#ifndef STORM_STORAGE_SPARSEMATRIX_H_ #define STORM_STORAGE_SPARSEMATRIX_H_ // To detect whether the usage of TBB is possible, this include is neccessary #include "storm-config.h" #ifdef STORM_HAVE_INTELTBB # include "utility/OsDetection.h" // This fixes a potential dependency ordering problem between GMM and TBB # include # include "tbb/tbb.h" # include #endif #include #include #include #include #include "src/storage/BitVector.h" #include "src/utility/constants.h" #include "src/exceptions/InvalidArgumentException.h" #include "src/exceptions/OutOfRangeException.h" // Forward declaration for adapter classes. namespace storm { namespace adapters { class GmmxxAdapter; class EigenAdapter; class StormAdapter; } } namespace storm { namespace storage { #ifdef STORM_HAVE_INTELTBB // Forward declaration of the TBB Helper class. template class tbbHelper_MatrixRowVectorScalarProduct; #endif /*! * A class that holds a possibly non-square matrix in the compressed row storage format. That is, it is supposed * to store non-zero entries only, but zeros may be explicitly stored if necessary for certain operations. * Likewise, the matrix is intended to store one value per column only. However, the functions provided by the * matrix are implemented in a way that makes it safe to store several entries per column. * * The creation of a matrix can be done in several ways. If the number of rows, columns and entries is known * prior to creating the matrix, the matrix can be constructed using this knowledge, which saves reallocations. * On the other hand, if either one of these values is not known a priori, the matrix can be constructed as an * empty matrix that needs to perform reallocations as more and more entries are inserted in the matrix. * * It should be observed that due to the nature of the sparse matrix format, entries can only be inserted in * order, i.e. row by row and column by column. */ template class SparseMatrix { public: // Declare adapter classes as friends to use internal data. friend class storm::adapters::GmmxxAdapter; friend class storm::adapters::EigenAdapter; friend class storm::adapters::StormAdapter; #ifdef STORM_HAVE_INTELTBB // Declare the helper class for TBB as friend. template friend class tbbHelper_MatrixRowVectorScalarProduct; #endif typedef typename std::vector>::iterator iterator; typedef typename std::vector>::const_iterator const_iterator; /*! * This class represents a number of consecutive rows of the matrix. */ class rows { public: /*! * Constructs an object that represents the rows defined by the value of the first entry, the column * of the first entry and the number of entries in this row set. * * @param columnAndValuePtr A pointer to the columnd and value of the first entry of the rows. * @param entryCount The number of entrys in the rows. */ rows(std::pair* columnAndValuePtr, uint_fast64_t entryCount); /*! * Retrieves an iterator that points to the beginning of the rows. * * @return An iterator that points to the beginning of the rows. */ iterator begin(); /*! * Retrieves an iterator that points past the last entry of the rows. * * @return An iterator that points past the last entry of the rows. */ iterator end(); private: // The pointer to the columnd and value of the first entry. std::pair* columnAndValuePtr; // The number of non-zero entries in the rows. uint_fast64_t entryCount; }; /*! * This class represents a number of consecutive rows of the matrix. */ class const_rows { public: /*! * Constructs an object that represents the rows defined by the value of the first entry, the column * of the first entry and the number of entries in this row set. * * @param columnAndValuePtr A pointer to the columnd and value of the first entry of the rows. * @param entryCount The number of entrys in the rows. */ const_rows(std::pair const* columnAndValuePtr, uint_fast64_t entryCount); /*! * Retrieves an iterator that points to the beginning of the rows. * * @return An iterator that points to the beginning of the rows. */ const_iterator begin() const; /*! * Retrieves an iterator that points past the last entry of the rows. * * @return An iterator that points past the last entry of the rows. */ const_iterator end() const; private: // The pointer to the columnd and value of the first entry. std::pair const* columnAndValuePtr; // The number of non-zero entries in the rows. uint_fast64_t entryCount; }; /*! * An enum representing the internal state of the matrix. After creation, the matrix is UNINITIALIZED. * Only after a call to finalize(), the status of the matrix is set to INITIALIZED and the matrix can be * used. */ enum MatrixStatus { UNINITIALIZED, INITIALIZED }; /*! * Constructs a sparse matrix object with the given number of rows, columns and number of entries. * * @param rows The number of rows of the matrix. * @param columns The number of columns of the matrix. * @param entries The number of entries of the matrix. */ SparseMatrix(uint_fast64_t rows = 0, uint_fast64_t columns = 0, uint_fast64_t entries = 0); /*! * Constructs a sparse matrix by performing a deep-copy of the given matrix. * * @param other The matrix from which to copy the content. */ SparseMatrix(SparseMatrix const& other); /*! * Constructs a sparse matrix by moving the contents of the given matrix to the newly created one. * * @param other The matrix from which to move the content. */ SparseMatrix(SparseMatrix&& other); /*! * Constructs a sparse matrix by copying the given contents. * * @param columnCount The number of columns of the matrix. * @param rowIndications The row indications vector of the matrix to be constructed. * @param columnsAndValues The vector containing the columns and values of the entries in the matrix. */ SparseMatrix(uint_fast64_t columnCount, std::vector const& rowIndications, std::vector> const& columnsAndValues); /*! * Constructs a sparse matrix by copying the given contents. * * @param columnCount The number of columns of the matrix. * @param rowIndications The row indications vector of the matrix to be constructed. * @param columnIndications The column indications vector of the matrix to be constructed. * @param values The vector containing the values of the entries in the matrix. */ SparseMatrix(uint_fast64_t columnCount, std::vector const& rowIndications, std::vector const& columnIndications, std::vector const& values); /*! * Constructs a sparse matrix by moving the given contents. * * @param columnCount The number of columns of the matrix. * @param rowIndications The row indications vector of the matrix to be constructed. * @param columnIndications The column indications vector of the matrix to be constructed. * @param values The vector containing the values of the entries in the matrix. */ SparseMatrix(uint_fast64_t columnCount, std::vector&& rowIndications, std::vector&& columnIndications, std::vector&& values); /*! * Constructs a sparse matrix by moving the given contents. * * @param columnCount The number of columns of the matrix. * @param rowIndications The row indications vector of the matrix to be constructed. * @param columnsAndValues The vector containing the columns and values of the entries in the matrix. */ SparseMatrix(uint_fast64_t columnCount, std::vector&& rowIndications, std::vector>&& columnsAndValues); /*! * Assigns the contents of the given matrix to the current one by deep-copying its contents. * * @param other The matrix from which to copy-assign. */ SparseMatrix& operator=(SparseMatrix const& other); /*! * Assigns the contents of the given matrix to the current one by moving its contents. * * @param other The matrix from which to move to contents. */ SparseMatrix& operator=(SparseMatrix&& other); /*! * Determines whether the current and the given matrix are semantically equal. * * @param other The matrix with which to compare the current matrix. * @return True iff the given matrix is semantically equal to the current one. */ bool operator==(SparseMatrix const& other) const; /*! * Sets the matrix entry at the given row and column to the given value. After all entries have been added, * a call to finalize(false) is mandatory. * * Note: this is a linear setter. That is, it must be called consecutively for each entry, row by row and * column by column. As multiple entries per column are admitted, consecutive calls to this method are * admitted to mention the same row-column-pair. If rows are skipped entirely, the corresponding rows are * treated as empty. If these constraints are not met, an exception is thrown. * * @param row The row in which the matrix entry is to be set. * @param column The column in which the matrix entry is to be set. * @param value The value that is to be set at the specified row and column. */ void addNextValue(uint_fast64_t row, uint_fast64_t column,T const& value); /* * Finalizes the sparse matrix to indicate that initialization process has been completed and the matrix * may now be used. This must be called after all entries have been added to the matrix via addNextValue. * * @param overriddenRowCount If this is set to a value that is greater than the current number of rows, * this will cause the finalize method to add empty rows at the end of the matrix until the given row count * has been matched. Note that this will *not* override the row count that has been given upon construction * (if any), but will only take effect if the matrix has been created without the number of rows given. * @param overriddenColumnCount If this is set to a value that is greater than the current number of columns, * this will cause the finalize method to set the number of columns to the given value. Note that this will * *not* override the column count that has been given upon construction (if any), but will only take effect * if the matrix has been created without the number of columns given. By construction, the matrix will have * no entries in the columns that have been added this way. */ void finalize(uint_fast64_t overriddenRowCount = 0, uint_fast64_t overriddenColumnCount = 0); /*! * Returns the number of rows of the matrix. * * @return The number of rows of the matrix. */ uint_fast64_t getRowCount() const; /*! * Returns the number of columns of the matrix. * * @return The number of columns of the matrix. */ uint_fast64_t getColumnCount() const; /*! * Returns the number of entries in the matrix. * * @return The number of entries in the matrix. */ uint_fast64_t getEntryCount() const; /*! * Checks whether the matrix was initialized properly and is ready for further use. * * @return True iff the matrix was initialized properly and is ready for further use. */ bool isInitialized() const; /*! * This function makes the given rows absorbing. * * @param rows A bit vector indicating which rows are to be made absorbing. */ void makeRowsAbsorbing(storm::storage::BitVector const& rows); /*! * This function makes the groups of rows given by the bit vector absorbing. * * @param rowGroupConstraint A bit vector indicating which row groups to make absorbing. * @param rowGroupIndices A vector indicating which rows belong to a given row group. */ void makeRowsAbsorbing(storm::storage::BitVector const& rowGroupConstraint, std::vector const& rowGroupIndices); /*! * This function makes the given row absorbing. This means that all entries will be set to 0 except the one * at the specified column, which is set to 1 instead. * * @param row The row to be made absorbing. * @param column The index of the column whose value is to be set to 1. */ void makeRowAbsorbing(const uint_fast64_t row, const uint_fast64_t column); /* * Sums the entries in the given row and columns. * * @param row The row whose entries to add. * @param columns A bit vector that indicates which columns to add. * @return The sum of the entries in the given row and columns. */ T getConstrainedRowSum(uint_fast64_t row, storm::storage::BitVector const& columns) const; /*! * Computes a vector whose i-th entry is the sum of the entries in the i-th selected row where only those * entries are added that are in selected columns. * * @param rowConstraint A bit vector that indicates for which rows to compute the constrained sum. * @param columnConstraint A bit vector that indicates which columns to add in the selected rows. * * @return A vector whose elements are the sums of the selected columns in each row. */ std::vector getConstrainedRowSumVector(storm::storage::BitVector const& rowConstraint, storm::storage::BitVector const& columnConstraint) const; /*! * Computes a vector whose entries represent the sums of selected columns for all rows in selected row * groups. * * @param rowGroupConstraint A bit vector that indicates which row groups are to be considered. * @param rowGroupIndices A vector indicating which rows belong to a given row group. * @param columnConstraint A bit vector that indicates which columns to sum. * @return A vector whose entries represent the sums of selected columns for all rows in selected row * groups. */ std::vector getConstrainedRowSumVector(storm::storage::BitVector const& rowGroupConstraint, std::vector const& rowGroupIndices, storm::storage::BitVector const& columnConstraint) const; /*! * Creates a submatrix of the current matrix by dropping all rows and columns whose bits are not * set to one in the given bit vector. * * @param constraint A bit vector indicating which rows and columns to keep. * @return A matrix corresponding to a submatrix of the current matrix in which only rows and columns given * by the constraint are kept and all others are dropped. */ SparseMatrix getSubmatrix(storm::storage::BitVector const& constraint) const; /*! * Creates a submatrix of the current matrix by keeping only certain row groups and columns. * * @param rowGroupConstraint A bit vector indicating which row groups and columns to keep. * @param rowGroupIndices A vector indicating which rows belong to a given row group. * @param insertDiagonalEntries If set to true, the resulting matrix will have zero entries in column i for * each row in row group i. This can then be used for inserting other values later. * @return A matrix corresponding to a submatrix of the current matrix in which only row groups and columns * given by the row group constraint are kept and all others are dropped. */ SparseMatrix getSubmatrix(storm::storage::BitVector const& rowGroupConstraint, std::vector const& rowGroupIndices, bool insertDiagonalEntries = false) const; /*! * Creates a submatrix of the current matrix by keeping only row groups and columns in the given row group * and column constraint, respectively. * * @param rowGroupConstraint A bit vector indicating which row groups to keep. * @param columnConstraint A bit vector indicating which columns to keep. * @param rowGroupIndices A vector indicating which rows belong to a given row group. * @param insertDiagonalEntries If set to true, the resulting matrix will have zero entries in column i for * each row in row group i. This can then be used for inserting other values later. * @return A matrix corresponding to a submatrix of the current matrix in which only row groups and columns * given by the row group constraint are kept and all others are dropped. */ SparseMatrix getSubmatrix(storm::storage::BitVector const& rowGroupConstraint, storm::storage::BitVector const& columnConstraint, std::vector const& rowGroupIndices, bool insertDiagonalEntries = false) const; /*! * Creates a submatrix of the current matrix by selecting one row out of each row group. * * @param rowGroupdToRowIndexMapping A mapping from each row group index to a selected row in this group. * @param rowGroupIndices A vector indicating which rows belong to a given row group. * @param insertDiagonalEntries If set to true, the resulting matrix will have zero entries in column i for * each row in row group i. This can then be used for inserting other values later. * @return A submatrix of the current matrix by selecting one row out of each row group. */ SparseMatrix getSubmatrix(std::vector const& rowGroupToRowIndexMapping, std::vector const& rowGroupIndices, bool insertDiagonalEntries = true) const; /*! * Transposes the matrix. * * @return A sparse matrix that represents the transpose of this matrix. */ storm::storage::SparseMatrix transpose() const; /*! * Transforms the matrix into an equation system. That is, it transforms the matrix A into a matrix (1-A). */ void convertToEquationSystem(); /*! * Inverts all entries on the diagonal, i.e. sets the diagonal values to one minus their previous value. * Requires the matrix to contain each diagonal entry and to be square. */ void invertDiagonal(); /*! * Negates (w.r.t. addition) all entries that are not on the diagonal. */ void negateAllNonDiagonalEntries(); /*! * Sets all diagonal elements to zero. */ void deleteDiagonalEntries(); /*! * Calculates the Jacobi decomposition of this sparse matrix. For this operation, the matrix must be square. * * @return A pair (L+U, D^-1) containing the matrix L+U and the inverted diagonal matrix D^-1. */ std::pair, storm::storage::SparseMatrix> getJacobiDecomposition() const; /*! * Performs a pointwise matrix multiplication of the matrix with the given matrix and returns a vector * containing the sum of the entries in each row of the resulting matrix. * * @param otherMatrix A reference to the matrix with which to perform the pointwise multiplication. This * matrix must be a submatrix of the current matrix in the sense that it may not have entries at indices * where there is no entry in the current matrix. * @return A vector containing the sum of the entries in each row of the matrix resulting from pointwise * multiplication of the current matrix with the given matrix. */ std::vector getPointwiseProductRowSumVector(storm::storage::SparseMatrix const& otherMatrix) const; /*! * Multiplies the matrix with the given vector and writes the result to given result vector. * * @param vector The vector with which to multiply the matrix. * @param result The vector that is supposed to hold the result of the multiplication after the operation. * @return The product of the matrix and the given vector as the content of the given result vector. */ void multiplyWithVector(std::vector const& vector, std::vector& result) const; /*! * Returns an object representing the consecutive rows given by the parameters. * * @param startRow The starting row. * @param endRow The ending row (which is included in the result). * @return An object representing the consecutive rows given by the parameters. */ const_rows getRows(uint_fast64_t startRow, uint_fast64_t endRow) const; /*! * Returns an object representing the consecutive rows given by the parameters. * * @param startRow The starting row. * @param endRow The ending row (which is included in the result). * @return An object representing the consecutive rows given by the parameters. */ rows getRows(uint_fast64_t startRow, uint_fast64_t endRow); /*! * Returns an object representing the given row. * * @param row The row to get. * @return An object representing the given row. */ const_rows getRow(uint_fast64_t row) const; /*! * Returns an object representing the given row. * * @param row The row to get. * @return An object representing the given row. */ rows getRow(uint_fast64_t row); /*! * Retrieves an iterator that points to the beginning of the given row. * * @param row The row to the beginning of which the iterator has to point. * @return An iterator that points to the beginning of the given row. */ const_iterator begin(uint_fast64_t row = 0) const; /*! * Retrieves an iterator that points to the beginning of the given row. * * @param row The row to the beginning of which the iterator has to point. * @return An iterator that points to the beginning of the given row. */ iterator begin(uint_fast64_t row = 0); /*! * Retrieves an iterator that points past the end of the given row. * * @param row The row past the end of which the iterator has to point. * @return An iterator that points past the end of the given row. */ const_iterator end(uint_fast64_t row = 0) const; /*! * Retrieves an iterator that points past the end of the given row. * * @param row The row past the end of which the iterator has to point. * @return An iterator that points past the end of the given row. */ iterator end(uint_fast64_t row = 0); /*! * Retrieves an iterator that points past the end of the last row of the matrix. * * @return An iterator that points past the end of the last row of the matrix. */ const_iterator end() const; /*! * Retrieves an iterator that points past the end of the last row of the matrix. * * @return An iterator that points past the end of the last row of the matrix. */ iterator end(); /*! * Computes the sum of the entries in a given row. * * @param row The row that is to be summed. * @return The sum of the selected row. */ T getRowSum(uint_fast64_t row) const; /*! * Checks if the current matrix is a submatrix of the given matrix, where a matrix A is called a submatrix * of B if B has no entries in position where A has none. Additionally, the matrices must be of equal size. * * @param matrix The matrix that possibly is a supermatrix of the current matrix. * @return True iff the current matrix is a submatrix of the given matrix. */ bool isSubmatrixOf(SparseMatrix const& matrix) const; template friend std::ostream& operator<<(std::ostream& out, SparseMatrix const& matrix); /*! * Returns the size of the matrix in memory measured in bytes. * * @return The size of the matrix in memory measured in bytes. */ uint_fast64_t getSizeInMemory() const; /*! * Calculates a hash value over all values contained in the matrix. * * @return size_t A hash value for this matrix. */ std::size_t hash() const; private: /*! * Prepares the internal storage of the matrix. This relies on the number of entries and the number of rows * being set correctly. They may, however, be zero, in which case the insertion of elements in the matrix * will cause occasional reallocations. */ void prepareInternalStorage(); /*! * Checks whether the matrix is properly initialized and throws an exception otherwise. */ void checkReady(std::string const& methodName) const; // A flag indicating whether the number of rows was set upon construction. bool rowCountSet; // The number of rows of the matrix. uint_fast64_t rowCount; // A flag indicating whether the number of columns was set upon construction. bool columnCountSet; // The number of columns of the matrix. uint_fast64_t columnCount; // The number of entries in the matrix. uint_fast64_t entryCount; // Stores whether the storage of the matrix was preallocated or not. bool storagePreallocated; // The storage for the columns and values of all entries in the matrix. std::vector> columnsAndValues; // A vector containing the indices at which each given row begins. This index is to be interpreted as an // index in the valueStorage and the columnIndications vectors. Put differently, the values of the entries // in row i are valueStorage[rowIndications[i]] to valueStorage[rowIndications[i + 1]] where the last // entry is not included anymore. std::vector rowIndications; // The internal status of the matrix. MatrixStatus internalStatus; // Stores the current number of entries in the matrix. This is used for inserting an entry into a matrix // with preallocated storage. uint_fast64_t currentEntryCount; // Stores the row of the last entry in the matrix. This is used for correctly inserting an entry into a // matrix. uint_fast64_t lastRow; // Stores the column of the currently last entry in the matrix. This is used for correctly inserting an // entry into a matrix. uint_fast64_t lastColumn; }; #ifdef STORM_HAVE_INTELTBB /*! * This function is a helper for the parallel execution of the multipliyWithVector method. * It uses Intel's TBB parallel_for paradigm to split up the row/vector multiplication and summation. */ template class tbbHelper_MatrixRowVectorScalarProduct { public: tbbHelper_MatrixRowVectorScalarProduct(M const* matrixA, V const* vectorX, V * resultVector); void operator() (const tbb::blocked_range& r) const; private: V * resultVector; V const* vectorX; M const* matrixA; }; #endif } // namespace storage } // namespace storm #endif // STORM_STORAGE_SPARSEMATRIX_H_