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serial/coo_sparse_matrix.c

@@ -15,9 +15,8 @@ void allocMemoryForCoo(CooSparseMatrix *sparseMatrix, int numberOfElements) {
 }
 
 void addElement(CooSparseMatrix *sparseMatrix, double value, int row, int column) {
+	// Checks if there is enough space allocated
 	if (sparseMatrix->numberOfNonZeroElements == sparseMatrix->size) {
-		printf("%d == %d |||| %d, %d\n", sparseMatrix->numberOfNonZeroElements,
-			sparseMatrix->size, row, column);
 		printf("Number of non zero elements exceeded size of matrix!\n");
 		exit(EXIT_FAILURE);
 	}
@@ -29,6 +28,7 @@ void addElement(CooSparseMatrix *sparseMatrix, double value, int row, int column
 	newElement->rowIndex = row;
 	newElement->columnIndex = column;
 
+	// Adds the new element to the first empty (NULL) address of the matrix
 	sparseMatrix->elements[sparseMatrix->numberOfNonZeroElements] = newElement;
 	sparseMatrix->numberOfNonZeroElements = sparseMatrix->numberOfNonZeroElements + 1;
 }
@@ -42,14 +42,19 @@ void transposeSparseMatrix(CooSparseMatrix *sparseMatrix) {
 	}
 }
 
+/*
+ * This function is a port of the one found here:
+ * https://github.com/scipy/scipy/blob/3b36a57/scipy/sparse/sparsetools/coo.h#L34
+*/
 void transformToCSR(CooSparseMatrix initialSparseMatrix,
 	CsrSparseMatrix *transformedSparseMatrix) {
-	// Taken from here: https://github.com/scipy/scipy/blob/3b36a57/scipy/sparse/sparsetools/coo.h#L34
+	// Checks if the sizes of the two matrices fit
 	if (initialSparseMatrix.numberOfNonZeroElements > transformedSparseMatrix->size) {
 		printf("Transformed CSR matrix does not have enough space!\n");
 		exit(EXIT_FAILURE);
 	}
 
+	// Calculates the elements per row
 	for (int i=0; i<initialSparseMatrix.numberOfNonZeroElements; ++i){
 		int rowIndex = initialSparseMatrix.elements[i]->rowIndex;
 		transformedSparseMatrix->rowCumulativeIndexes[rowIndex] = 
@@ -63,6 +68,7 @@ void transformToCSR(CooSparseMatrix initialSparseMatrix,
 		sum += temp;
 	}
 
+	// Copies the values and columns of the elements
 	for (int i=0; i<initialSparseMatrix.numberOfNonZeroElements; ++i){
 		int row  = initialSparseMatrix.elements[i]->rowIndex;
 		int destinationIndex = transformedSparseMatrix->rowCumulativeIndexes[row];
@@ -73,6 +79,7 @@ void transformToCSR(CooSparseMatrix initialSparseMatrix,
 		transformedSparseMatrix->rowCumulativeIndexes[row]++;
 	}
 
+	// Fixes the cumulative sum
 	for (int i=0, last=0; i<=transformedSparseMatrix->size; i++){
 		int temp = transformedSparseMatrix->rowCumulativeIndexes[i];
 		transformedSparseMatrix->rowCumulativeIndexes[i] = last;

serial/coo_sparse_matrix.h

@@ -1,6 +1,8 @@
 #ifndef COO_SPARSE_MATRIX_H	/* Include guard */
 #define COO_SPARSE_MATRIX_H
 
+/* ===== INCLUDES ===== */
+
 #include <stdbool.h>
 #include <stdlib.h>
 #include <stdio.h>
@@ -8,26 +10,51 @@
 
 #include "csr_sparse_matrix.h"
 
+/* ===== STRUCTURES ===== */
+
+// One element of the coordinate formated sparse matrix.
 typedef struct cooSparseMatrixElement {
 	double value;
 	int rowIndex, columnIndex;
 } CooSparseMatrixElement;
 
+// A sparse matrix in COOrdinate format (aka triplet format).
 typedef struct cooSparseMatrix {
 	int size, numberOfNonZeroElements;
 	CooSparseMatrixElement **elements;
 } CooSparseMatrix;
 
+/* ===== FUNCTION DEFINITIONS ===== */
+
+// initCooSparseMatrix creates and initializes the members of a CooSparseMatrix
+// structure instance.
 CooSparseMatrix initCooSparseMatrix();
+
+//allocMemoryForCoo allocates memory for the elements of the matrix.
 void allocMemoryForCoo(CooSparseMatrix *sparseMatrix, int numberOfElements);
+
+// addElement adds an element representing the triplet passed in the arguments
+// to the first empty address of the space allocated for the elements.
 void addElement(CooSparseMatrix *sparseMatrix, double value, int row,
 	int column);
+
+// transposeSparseMatrix transposes the matrix.
 void transposeSparseMatrix(CooSparseMatrix *sparseMatrix);
+
+// transformToCSR transforms the sparse matrix representation format from COO
+// to CSR.
 void transformToCSR(CooSparseMatrix initialSparseMatrix,
 	CsrSparseMatrix *transformedSparseMatrix);
+
+// cooSparseMatrixVectorMultiplication calculates the product of a
+// CooSparseMatrix and a vector.
 void cooSparseMatrixVectorMultiplication(CooSparseMatrix sparseMatrix,
 	double *vector, double **product, int vectorSize);
+
+// destroyCooSparseMatrix frees all space used by the CooSparseMatrix.
 void destroyCooSparseMatrix(CooSparseMatrix *sparseMatrix);
+
+// printCooSparseMatrix prints the values of a CooSparseMatrix.
 void printCooSparseMatrix(CooSparseMatrix sparseMatrix);
 
 #endif	// COO_SPARSE_MATRIX_H

serial/csr_sparse_matrix.c

@@ -24,8 +24,8 @@ void allocMemoryForCsr(CsrSparseMatrix *sparseMatrix, int numberOfElements) {
 	sparseMatrix->size = numberOfElements;
 }
 
-// Row indexes start from 0!
 void zeroOutRow(CsrSparseMatrix *sparseMatrix, int row) {
+	// Gets start and end indexes of the row's elements
 	int startIndex = sparseMatrix->rowCumulativeIndexes[row],
 	endIndex = sparseMatrix->rowCumulativeIndexes[row+1];
 	for (int i=startIndex; i<endIndex; ++i) {
@@ -36,7 +36,6 @@ void zeroOutRow(CsrSparseMatrix *sparseMatrix, int row) {
 void zeroOutColumn(CsrSparseMatrix *sparseMatrix, int column) {
 	for (int i=0; i<sparseMatrix->numberOfNonZeroElements; ++i){
 		if(sparseMatrix->columnIndexes[i] == column){
-			// Zeros out this element
 			sparseMatrix->values[i] = 0;
 		}
 	}

serial/csr_sparse_matrix.h

@@ -1,24 +1,47 @@
 #ifndef CSR_SPARSE_MATRIX_H	/* Include guard */
 #define CSR_SPARSE_MATRIX_H
 
+/* ===== INCLUDES ===== */
+
 #include <stdbool.h>
 #include <stdlib.h>
 #include <stdio.h>
 #include <stdlib.h>
 
+/* ===== STRUCTURES ===== */
+
+// A sparse matrix in compressed SparseRow format.
 typedef struct csrSparseMatrix {
 	int size, numberOfNonZeroElements;
 	int *rowCumulativeIndexes, *columnIndexes;
 	double *values;
 } CsrSparseMatrix;
 
+/* ===== FUNCTION DEFINITIONS ===== */
+
+// initCsrSparseMatrix creates and initializes the members of a CsrSparseMatrix
+// structure instance.
 CsrSparseMatrix initCsrSparseMatrix();
+
+// allocMemoryForCsr allocates memory for the elements of the matrix.
 void allocMemoryForCsr(CsrSparseMatrix *sparseMatrix, int numberOfElements);
+
+// zeroOutRow assigns a zero value to all the elements of a row in the matrix.
 void zeroOutRow(CsrSparseMatrix *sparseMatrix, int row);
+
+// zeroOutColumn assigns a zero value to all the elements of a column in the
+// matrix.
 void zeroOutColumn(CsrSparseMatrix *sparseMatrix, int column);
+
+// csrSparseMatrixVectorMultiplication calculates the product of a
+// CsrSparseMatrix and a vector.
 void csrSparseMatrixVectorMultiplication(CsrSparseMatrix sparseMatrix,
 	double *vector, double **product, int vectorSize);
+
+// destroyCsrSparseMatrix frees all space used by the CsrSparseMatrix.
 void destroyCsrSparseMatrix(CsrSparseMatrix *sparseMatrix);
+
+// printCsrSparseMatrix prints the values of a CsrSparseMatrix.
 void printCsrSparseMatrix(CsrSparseMatrix sparseMatrix);
 
 #endif	// CSR_SPARSE_MATRIX_H

serial/serial_gs_pagerank.c

@@ -3,7 +3,6 @@
 #include "serial_gs_pagerank_functions.h"
 
 struct timeval startwtime, endwtime;
-double seq_time;
 
 int main(int argc, char **argv) {
 	CsrSparseMatrix transitionMatrix = initCsrSparseMatrix();

serial/serial_gs_pagerank_functions.c

@@ -126,8 +126,8 @@ int pagerank(CsrSparseMatrix *transitionMatrix, double **pagerankVector,
 						}
 					}
 
-					// Increases sparsity of the transition matrix by
+					// Increases sparsity of the transition matrix by zeroing
-					// deleting elements that correspond to converged pages
+					// out elements that correspond to converged pages
 					zeroOutRow(transitionMatrix, i);
 					zeroOutColumn(transitionMatrix, i);
 
@@ -215,8 +215,6 @@ void calculateNextPagerank(CsrSparseMatrix *transitionMatrix,
 	double *linksFromConvergedPagesPagerankVector,
 	double *convergedPagerankVector, int vectorSize, double dampingFactor) {
 	// Calculates the web uniform probability once.
-	
-	
 	double webUniformProbability = 1. / vectorSize;
 
 	csrSparseMatrixVectorMultiplication(*transitionMatrix, previousPagerankVector,
@@ -232,7 +230,6 @@ void calculateNextPagerank(CsrSparseMatrix *transitionMatrix,
 	for (int i=0; i<vectorSize; ++i) {
 		(*pagerankVector)[i] += normDifference * webUniformProbability +
 		linksFromConvergedPagesPagerankVector[i] + convergedPagerankVector[i];
-		//(*pagerankVector)[i] += 0.5*normDifference* webUniformProbability +linksFromConvergedPagesPagerankVector[i] + convergedPagerankVector[i];
 	}
 }