Implement parallel openmp algorithm

openmp/Makefile

@@ -7,8 +7,8 @@ CC = gcc -std=gnu99 -fopenmp
 RM = rm -f
 CFLAGS_DEBUG=-O0 -ggdb3 -Wall -I.
 CFLAGS=-O3 -Wall -I.
-OBJ=serial_gs_pagerank.o serial_gs_pagerank_functions.o coo_sparse_matrix.o csr_sparse_matrix.o
+OBJ=openmp_gs_pagerank.o openmp_gs_pagerank_functions.o coo_sparse_matrix.o csr_sparse_matrix.o
-DEPS=serial_gs_pagerank_functions.h coo_sparse_matrix.h csr_sparse_matrix.h
+DEPS=openmp_gs_pagerank_functions.h coo_sparse_matrix.h csr_sparse_matrix.h
 
 # ==========================================
 # TARGETS

openmp/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) {
+	if (initialSparseMatrix.numberOfNonZeroElements > transformedSparseMatrix->numberOfElements) {
 		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];
@@ -73,13 +79,12 @@ 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;
 		last = temp;
 	}
-
-	transformedSparseMatrix->numberOfNonZeroElements = initialSparseMatrix.numberOfNonZeroElements;
 }
 
 void cooSparseMatrixVectorMultiplication(CooSparseMatrix sparseMatrix,

openmp/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

openmp/csr_sparse_matrix.c

@@ -3,7 +3,7 @@
 CsrSparseMatrix initCsrSparseMatrix() {
 	CsrSparseMatrix sparseMatrix;
 	sparseMatrix.size = 0;
-	sparseMatrix.numberOfNonZeroElements = 0;
+	sparseMatrix.numberOfElements = 0;
 
 	sparseMatrix.values = NULL;
 	sparseMatrix.columnIndexes = NULL;
@@ -11,21 +11,23 @@ CsrSparseMatrix initCsrSparseMatrix() {
 	return sparseMatrix;
 }
 
-void allocMemoryForCsr(CsrSparseMatrix *sparseMatrix, int numberOfElements) {
+void allocMemoryForCsr(CsrSparseMatrix *sparseMatrix, int size, int numberOfElements) {
 	sparseMatrix->values = (double *) malloc(numberOfElements * sizeof(double));
 	sparseMatrix->columnIndexes = (int *) malloc(
 		numberOfElements * sizeof(int));
 	sparseMatrix->rowCumulativeIndexes = (int *) malloc(
-		(numberOfElements + 1) * sizeof(int));
+		(size + 1) * sizeof(int));
 
-	for (int i=0; i<numberOfElements+1; ++i) {
+	for (int i=0; i<size+1; ++i) {
 		sparseMatrix->rowCumulativeIndexes[i] = 0;
 	}
-	sparseMatrix->size = numberOfElements;
+
+	sparseMatrix->size = size;
+	sparseMatrix->numberOfElements = 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) {
@@ -34,9 +36,8 @@ void zeroOutRow(CsrSparseMatrix *sparseMatrix, int row) {
 }
 
 void zeroOutColumn(CsrSparseMatrix *sparseMatrix, int column) {
-	for (int i=0; i<sparseMatrix->numberOfNonZeroElements; ++i){
+	for (int i=0; i<sparseMatrix->numberOfElements; ++i){
 		if(sparseMatrix->columnIndexes[i] == column){
-			// Zeros out this element
 			sparseMatrix->values[i] = 0;
 		}
 	}

openmp/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 size, numberOfElements;
 	int *rowCumulativeIndexes, *columnIndexes;
 	double *values;
 } CsrSparseMatrix;
 
+/* ===== FUNCTION DEFINITIONS ===== */
+
+// initCsrSparseMatrix creates and initializes the members of a CsrSparseMatrix
+// structure instance.
 CsrSparseMatrix initCsrSparseMatrix();
-void allocMemoryForCsr(CsrSparseMatrix *sparseMatrix, int numberOfElements);
+
+// allocMemoryForCsr allocates memory for the elements of the matrix.
+void allocMemoryForCsr(CsrSparseMatrix *sparseMatrix, int size, 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

openmp/openmp_gs_pagerank.c

@@ -0,0 +1,65 @@
+#include <sys/time.h>
+
+#include "openmp_gs_pagerank_functions.h"
+
+struct timeval startwtime, endwtime;
+
+int main(int argc, char **argv) {
+	CsrSparseMatrix transitionMatrix = initCsrSparseMatrix();
+	double *pagerankVector;
+	bool convergenceStatus;
+	Parameters parameters;
+	int maxIterationsForConvergence = 0;
+
+	parseArguments(argc, argv, &parameters);
+
+	initialize(&transitionMatrix, &pagerankVector, &parameters);
+
+	// Saves information about the dataset to the output file
+	{
+		FILE *outputFile;
+		outputFile = fopen(parameters.outputFilename, "w");
+
+		if (outputFile == NULL) {
+			printf("Error while opening the output file.\n");
+			exit(EXIT_FAILURE);
+		}
+
+		fprintf(outputFile, "Pagerank will run for the dataset %s\n"\
+			"Dataset contains %d pages with %d outlinks.\n",
+			parameters.graphFilename, parameters.numberOfPages, transitionMatrix.size);
+
+		fclose(outputFile);
+	}
+
+	// Starts wall-clock timer
+	gettimeofday (&startwtime, NULL);
+	int* iterations = (int *)malloc(parameters.numberOfPages*sizeof(int));
+
+	// Calculates pagerank
+	iterations = pagerank(&transitionMatrix, &pagerankVector,
+		&convergenceStatus, parameters, &maxIterationsForConvergence);
+
+	// Stops wall-clock timer
+	gettimeofday (&endwtime, NULL);
+	double seq_time = (double)((endwtime.tv_usec - startwtime.tv_usec)/1.0e6 +
+		endwtime.tv_sec - startwtime.tv_sec);
+	printf("%s wall clock time = %f\n","Pagerank (Gauss-Seidel method), serial implementation",
+		seq_time);
+
+	printf(ANSI_COLOR_YELLOW "\n----- RESULTS -----\n" ANSI_COLOR_RESET);
+	if (convergenceStatus) {
+		printf(ANSI_COLOR_GREEN "Pagerank converged after %d iterations!\n" \
+			ANSI_COLOR_RESET, maxIterationsForConvergence);
+	} else {
+		printf(ANSI_COLOR_RED "Pagerank did not converge after max number of" \
+			" iterations (%d) was reached!\n" ANSI_COLOR_RESET, maxIterationsForConvergence);
+	}
+
+	// Saves results to the output file
+	savePagerankToFile(parameters.outputFilename, iterations, pagerankVector,
+		parameters.numberOfPages, maxIterationsForConvergence);
+
+	free(pagerankVector);
+	destroyCsrSparseMatrix(&transitionMatrix);
+}

openmp/serial_gs_pagerank_functions.c → openmp/openmp_gs_pagerank_functions.c

@@ -1,12 +1,13 @@
 /* ===== INCLUDES ===== */
 
-#include "serial_gs_pagerank_functions.h"
+#include "openmp_gs_pagerank_functions.h"
-#include <omp.h>
+
 /* ===== CONSTANTS ===== */
 
 const char *ARGUMENT_CONVERGENCE_TOLERANCE = "-c";
 const char *ARGUMENT_MAX_ITERATIONS = "-m";
 const char *ARGUMENT_DAMPING_FACTOR = "-a";
+const char *ARGUMENT_THREADS_NUMBER = "-t";
 const char *ARGUMENT_VERBAL_OUTPUT = "-v";
 const char *ARGUMENT_OUTPUT_HISTORY = "-h";
 const char *ARGUMENT_OUTPUT_FILENAME = "-o";
@@ -15,26 +16,31 @@ const int NUMERICAL_BASE = 10;
 char *DEFAULT_OUTPUT_FILENAME = "pagerank_output";
 const int FILE_READ_BUFFER_SIZE = 4096;
 
-const int CONVERGENCE_CHECK_ITERATION_PERIOD = 3;
+const int CONVERGENCE_CHECK_ITERATION_PERIOD = 2;
-const int SPARSITY_INCREASE_ITERATION_PERIOD = 3;
+const int SPARSITY_INCREASE_ITERATION_PERIOD = 10;
+
+/* ===== GLOBAL VARIABLES ====== */
+
+int numberOfThreads;
 
 /* ===== FUNCTIONS ===== */
 
-int pagerank(CsrSparseMatrix *transitionMatrix, double **pagerankVector,
+int* pagerank(CsrSparseMatrix *transitionMatrix, double **pagerankVector,
-	bool *convergenceStatus, Parameters parameters) {
+	bool *convergenceStatus, Parameters parameters, int* maxIterationsForConvergence) {
 	// Variables declaration
-	int iterations = 0, numberOfPages = parameters.numberOfPages;
+	int numberOfPages = parameters.numberOfPages;
+	int *iterations;
 	double delta, *pagerankDifference, *previousPagerankVector,
 	*convergedPagerankVector, *linksFromConvergedPagesPagerankVector;
+	CsrSparseMatrix originalTransitionMatrix = initCsrSparseMatrix();
 	CooSparseMatrix linksFromConvergedPages = initCooSparseMatrix();
 	bool *convergenceMatrix;
 
-	int P = omp_get_max_threads();
-	omp_set_num_threads(P);
-	
 	// Space allocation
 	{
 		size_t sizeofDouble = sizeof(double);
+		// iterations until each page converged
+		iterations = (int *) malloc(numberOfPages * sizeof(int));
 		// pagerankDifference used to calculate delta
 		pagerankDifference = (double *) malloc(numberOfPages * sizeofDouble);
 		// previousPagerankVector holds last iteration's pagerank vector
@@ -50,12 +56,22 @@ int pagerank(CsrSparseMatrix *transitionMatrix, double **pagerankVector,
 		*convergenceStatus = false;
 
 		// Initialization
-		allocMemoryForCoo(&linksFromConvergedPages, transitionMatrix->numberOfNonZeroElements);
+		// originalTransitionMatrix used to run pagerank in phases
-		#pragma omp parallel for num_threads(P)
+		allocMemoryForCsr(&originalTransitionMatrix, transitionMatrix->size, transitionMatrix->numberOfElements);
+		memcpy(originalTransitionMatrix.rowCumulativeIndexes, transitionMatrix->rowCumulativeIndexes,
+			(transitionMatrix->size+1) * sizeof(int));
+		memcpy(originalTransitionMatrix.columnIndexes, transitionMatrix->columnIndexes,
+			transitionMatrix->numberOfElements * sizeof(int));
+		memcpy(originalTransitionMatrix.values, transitionMatrix->values,
+			transitionMatrix->numberOfElements * sizeof(double));
+
+		allocMemoryForCoo(&linksFromConvergedPages, transitionMatrix->numberOfElements);
+		#pragma omp parallel for num_threads(numberOfThreads)
 		for (int i=0; i<numberOfPages; ++i) {
 			convergedPagerankVector[i] = 0;
 			convergenceMatrix[i] = false;
 			linksFromConvergedPagesPagerankVector[i] = 0;
+			iterations[i] = 0;
 		}
 	}
 
@@ -75,14 +91,14 @@ int pagerank(CsrSparseMatrix *transitionMatrix, double **pagerankVector,
 
 		if (parameters.history) {
 			// Outputs pagerank vector to file
-			savePagerankToFile(parameters.outputFilename, iterations != 0,
+			savePagerankToFile(parameters.outputFilename, NULL, *pagerankVector,
-				*pagerankVector, numberOfPages, parameters.realIterations);
+				numberOfPages, *maxIterationsForConvergence);
 		}
 
 		// Periodically checks for convergence
-		if (!(iterations % CONVERGENCE_CHECK_ITERATION_PERIOD)) {
+		if (!((*maxIterationsForConvergence) % CONVERGENCE_CHECK_ITERATION_PERIOD)) {
 			// Builds pagerank vectors difference
-			#pragma omp parallel for num_threads(P)
+			#pragma omp parallel for num_threads(numberOfThreads)
 			for (int i=0; i<numberOfPages; ++i) {
 				pagerankDifference[i] = (*pagerankVector)[i] - previousPagerankVector[i];
 			}
@@ -95,11 +111,13 @@ int pagerank(CsrSparseMatrix *transitionMatrix, double **pagerankVector,
 			}
 		}
 
+		++(*maxIterationsForConvergence);
+
 		// Periodically increases sparsity
-		if (iterations && !(iterations % SPARSITY_INCREASE_ITERATION_PERIOD)) {
+		if ((*maxIterationsForConvergence) && !(*maxIterationsForConvergence % SPARSITY_INCREASE_ITERATION_PERIOD)) {
 			bool *newlyConvergedPages = (bool *) malloc(numberOfPages * sizeof(bool));
 			// Checks each individual page for convergence
-			#pragma omp parallel for num_threads(P)
+			#pragma omp parallel for num_threads(numberOfThreads)
 			for (int i=0; i<numberOfPages; ++i) {
 				double difference = fabs((*pagerankVector)[i] -
 					previousPagerankVector[i]) / fabs(previousPagerankVector[i]);
@@ -110,9 +128,11 @@ int pagerank(CsrSparseMatrix *transitionMatrix, double **pagerankVector,
 					newlyConvergedPages[i] = true;
 					convergenceMatrix[i] = true;
 					convergedPagerankVector[i] = (*pagerankVector)[i];
+					iterations[i] = *maxIterationsForConvergence;
 				}
 			}
-			#pragma omp parallel for num_threads(P)
+
+			#pragma omp parallel for num_threads(numberOfThreads)
 			for (int i=0; i<numberOfPages; ++i) {
 				// Filters newly converged pages
 				if (newlyConvergedPages[i] == true) {
@@ -132,10 +152,10 @@ 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);
+					//zeroOutColumn(transitionMatrix, i);
 
 					// Builds the new linksFromConvergedPagesPagerankVector
 					cooSparseMatrixVectorMultiplication(linksFromConvergedPages,
@@ -146,21 +166,29 @@ int pagerank(CsrSparseMatrix *transitionMatrix, double **pagerankVector,
 			free(newlyConvergedPages);
 		}
 
-		++iterations;
+		// Prunes the transition matrix every 8 iterations
+		if (*maxIterationsForConvergence != 0 && (*maxIterationsForConvergence%8 == 0)) {
+			memcpy(transitionMatrix->values, originalTransitionMatrix.values,
+				transitionMatrix->numberOfElements * sizeof(double));
+			#pragma omp parallel for num_threads(numberOfThreads)
+			for (int i=0; i<numberOfPages; ++i) {
+				convergedPagerankVector[i] = 0;
+				convergenceMatrix[i] = false;
+				linksFromConvergedPagesPagerankVector[i] = 0;
+			}
+			linksFromConvergedPages.numberOfNonZeroElements = 0;
+		}
+
 		// Outputs information about this iteration
-		if (iterations%2) {
+		if (parameters.verbose){
-			printf(ANSI_COLOR_BLUE "Iteration %d: delta = %f\n" ANSI_COLOR_RESET, iterations, delta);
+			if ((*maxIterationsForConvergence)%2) {
+				printf(ANSI_COLOR_BLUE "Iteration %d: delta = %f\n" ANSI_COLOR_RESET, *maxIterationsForConvergence, delta);
 			} else {
-			printf(ANSI_COLOR_CYAN "Iteration %d: delta = %f\n" ANSI_COLOR_RESET, iterations, delta);
+				printf(ANSI_COLOR_CYAN "Iteration %d: delta = %f\n" ANSI_COLOR_RESET, *maxIterationsForConvergence, delta);
 			}
-	} while (!*convergenceStatus && (parameters.maxIterations == 0 ||
-		iterations < parameters.maxIterations));
-	parameters.realIterations = iterations;
-	if (!parameters.history) {
-		// Outputs last pagerank vector to file
-		savePagerankToFile(parameters.outputFilename, false, *pagerankVector,
-			numberOfPages, parameters.realIterations);
 		}
+	} while (!*convergenceStatus && (parameters.maxIterations == 0 ||
+		*maxIterationsForConvergence < parameters.maxIterations));
 
 	// Frees memory
 	free(pagerankDifference);
@@ -181,6 +209,9 @@ int pagerank(CsrSparseMatrix *transitionMatrix, double **pagerankVector,
 void initialize(CsrSparseMatrix *transitionMatrix,
 	double **pagerankVector, Parameters *parameters) {
 
+	// Sets the number of threads to be used
+	omp_set_num_threads(numberOfThreads);
+
 	// Reads web graph from file
 	if ((*parameters).verbose) {
 		printf(ANSI_COLOR_YELLOW "----- Reading graph from file -----\n" ANSI_COLOR_RESET);
@@ -190,7 +221,8 @@ void initialize(CsrSparseMatrix *transitionMatrix,
 	// Outputs the algorithm parameters to the console
 	if ((*parameters).verbose) {
 		printf(ANSI_COLOR_YELLOW "\n----- Running with parameters -----\n" ANSI_COLOR_RESET\
-			"Number of pages: %d", (*parameters).numberOfPages);
+			"Number of pages: %d"\
+			"\nNumber of threads: %d", (*parameters).numberOfPages, numberOfThreads);
 		if (!(*parameters).maxIterations) {
 			printf("\nMaximum number of iterations: inf");
 		} else {
@@ -201,7 +233,7 @@ void initialize(CsrSparseMatrix *transitionMatrix,
 			"\nGraph filename: %s\n", (*parameters).convergenceCriterion,
 			(*parameters).dampingFactor, (*parameters).graphFilename);
 	}
-	(*parameters).realIterations = 0;
+
 	// Allocates memory for the pagerank vector
 	(*pagerankVector) = (double *) malloc((*parameters).numberOfPages * sizeof(double));
 	double webUniformProbability = 1. / (*parameters).numberOfPages;
@@ -221,24 +253,22 @@ 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,
 		pagerankVector, vectorSize);
-	#pragma omp parallel for
+
+	#pragma omp parallel for num_threads(4)
 	for (int i=0; i<vectorSize; ++i) {
 		(*pagerankVector)[i] = dampingFactor * (*pagerankVector)[i];
 	}
 
 	double normDifference = vectorNorm(previousPagerankVector, vectorSize) -
 	vectorNorm(*pagerankVector, vectorSize);
-	#pragma omp parallel for
+
 	for (int i=0; i<vectorSize; ++i) {
-		//(*pagerankVector)[i] += normDifference * webUniformProbability +
+		(*pagerankVector)[i] += normDifference * webUniformProbability +
-		//linksFromConvergedPagesPagerankVector[i] + convergedPagerankVector[i];
+		linksFromConvergedPagesPagerankVector[i] + convergedPagerankVector[i];
-		(*pagerankVector)[i] += 0.5*normDifference* webUniformProbability +linksFromConvergedPagesPagerankVector[i] + convergedPagerankVector[i];
 	}
 }
 
@@ -261,13 +291,15 @@ double vectorNorm(double *vector, int vectorSize) {
  * parseArguments parses the command line arguments given by the user.
 */
 void parseArguments(int argumentCount, char **argumentVector, Parameters *parameters) {
-	if (argumentCount < 2 || argumentCount > 10) {
+	if (argumentCount < 2 || argumentCount > 16) {
 		validUsage(argumentVector[0]);
 	}
 
+	numberOfThreads = omp_get_max_threads();
+
 	(*parameters).numberOfPages = 0;
 	(*parameters).maxIterations = 0;
-	(*parameters).convergenceCriterion = 1;
+	(*parameters).convergenceCriterion = 0.001;
 	(*parameters).dampingFactor = 0.85;
 	(*parameters).verbose = false;
 	(*parameters).history = false;
@@ -304,6 +336,15 @@ void parseArguments(int argumentCount, char **argumentVector, Parameters *parame
 				exit(EXIT_FAILURE);
 			}
 			(*parameters).dampingFactor = alphaInput;
+		} else if (!strcmp(argumentVector[argumentIndex], ARGUMENT_THREADS_NUMBER)) {
+			argumentIndex = checkIncrement(argumentIndex, argumentCount, argumentVector[0]);
+
+			size_t threadsInput = strtol(argumentVector[argumentIndex], &endPointer, NUMERICAL_BASE);
+			if (threadsInput == 0 && endPointer) {
+				printf("Invalid iterations argument\n");
+				exit(EXIT_FAILURE);
+			}
+			numberOfThreads = threadsInput;
 		} else if (!strcmp(argumentVector[argumentIndex], ARGUMENT_VERBAL_OUTPUT)) {
 			(*parameters).verbose = true;
 		} else if (!strcmp(argumentVector[argumentIndex], ARGUMENT_OUTPUT_HISTORY)) {
@@ -423,33 +464,27 @@ void generateNormalizedTransitionMatrixFromFile(CsrSparseMatrix *transitionMatri
 
 	// Calculates the outdegree of each page and assigns the uniform probability
 	// of transition to the elements of the corresponding row
-
 	int* pageOutdegree = malloc((*parameters).numberOfPages*sizeof(int));
 	for (int i=0; i<(*parameters).numberOfPages; ++i){
 		pageOutdegree[i] = 0;
 	}
 
-	
 	for (int i=0; i<numberOfEdges; ++i) {
 		int currentRow = tempMatrix.elements[i]->rowIndex;
-
-				if (currentRow == tempMatrix.elements[i]->rowIndex) {
 		++pageOutdegree[currentRow];
 	}
 
-			
-	}
-
 	for (int i=0; i<tempMatrix.size; ++i) {
 		tempMatrix.elements[i]->value = 1./pageOutdegree[tempMatrix.elements[i]->rowIndex];
 	}
+	free(pageOutdegree);
 
 	// Transposes the temporary transition matrix (P^T).
 	transposeSparseMatrix(&tempMatrix);
-	allocMemoryForCsr(transitionMatrix, numberOfEdges);
+
+	allocMemoryForCsr(transitionMatrix, (*parameters).numberOfPages, numberOfEdges);
 	// Transforms the temporary COO matrix to the desired CSR format
 	transformToCSR(tempMatrix, transitionMatrix);
-	//printCsrSparseMatrix(*transitionMatrix);
 	destroyCooSparseMatrix(&tempMatrix);
 
 	fclose(graphFile);
@@ -486,27 +521,34 @@ int checkIncrement(int previousIndex, int maxIndex, char *programName) {
 	return ++previousIndex;
 }
 
-void savePagerankToFile(char *filename, bool append, double *pagerankVector,
+void savePagerankToFile(char *filename, int *iterationsUntilConvergence,
-	int vectorSize, int realIterations) {
+	double *pagerankVector, int vectorSize, int iteration) {
 	FILE *outputFile;
 
-	if (append) {
 	outputFile = fopen(filename, "a");
-	} else {
-		outputFile = fopen(filename, "w");
-	}
 
 	if (outputFile == NULL) {
 		printf("Error while opening the output file.\n");
 		return;
 	}
-	//Save numberofPages and convergence time
 
+	fprintf(outputFile, "\n----- Iteration %d -----\n", iteration);
+
+	// Saves the pagerank vector
+	double sum = 0;
+	for (int i=0; i<vectorSize; ++i) {
+		sum += pagerankVector[i];
+	}
+	if (iterationsUntilConvergence == NULL){
 		for (int i=0; i<vectorSize; ++i) {
-		fprintf(outputFile, "%f ", pagerankVector[i]);
+			fprintf(outputFile, "%d = %.10g\n", i, pagerankVector[i]/sum);
 		}
-	fprintf(outputFile, "\n");
+	} else {
-	//fprintf(outputFile, "%d\t", vectorSize);
+		for (int i=0; i<vectorSize; ++i) {
-	//fprintf(outputFile, "%d\t", realIterations);
+			fprintf(outputFile, "%d\t%d\t%.10g\n", i, iterationsUntilConvergence[i],
+				pagerankVector[i]/sum);
+		}
+	}
+
 	fclose(outputFile);
 }

openmp/serial_gs_pagerank_functions.h → openmp/openmp_gs_pagerank_functions.h

@@ -1,5 +1,5 @@
-#ifndef SERIAL_GS_PAGERANK_FUNCTIONS_H	/* Include guard */
+#ifndef OPENMP_GS_PAGERANK_FUNCTIONS_H	/* Include guard */
-#define SERIAL_GS_PAGERANK_FUNCTIONS_H
+#define OPENMP_GS_PAGERANK_FUNCTIONS_H
 
 /* ===== INCLUDES ===== */
 
@@ -8,6 +8,7 @@
 #include <stdlib.h>
 #include <string.h>
 #include <math.h>
+#include <omp.h>
 
 #include "coo_sparse_matrix.h"
 
@@ -27,6 +28,7 @@
 extern const char *ARGUMENT_CONVERGENCE_TOLERANCE;
 extern const char *ARGUMENT_MAX_ITERATIONS;
 extern const char *ARGUMENT_DAMPING_FACTOR;
+extern const char *ARGUMENT_THREADS_NUMBER;
 extern const char *ARGUMENT_VERBAL_OUTPUT;
 extern const char *ARGUMENT_OUTPUT_HISTORY;
 extern const char *ARGUMENT_OUTPUT_FILENAME;
@@ -41,7 +43,7 @@ extern const int FILE_READ_BUFFER_SIZE;
 
 // A data structure to conveniently hold the algorithm's parameters.
 typedef struct parameters {
-	int numberOfPages, maxIterations, realIterations;
+	int numberOfPages, maxIterations;
 	double convergenceCriterion, dampingFactor;
 	bool verbose, history;
 	char *outputFilename, *graphFilename;
@@ -71,8 +73,8 @@ void generateNormalizedTransitionMatrixFromFile(CsrSparseMatrix *transitionMatri
 
 // Function savePagerankToFile appends or overwrites the pagerank vector
 // "pagerankVector" to the file with the filename supplied in the arguments.
-void savePagerankToFile(char *filename, bool append, double *pagerankVector,
+void savePagerankToFile(char *filename, int *iterationsUntilConvergence,
-	int vectorSize, int realIterations);
+	double *pagerankVector, int vectorSize, int iteration);
 
 // Function initialize allocates memory for the pagerank vector, reads the
 // dataset from the file and creates the transition probability distribution
@@ -92,7 +94,7 @@ void calculateNextPagerank(CsrSparseMatrix *transitionMatrix,
 // Function pagerank iteratively calculates the pagerank of each page until
 // either the convergence criterion is met or the maximum number of iterations
 // is reached.
-int pagerank(CsrSparseMatrix *transitionMatrix, double **pagerankVector,
+int* pagerank(CsrSparseMatrix *transitionMatrix, double **pagerankVector,
-	bool *convergenceStatus, Parameters parameters);
+	bool *convergenceStatus, Parameters parameters, int* maxIterationsForConvergence);
 
-#endif	// SERIAL_GS_PAGERANK_FUNCTIONS_H
+#endif	// OPENMP_GS_PAGERANK_FUNCTIONS_H

openmp/serial_gs_pagerank.c

@@ -1,44 +0,0 @@
-#include <sys/time.h>
-#include <omp.h>
-#include "serial_gs_pagerank_functions.h"
-//#include "coo_sparse_matrix.h"
-
-struct timeval startwtime, endwtime;
-double seq_time;
-
-int main(int argc, char **argv) {
-	CsrSparseMatrix transitionMatrix = initCsrSparseMatrix();
-	double *pagerankVector;
-	bool convergenceStatus;
-	Parameters parameters;
-	omp_set_dynamic(0);
-	parseArguments(argc, argv, &parameters);
-
-	initialize(&transitionMatrix, &pagerankVector, &parameters);
-
-	// Starts wall-clock timer
-	gettimeofday (&startwtime, NULL);
-
-	int iterations = pagerank(&transitionMatrix, &pagerankVector,
-		&convergenceStatus, parameters);
-	if (parameters.verbose) {
-		printf(ANSI_COLOR_YELLOW "\n----- RESULTS -----\n" ANSI_COLOR_RESET);
-		if (convergenceStatus) {
-			printf(ANSI_COLOR_GREEN "Pagerank converged after %d iterations!\n" \
-				ANSI_COLOR_RESET, iterations);
-		} else {
-			printf(ANSI_COLOR_RED "Pagerank did not converge after max number of" \
-				" iterations (%d) was reached!\n" ANSI_COLOR_RESET, iterations);
-		}
-	}
-
-	// Stops wall-clock timer
-	gettimeofday (&endwtime, NULL);
-	double seq_time = (double)((endwtime.tv_usec - startwtime.tv_usec)/1.0e6 +
-		endwtime.tv_sec - startwtime.tv_sec);
-	printf("%s wall clock time = %f\n","Pagerank (Gauss-Seidel method), serial implementation",
-		seq_time);
-
-	free(pagerankVector);
-	destroyCsrSparseMatrix(&transitionMatrix);
-}