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added more descriptions for matrix components and changed AD to LU
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Sam Shaner committed Mar 27, 2016
1 parent 36db653 commit fb76086
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Showing 3 changed files with 89 additions and 75 deletions.
138 changes: 76 additions & 62 deletions src/Matrix.cpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -7,10 +7,14 @@
* a map of lists) to allow for easy setting and incrementing of the
* values in the object. When the matrix is needed to perform linear
* algebra operations, it is converted to compressed row storage (CSR)
* form. The matrix is ordered by cell (as opposed to by group) on the
* outside. Locks are used to make the matrix thread-safe against
* form [1]. The matrix is ordered by cell (as opposed to by group) on
* the outside. Locks are used to make the matrix thread-safe against
* concurrent writes the same value. One lock locks out multiple rows of
* the matrix at a time reprsenting multiple groups in the same cell.
*
* [1] "Sparse matrix", Wikipedia,
* https://en.wikipedia.org/wiki/Sparse_matrix.
*
* @param cell_locks Omp locks for atomic cell operations
* @param num_x The number of cells in the x direction.
* @param num_y The number of cells in the y direction.
Expand All @@ -28,15 +32,15 @@ Matrix::Matrix(omp_lock_t* cell_locks, int num_x, int num_y, int num_groups) {
_LIL.push_back(std::map<int, FP_PRECISION>());

_A = NULL;
_AD = NULL;
_LU = NULL;
_IA = NULL;
_IAD = NULL;
_ILU = NULL;
_JA = NULL;
_JAD = NULL;
_JLU = NULL;
_DIAG = NULL;
_modified = true;
_NNZ = 0;
_NNZD = 0;
_NNZLU = 0;

/* Set OpenMP locks for each Matrix cell */
if (cell_locks == NULL)
Expand All @@ -56,20 +60,20 @@ Matrix::~Matrix() {
if (_A != NULL)
delete [] _A;

if (_AD != NULL)
delete [] _AD;
if (_LU != NULL)
delete [] _LU;

if (_IA != NULL)
delete [] _IA;

if (_IAD != NULL)
delete [] _IAD;
if (_ILU != NULL)
delete [] _ILU;

if (_JA != NULL)
delete [] _JA;

if (_JAD != NULL)
delete [] _JAD;
if (_JLU != NULL)
delete [] _JLU;

if (_DIAG != NULL)
delete [] _DIAG;
Expand Down Expand Up @@ -189,54 +193,54 @@ void Matrix::convertToCSR() {

/* Get number of nonzero values */
int NNZ = getNNZ();
int NNZD = getNNZD();
int NNZLU = getNNZLU();

if (NNZ != _NNZ || NNZD != _NNZD) {
if (NNZ != _NNZ || NNZLU != _NNZLU) {

/* Deallocate memory for arrays if previously allocated */
if (_A != NULL)
delete [] _A;

if (_AD != NULL)
delete [] _AD;
if (_LU != NULL)
delete [] _LU;

if (_IA != NULL)
delete [] _IA;

if (_IAD != NULL)
delete [] _IAD;
if (_ILU != NULL)
delete [] _ILU;

if (_JA != NULL)
delete [] _JA;

if (_JAD != NULL)
delete [] _JAD;
if (_JLU != NULL)
delete [] _JLU;

if (_DIAG != NULL)
delete [] _DIAG;

/* Allocate memory for arrays */
_A = new FP_PRECISION[NNZ];
_AD = new FP_PRECISION[NNZD];
_LU = new FP_PRECISION[NNZLU];
_IA = new int[_num_rows+1];
_IAD = new int[_num_rows+1];
_ILU = new int[_num_rows+1];
_JA = new int[NNZ];
_JAD = new int[NNZD];
_JLU = new int[NNZLU];
_DIAG = new FP_PRECISION[_num_rows];

_NNZ = NNZ;
_NNZD = NNZD;
_NNZLU = NNZLU;
}

std::fill_n(_DIAG, _num_rows, 0.0);

/* Form arrays */
int j = 0;
int jd = 0;
int jlu = 0;
std::map<int, FP_PRECISION>::iterator iter;
for (int row=0; row < _num_rows; row++) {
_IA[row] = j;
_IAD[row] = jd;
_ILU[row] = jlu;
for (iter = _LIL[row].begin(); iter != _LIL[row].end(); ++iter) {
if (iter->second != 0.0) {
_JA[j] = iter->first;
Expand All @@ -245,9 +249,9 @@ void Matrix::convertToCSR() {
if (row == iter->first)
_DIAG[row] = iter->second;
else {
_JAD[jd] = iter->first;
_AD[jd] = iter->second;
jd++;
_JLU[jlu] = iter->first;
_LU[jlu] = iter->second;
jlu++;
}

j++;
Expand All @@ -256,7 +260,7 @@ void Matrix::convertToCSR() {
}

_IA[_num_rows] = NNZ;
_IAD[_num_rows] = NNZD;
_ILU[_num_rows] = NNZLU;

/* Reset flat indicating the CSR objects have the same values as the
* LIL object */
Expand Down Expand Up @@ -312,11 +316,13 @@ FP_PRECISION Matrix::getValue(int cell_from, int group_from,


/**
* @brief Get the A component of the CSR form of the matrix object.
* @brief Get the full matrix (A) component of the CSR form of the matrix
* object.
* @return A pointer to the A component of the CSR form matrix object.
*/
FP_PRECISION* Matrix::getA() {

/* If the matrix has been modified, regenerate its' CSR attributes */
if (_modified)
convertToCSR();

Expand All @@ -325,26 +331,29 @@ FP_PRECISION* Matrix::getA() {


/**
* @brief Get the A component (excluding the diagonal) of the CSR form of the
* matrix object.
* @return A pointer to the A component (excluding the diagonal) of the CSR
* form matrix object.
* @brief Get the lower + upper (LU) component of the CSR form of the matrix
* object.
* @return A pointer to the lower + upper (LU) component of the CSR form matrix
* object.
*/
FP_PRECISION* Matrix::getAD() {
FP_PRECISION* Matrix::getLU() {

/* If the matrix has been modified, regenerate its' CSR attributes */
if (_modified)
convertToCSR();

return _AD;
return _LU;
}


/**
* @brief Get the IA component of the CSR form of the matrix object.
* @return A pointer to the IA component of the CSR form matrix object.
* @brief Get an array of the row indices (I) component of the CSR form of the
* full matrix (A).
* @return A pointer to the I component of the CSR form of the full matrix (A).
*/
int* Matrix::getIA() {

/* If the matrix has been modified, regenerate its' CSR attributes */
if (_modified)
convertToCSR();

Expand All @@ -353,26 +362,29 @@ int* Matrix::getIA() {


/**
* @brief Get the IA component (excluding the diagonal) of the CSR form of the
* matrix object.
* @return A pointer to the IA component (excluding the diagonal) of the CSR
* form matrix object.
* @brief Get an array of the row indices (I) component of the CSR form of the
* lower + upper (LU) components of the matrix.
* @return A pointer to the I component of the CSR form of the LU components
* of the matrix.
*/
int* Matrix::getIAD() {
int* Matrix::getILU() {

/* If the matrix has been modified, regenerate its' CSR attributes */
if (_modified)
convertToCSR();

return _IAD;
return _ILU;
}


/**
* @brief Get the JA component of the CSR form of the matrix object.
* @return A pointer to the JA component of the CSR form matrix object.
* @brief Get an array of the column indices (J) component of the CSR form of
* the full matrix (A).
* @return A pointer to the J component of the CSR form of the full matrix (A).
*/
int* Matrix::getJA() {

/* If the matrix has been modified, regenerate its' CSR attributes */
if (_modified)
convertToCSR();

Expand All @@ -381,17 +393,18 @@ int* Matrix::getJA() {


/**
* @brief Get the JA component (excluding the diagonal) of the CSR form of the
* matrix object.
* @return A pointer to the JA component (excluding the diagonal) of the CSR
* form matrix object.
* @brief Get an array of the column indices (J) component of the CSR form of
* the lower + upper (LU) components of the matrix.
* @return A pointer to the J component of the CSR form of the LU components
* of the matrix.
*/
int* Matrix::getJAD() {
int* Matrix::getJLU() {

/* If the matrix has been modified, regenerate its' CSR attributes */
if (_modified)
convertToCSR();

return _JAD;
return _JLU;
}


Expand Down Expand Up @@ -445,8 +458,8 @@ int Matrix::getNumRows() {


/**
* @brief Get the number of non-zero values in the matrix.
* @return The number of non-zero values in the matrix.
* @brief Get the number of non-zero values in the full matrix.
* @return The number of non-zero values in the full matrix.
*/
int Matrix::getNNZ() {

Expand All @@ -464,22 +477,23 @@ int Matrix::getNNZ() {


/**
* @brief Get the number of non-zero values in the matrix, excluding the
* diagonal.
* @return The number of non-zero values in the matrix, excluding the diagonal.
* @brief Get the number of non-zero values in the lower + upper components of
* the matrix.
* @return The number of non-zero values in the lower + upper components of the
* matrix.
*/
int Matrix::getNNZD() {
int Matrix::getNNZLU() {

int NNZD = 0;
int NNZLU = 0;
std::map<int, FP_PRECISION>::iterator iter;
for (int row=0; row < _num_rows; row++) {
for (iter = _LIL[row].begin(); iter != _LIL[row].end(); ++iter) {
if (iter->second != 0.0 && iter->first != row)
NNZD++;
NNZLU++;
}
}

return NNZD;
return NNZLU;
}


Expand Down
16 changes: 8 additions & 8 deletions src/Matrix.h
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Original file line number Diff line number Diff line change
Expand Up @@ -34,11 +34,11 @@ class Matrix {

/** The CSR matrix variables */
FP_PRECISION* _A;
FP_PRECISION* _AD;
FP_PRECISION* _LU;
int* _IA;
int* _JA;
int* _IAD;
int* _JAD;
int* _ILU;
int* _JLU;
FP_PRECISION* _DIAG;

bool _modified;
Expand All @@ -47,7 +47,7 @@ class Matrix {
int _num_groups;
int _num_rows;
int _NNZ;
int _NNZD;
int _NNZLU;

/** OpenMP mutual exclusion locks for atomic cell updates */
omp_lock_t* _cell_locks;
Expand All @@ -72,18 +72,18 @@ class Matrix {
FP_PRECISION getValue(int cell_from, int group_from, int cell_to,
int group_to);
FP_PRECISION* getA();
FP_PRECISION* getAD();
FP_PRECISION* getLU();
int* getIA();
int* getIAD();
int* getILU();
int* getJA();
int* getJAD();
int* getJLU();
FP_PRECISION* getDiag();
int getNumX();
int getNumY();
int getNumGroups();
int getNumRows();
int getNNZ();
int getNNZD();
int getNNZLU();
omp_lock_t* getCellLocks();

/* Setter functions */
Expand Down
10 changes: 5 additions & 5 deletions src/linalg.cpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -138,10 +138,10 @@ void linearSolve(Matrix* A, Matrix* M, Vector* X, Vector* B, FP_PRECISION tol,
int num_rows = X->getNumRows();
Vector X_old(cell_locks, num_x, num_y, num_groups);
FP_PRECISION* x_old = X_old.getArray();
int* IAD = A->getIAD();
int* JAD = A->getJAD();
int* ILU = A->getILU();
int* JLU = A->getJLU();
FP_PRECISION* DIAG = A->getDiag();
FP_PRECISION* ad = A->getAD();
FP_PRECISION* lu = A->getLU();
FP_PRECISION* x = X->getArray();
FP_PRECISION* b = B->getArray();
int row;
Expand Down Expand Up @@ -169,8 +169,8 @@ void linearSolve(Matrix* A, Matrix* M, Vector* X, Vector* B, FP_PRECISION tol,

/* Accumulate off diagonals multiplied by corresponding fluxes */
val = 0.0;
for (int i = IAD[row]; i < IAD[row+1]; i++)
val += ad[i] * x[JAD[i]];
for (int i = ILU[row]; i < ILU[row+1]; i++)
val += lu[i] * x[JLU[i]];

/* Update the flux for this row */
x[row] += SOR_factor * ((b[row] - val) / DIAG[row] - x[row]);
Expand Down

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