::read_header(), libMesh::CheckpointIO::read_nodes(), libMesh::System::read_parallel_data(), libMesh::System::read_SCALAR_dofs(), libMesh::System::read_serialized_blocked_dof_objects(), libMesh::System::read_serialized_vector(), libMesh::DistributedMesh::renumber_dof_objects(), libMesh::Partitioner::repartition(), OverlappingFunctorTest::run_partitioner_test(), libMesh::DofMap::scatter_constraints(), libMesh::DistributedMesh::set_next_unique_id(), libMesh::DofMap::set_nonlocal_dof_objects(), libMesh::PetscDMWrapper::set_point_range_in_section(), WriteVecAndScalar::setupTests(), libMesh::RBEIMEvaluation::side_gather_bfs(), DistributedMeshTest::testRemoteElemError(), CheckpointIOTest::testSplitter(), libMesh::MeshRefinement::uniformly_coarsen(), libMesh::DistributedMesh::update_parallel_id_counts(), libMesh::GMVIO::write_binary(), libMesh::GMVIO::write_discontinuous_gmv(), libMesh::ExodusII_IO_Helper::write_nodal_coordinates(), libMesh::VTKIO::write_nodal_data(), libMesh::ExodusII_IO::write_nodal_data(), libMesh::System::write_parallel_data(), libMesh::System::write_SCALAR_dofs(), libMesh::XdrIO::write_serialized_bcs_helper(), libMesh::System::write_serialized_blocked_dof_objects(), libMesh::XdrIO::write_serialized_connectivity(), libMesh::XdrIO::write_serialized_nodes(), and libMesh::XdrIO::write_serialized_nodesets().

104  {
105  processor_id_type returnval =
106  cast_int<processor_id_type>(_communicator.size());
107  libmesh_assert(returnval); // We never have an empty comm
108  return returnval;
109  }
const Parallel::Communicator & _communicator
processor_id_type size() const
uint8_t processor_id_type
libmesh_assert(ctx)

◆ need_full_sparsity_pattern()

template<typename T>
virtual bool libMesh::SparseMatrix< T >::need_full_sparsity_pattern ( ) const
inlinevirtualinherited
Returns
true if this sparse matrix format needs to be fed the graph of the sparse matrix.

This is true for LaspackMatrix, but not PetscMatrixBase subclasses. In the case where the full graph is not required, we can efficiently approximate it to provide a good estimate of the required size of the sparse matrix.

Reimplemented in libMesh::EpetraMatrix< T >, and libMesh::LaspackMatrix< T >.

Definition at line 162 of file sparse_matrix.h.

Referenced by libMesh::DofMap::attach_matrix(), and libMesh::DofMap::update_sparsity_pattern().

163  { return false; }

◆ norm()

template<typename T >
template<NormType N>
Real libMesh::PetscMatrix< T >::norm ( ) const
private
Returns
A norm of the matrix, where the type of norm to compute is determined by the template parameter N of the PETSc-defined type NormType. The valid template arguments are NORM_1, NORM_FROBENIUS and NORM_INFINITY, as used to define l1_norm(), frobenius_norm() and linfty_norm().

Definition at line 474 of file petsc_matrix.C.

References libMesh::closed(), libMesh::initialized(), libMesh::libmesh_assert(), libMesh::Real, and value.

475 {
476  libmesh_assert (this->initialized());
477 
478  semiparallel_only();
479 
480  PetscReal petsc_value;
481  Real value;
482 
483  libmesh_assert (this->closed());
484 
485  LibmeshPetscCall(MatNorm(this->_mat, N, &petsc_value));
486 
487  value = static_cast<Real>(petsc_value);
488 
489  return value;
490 }
virtual bool initialized() const
libmesh_assert(ctx)
Mat _mat
PETSc matrix datatype to store values.
virtual bool closed() const override
DIE A HORRIBLE DEATH HERE typedef LIBMESH_DEFAULT_SCALAR_TYPE Real
static const bool value
Definition: xdr_io.C:55

◆ operator()()

template<typename T >
T libMesh::PetscMatrix< T >::operator() ( const numeric_index_type  i,
const numeric_index_type  j 
) const
overridevirtual
Returns
A copy of matrix entry (i,j).
Note
This may be an expensive operation, and you should always be careful where you call this function.

Implements libMesh::SparseMatrix< T >.

Definition at line 1119 of file petsc_matrix.C.

References libMesh::closed(), libMesh::initialized(), libMesh::libmesh_assert(), and value.

1121 {
1122  libmesh_assert (this->initialized());
1123 
1124  // If the entry is not in the sparse matrix, it is 0.
1125  T value=0.;
1126 
1127  PetscInt
1128  i_val=static_cast<PetscInt>(i_in),
1129  j_val=static_cast<PetscInt>(j_in);
1130 
1131 
1132  // the matrix needs to be closed for this to work
1133  // this->close();
1134  // but closing it is a semiparallel operation; we want operator()
1135  // to run on one processor.
1136  libmesh_assert(this->closed());
1137 
1138  LibmeshPetscCall(MatGetValue(this->_mat, i_val, j_val, &value));
1139 
1140  return value;
1141 }
virtual bool initialized() const
libmesh_assert(ctx)
Mat _mat
PETSc matrix datatype to store values.
virtual bool closed() const override
static const bool value
Definition: xdr_io.C:55

◆ operator=() [1/3]

template<typename T>
PetscMatrix& libMesh::PetscMatrix< T >::operator= ( PetscMatrix< T > &&  )
delete

◆ operator=() [2/3]

template<typename T >
PetscMatrix< T > & libMesh::PetscMatrix< T >::operator= ( const PetscMatrix< T > &  v)

Definition at line 1194 of file petsc_matrix.C.

References libMesh::libMeshPrivateData::_is_initialized, libMesh::PetscMatrixBase< T >::_mat, and libMesh::libmesh_assert().

1195 {
1196  semiparallel_only();
1197 
1198  if (this->_mat)
1199  {
1200  PetscBool assembled;
1201  LibmeshPetscCall(MatAssembled(this->_mat, &assembled));
1202 #ifndef NDEBUG
1203  const bool cxx_assembled = (assembled == PETSC_TRUE) ? true : false;
1204  libmesh_assert(this->_communicator.verify(cxx_assembled));
1205 #endif
1206 
1207  if (!assembled)
1208  // MatCopy does not work with an unassembled matrix. We could use MatDuplicate but then we
1209  // would have to destroy the matrix we manage and others might be relying on that data. So
1210  // we just assemble here regardless of the preceding level of matrix fill
1211  this->close();
1212  LibmeshPetscCall(MatCopy(v._mat, this->_mat, DIFFERENT_NONZERO_PATTERN));
1213  }
1214  else
1215  LibmeshPetscCall(MatDuplicate(v._mat, MAT_COPY_VALUES, &this->_mat));
1216 
1217  this->_is_initialized = true;
1218 
1219  return *this;
1220 }
const Parallel::Communicator & _communicator
bool _is_initialized
Flag indicating whether or not the matrix has been initialized.
libmesh_assert(ctx)
virtual void close() override
Calls the SparseMatrix&#39;s internal assembly routines, ensuring that the values are consistent across p...
Mat _mat
PETSc matrix datatype to store values.
timpi_pure bool verify(const T &r) const

◆ operator=() [3/3]

template<typename T >
SparseMatrix< T > & libMesh::PetscMatrix< T >::operator= ( const SparseMatrix< T > &  )
overridevirtual

This looks like a copy assignment operator, but note that, unlike normal copy assignment operators, it is pure virtual.

This function should be overridden in derived classes so that they can be copied correctly via references to the base class. This design usually isn't a good idea in general, but in this context it works because we usually don't have a mix of different kinds of SparseMatrix active in the library at a single time.

Returns
A reference to *this as the base type.

Reimplemented from libMesh::SparseMatrix< T >.

Definition at line 1223 of file petsc_matrix.C.

1224 {
1225  *this = cast_ref<const PetscMatrix<T> &>(v);
1226  return *this;
1227 }

◆ preallocate()

template<typename T>
void libMesh::PetscMatrix< T >::preallocate ( numeric_index_type  m_l,
const std::vector< numeric_index_type > &  n_nz,
const std::vector< numeric_index_type > &  n_oz,
numeric_index_type  blocksize 
)
protected

Definition at line 260 of file petsc_matrix.C.

References libMesh::AIJ, libMesh::HYPRE, libMesh::libmesh_ignore(), and libMesh::numeric_petsc_cast().

264 {
265  // Make sure the sparsity pattern isn't empty unless the matrix is 0x0
266  libmesh_assert_equal_to (n_nz.size(), m_l);
267  libmesh_assert_equal_to (n_oz.size(), m_l);
268  // Avoid unused warnings when not configured with block storage
269  libmesh_ignore(blocksize_in);
270 
271 #ifdef LIBMESH_ENABLE_BLOCKED_STORAGE
272  PetscInt blocksize = static_cast<PetscInt>(blocksize_in);
273 
274  if (blocksize > 1)
275  {
276  // transform the per-entry n_nz and n_oz arrays into their block counterparts.
277  std::vector<numeric_index_type> b_n_nz, b_n_oz;
278 
279  transform_preallocation_arrays (blocksize,
280  n_nz, n_oz,
281  b_n_nz, b_n_oz);
282 
283  LibmeshPetscCall(MatSeqBAIJSetPreallocation (this->_mat,
284  blocksize,
285  0,
286  numeric_petsc_cast(b_n_nz.empty() ? nullptr : b_n_nz.data())));
287 
288  LibmeshPetscCall(MatMPIBAIJSetPreallocation (this->_mat,
289  blocksize,
290  0,
291  numeric_petsc_cast(b_n_nz.empty() ? nullptr : b_n_nz.data()),
292  0,
293  numeric_petsc_cast(b_n_oz.empty() ? nullptr : b_n_oz.data())));
294  }
295  else
296 #endif
297  {
298  switch (this->_mat_type) {
299  case AIJ:
300  LibmeshPetscCall(MatSeqAIJSetPreallocation (this->_mat,
301  0,
302  numeric_petsc_cast(n_nz.empty() ? nullptr : n_nz.data())));
303  LibmeshPetscCall(MatMPIAIJSetPreallocation (this->_mat,
304  0,
305  numeric_petsc_cast(n_nz.empty() ? nullptr : n_nz.data()),
306  0,
307  numeric_petsc_cast(n_oz.empty() ? nullptr : n_oz.data())));
308  break;
309 
310  case HYPRE:
311 #if !PETSC_VERSION_LESS_THAN(3,9,4) && LIBMESH_HAVE_PETSC_HYPRE
312  LibmeshPetscCall(MatHYPRESetPreallocation (this->_mat,
313  0,
314  numeric_petsc_cast(n_nz.empty() ? nullptr : n_nz.data()),
315  0,
316  numeric_petsc_cast(n_oz.empty() ? nullptr : n_oz.data())));
317 #else
318  libmesh_error_msg("PETSc 3.9.4 or higher with hypre is required for MatHypre");
319 #endif
320  break;
321 
322  default: libmesh_error_msg("Unsupported petsc matrix type");
323  }
324 
325  }
326 }
PetscInt * numeric_petsc_cast(const numeric_index_type *p)
void libmesh_ignore(const Args &...)
Mat _mat
PETSc matrix datatype to store values.
PetscMatrixType _mat_type
Definition: petsc_matrix.h:349

◆ print() [1/2]

template<>
void libMesh::SparseMatrix< Complex >::print ( std::ostream &  os,
const bool  sparse 
) const
inherited

Definition at line 136 of file sparse_matrix.C.

137 {
138  // std::complex<>::operator<<() is defined, but use this form
139 
140  if (sparse)
141  {
142  libmesh_not_implemented();
143  }
144 
145  os << "Real part:" << std::endl;
146  for (auto i : make_range(this->m()))
147  {
148  for (auto j : make_range(this->n()))
149  os << std::setw(8) << (*this)(i,j).real() << " ";
150  os << std::endl;
151  }
152 
153  os << std::endl << "Imaginary part:" << std::endl;
154  for (auto i : make_range(this->m()))
155  {
156  for (auto j : make_range(this->n()))
157  os << std::setw(8) << (*this)(i,j).imag() << " ";
158  os << std::endl;
159  }
160 }
boost::multiprecision::float128 real(const boost::multiprecision::float128 in)
virtual numeric_index_type m() const =0
IntRange< T > make_range(T beg, T end)
The 2-parameter make_range() helper function returns an IntRange<T> when both input parameters are of...
Definition: int_range.h:140
boost::multiprecision::float128 imag(const boost::multiprecision::float128)
virtual numeric_index_type n() const =0

◆ print() [2/2]

template<typename T >
void libMesh::SparseMatrix< T >::print ( std::ostream &  os = libMesh::out,
const bool  sparse = false 
) const
inherited

Print the contents of the matrix to the screen in a uniform style, regardless of matrix/solver package being used.

Definition at line 252 of file sparse_matrix.C.

Referenced by libMesh::EigenSparseMatrix< T >::print_personal(), and libMesh::LaspackMatrix< T >::print_personal().

253 {
254  parallel_object_only();
255 
256  libmesh_assert (this->initialized());
257 
258  const numeric_index_type first_dof = this->row_start(),
259  end_dof = this->row_stop();
260 
261  // We'll print the matrix from processor 0 to make sure
262  // it's serialized properly
263  if (this->processor_id() == 0)
264  {
265  libmesh_assert_equal_to (first_dof, 0);
266  for (numeric_index_type i : make_range(end_dof))
267  {
268  if (sparse)
269  {
270  for (auto j : make_range(this->n()))
271  {
272  T c = (*this)(i,j);
273  if (c != static_cast<T>(0.0))
274  {
275  os << i << " " << j << " " << c << std::endl;
276  }
277  }
278  }
279  else
280  {
281  for (auto j : make_range(this->n()))
282  os << (*this)(i,j) << " ";
283  os << std::endl;
284  }
285  }
286 
287  std::vector<numeric_index_type> ibuf, jbuf;
288  std::vector<T> cbuf;
289  numeric_index_type currenti = end_dof;
290  for (auto p : IntRange<processor_id_type>(1, this->n_processors()))
291  {
292  this->comm().receive(p, ibuf);
293  this->comm().receive(p, jbuf);
294  this->comm().receive(p, cbuf);
295  libmesh_assert_equal_to (ibuf.size(), jbuf.size());
296  libmesh_assert_equal_to (ibuf.size(), cbuf.size());
297 
298  if (ibuf.empty())
299  continue;
300  libmesh_assert_greater_equal (ibuf.front(), currenti);
301  libmesh_assert_greater_equal (ibuf.back(), ibuf.front());
302 
303  std::size_t currentb = 0;
304  for (;currenti <= ibuf.back(); ++currenti)
305  {
306  if (sparse)
307  {
308  for (numeric_index_type j=0; j<this->n(); j++)
309  {
310  if (currentb < ibuf.size() &&
311  ibuf[currentb] == currenti &&
312  jbuf[currentb] == j)
313  {
314  os << currenti << " " << j << " " << cbuf[currentb] << std::endl;
315  currentb++;
316  }
317  }
318  }
319  else
320  {
321  for (auto j : make_range(this->n()))
322  {
323  if (currentb < ibuf.size() &&
324  ibuf[currentb] == currenti &&
325  jbuf[currentb] == j)
326  {
327  os << cbuf[currentb] << " ";
328  currentb++;
329  }
330  else
331  os << static_cast<T>(0.0) << " ";
332  }
333  os << std::endl;
334  }
335  }
336  }
337  if (!sparse)
338  {
339  for (; currenti != this->m(); ++currenti)
340  {
341  for (numeric_index_type j=0; j<this->n(); j++)
342  os << static_cast<T>(0.0) << " ";
343  os << std::endl;
344  }
345  }
346  }
347  else
348  {
349  std::vector<numeric_index_type> ibuf, jbuf;
350  std::vector<T> cbuf;
351 
352  // We'll assume each processor has access to entire
353  // matrix rows, so (*this)(i,j) is valid if i is a local index.
354  for (numeric_index_type i : make_range(first_dof, end_dof))
355  {
356  for (auto j : make_range(this->n()))
357  {
358  T c = (*this)(i,j);
359  if (c != static_cast<T>(0.0))
360  {
361  ibuf.push_back(i);
362  jbuf.push_back(j);
363  cbuf.push_back(c);
364  }
365  }
366  }
367  this->comm().send(0,ibuf);
368  this->comm().send(0,jbuf);
369  this->comm().send(0,cbuf);
370  }
371 }
virtual bool initialized() const
const Parallel::Communicator & comm() const
virtual numeric_index_type row_stop() const =0
processor_id_type n_processors() const
Status receive(const unsigned int dest_processor_id, T &buf, const MessageTag &tag=any_tag) const
dof_id_type numeric_index_type
Definition: id_types.h:99
virtual numeric_index_type m() const =0
libmesh_assert(ctx)
virtual numeric_index_type row_start() const =0
void send(const unsigned int dest_processor_id, const T &buf, const MessageTag &tag=no_tag) const
IntRange< T > make_range(T beg, T end)
The 2-parameter make_range() helper function returns an IntRange<T> when both input parameters are of...
Definition: int_range.h:140
processor_id_type processor_id() const
virtual numeric_index_type n() const =0

◆ print_info()

void libMesh::ReferenceCounter::print_info ( std::ostream &  out_stream = libMesh::out)
staticinherited

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

Definition at line 81 of file reference_counter.C.

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

Referenced by libMesh::LibMeshInit::~LibMeshInit().

82 {
84  out_stream << ReferenceCounter::get_info();
85 }
static std::string get_info()
Gets a string containing the reference information.
static bool _enable_print_counter
Flag to control whether reference count information is printed when print_info is called...

◆ print_matlab()

template<typename T >
void libMesh::PetscMatrix< T >::print_matlab ( const std::string &  name = "") const
overridevirtual

Print the contents of the matrix in Matlab's sparse matrix format.

Optionally prints the matrix to the file named name. If name is not specified it is dumped to the screen.

Reimplemented from libMesh::SparseMatrix< T >.

Definition at line 510 of file petsc_matrix.C.

References libMesh::closed(), libMesh::WrappedPetsc< T >::get(), libMesh::initialized(), libMesh::libmesh_assert(), and libMesh::Quality::name().

511 {
512  libmesh_assert (this->initialized());
513 
514  semiparallel_only();
515 
516  if (!this->closed())
517  {
518  libmesh_deprecated();
519  libmesh_warning("The matrix must be assembled before calling PetscMatrix::print_matlab().\n"
520  "Please update your code, as this warning will become an error in a future release.");
521  const_cast<PetscMatrix<T> *>(this)->close();
522  }
523 
524  // Create an ASCII file containing the matrix
525  // if a filename was provided.
526  if (name != "")
527  {
528  WrappedPetsc<PetscViewer> petsc_viewer;
529 
530  LibmeshPetscCall(PetscViewerASCIIOpen( this->comm().get(),
531  name.c_str(),
532  petsc_viewer.get()));
533 
534 #if PETSC_VERSION_LESS_THAN(3,7,0)
535  LibmeshPetscCall(PetscViewerSetFormat (petsc_viewer,
536  PETSC_VIEWER_ASCII_MATLAB));
537 #else
538  LibmeshPetscCall(PetscViewerPushFormat (petsc_viewer,
539  PETSC_VIEWER_ASCII_MATLAB));
540 #endif
541 
542  LibmeshPetscCall(MatView (this->_mat, petsc_viewer));
543  }
544 
545  // Otherwise the matrix will be dumped to the screen.
546  else
547  {
548 #if PETSC_VERSION_LESS_THAN(3,7,0)
549  LibmeshPetscCall(PetscViewerSetFormat (PETSC_VIEWER_STDOUT_WORLD,
550  PETSC_VIEWER_ASCII_MATLAB));
551 #else
552  LibmeshPetscCall(PetscViewerPushFormat (PETSC_VIEWER_STDOUT_WORLD,
553  PETSC_VIEWER_ASCII_MATLAB));
554 #endif
555 
556  LibmeshPetscCall(MatView (this->_mat, PETSC_VIEWER_STDOUT_WORLD));
557  }
558 }
std::string name(const ElemQuality q)
This function returns a string containing some name for q.
Definition: elem_quality.C:42
virtual bool initialized() const
const Parallel::Communicator & comm() const
libmesh_assert(ctx)
virtual void close() override
Calls the SparseMatrix&#39;s internal assembly routines, ensuring that the values are consistent across p...
Mat _mat
PETSc matrix datatype to store values.
virtual bool closed() const override
This class provides a nice interface to the PETSc C-based AIJ data structures for parallel...
Definition: petsc_matrix.h:61

◆ print_personal()

template<typename T >
void libMesh::PetscMatrix< T >::print_personal ( std::ostream &  os = libMesh::out) const
overridevirtual

Print the contents of the matrix to the screen with the PETSc viewer.

This function only allows printing to standard out since we have limited ourselves to one PETSc implementation for writing.

Implements libMesh::SparseMatrix< T >.

Definition at line 565 of file petsc_matrix.C.

References libMesh::closed(), libMesh::initialized(), libMesh::libmesh_assert(), and mkstemp().

566 {
567  libmesh_assert (this->initialized());
568 
569  // Routine must be called in parallel on parallel matrices
570  // and serial on serial matrices.
571  semiparallel_only();
572 
573  // #ifndef NDEBUG
574  // if (os != std::cout)
575  // libMesh::err << "Warning! PETSc can only print to std::cout!" << std::endl;
576  // #endif
577 
578  // Matrix must be in an assembled state to be printed
579  if (!this->closed())
580  {
581  libmesh_deprecated();
582  libmesh_warning("The matrix must be assembled before calling PetscMatrix::print_personal().\n"
583  "Please update your code, as this warning will become an error in a future release.");
584  const_cast<PetscMatrix<T> *>(this)->close();
585  }
586 
587  // Print to screen if ostream is stdout
588  if (os.rdbuf() == std::cout.rdbuf())
589  LibmeshPetscCall(MatView(this->_mat, NULL));
590 
591  // Otherwise, print to the requested file, in a roundabout way...
592  else
593  {
594  // We will create a temporary filename, and file, for PETSc to
595  // write to.
596  std::string temp_filename;
597 
598  {
599  // Template for temporary filename
600  char c[] = "temp_petsc_matrix.XXXXXX";
601 
602  // Generate temporary, unique filename only on processor 0. We will
603  // use this filename for PetscViewerASCIIOpen, before copying it into
604  // the user's stream
605  if (this->processor_id() == 0)
606  {
607  int fd = mkstemp(c);
608 
609  // Check to see that mkstemp did not fail.
610  libmesh_error_msg_if(fd == -1, "mkstemp failed in PetscMatrix::print_personal()");
611 
612  // mkstemp returns a file descriptor for an open file,
613  // so let's close it before we hand it to PETSc!
614  ::close (fd);
615  }
616 
617  // Store temporary filename as string, makes it easier to broadcast
618  temp_filename = c;
619  }
620 
621  // Now broadcast the filename from processor 0 to all processors.
622  this->comm().broadcast(temp_filename);
623 
624  // PetscViewer object for passing to MatView
625  PetscViewer petsc_viewer;
626 
627  // This PETSc function only takes a string and handles the opening/closing
628  // of the file internally. Since print_personal() takes a reference to
629  // an ostream, we have to do an extra step... print_personal() should probably
630  // have a version that takes a string to get rid of this problem.
631  LibmeshPetscCall(PetscViewerASCIIOpen( this->comm().get(),
632  temp_filename.c_str(),
633  &petsc_viewer));
634 
635  // Probably don't need to set the format if it's default...
636  // ierr = PetscViewerSetFormat (petsc_viewer,
637  // PETSC_VIEWER_DEFAULT);
638  // LIBMESH_CHKERR(ierr);
639 
640  // Finally print the matrix using the viewer
641  LibmeshPetscCall(MatView (this->_mat, petsc_viewer));
642 
643  if (this->processor_id() == 0)
644  {
645  // Now the inefficient bit: open temp_filename as an ostream and copy the contents
646  // into the user's desired ostream. We can't just do a direct file copy, we don't even have the filename!
647  std::ifstream input_stream(temp_filename.c_str());
648  os << input_stream.rdbuf(); // The "most elegant" way to copy one stream into another.
649  // os.close(); // close not defined in ostream
650 
651  // Now remove the temporary file
652  input_stream.close();
653  std::remove(temp_filename.c_str());
654  }
655  }
656 }
virtual bool initialized() const
const Parallel::Communicator & comm() const
int mkstemp(char *tmpl)
Definition: win_mkstemp.h:13
libmesh_assert(ctx)
virtual void close() override
Calls the SparseMatrix&#39;s internal assembly routines, ensuring that the values are consistent across p...
void broadcast(T &data, const unsigned int root_id=0, const bool identical_sizes=false) const
Mat _mat
PETSc matrix datatype to store values.
virtual bool closed() const override
This class provides a nice interface to the PETSc C-based AIJ data structures for parallel...
Definition: petsc_matrix.h:61
processor_id_type processor_id() const

◆ print_petsc_binary()

template<typename T >
void libMesh::PetscMatrix< T >::print_petsc_binary ( const std::string &  filename)
overridevirtual

Write the contents of the matrix to a file in PETSc's binary sparse matrix format.

Reimplemented from libMesh::SparseMatrix< T >.

Definition at line 691 of file petsc_matrix.C.

References libMesh::initialized(), and libMesh::libmesh_assert().

692 {
693  libmesh_assert (this->initialized());
694 
695  this->_petsc_viewer(filename, PETSCVIEWERBINARY, FILE_MODE_WRITE);
696 }
virtual bool initialized() const
libmesh_assert(ctx)
void _petsc_viewer(const std::string &filename, PetscViewerType viewertype, PetscFileMode filemode)
Definition: petsc_matrix.C:661

◆ print_petsc_hdf5()

template<typename T >
void libMesh::PetscMatrix< T >::print_petsc_hdf5 ( const std::string &  filename)
overridevirtual

Write the contents of the matrix to a file in PETSc's HDF5 sparse matrix format.

Reimplemented from libMesh::SparseMatrix< T >.

Definition at line 701 of file petsc_matrix.C.

References libMesh::initialized(), and libMesh::libmesh_assert().

702 {
703  libmesh_assert (this->initialized());
704 
705  this->_petsc_viewer(filename, PETSCVIEWERHDF5, FILE_MODE_WRITE);
706 }
virtual bool initialized() const
libmesh_assert(ctx)
void _petsc_viewer(const std::string &filename, PetscViewerType viewertype, PetscFileMode filemode)
Definition: petsc_matrix.C:661

◆ processor_id()

processor_id_type libMesh::ParallelObject::processor_id ( ) const
inlineinherited
Returns
The rank of this processor in the group.

Definition at line 114 of file parallel_object.h.

References libMesh::ParallelObject::_communicator, and TIMPI::Communicator::rank().

Referenced by libMesh::BoundaryInfo::_find_id_maps(), libMesh::PetscDMWrapper::add_dofs_to_section(), libMesh::DistributedMesh::add_elem(), libMesh::BoundaryInfo::add_elements(), libMesh::DofMap::add_neighbors_to_send_list(), libMesh::DistributedMesh::add_node(), libMesh::MeshTools::Modification::all_tri(), libMesh::DofMap::allgather_recursive_constraints(), libMesh::FEMSystem::assembly(), libMesh::Nemesis_IO::assert_symmetric_cmaps(), libMesh::Partitioner::assign_partitioning(), libMesh::Nemesis_IO_Helper::build_element_and_node_maps(), libMesh::Partitioner::build_graph(), libMesh::InfElemBuilder::build_inf_elem(), libMesh::BoundaryInfo::build_node_list_from_side_list(), libMesh::EquationSystems::build_parallel_elemental_solution_vector(), libMesh::EquationSystems::build_parallel_solution_vector(), libMesh::MeshFunction::check_found_elem(), libMesh::DistributedMesh::clear(), libMesh::DistributedMesh::clear_elems(), libMesh::ExodusII_IO_Helper::close(), libMesh::Nemesis_IO_Helper::compute_border_node_ids(), libMesh::Nemesis_IO_Helper::compute_communication_map_parameters(), libMesh::Nemesis_IO_Helper::compute_internal_and_border_elems_and_internal_nodes(), libMesh::RBConstruction::compute_max_error_bound(), libMesh::Nemesis_IO_Helper::compute_node_communication_maps(), libMesh::Nemesis_IO_Helper::compute_num_global_elem_blocks(), libMesh::Nemesis_IO_Helper::compute_num_global_nodesets(), libMesh::Nemesis_IO_Helper::compute_num_global_sidesets(), libMesh::Nemesis_IO_Helper::construct_nemesis_filename(), libMesh::ExodusII_IO::copy_elemental_solution(), libMesh::ExodusII_IO::copy_nodal_solution(), libMesh::ExodusII_IO::copy_scalar_solution(), libMesh::Nemesis_IO::copy_scalar_solution(), libMesh::MeshTools::correct_node_proc_ids(), libMesh::ExodusII_IO_Helper::create(), libMesh::DistributedMesh::delete_elem(), libMesh::MeshCommunication::delete_remote_elements(), libMesh::DofMap::distribute_dofs(), libMesh::DofMap::distribute_scalar_dofs(), libMesh::DistributedMesh::DistributedMesh(), libMesh::DofMapBase::end_dof(), libMesh::DofMapBase::end_old_dof(), libMesh::EnsightIO::EnsightIO(), libMesh::GenericProjector< FFunctor, GFunctor, FValue, ProjectionAction >::SubFunctor::find_dofs_to_send(), libMesh::UnstructuredMesh::find_neighbors(), libMesh::DofMapBase::first_dof(), libMesh::DofMapBase::first_old_dof(), libMesh::RBEIMEvaluation::gather_bfs(), libMesh::Nemesis_IO_Helper::get_cmap_params(), libMesh::Nemesis_IO_Helper::get_eb_info_global(), libMesh::Nemesis_IO_Helper::get_elem_cmap(), libMesh::Nemesis_IO_Helper::get_elem_map(), libMesh::MeshBase::get_info(), libMesh::DofMap::get_info(), libMesh::Nemesis_IO_Helper::get_init_global(), libMesh::Nemesis_IO_Helper::get_init_info(), libMesh::RBEIMEvaluation::get_interior_basis_functions_as_vecs(), libMesh::Nemesis_IO_Helper::get_loadbal_param(), libMesh::DofMap::get_local_constraints(), libMesh::MeshBase::get_local_constraints(), libMesh::Nemesis_IO_Helper::get_node_cmap(), libMesh::Nemesis_IO_Helper::get_node_map(), libMesh::Nemesis_IO_Helper::get_ns_param_global(), libMesh::Nemesis_IO_Helper::get_ss_param_global(), libMesh::SparsityPattern::Build::handle_vi_vj(), libMesh::LaplaceMeshSmoother::init(), libMesh::SystemSubsetBySubdomain::init(), HeatSystem::init_data(), libMesh::ExodusII_IO_Helper::initialize(), libMesh::ExodusII_IO_Helper::initialize_element_variables(), libMesh::ExodusII_IO_Helper::initialize_global_variables(), libMesh::ExodusII_IO_Helper::initialize_nodal_variables(), libMesh::DistributedMesh::insert_elem(), libMesh::DofMap::is_evaluable(), libMesh::SparsityPattern::Build::join(), libMesh::TransientRBEvaluation::legacy_write_offline_data_to_files(), libMesh::RBSCMEvaluation::legacy_write_offline_data_to_files(), libMesh::RBEvaluation::legacy_write_offline_data_to_files(), libMesh::MeshTools::libmesh_assert_consistent_distributed(), libMesh::MeshTools::libmesh_assert_consistent_distributed_nodes(), libMesh::MeshTools::libmesh_assert_contiguous_dof_ids(), libMesh::MeshTools::libmesh_assert_parallel_consistent_procids< Elem >(), libMesh::MeshTools::libmesh_assert_valid_neighbors(), libMesh::DistributedMesh::libmesh_assert_valid_parallel_object_ids(), libMesh::DofMap::local_variable_indices(), main(), libMesh::MeshRefinement::make_coarsening_compatible(), AugmentSparsityOnInterface::mesh_reinit(), libMesh::TriangulatorInterface::MeshedHole::MeshedHole(), libMesh::MeshBase::n_active_local_elem(), libMesh::BoundaryInfo::n_boundary_conds(), libMesh::MeshTools::n_connected_components(), libMesh::MeshBase::n_constraint_rows(), libMesh::BoundaryInfo::n_edge_conds(), libMesh::DofMapBase::n_local_dofs(), libMesh::MeshBase::n_local_elem(), libMesh::MeshBase::n_local_nodes(), libMesh::BoundaryInfo::n_nodeset_conds(), libMesh::BoundaryInfo::n_shellface_conds(), libMesh::RBEIMEvaluation::node_gather_bfs(), libMesh::DistributedMesh::own_node(), libMesh::BoundaryInfo::parallel_sync_node_ids(), libMesh::BoundaryInfo::parallel_sync_side_ids(), libMesh::System::point_gradient(), libMesh::System::point_hessian(), libMesh::System::point_value(), libMesh::MeshBase::print_constraint_rows(), libMesh::DofMap::print_dof_constraints(), libMesh::DofMap::process_mesh_constraint_rows(), libMesh::Nemesis_IO_Helper::put_cmap_params(), libMesh::Nemesis_IO_Helper::put_elem_cmap(), libMesh::Nemesis_IO_Helper::put_elem_map(), libMesh::Nemesis_IO_Helper::put_loadbal_param(), libMesh::Nemesis_IO_Helper::put_node_cmap(), libMesh::Nemesis_IO_Helper::put_node_map(), libMesh::NameBasedIO::read(), libMesh::Nemesis_IO::read(), libMesh::XdrIO::read(), libMesh::CheckpointIO::read(), libMesh::EquationSystems::read(), libMesh::ExodusII_IO_Helper::read_elem_num_map(), libMesh::ExodusII_IO_Helper::read_global_values(), libMesh::ExodusII_IO::read_header(), libMesh::CheckpointIO::read_header(), libMesh::XdrIO::read_header(), libMesh::System::read_header(), libMesh::System::read_legacy_data(), libMesh::DynaIO::read_mesh(), libMesh::ExodusII_IO_Helper::read_node_num_map(), libMesh::System::read_parallel_data(), libMesh::TransientRBConstruction::read_riesz_representors_from_files(), libMesh::RBConstruction::read_riesz_representors_from_files(), libMesh::System::read_SCALAR_dofs(), libMesh::XdrIO::read_serialized_bc_names(), libMesh::XdrIO::read_serialized_bcs_helper(), libMesh::System::read_serialized_blocked_dof_objects(), libMesh::XdrIO::read_serialized_connectivity(), libMesh::System::read_serialized_data(), libMesh::XdrIO::read_serialized_nodes(), libMesh::XdrIO::read_serialized_nodesets(), libMesh::XdrIO::read_serialized_subdomain_names(), libMesh::System::read_serialized_vector(), libMesh::System::read_serialized_vectors(), libMesh::Nemesis_IO_Helper::read_var_names_impl(), libMesh::SimplexRefiner::refine_via_edges(), libMesh::StaticCondensationDofMap::reinit(), libMesh::DistributedMesh::renumber_dof_objects(), libMesh::DistributedMesh::renumber_nodes_and_elements(), libMesh::DofMap::scatter_constraints(), libMesh::CheckpointIO::select_split_config(), libMesh::DistributedMesh::set_next_unique_id(), libMesh::DofMap::set_nonlocal_dof_objects(), libMesh::PetscDMWrapper::set_point_range_in_section(), libMesh::RBEIMEvaluation::side_gather_bfs(), ExodusTest< elem_type >::test_read_gold(), ExodusTest< elem_type >::test_write(), MeshInputTest::testAbaqusRead(), MeshInputTest::testBadGmsh(), MeshInputTest::testCopyElementSolutionImpl(), MeshInputTest::testCopyElementVectorImpl(), MeshInputTest::testCopyNodalSolutionImpl(), DefaultCouplingTest::testCoupling(), PointNeighborCouplingTest::testCoupling(), MeshInputTest::testDynaFileMappings(), MeshInputTest::testDynaNoSplines(), MeshInputTest::testDynaReadElem(), MeshInputTest::testDynaReadPatch(), MeshInputTest::testExodusFileMappings(), MeshInputTest::testExodusIGASidesets(), MeshInputTest::testExodusWriteElementDataFromDiscontinuousNodalData(), MeshInputTest::testGmshBCIDOverlap(), MeshInputTest::testGoodGmsh(), MeshInputTest::testGoodSTL(), MeshInputTest::testGoodSTLBinary(), MeshInputTest::testLowOrderEdgeBlocks(), SystemsTest::testProjectMatrix3D(), BoundaryInfoTest::testShellFaceConstraints(), MeshInputTest::testSingleElementImpl(), WriteVecAndScalar::testSolution(), CheckpointIOTest::testSplitter(), MeshInputTest::testTetgenIO(), libMesh::MeshTools::total_weight(), libMesh::NetGenMeshInterface::triangulate(), libMesh::MeshRefinement::uniformly_coarsen(), libMesh::DistributedMesh::update_parallel_id_counts(), libMesh::DTKAdapter::update_variable_values(), libMesh::MeshTools::volume(), libMesh::STLIO::write(), libMesh::NameBasedIO::write(), libMesh::XdrIO::write(), libMesh::CheckpointIO::write(), libMesh::EquationSystems::write(), libMesh::GMVIO::write_discontinuous_gmv(), libMesh::ExodusII_IO::write_element_data(), libMesh::ExodusII_IO_Helper::write_element_values(), libMesh::ExodusII_IO_Helper::write_element_values_element_major(), libMesh::ExodusII_IO_Helper::write_elements(), libMesh::ExodusII_IO_Helper::write_elemset_data(), libMesh::ExodusII_IO_Helper::write_elemsets(), libMesh::ExodusII_IO::write_global_data(), libMesh::ExodusII_IO_Helper::write_global_values(), libMesh::System::write_header(), libMesh::ExodusII_IO::write_information_records(), libMesh::ExodusII_IO_Helper::write_information_records(), libMesh::ExodusII_IO_Helper::write_nodal_coordinates(), libMesh::UCDIO::write_nodal_data(), libMesh::VTKIO::write_nodal_data(), libMesh::ExodusII_IO::write_nodal_data(), libMesh::ExodusII_IO::write_nodal_data_common(), libMesh::ExodusII_IO::write_nodal_data_discontinuous(), libMesh::ExodusII_IO_Helper::write_nodal_values(), libMesh::ExodusII_IO_Helper::write_nodeset_data(), libMesh::Nemesis_IO_Helper::write_nodesets(), libMesh::ExodusII_IO_Helper::write_nodesets(), libMesh::RBEIMEvaluation::write_out_interior_basis_functions(), libMesh::RBEIMEvaluation::write_out_node_basis_functions(), libMesh::RBEIMEvaluation::write_out_side_basis_functions(), write_output_solvedata(), libMesh::System::write_parallel_data(), libMesh::RBConstruction::write_riesz_representors_to_files(), libMesh::System::write_SCALAR_dofs(), libMesh::XdrIO::write_serialized_bc_names(), libMesh::XdrIO::write_serialized_bcs_helper(), libMesh::System::write_serialized_blocked_dof_objects(), libMesh::XdrIO::write_serialized_connectivity(), libMesh::System::write_serialized_data(), libMesh::XdrIO::write_serialized_nodes(), libMesh::XdrIO::write_serialized_nodesets(), libMesh::XdrIO::write_serialized_subdomain_names(), libMesh::System::write_serialized_vector(), libMesh::System::write_serialized_vectors(), libMesh::ExodusII_IO_Helper::write_sideset_data(), libMesh::Nemesis_IO_Helper::write_sidesets(), libMesh::ExodusII_IO_Helper::write_sidesets(), libMesh::ExodusII_IO::write_timestep(), libMesh::ExodusII_IO_Helper::write_timestep(), and libMesh::ExodusII_IO::write_timestep_discontinuous().

115  { return cast_int<processor_id_type>(_communicator.rank()); }
processor_id_type rank() const
const Parallel::Communicator & _communicator

◆ read()

template<typename T >
void libMesh::SparseMatrix< T >::read ( const std::string &  filename)
virtualinherited

Read the contents of the matrix from a file, with the file format inferred from the extension of filename.

Definition at line 516 of file sparse_matrix.C.

517 {
518  {
519  std::ifstream in (filename.c_str());
520  libmesh_error_msg_if
521  (!in.good(), "ERROR: cannot read file:\n\t" <<
522  filename);
523  }
524 
525  std::string_view basename = Utility::basename_of(filename);
526 
527  const bool gzipped_file = Utility::ends_with(filename, ".gz");
528 
529  if (gzipped_file)
530  basename.remove_suffix(3);
531 
532  if (Utility::ends_with(basename, ".matlab") ||
533  Utility::ends_with(basename, ".m"))
534  this->read_matlab(filename);
535  else if (Utility::ends_with(basename, ".petsc64"))
536  {
537 #ifndef LIBMESH_HAVE_PETSC
538  libmesh_error_msg("Cannot load PETSc matrix file " <<
539  filename << " without PETSc-enabled libMesh.");
540 #endif
541 #if LIBMESH_DOF_ID_BYTES != 8
542  libmesh_error_msg("Cannot load 64-bit PETSc matrix file " <<
543  filename << " with non-64-bit libMesh.");
544 #endif
545  this->read_petsc_binary(filename);
546  }
547  else if (Utility::ends_with(basename, ".petsc32"))
548  {
549 #ifndef LIBMESH_HAVE_PETSC
550  libmesh_error_msg("Cannot load PETSc matrix file " <<
551  filename << " without PETSc-enabled libMesh.");
552 #endif
553 #if LIBMESH_DOF_ID_BYTES != 4
554  libmesh_error_msg("Cannot load 32-bit PETSc matrix file " <<
555  filename << " with non-32-bit libMesh.");
556 #endif
557  this->read_petsc_binary(filename);
558  }
559  else if (Utility::ends_with(basename, ".h5"))
560  {
561  this->read_coreform_hdf5(filename);
562  }
563  else
564  libmesh_error_msg(" ERROR: Unrecognized matrix file extension on: "
565  << basename
566  << "\n I understand the following:\n\n"
567  << " *.h5 -- CoreForm HDF5 sparse matrix format\n"
568  << " *.matlab -- Matlab sparse matrix format\n"
569  << " *.m -- Matlab sparse matrix format\n"
570  << " *.petsc32 -- PETSc binary format, 32-bit\n"
571  << " *.petsc64 -- PETSc binary format, 64-bit\n"
572  );
573 }
bool ends_with(std::string_view superstring, std::string_view suffix)
Look for a substring at the very end of a string.
Definition: utility.C:213
virtual void read_coreform_hdf5(const std::string &filename, const std::string &groupname="extraction")
Read the contents of the matrix from a file, with the HDF5 sparse matrix format used by CoreForm...
virtual void read_matlab(const std::string &filename)
Read the contents of the matrix from the Matlab-script sparse matrix format used by PETSc...
virtual void read_petsc_binary(const std::string &filename)
Read the contents of the matrix from a file in PETSc&#39;s binary sparse matrix format.
std::string_view basename_of(const std::string &fullname)
Definition: utility.C:108

◆ read_coreform_hdf5()

template<typename T >
void libMesh::SparseMatrix< T >::read_coreform_hdf5 ( const std::string &  filename,
const std::string &  groupname = "extraction" 
)
virtualinherited

Read the contents of the matrix from a file, with the HDF5 sparse matrix format used by CoreForm, expecing sparse matrix data in the group given by groupname.

This will be initialized with the sparsity from the file, linearly partitioned onto the number of processors available unless this matrix is pre-sized and pre-partitionsed.

Definition at line 578 of file sparse_matrix.C.

580 {
581 #ifndef LIBMESH_HAVE_HDF5
582  libmesh_ignore(filename, groupname);
583  libmesh_error_msg("ERROR: need HDF5 support to handle .h5 files!!!");
584 #else
585  LOG_SCOPE("read_coreform_hdf5()", "SparseMatrix");
586 
587  std::size_t num_rows, num_cols;
588 
589  hid_t group;
590 
591  auto check_open = [&filename](hid_t id, const std::string & objname)
592  {
593  if (id == H5I_INVALID_HID)
594  libmesh_error_msg("Couldn't open " + objname + " in " + filename);
595  };
596 
597  auto check_hdf5 = [&filename](auto hdf5val, const std::string & objname)
598  {
599  if (hdf5val < 0)
600  libmesh_error_msg("HDF5 error from " + objname + " in " + filename);
601  };
602 
603 
604  if (this->processor_id() == 0)
605  {
606  const hid_t file = H5Fopen(filename.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT);
607 
608  if (file == H5I_INVALID_HID)
609  libmesh_file_error(filename);
610 
611  group = H5Gopen(file, groupname.c_str(), H5P_DEFAULT);
612  check_open(group, groupname);
613 
614  auto read_size_attribute = [&filename, &group, &check_open, &check_hdf5]
615  (const std::string & attribute_name)
616  {
617  unsigned long long returnval = 0;
618 
619  const hid_t attr = H5Aopen(group, attribute_name.c_str(), H5P_DEFAULT);
620  check_open(attr, attribute_name);
621 
622  const hid_t attr_type = H5Aget_type(attr);
623  check_hdf5(attr_type, attribute_name + " type");
624 
625  // HDF5 will convert between the file's integer type and ours, but
626  // we do expect an integer type.
627  if (H5Tget_class(attr_type) != H5T_INTEGER)
628  libmesh_error_msg("Non-integer type for " + attribute_name + " in " + filename);
629 
630  H5Tclose(attr_type);
631 
632  // HDF5 is supposed to handle both upscaling and endianness
633  // conversions here
634  herr_t errval = H5Aread(attr, H5T_NATIVE_ULLONG, &returnval);
635  check_hdf5(errval, attribute_name + " read");
636 
637  H5Aclose(attr);
638 
639  return returnval;
640  };
641 
642  num_cols = read_size_attribute("num_cols");
643  num_rows = read_size_attribute("num_rows");
644 
645  this->comm().broadcast(num_cols);
646  this->comm().broadcast(num_rows);
647  }
648  else
649  {
650  this->comm().broadcast(num_cols);
651  this->comm().broadcast(num_rows);
652  }
653 
654  numeric_index_type new_row_start, new_row_stop,
655  new_col_start, new_col_stop;
656 
657  // If we need to reinit, we need to determine which rows+columns
658  // each processor is in charge of.
659  std::vector<numeric_index_type> new_row_starts, new_row_stops,
660  new_col_starts, new_col_stops;
661 
662  if (this->initialized() &&
663  num_cols == this->m() &&
664  num_rows == this->n())
665  {
666  new_row_start = this->row_start(),
667  new_row_stop = this->row_stop();
668 
669  new_col_start = this->col_start(),
670  new_col_stop = this->col_stop();
671  }
672  else
673  {
674  // Determine which rows/columns each processor will be in charge of
675  new_row_start = this->processor_id() * num_rows / this->n_processors(),
676  new_row_stop = (this->processor_id()+1) * num_rows / this->n_processors();
677 
678  new_col_start = this->processor_id() * num_cols / this->n_processors(),
679  new_col_stop = (this->processor_id()+1) * num_cols / this->n_processors();
680  }
681 
682  this->comm().gather(0, new_row_start, new_row_starts);
683  this->comm().gather(0, new_row_stop, new_row_stops);
684  this->comm().gather(0, new_col_start, new_col_starts);
685  this->comm().gather(0, new_col_stop, new_col_stops);
686 
687  numeric_index_type on_diagonal_nonzeros = 0,
688  off_diagonal_nonzeros = 0;
689 
690  std::vector<std::size_t> cols, row_offsets;
691  std::vector<double> vals;
692 
693  if (this->processor_id() == 0)
694  {
695  auto read_vector = [&filename, &group, &check_open, &check_hdf5]
696  (const std::string & dataname, auto hdf5_class,
697  auto hdf5_type, auto & datavec)
698  {
699  const hid_t data = H5Dopen1(group, dataname.c_str());
700  check_open(data, dataname.c_str());
701 
702  const hid_t data_type = H5Dget_type(data);
703  check_hdf5(data_type, dataname + " type");
704 
705  // HDF5 will convert between the file's integer type and ours, but
706  // we do expect an integer type.
707  if (H5Tget_class(data_type) != hdf5_class)
708  libmesh_error_msg("Unexpected type for " + dataname + " in " + filename);
709 
710  H5Tclose(data_type);
711 
712  const hid_t dataspace = H5Dget_space(data);
713  check_hdf5(dataspace, dataname + " space");
714 
715  int ndims = H5Sget_simple_extent_ndims(dataspace);
716  if (ndims != 1)
717  libmesh_error_msg("Non-vector space for " + dataname + " in " + filename);
718 
719  hsize_t len, maxlen;
720  herr_t errval = H5Sget_simple_extent_dims(dataspace, &len, &maxlen);
721  check_hdf5(errval, dataname + " dims");
722 
723  datavec.resize(len);
724 
725  errval = H5Dread(data, hdf5_type, H5S_ALL, H5S_ALL, H5P_DEFAULT, datavec.data());
726  check_hdf5(errval, dataname + " read");
727  };
728 
729  read_vector("cols", H5T_INTEGER, H5T_NATIVE_ULLONG, cols);
730  read_vector("row_offsets", H5T_INTEGER, H5T_NATIVE_ULLONG, row_offsets);
731  read_vector("vals", H5T_FLOAT, H5T_NATIVE_DOUBLE, vals);
732 
733  if (cols.size() != vals.size())
734  libmesh_error_msg("Inconsistent cols/vals sizes in " + filename);
735 
736  if (row_offsets.size() != num_rows + 1)
737  libmesh_error_msg("Inconsistent row_offsets size in " + filename);
738 
739  // Data for the row we're working on
740  numeric_index_type current_row = 0;
741  processor_id_type current_proc = 0;
742  numeric_index_type current_on_diagonal_nonzeros = 0;
743  numeric_index_type current_off_diagonal_nonzeros = 0;
744  if (row_offsets[0] != 0)
745  libmesh_error_msg("Unexpected row_offsets[0] in " + filename);
746 
747  for (auto i : index_range(cols))
748  {
749  while (row_offsets[current_row+1] <= i)
750  {
751  ++current_row;
752  if (row_offsets[current_row] < row_offsets[current_row-1])
753  libmesh_error_msg("Non-monotonic row_offsets in " + filename);
754  current_on_diagonal_nonzeros = 0;
755  current_off_diagonal_nonzeros = 0;
756  }
757 
758  while (current_row >= (new_row_stops[current_proc]+1))
759  ++current_proc;
760 
761  // 0-based indexing in file
762  if (cols[i] >= new_col_starts[current_proc] &&
763  cols[i] < new_col_stops[current_proc])
764  {
765  ++current_on_diagonal_nonzeros;
766  on_diagonal_nonzeros =
767  std::max(on_diagonal_nonzeros,
768  current_on_diagonal_nonzeros);
769  }
770  else
771  {
772  ++current_off_diagonal_nonzeros;
773  off_diagonal_nonzeros =
774  std::max(off_diagonal_nonzeros,
775  current_off_diagonal_nonzeros);
776  }
777  }
778  }
779 
780  this->comm().broadcast(on_diagonal_nonzeros);
781  this->comm().broadcast(off_diagonal_nonzeros);
782 
783  this->init(num_rows, num_cols,
784  new_row_stop-new_row_start,
785  new_col_stop-new_col_start,
786  on_diagonal_nonzeros,
787  off_diagonal_nonzeros);
788 
789  // Set the matrix values last.
790  if (this->processor_id() == 0)
791  {
792  numeric_index_type current_row = 0;
793  for (auto i : index_range(cols))
794  {
795  while (row_offsets[current_row+1] <= i)
796  {
797  ++current_row;
798  libmesh_assert_greater_equal (row_offsets[current_row],
799  row_offsets[current_row-1]);
800  }
801  this->set(current_row, cols[i], vals[i]);
802  }
803  }
804 
805  this->close();
806 #endif // LIBMESH_HAVE_HDF5
807 }
virtual bool initialized() const
MPI_Datatype data_type
void gather(const unsigned int root_id, const T &send_data, std::vector< T, A > &recv) const
const Parallel::Communicator & comm() const
virtual numeric_index_type row_stop() const =0
uint8_t processor_id_type
processor_id_type n_processors() const
void libmesh_ignore(const Args &...)
dof_id_type numeric_index_type
Definition: id_types.h:99
virtual numeric_index_type m() const =0
virtual numeric_index_type col_stop() const =0
virtual numeric_index_type col_start() const =0
void broadcast(T &data, const unsigned int root_id=0, const bool identical_sizes=false) const
virtual void close()=0
Calls the SparseMatrix&#39;s internal assembly routines, ensuring that the values are consistent across p...
virtual numeric_index_type row_start() const =0
processor_id_type processor_id() const
auto index_range(const T &sizable)
Helper function that returns an IntRange<std::size_t> representing all the indices of the passed-in v...
Definition: int_range.h:117
virtual numeric_index_type n() const =0
virtual void init(const numeric_index_type m, const numeric_index_type n, const numeric_index_type m_l, const numeric_index_type n_l, const numeric_index_type nnz=30, const numeric_index_type noz=10, const numeric_index_type blocksize=1)=0
Initialize SparseMatrix with the specified sizes.

◆ read_matlab()

template<typename T >
void libMesh::SparseMatrix< T >::read_matlab ( const std::string &  filename)
virtualinherited

Read the contents of the matrix from the Matlab-script sparse matrix format used by PETSc.

If the size and sparsity of the matrix in filename appears consistent with the existing sparsity of this then the existing parallel decomposition and sparsity will be retained. If not, then this will be initialized with the sparsity from the file, linearly partitioned onto the number of processors available.

Definition at line 812 of file sparse_matrix.C.

Referenced by ConstraintOperatorTest::test1DCoarseningNewNodes().

813 {
814  LOG_SCOPE("read_matlab()", "SparseMatrix");
815 
816 #ifndef LIBMESH_HAVE_CXX11_REGEX
817  libmesh_not_implemented(); // What is your compiler?!? Email us!
818  libmesh_ignore(filename);
819 #else
820  parallel_object_only();
821 
822  const bool gzipped_file = Utility::ends_with(filename, ".gz");
823 
824  // The sizes we get from the file
825  std::size_t m = 0,
826  n = 0;
827 
828  // If we don't already have this size, we'll need to reinit, and
829  // determine which rows+columns each processor is in charge of.
830  std::vector<numeric_index_type> new_row_starts, new_row_stops,
831  new_col_starts, new_col_stops;
832 
833  numeric_index_type new_row_start, new_row_stop,
834  new_col_start, new_col_stop;
835 
836  // We'll read through the file three times: once to get a reliable
837  // value for the matrix size (so we can divvy it up among
838  // processors), then again to get the sparsity to send to each
839  // processor, then a final time to get the entries to send to each
840  // processor.
841  //
842  // We'll use an istream here; it might be an ifstream if we're
843  // opening a raw ASCII file or a gzstream if we're opening a
844  // compressed one.
845  std::unique_ptr<std::istream> file;
846 
847  // We'll need a temporary structure to cache matrix entries, because
848  // we need to read through the whole file before we know the size
849  // and sparsity structure with which we can init().
850  //
851  // Reading through the file three times via `seekg` doesn't work
852  // with our gzstream wrapper, and seems to take three times as long
853  // even with a plain ifstream. What happened to disk caching!?
854  std::vector<std::tuple<numeric_index_type, numeric_index_type, T>> entries;
855 
856  // First read through the file, saving size and entry data
857  {
858  // We'll read the matrix on processor 0 rather than try to juggle
859  // parallel I/O.
860  if (this->processor_id() == 0)
861  {
862  // We'll be using regular expressions to make ourselves slightly
863  // more robust to formatting.
864  const std::regex start_regex // assignment like "zzz = ["
865  ("\\s*\\w+\\s*=\\s*\\[");
866  const std::regex end_regex // end of assignment
867  ("^[^%]*\\]");
868 
869  if (gzipped_file)
870  {
871 #ifdef LIBMESH_HAVE_GZSTREAM
872  auto inf = std::make_unique<igzstream>();
873  libmesh_assert(inf);
874  inf->open(filename.c_str(), std::ios::in);
875  file = std::move(inf);
876 #else
877  libmesh_error_msg("ERROR: need gzstream to handle .gz files!!!");
878 #endif
879  }
880  else
881  {
882  auto inf = std::make_unique<std::ifstream>();
883  libmesh_assert(inf);
884 
885  std::string new_name = Utility::unzip_file(filename);
886 
887  inf->open(new_name.c_str(), std::ios::in);
888  file = std::move(inf);
889  }
890 
891  // If we have a matrix with all-zero trailing rows, the only
892  // way to get the size is if it ended up in a comment
893  const std::regex size_regex // comment like "% size = 8 8"
894  ("%\\s*[Ss][Ii][Zz][Ee]\\s*=\\s*(\\d+)\\s+(\\d+)");
895  const std::string whitespace = " \t";
896 
897  bool have_started = false;
898  bool have_ended = false;
899  std::size_t largest_i_seen = 0, largest_j_seen = 0;
900 
901  // Data for the row we're working on
902  // Use 1-based indexing for current_row, as in the file
903  std::size_t current_row = 1;
904 
905  for (std::string line; std::getline(*file, line);)
906  {
907  std::smatch sm;
908 
909  // First, try to match an entry. This is the most common
910  // case so we won't rely on slow std::regex for it.
911  // stringstream is at least an improvement over that.
912 
913  // Look for row/col/val like "1 1 -2.0e-4"
914 
915  std::istringstream l(line);
916 
917  std::size_t i, j;
918  T value;
919 
920  l >> i >> j >> value;
921 
922  if (!l.fail())
923  {
924  libmesh_error_msg_if
925  (!have_started, "Confused by premature entries in matrix file " << filename);
926 
927  entries.emplace_back(cast_int<numeric_index_type>(i),
928  cast_int<numeric_index_type>(j),
929  value);
930 
931  libmesh_error_msg_if
932  (!i || !j, "Expected 1-based indexing in matrix file "
933  << filename);
934 
935  current_row = std::max(current_row, i);
936 
937  libmesh_error_msg_if
938  (i < current_row,
939  "Can't handle out-of-order entries in matrix file "
940  << filename);
941 
942  largest_i_seen = std::max(i, largest_i_seen);
943  largest_j_seen = std::max(j, largest_j_seen);
944  }
945 
946  else if (std::regex_search(line, sm, size_regex))
947  {
948  const std::string msize = sm[1];
949  const std::string nsize = sm[2];
950  m = std::stoull(msize);
951  n = std::stoull(nsize);
952  }
953 
954  else if (std::regex_search(line, start_regex))
955  have_started = true;
956 
957  else if (std::regex_search(line, end_regex))
958  {
959  have_ended = true;
960  break;
961  }
962  }
963 
964  libmesh_error_msg_if
965  (!have_started, "Confused by missing assignment beginning in matrix file " << filename);
966 
967  libmesh_error_msg_if
968  (!have_ended, "Confused by missing assignment ending in matrix file " << filename);
969 
970  libmesh_error_msg_if
971  (m > largest_i_seen, "Confused by missing final row(s) in matrix file " << filename);
972 
973  libmesh_error_msg_if
974  (m > 0 && m < largest_i_seen, "Confused by extra final row(s) in matrix file " << filename);
975 
976  if (!m)
977  m = largest_i_seen;
978 
979  libmesh_error_msg_if
980  (n > largest_j_seen, "Confused by missing final column(s) in matrix file " << filename);
981 
982  libmesh_error_msg_if
983  (n > 0 && n < largest_j_seen, "Confused by extra final column(s) in matrix file " << filename);
984 
985  if (!n)
986  n = largest_j_seen;
987 
988  this->comm().broadcast(m);
989  this->comm().broadcast(n);
990  }
991  else
992  {
993  this->comm().broadcast(m);
994  this->comm().broadcast(n);
995  }
996 
997  if (this->initialized() &&
998  m == this->m() &&
999  n == this->n())
1000  {
1001  new_row_start = this->row_start(),
1002  new_row_stop = this->row_stop();
1003 
1004  new_col_start = this->col_start(),
1005  new_col_stop = this->col_stop();
1006  }
1007  else
1008  {
1009  // Determine which rows/columns each processor will be in charge of
1010  new_row_start = this->processor_id() * m / this->n_processors(),
1011  new_row_stop = (this->processor_id()+1) * m / this->n_processors();
1012 
1013  new_col_start = this->processor_id() * n / this->n_processors(),
1014  new_col_stop = (this->processor_id()+1) * n / this->n_processors();
1015  }
1016 
1017  this->comm().gather(0, new_row_start, new_row_starts);
1018  this->comm().gather(0, new_row_stop, new_row_stops);
1019  this->comm().gather(0, new_col_start, new_col_starts);
1020  this->comm().gather(0, new_col_stop, new_col_stops);
1021 
1022  } // Done reading entry data and broadcasting matrix size
1023 
1024  // Calculate the matrix sparsity and initialize it second
1025  {
1026  // Deduce the sparsity pattern, or at least the maximum number of
1027  // on- and off- diagonal non-zeros per row.
1028  numeric_index_type on_diagonal_nonzeros =0,
1029  off_diagonal_nonzeros =0;
1030 
1031  if (this->processor_id() == 0)
1032  {
1033  // Data for the row we're working on
1034  // Use 1-based indexing for current_row, as in the file
1035  numeric_index_type current_row = 1;
1036  processor_id_type current_proc = 0;
1037  numeric_index_type current_on_diagonal_nonzeros = 0;
1038  numeric_index_type current_off_diagonal_nonzeros = 0;
1039 
1040  for (auto [i, j, value] : entries)
1041  {
1042  if (i > current_row)
1043  {
1044  current_row = i;
1045  // +1 for 1-based indexing in file
1046  while (current_row >= (new_row_stops[current_proc]+1))
1047  ++current_proc;
1048  current_on_diagonal_nonzeros = 0;
1049  current_off_diagonal_nonzeros = 0;
1050  }
1051 
1052  // +1 for 1-based indexing in file
1053  if (j >= (new_col_starts[current_proc]+1) &&
1054  j < (new_col_stops[current_proc]+1))
1055  {
1056  ++current_on_diagonal_nonzeros;
1057  on_diagonal_nonzeros =
1058  std::max(on_diagonal_nonzeros,
1059  current_on_diagonal_nonzeros);
1060  }
1061  else
1062  {
1063  ++current_off_diagonal_nonzeros;
1064  off_diagonal_nonzeros =
1065  std::max(off_diagonal_nonzeros,
1066  current_off_diagonal_nonzeros);
1067  }
1068  }
1069  }
1070 
1071  this->comm().broadcast(on_diagonal_nonzeros);
1072  this->comm().broadcast(off_diagonal_nonzeros);
1073 
1074  this->init(m, n,
1075  new_row_stop-new_row_start,
1076  new_col_stop-new_col_start,
1077  on_diagonal_nonzeros,
1078  off_diagonal_nonzeros);
1079  }
1080 
1081  // Set the matrix values last.
1082  // Convert from 1-based to 0-based indexing
1083  if (this->processor_id() == 0)
1084  for (auto [i, j, value] : entries)
1085  this->set(i-1, j-1, value);
1086 
1087  this->close();
1088 #endif
1089 }
virtual bool initialized() const
bool ends_with(std::string_view superstring, std::string_view suffix)
Look for a substring at the very end of a string.
Definition: utility.C:213
void gather(const unsigned int root_id, const T &send_data, std::vector< T, A > &recv) const
const Parallel::Communicator & comm() const
virtual numeric_index_type row_stop() const =0
uint8_t processor_id_type
processor_id_type n_processors() const
void libmesh_ignore(const Args &...)
dof_id_type numeric_index_type
Definition: id_types.h:99
virtual numeric_index_type m() const =0
std::string unzip_file(std::string_view name)
Create an unzipped copy of a bz2 or xz file, returning the name of the now-unzipped file that can be ...
Definition: utility.C:164
libmesh_assert(ctx)
virtual numeric_index_type col_stop() const =0
virtual numeric_index_type col_start() const =0
void broadcast(T &data, const unsigned int root_id=0, const bool identical_sizes=false) const
virtual void close()=0
Calls the SparseMatrix&#39;s internal assembly routines, ensuring that the values are consistent across p...
virtual numeric_index_type row_start() const =0
static const bool value
Definition: xdr_io.C:55
processor_id_type processor_id() const
virtual numeric_index_type n() const =0
virtual void init(const numeric_index_type m, const numeric_index_type n, const numeric_index_type m_l, const numeric_index_type n_l, const numeric_index_type nnz=30, const numeric_index_type noz=10, const numeric_index_type blocksize=1)=0
Initialize SparseMatrix with the specified sizes.

◆ read_petsc_binary()

template<typename T >
void libMesh::PetscMatrix< T >::read_petsc_binary ( const std::string &  filename)
overridevirtual

Read the contents of the matrix from a file in PETSc's binary sparse matrix format.

Reimplemented from libMesh::SparseMatrix< T >.

Definition at line 711 of file petsc_matrix.C.

712 {
713  LOG_SCOPE("read_petsc_binary()", "PetscMatrix");
714 
715  this->_petsc_viewer(filename, PETSCVIEWERBINARY, FILE_MODE_READ);
716 }
void _petsc_viewer(const std::string &filename, PetscViewerType viewertype, PetscFileMode filemode)
Definition: petsc_matrix.C:661

◆ read_petsc_hdf5()

template<typename T >
void libMesh::PetscMatrix< T >::read_petsc_hdf5 ( const std::string &  filename)
overridevirtual

Read the contents of the matrix from a file in PETSc's HDF5 sparse matrix format.

Reimplemented from libMesh::SparseMatrix< T >.

Definition at line 721 of file petsc_matrix.C.

722 {
723  LOG_SCOPE("read_petsc_hdf5()", "PetscMatrix");
724 
725  this->_petsc_viewer(filename, PETSCVIEWERHDF5, FILE_MODE_READ);
726 }
void _petsc_viewer(const std::string &filename, PetscViewerType viewertype, PetscFileMode filemode)
Definition: petsc_matrix.C:661

◆ reinit_submatrix()

template<typename T>
virtual void libMesh::SparseMatrix< T >::reinit_submatrix ( SparseMatrix< T > &  submatrix,
const std::vector< numeric_index_type > &  rows,
const std::vector< numeric_index_type > &  cols 
) const
inlinevirtualinherited

This function is similar to the one above, but it allows you to reuse the existing sparsity pattern of "submatrix" instead of reallocating it again.

This should hopefully be more efficient if you are frequently extracting submatrices of the same size.

Definition at line 551 of file sparse_matrix.h.

554  {
555  this->_get_submatrix(submatrix,
556  rows,
557  cols,
558  true); // true means REUSE submatrix
559  }
virtual void _get_submatrix(SparseMatrix< T > &, const std::vector< numeric_index_type > &, const std::vector< numeric_index_type > &, const bool) const
Protected implementation of the create_submatrix and reinit_submatrix routines.

◆ require_sparsity_pattern()

template<typename T>
virtual bool libMesh::SparseMatrix< T >::require_sparsity_pattern ( ) const
inlinevirtualinherited
Returns
Whether this matrix needs the sparsity pattern computed by the DofMap

Reimplemented in libMesh::StaticCondensation, libMesh::PetscMatrixShellMatrix< T >, and libMesh::PetscMatrixShellMatrix< Number >.

Definition at line 168 of file sparse_matrix.h.

168 { return !this->use_hash_table(); }
bool use_hash_table() const

◆ reset_preallocation()

template<typename T >
void libMesh::PetscMatrix< T >::reset_preallocation ( )

Reset matrix to use the original nonzero pattern provided by users.

Definition at line 385 of file petsc_matrix.C.

References libMesh::initialized(), and libMesh::libmesh_assert().

386 {
387  semiparallel_only();
388 
389 #if !PETSC_VERSION_LESS_THAN(3,9,0)
390  libmesh_assert (this->initialized());
391 
392  LibmeshPetscCall(MatResetPreallocation(this->_mat));
393 #else
394  libmesh_warning("Your version of PETSc doesn't support resetting of "
395  "preallocation, so we will use your most recent sparsity "
396  "pattern. This may result in a degradation of performance\n");
397 #endif
398 }
virtual bool initialized() const
libmesh_assert(ctx)
Mat _mat
PETSc matrix datatype to store values.

◆ restore_original_nonzero_pattern()

template<typename T >
void libMesh::PetscMatrix< T >::restore_original_nonzero_pattern ( )
overridevirtual

Reset the memory storage of the matrix.

Unlike clear(), this does not destroy the matrix but rather will reset the matrix to use the original preallocation or when using hash table matrix assembly (see use_hash_table()) will reset (clear) the hash table used for assembly. In the words of the MatResetPreallocation documentation in PETSc, 'current values in the matrix are lost in this call', so a user can expect to have back their original sparsity pattern in a zeroed state

Reimplemented from libMesh::SparseMatrix< T >.

Definition at line 1263 of file petsc_matrix.C.

1264 {
1265  semiparallel_only();
1266 
1267  if (this->_use_hash_table)
1268 #if PETSC_RELEASE_GREATER_EQUALS(3, 23, 0)
1269  // This performs MatReset plus re-establishes the hash table
1270  LibmeshPetscCall(MatResetHash(this->_mat));
1271 #else
1272  libmesh_error_msg("Resetting hash tables not supported until PETSc version 3.23");
1273 #endif
1274  else
1275  this->reset_preallocation();
1276 }
void reset_preallocation()
Reset matrix to use the original nonzero pattern provided by users.
Definition: petsc_matrix.C:385
Mat _mat
PETSc matrix datatype to store values.
bool _use_hash_table
Flag indicating whether the matrix is assembled using a hash table.

◆ row_start()

template<typename T >
numeric_index_type libMesh::PetscMatrixBase< T >::row_start ( ) const
overridevirtualinherited
Returns
The index of the first matrix row stored on this processor.

Implements libMesh::SparseMatrix< T >.

Reimplemented in libMesh::StaticCondensation, and libMesh::StaticCondensation.

Definition at line 178 of file petsc_matrix_base.C.

179 {
180  libmesh_assert (this->initialized());
181 
182  PetscInt start=0, stop=0;
183 
184  LibmeshPetscCall(MatGetOwnershipRange(this->_mat, &start, &stop));
185 
186  return static_cast<numeric_index_type>(start);
187 }
virtual bool initialized() const
dof_id_type numeric_index_type
Definition: id_types.h:99
libmesh_assert(ctx)
void stop(const char *file, int line, const char *date, const char *time)
Mat _mat
PETSc matrix datatype to store values.

◆ row_stop()

template<typename T >
numeric_index_type libMesh::PetscMatrixBase< T >::row_stop ( ) const
overridevirtualinherited
Returns
The index of the last matrix row (+1) stored on this processor.

Implements libMesh::SparseMatrix< T >.

Reimplemented in libMesh::StaticCondensation, and libMesh::StaticCondensation.

Definition at line 190 of file petsc_matrix_base.C.

191 {
192  libmesh_assert (this->initialized());
193 
194  PetscInt start=0, stop=0;
195 
196  LibmeshPetscCall(MatGetOwnershipRange(this->_mat, &start, &stop));
197 
198  return static_cast<numeric_index_type>(stop);
199 }
virtual bool initialized() const
dof_id_type numeric_index_type
Definition: id_types.h:99
libmesh_assert(ctx)
void stop(const char *file, int line, const char *date, const char *time)
Mat _mat
PETSc matrix datatype to store values.

◆ scale()

template<typename T >
void libMesh::PetscMatrix< T >::scale ( const T  scale)
overridevirtual

Scales all elements of this matrix by scale.

Reimplemented from libMesh::SparseMatrix< T >.

Definition at line 1230 of file petsc_matrix.C.

References libMesh::closed(), libMesh::libmesh_assert(), libMesh::PS(), and libMesh::MeshTools::Modification::scale().

1231 {
1232  libmesh_assert(this->closed());
1233 
1234  LibmeshPetscCall(MatScale(this->_mat, PS(scale)));
1235 }
PetscScalar PS(T val)
Definition: petsc_macro.h:168
libmesh_assert(ctx)
Mat _mat
PETSc matrix datatype to store values.
virtual bool closed() const override
virtual void scale(const T scale) override
Scales all elements of this matrix by scale.

◆ set()

template<typename T >
void libMesh::PetscMatrix< T >::set ( const numeric_index_type  i,
const numeric_index_type  j,
const T  value 
)
overridevirtual

Set the element (i,j) to value.

Throws an error if the entry does not exist. Zero values can be "stored" in non-existent fields.

Implements libMesh::SparseMatrix< T >.

Definition at line 968 of file petsc_matrix.C.

References libMesh::initialized(), libMesh::libmesh_assert(), and value.

971 {
972  libmesh_assert (this->initialized());
973 
974  PetscInt i_val=i, j_val=j;
975 
976  PetscScalar petsc_value = static_cast<PetscScalar>(value);
977  std::scoped_lock lock(this->_petsc_matrix_mutex);
978  LibmeshPetscCall(MatSetValues(this->_mat, 1, &i_val, 1, &j_val,
979  &petsc_value, INSERT_VALUES));
980 }
virtual bool initialized() const
std::mutex _petsc_matrix_mutex
Definition: petsc_matrix.h:353
libmesh_assert(ctx)
Mat _mat
PETSc matrix datatype to store values.
static const bool value
Definition: xdr_io.C:55

◆ set_context()

template<typename T >
void libMesh::PetscMatrixBase< T >::set_context ( )
inherited

Set the context (ourself) for _mat.

Definition at line 105 of file petsc_matrix_base.C.

106 {
107  libmesh_assert(this->_mat);
108  PetscContainer container;
109  LibmeshPetscCall(PetscContainerCreate(this->comm().get(), &container));
110  LibmeshPetscCall(PetscContainerSetPointer(container, this));
111  LibmeshPetscCall(PetscObjectCompose((PetscObject)(Mat)this->_mat, "PetscMatrixCtx", (PetscObject)container));
112  LibmeshPetscCall(PetscContainerDestroy(&container));
113 }
const Parallel::Communicator & comm() const
libmesh_assert(ctx)
Mat _mat
PETSc matrix datatype to store values.

◆ set_destroy_mat_on_exit()

template<typename T >
void libMesh::PetscMatrixBase< T >::set_destroy_mat_on_exit ( bool  destroy = true)
inherited

If set to false, we don't delete the Mat on destruction and allow instead for PETSc to manage it.

Definition at line 91 of file petsc_matrix_base.C.

92 {
94 }
bool _destroy_mat_on_exit
This boolean value should only be set to false for the constructor which takes a PETSc Mat object...
void destroy(triangulateio &t, IO_Type)
Frees any memory which has been dynamically allocated by Triangle.

◆ solver_package()

template<typename T>
virtual SolverPackage libMesh::PetscMatrixBase< T >::solver_package ( )
inlineoverridevirtualinherited

Implements libMesh::SparseMatrix< T >.

Reimplemented in libMesh::StaticCondensation, and libMesh::StaticCondensation.

Definition at line 107 of file petsc_matrix_base.h.

108  {
109  return PETSC_SOLVERS;
110  }

◆ supports_hash_table()

template<typename T >
bool libMesh::PetscMatrix< T >::supports_hash_table ( ) const
overridevirtual
Returns
Whether the matrix supports hash table assembly

Reimplemented from libMesh::SparseMatrix< T >.

Definition at line 1238 of file petsc_matrix.C.

1239 {
1240 #if PETSC_RELEASE_LESS_THAN(3,19,0)
1241  return false;
1242 #else
1243  return true;
1244 #endif
1245 }

◆ swap()

template<typename T>
void libMesh::PetscMatrixBase< T >::swap ( PetscMatrixBase< T > &  m_in)
inherited

Swaps the internal data pointers of two PetscMatrices, no actual values are swapped.

Definition at line 98 of file petsc_matrix_base.C.

Referenced by DMlibMeshJacobian().

99 {
100  std::swap(_mat, m_in._mat);
101  std::swap(_destroy_mat_on_exit, m_in._destroy_mat_on_exit);
102 }
bool _destroy_mat_on_exit
This boolean value should only be set to false for the constructor which takes a PETSc Mat object...
Mat _mat
PETSc matrix datatype to store values.

◆ update_preallocation_and_zero()

template<typename T >
void libMesh::PetscMatrix< T >::update_preallocation_and_zero ( )

Update the sparsity pattern based on dof_map, and set the matrix to zero.

This is useful in cases where the sparsity pattern changes during a computation.

Definition at line 379 of file petsc_matrix.C.

380 {
381  libmesh_not_implemented();
382 }

◆ update_sparsity_pattern()

template<typename T>
virtual void libMesh::SparseMatrix< T >::update_sparsity_pattern ( const SparsityPattern::Graph )
inlinevirtualinherited

Updates the matrix sparsity pattern.

When your SparseMatrix<T> implementation does not need this data, simply do not override this method.

Reimplemented in libMesh::EpetraMatrix< T >, and libMesh::LaspackMatrix< T >.

Definition at line 175 of file sparse_matrix.h.

Referenced by libMesh::DofMap::update_sparsity_pattern().

175 {}

◆ use_hash_table() [1/2]

template<typename T >
void libMesh::SparseMatrix< T >::use_hash_table ( bool  use_hash)
inherited

Sets whether to use hash table assembly.

This will error if the passed-in value is true and the matrix type does not support hash tables. Hash table or hash map assembly means storing maps from i-j locations in the matrix to values. Because it is a hash map as opposed to a contiguous array of data, no preallocation is required to use it

Definition at line 678 of file sparse_matrix.h.

Referenced by PetscMatrixTest::testPetscCopyFromHash().

679 {
680  libmesh_error_msg_if(use_hash && !this->supports_hash_table(),
681  "This matrix class does not support hash table assembly");
682  this->_use_hash_table = use_hash;
683 }
bool _use_hash_table
Flag indicating whether the matrix is assembled using a hash table.
virtual bool supports_hash_table() const

◆ use_hash_table() [2/2]

template<typename T>
bool libMesh::SparseMatrix< T >::use_hash_table ( ) const
inlineinherited
Returns
Whether this matrix is using hash table assembly. Hash table or hash map assembly means storing maps from i-j locations in the matrix to values. Because it is a hash map as opposed to a contiguous array of data, no preallocation is required to use it

Definition at line 620 of file sparse_matrix.h.

Referenced by libMesh::SparseMatrix< ValOut >::require_sparsity_pattern().

620 { return _use_hash_table; }
bool _use_hash_table
Flag indicating whether the matrix is assembled using a hash table.

◆ vector_mult()

template<typename T>
void libMesh::SparseMatrix< T >::vector_mult ( NumericVector< T > &  dest,
const NumericVector< T > &  arg 
) const
inherited

Multiplies the matrix by the NumericVector arg and stores the result in NumericVector dest.

Definition at line 214 of file sparse_matrix.C.

Referenced by libMesh::TransientRBConstruction::add_IC_to_RB_space(), libMesh::RBSCMConstruction::Aq_inner_product(), libMesh::AdvectionSystem::assemble_claw_rhs(), libMesh::RBSCMConstruction::B_inner_product(), libMesh::RBConstruction::compute_Fq_representor_innerprods(), libMesh::RBConstruction::compute_output_dual_innerprods(), libMesh::RBConstruction::compute_residual_dual_norm_slow(), libMesh::TransientRBConstruction::enrich_RB_space(), libMesh::RBConstruction::enrich_RB_space(), AssembleOptimization::gradient(), libMesh::TransientRBConstruction::mass_matrix_scaled_matvec(), AssembleOptimization::objective(), libMesh::RBConstruction::print_basis_function_orthogonality(), libMesh::ImplicitSystem::qoi_parameter_hessian(), libMesh::ImplicitSystem::qoi_parameter_hessian_vector_product(), libMesh::TransientRBConstruction::set_error_temporal_data(), libMesh::RBConstruction::train_reduced_basis_with_POD(), libMesh::TransientRBConstruction::truth_assembly(), libMesh::RBConstruction::truth_solve(), libMesh::TransientRBConstruction::update_RB_system_matrices(), libMesh::RBConstruction::update_RB_system_matrices(), libMesh::TransientRBConstruction::update_residual_terms(), and libMesh::RBConstruction::update_residual_terms().

216 {
217  dest.zero();
218  this->vector_mult_add(dest,arg);
219 }
void vector_mult_add(NumericVector< T > &dest, const NumericVector< T > &arg) const
Multiplies the matrix by the NumericVector arg and adds the result to the NumericVector dest...

◆ vector_mult_add()

template<typename T>
void libMesh::SparseMatrix< T >::vector_mult_add ( NumericVector< T > &  dest,
const NumericVector< T > &  arg 
) const
inherited

Multiplies the matrix by the NumericVector arg and adds the result to the NumericVector dest.

Definition at line 224 of file sparse_matrix.C.

Referenced by libMesh::ImplicitSystem::weighted_sensitivity_adjoint_solve().

226 {
227  /* This functionality is actually implemented in the \p
228  NumericVector class. */
229  dest.add_vector(arg,*this);
230 }

◆ zero()

template<typename T >
void libMesh::PetscMatrix< T >::zero ( )
overridevirtual

Set all entries to 0.

Implements libMesh::SparseMatrix< T >.

Definition at line 401 of file petsc_matrix.C.

References libMesh::initialized(), and libMesh::libmesh_assert().

402 {
403  libmesh_assert (this->initialized());
404 
405  semiparallel_only();
406 
407  PetscInt m_l, n_l;
408 
409  LibmeshPetscCall(MatGetLocalSize(this->_mat,&m_l,&n_l));
410 
411  if (n_l)
412  LibmeshPetscCall(MatZeroEntries(this->_mat));
413 }
virtual bool initialized() const
libmesh_assert(ctx)
Mat _mat
PETSc matrix datatype to store values.

◆ zero_clone()

template<typename T >
std::unique_ptr< SparseMatrix< T > > libMesh::PetscMatrix< T >::zero_clone ( ) const
overridevirtual
Returns
A smart pointer to a copy of this matrix with the same type, size, and partitioning, but with all zero entries.
Note
This must be overridden in the derived classes.

Implements libMesh::SparseMatrix< T >.

Definition at line 435 of file petsc_matrix.C.

References libMesh::closed().

436 {
437  libmesh_error_msg_if(!this->closed(), "Matrix must be closed before it can be cloned!");
438 
439  // Copy the nonzero pattern only
440  Mat copy;
441  LibmeshPetscCall(MatDuplicate(this->_mat, MAT_DO_NOT_COPY_VALUES, &copy));
442 
443  // Call wrapping PetscMatrix constructor, have it take over
444  // ownership.
445  auto ret = std::make_unique<PetscMatrix<T>>(copy, this->comm());
446  ret->set_destroy_mat_on_exit(true);
447 
448  return ret;
449 }
const Parallel::Communicator & comm() const
Mat _mat
PETSc matrix datatype to store values.
virtual bool closed() const override

◆ zero_rows()

template<typename T >
void libMesh::PetscMatrix< T >::zero_rows ( std::vector< numeric_index_type > &  rows,
diag_value = 0.0 
)
overridevirtual

Sets all row entries to 0 then puts diag_value in the diagonal entry.

Reimplemented from libMesh::SparseMatrix< T >.

Definition at line 416 of file petsc_matrix.C.

References libMesh::initialized(), libMesh::libmesh_assert(), libMesh::numeric_petsc_cast(), and libMesh::PS().

417 {
418  libmesh_assert (this->initialized());
419 
420  semiparallel_only();
421 
422  // As of petsc-dev at the time of 3.1.0, MatZeroRows now takes two additional
423  // optional arguments. The optional arguments (x,b) can be used to specify the
424  // solutions for the zeroed rows (x) and right hand side (b) to update.
425  // Could be useful for setting boundary conditions...
426  if (!rows.empty())
427  LibmeshPetscCall(MatZeroRows(this->_mat, cast_int<PetscInt>(rows.size()),
428  numeric_petsc_cast(rows.data()), PS(diag_value),
429  NULL, NULL));
430  else
431  LibmeshPetscCall(MatZeroRows(this->_mat, 0, NULL, PS(diag_value), NULL, NULL));
432 }
virtual bool initialized() const
PetscInt * numeric_petsc_cast(const numeric_index_type *p)
PetscScalar PS(T val)
Definition: petsc_macro.h:168
libmesh_assert(ctx)
Mat _mat
PETSc matrix datatype to store values.

Friends And Related Function Documentation

◆ ::PetscMatrixTest

template<typename T>
friend class ::PetscMatrixTest
friend

Definition at line 366 of file petsc_matrix.h.

Member Data Documentation

◆ _communicator

const Parallel::Communicator& libMesh::ParallelObject::_communicator
protectedinherited

◆ _counts

ReferenceCounter::Counts libMesh::ReferenceCounter::_counts
staticprotectedinherited

Actually holds the data.

Definition at line 124 of file reference_counter.h.

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

◆ _destroy_mat_on_exit

template<typename T>
bool libMesh::PetscMatrixBase< T >::_destroy_mat_on_exit
protectedinherited

This boolean value should only be set to false for the constructor which takes a PETSc Mat object.

Definition at line 186 of file petsc_matrix_base.h.

Referenced by libMesh::PetscMatrixBase< Number >::swap().

◆ _dof_map

template<typename T>
DofMap const* libMesh::SparseMatrix< T >::_dof_map
protectedinherited

The DofMap object associated with this object.

May be queried for degree-of-freedom counts on processors.

Definition at line 652 of file sparse_matrix.h.

◆ _enable_print_counter

bool libMesh::ReferenceCounter::_enable_print_counter = true
staticprotectedinherited

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

Definition at line 143 of file reference_counter.h.

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

◆ _is_initialized

template<typename T>
bool libMesh::SparseMatrix< T >::_is_initialized
protectedinherited

◆ _mat

template<typename T>
Mat libMesh::PetscMatrixBase< T >::_mat
protectedinherited

◆ _mat_type

template<typename T>
PetscMatrixType libMesh::PetscMatrix< T >::_mat_type
protected

Definition at line 349 of file petsc_matrix.h.

Referenced by libMesh::PetscMatrix< T >::PetscMatrix().

◆ _mutex

Threads::spin_mutex libMesh::ReferenceCounter::_mutex
staticprotectedinherited

Mutual exclusion object to enable thread-safe reference counting.

Definition at line 137 of file reference_counter.h.

◆ _n_objects

Threads::atomic< unsigned int > libMesh::ReferenceCounter::_n_objects
staticprotectedinherited

The number of objects.

Print the reference count information when the number returns to 0.

Definition at line 132 of file reference_counter.h.

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

◆ _petsc_matrix_mutex [1/2]

template<typename T>
std::mutex libMesh::PetscMatrix< T >::_petsc_matrix_mutex
mutableprivate

Definition at line 353 of file petsc_matrix.h.

◆ _petsc_matrix_mutex [2/2]

template<typename T>
Threads::spin_mutex libMesh::PetscMatrix< T >::_petsc_matrix_mutex
mutableprivate

Definition at line 355 of file petsc_matrix.h.

◆ _sp

template<typename T>
SparsityPattern::Build const* libMesh::SparseMatrix< T >::_sp
protectedinherited

The sparsity pattern associated with this object.

Should be queried for entry counts (or with need_full_sparsity_pattern, patterns) when needed.

Definition at line 659 of file sparse_matrix.h.

◆ _use_hash_table

template<typename T>
bool libMesh::SparseMatrix< T >::_use_hash_table
protectedinherited

Flag indicating whether the matrix is assembled using a hash table.

Definition at line 669 of file sparse_matrix.h.

Referenced by libMesh::SparseMatrix< ValOut >::use_hash_table().


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