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pthread/Makefile

@@ -0,0 +1,37 @@
+SHELL := /bin/bash
+
+# ============================================
+# COMMANDS
+
+CC = gcc -std=gnu99 -pthread
+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
+DEPS=serial_gs_pagerank_functions.h coo_sparse_matrix.h csr_sparse_matrix.h
+
+# ==========================================
+# TARGETS
+
+EXECUTABLES = pagerank.out
+
+.PHONY: all clean
+
+all: $(EXECUTABLES)
+
+# ==========================================
+# DEPENDENCIES (HEADERS)
+
+%.o: %.c $(DEPS)
+	$(CC) -c -o $@ $< $(CFLAGS)
+
+.PRECIOUS: $(EXECUTABLES) $(OBJ)
+
+# ==========================================
+# EXECUTABLE (MAIN)
+
+$(EXECUTABLES): $(OBJ)
+	$(CC) -o $@ $^ $(CFLAGS)
+
+clean:
+	$(RM) *.o *~ $(EXECUTABLES)

pthread/coo_sparse_matrix.c

@@ -0,0 +1,132 @@
+#include "coo_sparse_matrix.h"
+
+CooSparseMatrix initCooSparseMatrix() {
+	CooSparseMatrix sparseMatrix;
+	sparseMatrix.size = 0;
+	sparseMatrix.numberOfNonZeroElements = 0;
+	sparseMatrix.elements = NULL;
+	return sparseMatrix;
+}
+
+void allocMemoryForCoo(CooSparseMatrix *sparseMatrix, int numberOfElements) {
+	sparseMatrix->elements = (CooSparseMatrixElement **) malloc(
+		numberOfElements * sizeof(CooSparseMatrixElement *));
+	sparseMatrix->size = numberOfElements;
+}
+
+void addElement(CooSparseMatrix *sparseMatrix, double value, int row, int column) {
+	// Checks if there is enough space allocated
+	if (sparseMatrix->numberOfNonZeroElements == sparseMatrix->size) {
+		printf("Number of non zero elements exceeded size of matrix!\n");
+		exit(EXIT_FAILURE);
+	}
+
+	// Creates the new element
+	CooSparseMatrixElement *newElement = (CooSparseMatrixElement *) malloc(
+		sizeof(CooSparseMatrixElement));
+	newElement->value = value;
+	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;
+}
+
+void transposeSparseMatrix(CooSparseMatrix *sparseMatrix) {
+	for (int i=0; i<sparseMatrix->numberOfNonZeroElements; ++i) {
+		CooSparseMatrixElement *element = sparseMatrix->elements[i];
+		int tempRow = element->rowIndex;
+		element->rowIndex = element->columnIndex;
+		element->columnIndex = tempRow;
+	}
+}
+
+/*
+ * 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) {
+	// 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] = 
+		transformedSparseMatrix->rowCumulativeIndexes[rowIndex] + 1;
+	}
+
+	// Cumulative sums the non zero elements per row
+	for (int i=0, sum=0; i<transformedSparseMatrix->size+1; ++i){
+		int temp = transformedSparseMatrix->rowCumulativeIndexes[i];
+		transformedSparseMatrix->rowCumulativeIndexes[i] = sum;
+		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];
+
+		transformedSparseMatrix->columnIndexes[destinationIndex] = initialSparseMatrix.elements[i]->columnIndex;
+		transformedSparseMatrix->values[destinationIndex] = initialSparseMatrix.elements[i]->value;
+
+		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,
+	double *vector, double **product, int vectorSize) {
+	// Initializes the elements of the product vector to zero
+	for (int i=0; i<vectorSize; ++i) {
+		(*product)[i] = 0;
+	}
+
+	CooSparseMatrixElement *element;
+	for (int i=0; i<sparseMatrix.numberOfNonZeroElements; ++i) {
+		element = sparseMatrix.elements[i];
+		int row = element->rowIndex, column = element->columnIndex;
+
+		if (row >= vectorSize) {
+			printf("Error at sparseMatrixVectorMultiplication. Matrix has more rows than vector!\n");
+			printf("row = %d\n", row);
+			exit(EXIT_FAILURE);
+		}
+
+		(*product)[row] = (*product)[row] + element->value * vector[column];
+	}
+}
+
+void destroyCooSparseMatrix(CooSparseMatrix *sparseMatrix) {
+	for (int i=0; i<sparseMatrix->numberOfNonZeroElements; ++i) {
+		free(sparseMatrix->elements[i]);
+	}
+	free(sparseMatrix->elements);
+}
+
+void printCooSparseMatrix(CooSparseMatrix sparseMatrix) {
+	if (sparseMatrix.numberOfNonZeroElements == 0) {
+		return;
+	}
+
+	CooSparseMatrixElement *element;
+	for (int i=0; i<sparseMatrix.numberOfNonZeroElements; ++i) {
+		element = sparseMatrix.elements[i];
+		printf("[%d,%d] = %f\n", element->rowIndex, element->columnIndex,
+			element->value);
+	}
+}

pthread/coo_sparse_matrix.h

@@ -0,0 +1,60 @@
+#ifndef COO_SPARSE_MATRIX_H	/* Include guard */
+#define COO_SPARSE_MATRIX_H
+
+/* ===== INCLUDES ===== */
+
+#include <stdbool.h>
+#include <stdlib.h>
+#include <stdio.h>
+#include <stdlib.h>
+
+#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

pthread/csr_sparse_matrix.c

@@ -0,0 +1,92 @@
+#include "csr_sparse_matrix.h"
+
+CsrSparseMatrix initCsrSparseMatrix() {
+	CsrSparseMatrix sparseMatrix;
+	sparseMatrix.size = 0;
+	sparseMatrix.numberOfNonZeroElements = 0;
+
+	sparseMatrix.values = NULL;
+	sparseMatrix.columnIndexes = NULL;
+	sparseMatrix.rowCumulativeIndexes = NULL;
+	return sparseMatrix;
+}
+
+void allocMemoryForCsr(CsrSparseMatrix *sparseMatrix, int numberOfElements) {
+	sparseMatrix->values = (double *) malloc(numberOfElements * sizeof(double));
+	sparseMatrix->columnIndexes = (int *) malloc(
+		numberOfElements * sizeof(int));
+	sparseMatrix->rowCumulativeIndexes = (int *) malloc(
+		(numberOfElements + 1) * sizeof(int));
+
+	for (int i=0; i<numberOfElements+1; ++i) {
+		sparseMatrix->rowCumulativeIndexes[i] = 0;
+	}
+	sparseMatrix->size = numberOfElements;
+}
+
+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) {
+		sparseMatrix->values[i] = 0;
+	}
+}
+
+void zeroOutColumn(CsrSparseMatrix *sparseMatrix, int column) {
+	for (int i=0; i<sparseMatrix->numberOfNonZeroElements; ++i){
+		if(sparseMatrix->columnIndexes[i] == column){
+			sparseMatrix->values[i] = 0;
+		}
+	}
+}
+
+void csrSparseMatrixVectorMultiplication(CsrSparseMatrix sparseMatrix,
+	double *vector, double **product, int vectorSize) {
+	// Initializes the elements of the product vector to zero
+	for (int i=0; i<vectorSize; ++i) {
+		(*product)[i] = 0;
+	}
+
+	for (int i=0; i<sparseMatrix.size; ++i) {
+		// Gets start and end indexes of this row's elements
+		int startIndex = sparseMatrix.rowCumulativeIndexes[i],
+		endIndex = sparseMatrix.rowCumulativeIndexes[i+1];
+
+		if (startIndex == endIndex) {
+			// This row has no elements
+			continue;
+		}
+
+		double sum = 0;
+		for(int j=startIndex; j<endIndex; ++j){
+			int elementColumn = sparseMatrix.columnIndexes[j];
+			sum += sparseMatrix.values[j] * vector[elementColumn];
+		}
+
+		(*product)[i] = sum;
+	}
+}
+
+void destroyCsrSparseMatrix(CsrSparseMatrix *sparseMatrix) {
+	free(sparseMatrix->values);
+	free(sparseMatrix->rowCumulativeIndexes);
+	free(sparseMatrix->columnIndexes);
+}
+
+void printCsrSparseMatrix(CsrSparseMatrix sparseMatrix) {
+	if (sparseMatrix.size == 0) {
+		return;
+	}
+
+	for (int i=0; i<sparseMatrix.size; ++i){
+		int startIndex = sparseMatrix.rowCumulativeIndexes[i],
+		endIndex = sparseMatrix.rowCumulativeIndexes[i+1];
+		for(int j=startIndex; j<endIndex; ++j){
+			printf("Row [%d] has [%d] nz elements: \n at column[%d] is value = %f \n",
+				i, endIndex-startIndex,
+				sparseMatrix.columnIndexes[j],
+				sparseMatrix.values[j]);
+		}
+	}
+}

pthread/csr_sparse_matrix.h

@@ -0,0 +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

pthread/serial_gs_pagerank.c

@@ -0,0 +1,42 @@
+#include <sys/time.h>
+
+#include "serial_gs_pagerank_functions.h"
+
+struct timeval startwtime, endwtime;
+
+int main(int argc, char **argv) {
+	CsrSparseMatrix transitionMatrix = initCsrSparseMatrix();
+	double *pagerankVector;
+	bool convergenceStatus;
+	Parameters parameters;
+
+	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);
+}

pthread/serial_gs_pagerank_functions.c

@@ -0,0 +1,610 @@
+/* ===== INCLUDES ===== */
+
+#include "serial_gs_pagerank_functions.h"
+#include <pthread.h>
+
+/* ===== CONSTANTS ===== */
+
+const char *ARGUMENT_CONVERGENCE_TOLERANCE = "-c";
+const char *ARGUMENT_MAX_ITERATIONS = "-m";
+const char *ARGUMENT_DAMPING_FACTOR = "-a";
+const char *ARGUMENT_VERBAL_OUTPUT = "-v";
+const char *ARGUMENT_OUTPUT_HISTORY = "-h";
+const char *ARGUMENT_OUTPUT_FILENAME = "-o";
+
+const int NUMERICAL_BASE = 10;
+char *DEFAULT_OUTPUT_FILENAME = "pagerank_output";
+const int FILE_READ_BUFFER_SIZE = 4096;
+
+const int CONVERGENCE_CHECK_ITERATION_PERIOD = 2;
+const int SPARSITY_INCREASE_ITERATION_PERIOD = 10;
+
+/* ===== THREAD STUFF ====== */
+
+pthread_mutex_t Q = PTHREAD_MUTEX_INITIALIZER;;
+
+typedef struct threadArgs{
+	CsrSparseMatrix* transitionMatrix;
+	double* pagerankVector;
+	double* previousPagerankVector;
+	int numberOfPages;
+	double webUniformProbability;
+	double *linksFromConvergedPagesPagerankVector;
+	double *convergedPagerankVector;
+	int position;
+	double dF;
+}threadArgs;
+
+/* ===== FUNCTIONS ===== */
+
+int pagerank(CsrSparseMatrix *transitionMatrix, double **pagerankVector,
+	bool *convergenceStatus, Parameters parameters) {
+	// Variables declaration
+	int iterations = 0, numberOfPages = parameters.numberOfPages;
+	double delta, *pagerankDifference, *previousPagerankVector,
+	*convergedPagerankVector, *linksFromConvergedPagesPagerankVector;
+	CooSparseMatrix linksFromConvergedPages = initCooSparseMatrix();
+	bool *convergenceMatrix;
+
+	
+	int threadNum = parameters.numberOfPages;
+	pthread_t* threads = (pthread_t *)malloc(threadNum*sizeof(pthread_t));
+	
+	// Space allocation
+	{
+		size_t sizeofDouble = sizeof(double);
+		// pagerankDifference used to calculate delta
+		pagerankDifference = (double *) malloc(numberOfPages * sizeofDouble);
+		// previousPagerankVector holds last iteration's pagerank vector
+		previousPagerankVector = (double *) malloc(numberOfPages * sizeofDouble);
+		// convergedPagerankVector is the pagerank vector of converged pages only
+		convergedPagerankVector = (double *) malloc(numberOfPages * sizeofDouble);
+		// linksFromConvergedPagesPagerankVector holds the partial sum of the
+		// pagerank vector, that describes effect of the links from converged
+		// pages to non converged pages
+		linksFromConvergedPagesPagerankVector = (double *) malloc(numberOfPages * sizeofDouble);
+		// convergenceMatrix indicates which pages have converged
+		convergenceMatrix = (bool *) malloc(numberOfPages * sizeof(bool));
+		*convergenceStatus = false;
+
+		// Initialization
+		allocMemoryForCoo(&linksFromConvergedPages, transitionMatrix->numberOfNonZeroElements);
+		for (int i=0; i<numberOfPages; ++i) {
+			convergedPagerankVector[i] = 0;
+			convergenceMatrix[i] = false;
+			linksFromConvergedPagesPagerankVector[i] = 0;
+		}
+	}
+
+	if (parameters.verbose) {
+		printf(ANSI_COLOR_YELLOW "\n----- Starting iterations -----\n" ANSI_COLOR_RESET);
+	}
+
+	do {
+		// Stores previous pagerank vector
+		memcpy(previousPagerankVector, *pagerankVector, numberOfPages * sizeof(double));
+
+		// Calculates new pagerank vector
+		calculateNextPagerank(transitionMatrix, previousPagerankVector,
+			pagerankVector, linksFromConvergedPagesPagerankVector,
+			convergedPagerankVector, numberOfPages,
+			parameters.dampingFactor, threads, threadNum);
+
+		if (parameters.history) {
+			// Outputs pagerank vector to file
+			savePagerankToFile(parameters.outputFilename, iterations != 0,
+				*pagerankVector, numberOfPages, iterations);
+		}
+
+		// Periodically checks for convergence
+		if (!(iterations % CONVERGENCE_CHECK_ITERATION_PERIOD)) {
+			// Builds pagerank vectors difference
+			for (int i=0; i<numberOfPages; ++i) {
+				pagerankDifference[i] = (*pagerankVector)[i] - previousPagerankVector[i];
+			}
+			// Calculates convergence
+			delta = vectorNorm(pagerankDifference, numberOfPages);
+
+			if (delta < parameters.convergenceCriterion) {
+				// Converged
+				*convergenceStatus = true;
+			}
+		}
+
+		// Periodically increases sparsity
+		if (iterations && !(iterations % SPARSITY_INCREASE_ITERATION_PERIOD)) {
+			bool *newlyConvergedPages = (bool *) malloc(numberOfPages * sizeof(bool));
+			// Checks each individual page for convergence
+			for (int i=0; i<numberOfPages; ++i) {
+				double difference = fabs((*pagerankVector)[i] -
+					previousPagerankVector[i]) / fabs(previousPagerankVector[i]);
+
+				newlyConvergedPages[i] = false;
+				if (!convergenceMatrix[i] && difference < parameters.convergenceCriterion){
+					// Page converged
+					newlyConvergedPages[i] = true;
+					convergenceMatrix[i] = true;
+					convergedPagerankVector[i] = (*pagerankVector)[i];
+				}
+			}
+
+			for (int i=0; i<numberOfPages; ++i) {
+				// Filters newly converged pages
+				if (newlyConvergedPages[i] == true) {
+					// Checks if this converged page has an out-link to a non converged one
+					int rowStartIndex = transitionMatrix->rowCumulativeIndexes[i],
+					rowEndIndex = transitionMatrix->rowCumulativeIndexes[i+1];
+					if (rowEndIndex > rowStartIndex) {
+						// This row (page) has non zero elements (out-links)
+						for (int j=rowStartIndex; j<rowEndIndex; ++j) {
+							// Checks for links from converged pages to non converged
+							int pageLinksTo = transitionMatrix->columnIndexes[j];
+							if (convergenceMatrix[pageLinksTo] == false){
+								// Link exists, adds element to the vector
+								addElement(&linksFromConvergedPages,
+									transitionMatrix->values[j], i, pageLinksTo);
+							}
+						}
+					}
+
+					// Increases sparsity of the transition matrix by zeroing
+					// out elements that correspond to converged pages
+					zeroOutRow(transitionMatrix, i);
+					zeroOutColumn(transitionMatrix, i);
+
+					// Builds the new linksFromConvergedPagesPagerankVector
+					cooSparseMatrixVectorMultiplication(linksFromConvergedPages,
+						*pagerankVector, &linksFromConvergedPagesPagerankVector,
+						numberOfPages);
+				}
+			}
+			free(newlyConvergedPages);
+		}
+
+		++iterations;
+		// Outputs information about this iteration
+		if (iterations%2) {
+			printf(ANSI_COLOR_BLUE "Iteration %d: delta = %f\n" ANSI_COLOR_RESET, iterations, delta);
+		} else {
+			printf(ANSI_COLOR_CYAN "Iteration %d: delta = %f\n" ANSI_COLOR_RESET, iterations, delta);
+		}
+	} while (!*convergenceStatus && (parameters.maxIterations == 0 ||
+		iterations < parameters.maxIterations));
+
+	if (!parameters.history) {
+		// Always outputs last pagerank vector to file
+		savePagerankToFile(parameters.outputFilename, false, *pagerankVector,
+			numberOfPages, iterations);
+	}
+
+	// Frees memory
+	free(pagerankDifference);
+	free(previousPagerankVector);
+	free(convergedPagerankVector);
+	free(linksFromConvergedPagesPagerankVector);
+	free(convergenceMatrix);
+	destroyCooSparseMatrix(&linksFromConvergedPages);
+
+	return iterations;
+}
+
+/*
+ * initialize allocates required memory for arrays, reads the web graph from the
+ * from the file and creates the initial transition probability distribution
+ * matrix.
+*/
+void initialize(CsrSparseMatrix *transitionMatrix,
+	double **pagerankVector, Parameters *parameters) {
+
+	// Reads web graph from file
+	if ((*parameters).verbose) {
+		printf(ANSI_COLOR_YELLOW "----- Reading graph from file -----\n" ANSI_COLOR_RESET);
+	}
+	generateNormalizedTransitionMatrixFromFile(transitionMatrix, parameters);
+
+	// 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);
+		if (!(*parameters).maxIterations) {
+			printf("\nMaximum number of iterations: inf");
+		} else {
+			printf("\nMaximum number of iterations: %d", (*parameters).maxIterations);
+		}
+		printf("\nConvergence criterion: %f" \
+			"\nDamping factor: %f" \
+			"\nGraph filename: %s\n", (*parameters).convergenceCriterion,
+			(*parameters).dampingFactor, (*parameters).graphFilename);
+	}
+
+	// Allocates memory for the pagerank vector
+	(*pagerankVector) = (double *) malloc((*parameters).numberOfPages * sizeof(double));
+	double webUniformProbability = 1. / (*parameters).numberOfPages;
+	for (int i=0; i<(*parameters).numberOfPages; ++i) {
+		(*pagerankVector)[i] = webUniformProbability;
+	}
+}
+
+// ==================== MATH UTILS ====================
+
+/*
+ * calculateNextPagerank calculates the product of the multiplication
+ * between a matrix and the a vector in a cheap way.
+*/
+void calculateNextPagerank(CsrSparseMatrix *transitionMatrix,
+	double *previousPagerankVector, double **pagerankVector,
+	double *linksFromConvergedPagesPagerankVector,
+	double *convergedPagerankVector, int vectorSize, double dampingFactor, pthread_t *threads, int threadNum) {
+		
+	pthread_attr_t attr;
+	pthread_attr_init(&attr);
+	pthread_attr_setdetachstate(&attr, PTHREAD_CREATE_JOINABLE);
+		
+	// Calculates the web uniform probability once.
+	double webUniformProbability = 1. / vectorSize;
+	int runningThreads = 0;
+		
+	for (int i=0; i<vectorSize; ++i) {
+		pthread_mutex_lock(&Q);
+		threadArgs arg;
+		arg.position = i;
+		arg.transitionMatrix = transitionMatrix;
+		arg.pagerankVector = *pagerankVector;
+		arg.previousPagerankVector = previousPagerankVector;
+		arg.linksFromConvergedPagesPagerankVector = linksFromConvergedPagesPagerankVector;
+		arg.convergedPagerankVector = convergedPagerankVector;
+		arg.webUniformProbability = webUniformProbability;
+		arg.dF = dampingFactor;
+		if(runningThreads < threadNum){
+			if(pthread_create(&threads[i], &attr, csrSparseMatrixVectorMultiplication_threads, (void *) &arg)){
+				printf("Error creating thread %d", i);
+				pthread_mutex_unlock(&Q);
+				exit(-1);
+			}
+			else{
+				++runningThreads;
+				pthread_mutex_unlock(&Q);
+			}
+		}
+		else{
+			pthread_mutex_unlock(&Q);
+			printf("not enough threads\n");
+			exit(-1);
+		}
+		pthread_join(threads[i], NULL);
+		if(runningThreads < threadNum){
+			if(pthread_create(&threads[i], &attr, compPagerankVector_threads, (void *) &arg)){
+				printf("Error creating thread %d", i);
+				pthread_mutex_unlock(&Q);
+				exit(-1);
+			}
+			else{
+				++runningThreads;
+				pthread_mutex_unlock(&Q);
+			}
+		}
+		else{
+			printf("You have a problem \n");
+			exit(-1);
+			pthread_mutex_unlock(&Q);
+		}
+		
+	}
+	for(int i=0; i<vectorSize; ++i){
+		pthread_join(threads[i], NULL);
+	}
+	free(threads);
+	
+}
+
+void compPagerankVector_threads(void* arg){
+	threadArgs* co = (threadArgs *)arg;
+	co->pagerankVector[co->position] = co->dF * co->pagerankVector[co->position];
+	
+
+	double normDifference = vectorNorm(co->previousPagerankVector, co->numberOfPages) -
+	vectorNorm(co->pagerankVector, co->numberOfPages);
+
+	
+	co->pagerankVector[co->position] += normDifference * co->webUniformProbability +
+	co->linksFromConvergedPagesPagerankVector[co->position] + co->convergedPagerankVector[co->position];
+
+}
+
+void csrSparseMatrixVectorMultiplication_threads(void* arg){
+	threadArgs* co = (threadArgs *)arg;
+	//(CsrSparseMatrix sparseMatrix,
+	//double *vector, double **product, int vectorSize) {
+	// Initializes the elements of the product vector to zero
+	//for (int i=0; i<vectorSize; ++i) {
+		 co->pagerankVector[co->position] = 0;
+	//}
+
+	//for (int i=0; i<sparseMatrix.size; ++i) {
+		// Gets start and end indexes of this row's elements
+		int startIndex = co->transitionMatrix[co->position].rowCumulativeIndexes[co->position],
+		endIndex = co->transitionMatrix[co->position].rowCumulativeIndexes[co->position+1];
+
+		if (startIndex == endIndex) {
+			// This row has no elements
+			return;
+		}
+
+		double sum = 0;
+		for(int j=startIndex; j<endIndex; ++j){
+			int elementColumn = co->transitionMatrix[co->position].columnIndexes[j];
+			sum += co->transitionMatrix[co->position].values[j] * co->previousPagerankVector[elementColumn];
+		}
+
+		co->pagerankVector[co->position] = sum;
+	//}
+}
+
+
+/*
+ * vectorNorm calculates the first norm of a vector.
+*/
+double vectorNorm(double *vector, int vectorSize) {
+	double norm = 0.;
+
+	for (int i=0; i<vectorSize; ++i) {
+		norm += fabs(vector[i]);
+	}
+
+	return norm;
+}
+
+// ==================== PROGRAM INPUT AND OUTPUT UTILS ====================
+
+/*
+ * parseArguments parses the command line arguments given by the user.
+*/
+void parseArguments(int argumentCount, char **argumentVector, Parameters *parameters) {
+	if (argumentCount < 2 || argumentCount > 10) {
+		validUsage(argumentVector[0]);
+	}
+
+	(*parameters).numberOfPages = 0;
+	(*parameters).maxIterations = 0;
+	(*parameters).convergenceCriterion = 1;
+	(*parameters).dampingFactor = 0.85;
+	(*parameters).verbose = false;
+	(*parameters).history = false;
+	(*parameters).outputFilename = DEFAULT_OUTPUT_FILENAME;
+
+	char *endPointer;
+	int argumentIndex = 1;
+
+	while (argumentIndex < argumentCount) {
+		if (!strcmp(argumentVector[argumentIndex], ARGUMENT_CONVERGENCE_TOLERANCE)) {
+			argumentIndex = checkIncrement(argumentIndex, argumentCount, argumentVector[0]);
+
+			double convergenceInput = strtod(argumentVector[argumentIndex], &endPointer);
+			if (convergenceInput == 0) {
+				printf("Invalid convergence argument\n");
+				exit(EXIT_FAILURE);
+			}
+			(*parameters).convergenceCriterion = convergenceInput;
+		} else if (!strcmp(argumentVector[argumentIndex], ARGUMENT_MAX_ITERATIONS)) {
+			argumentIndex = checkIncrement(argumentIndex, argumentCount, argumentVector[0]);
+
+			size_t iterationsInput = strtol(argumentVector[argumentIndex], &endPointer, NUMERICAL_BASE);
+			if (iterationsInput == 0 && endPointer) {
+				printf("Invalid iterations argument\n");
+				exit(EXIT_FAILURE);
+			}
+			(*parameters).maxIterations = iterationsInput;
+		} else if (!strcmp(argumentVector[argumentIndex], ARGUMENT_DAMPING_FACTOR)) {
+			argumentIndex = checkIncrement(argumentIndex, argumentCount, argumentVector[0]);
+
+			double alphaInput = strtod(argumentVector[argumentIndex], &endPointer);
+			if ((alphaInput == 0 || alphaInput > 1) && endPointer) {
+				printf("Invalid alpha argument\n");
+				exit(EXIT_FAILURE);
+			}
+			(*parameters).dampingFactor = alphaInput;
+		} else if (!strcmp(argumentVector[argumentIndex], ARGUMENT_VERBAL_OUTPUT)) {
+			(*parameters).verbose = true;
+		} else if (!strcmp(argumentVector[argumentIndex], ARGUMENT_OUTPUT_HISTORY)) {
+			(*parameters).history = true;
+		} else if (!strcmp(argumentVector[argumentIndex], ARGUMENT_OUTPUT_FILENAME)) {
+			argumentIndex = checkIncrement(argumentIndex, argumentCount, argumentVector[0]);
+
+			if (fopen(argumentVector[argumentIndex], "w") == NULL) {
+				printf("Invalid output filename. Reverting to default.\n");
+				continue;
+			}
+			(*parameters).outputFilename = argumentVector[argumentIndex];
+		} else if (argumentIndex == argumentCount - 1) {
+			(*parameters).graphFilename = argumentVector[argumentIndex];
+		} else {
+			validUsage(argumentVector[0]);
+			exit(EXIT_FAILURE);
+		}
+		++argumentIndex;
+	}
+}
+
+/*
+ * readGraphFromFile loads the file supplied in the command line arguments to an
+ * array (directedWebGraph) that represents the graph.
+*/
+void generateNormalizedTransitionMatrixFromFile(CsrSparseMatrix *transitionMatrix,
+	Parameters *parameters){
+	FILE *graphFile;
+
+	// Opens the file for reading
+	graphFile = fopen((*parameters).graphFilename, "r+");
+	if (!graphFile) {
+		printf("Error opening file \n");
+		exit(EXIT_FAILURE);
+	}
+
+	char buffer[FILE_READ_BUFFER_SIZE];
+	char *readResult;
+	// Skips the first two lines
+	readResult = fgets(buffer, FILE_READ_BUFFER_SIZE, graphFile);
+	readResult = fgets(buffer, FILE_READ_BUFFER_SIZE, graphFile);
+	if (readResult == NULL) {
+		printf("Error while reading from the file. Does the file have the correct format?\n");
+		exit(EXIT_FAILURE);
+	}
+
+	// Third line contains the numbers of nodes and edges
+	int numberOfNodes = 0, numberOfEdges = 0;
+
+	readResult = fgets(buffer, FILE_READ_BUFFER_SIZE, graphFile);
+	if (readResult == NULL) {
+		printf("Error while reading from the file. Does the file have the correct format?\n");
+		exit(EXIT_FAILURE);
+	}
+
+	// Parses the number of nodes and number of edges
+	{
+		// Splits string to whitespace
+		char *token = strtok(buffer, " ");
+		bool nextIsNodes = false, nextIsEdges = false;
+
+		while (token != NULL) {
+			if (strcmp(token, "Nodes:") == 0) {
+				nextIsNodes = true;
+			} else if (nextIsNodes) {
+				numberOfNodes = atoi(token);
+				nextIsNodes = false;
+			} else if (strcmp(token, "Edges:") == 0) {
+				nextIsEdges = true;
+			} else if (nextIsEdges) {
+				numberOfEdges = atoi(token);
+				break;
+			}
+
+			// Gets next string token
+			token = strtok (NULL, " ,.-");
+		}
+	}
+
+	if ((*parameters).verbose) {
+		printf("File claims number of pages is: %d\nThe number of edges is: %d\n",
+			numberOfNodes, numberOfEdges);
+	}
+
+	// Skips the fourth line
+	readResult = fgets(buffer, 512, graphFile);
+	if (readResult == NULL) {
+		printf("Error while reading from the file. Does the file have the correct format?\n");
+		exit(EXIT_FAILURE);
+	}
+
+	
+	int maxPageIndex = 0;
+	CooSparseMatrix tempMatrix = initCooSparseMatrix();
+	allocMemoryForCoo(&tempMatrix, numberOfEdges);
+
+	for (int i=0; i<numberOfEdges; i++) {
+		int fileFrom = 0, fileTo = 0;
+		if (!fscanf(graphFile, "%d %d", &fileFrom, &fileTo)) {
+			break;
+		}
+
+		if (fileFrom > maxPageIndex) {
+			maxPageIndex = fileFrom;
+		}
+		if (fileTo > maxPageIndex) {
+			maxPageIndex = fileTo;
+		}
+		addElement(&tempMatrix, 1, fileFrom, fileTo);
+	}
+
+	if ((*parameters).verbose) {
+		printf("Max page index found is: %d\n", maxPageIndex);
+	}
+	(*parameters).numberOfPages = maxPageIndex + 1;
+
+	// 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;
+		++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);
+	// Transforms the temporary COO matrix to the desired CSR format
+	transformToCSR(tempMatrix, transitionMatrix);
+	destroyCooSparseMatrix(&tempMatrix);
+
+	fclose(graphFile);
+}
+
+/*
+ * validUsage outputs a message to the console that informs the user of the
+ * correct (valid) way to use the program.
+*/
+void validUsage(char *programName) {
+	printf("%s [-c convergence_criterion] [-m max_iterations] [-a alpha] [-v] [-h] [-o output_filename] <graph_file>" \
+		"\n-c convergence_criterion" \
+		"\n\tthe convergence tolerance criterion" \
+		"\n-m max_iterations" \
+		"\n\tmaximum number of iterations to perform" \
+		"\n-a alpha" \
+		"\n\tthe damping factor" \
+		"\n-v enable verbal output" \
+		"\n-h enable history output to file" \
+		"\n-o output_filename" \
+		"\n\tfilename and path for the output" \
+		"\n", programName);
+	exit(EXIT_FAILURE);
+}
+
+/*
+ * checkIncrement is a helper function for parseArguments function.
+*/
+int checkIncrement(int previousIndex, int maxIndex, char *programName) {
+	if (previousIndex == maxIndex) {
+		validUsage(programName);
+		exit(EXIT_FAILURE);
+	}
+	return ++previousIndex;
+}
+
+void savePagerankToFile(char *filename, bool append, 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;
+	}
+
+	// Saves the pagerank vector
+	//fprintf(outputFile, "Iteration %d:\t", iteration);
+	double sum = 0;
+	for (int i=0; i<vectorSize; ++i) {
+		sum += pagerankVector[i];
+	}
+	//fprintf(outputFile, "%f\n", sum);
+
+	for (int i=0; i<vectorSize; ++i) {
+		fprintf(outputFile, "%d = %.10g\n", i, pagerankVector[i]/sum);
+	}
+
+	fclose(outputFile);
+}

pthread/serial_gs_pagerank_functions.h

@@ -0,0 +1,100 @@
+#ifndef SERIAL_GS_PAGERANK_FUNCTIONS_H	/* Include guard */
+#define SERIAL_GS_PAGERANK_FUNCTIONS_H
+
+/* ===== INCLUDES ===== */
+
+#include <stdbool.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <math.h>
+
+#include "coo_sparse_matrix.h"
+
+/* ===== DEFINITIONS ===== */
+
+//Colors used for better console output formating.
+#define ANSI_COLOR_RED     "\x1B[31m"
+#define ANSI_COLOR_GREEN   "\x1B[32m"
+#define ANSI_COLOR_YELLOW  "\x1B[33m"
+#define ANSI_COLOR_BLUE    "\x1B[34m"
+#define ANSI_COLOR_CYAN    "\x1B[36m"
+#define ANSI_COLOR_RESET   "\x1B[0m"
+
+/* ===== CONSTANTS DEFINITION ===== */
+
+// Constant strings that store the command line options available.
+extern const char *ARGUMENT_CONVERGENCE_TOLERANCE;
+extern const char *ARGUMENT_MAX_ITERATIONS;
+extern const char *ARGUMENT_DAMPING_FACTOR;
+extern const char *ARGUMENT_VERBAL_OUTPUT;
+extern const char *ARGUMENT_OUTPUT_HISTORY;
+extern const char *ARGUMENT_OUTPUT_FILENAME;
+// The numerical base used when parsing numerical command line arguments.
+extern const int NUMERICAL_BASE;
+// Default filename used for the output.
+extern char *DEFAULT_OUTPUT_FILENAME;
+// The size of the buffer used for reading the graph input file.
+extern const int FILE_READ_BUFFER_SIZE;
+
+/* ===== STRUCTURES ===== */
+
+// A data structure to conveniently hold the algorithm's parameters.
+typedef struct parameters {
+	int numberOfPages, maxIterations;
+	double convergenceCriterion, dampingFactor;
+	bool verbose, history;
+	char *outputFilename, *graphFilename;
+} Parameters;
+
+/* ===== FUNCTION DEFINITIONS ===== */
+
+// Function validUsage outputs the correct way to use the program with command
+// line arguments.
+void validUsage(char *programName);
+
+// Function checkIncrement is a helper function used in parseArguments (see
+// bellow).
+int checkIncrement(int previousIndex, int maxIndex, char *programName);
+
+// Function parseArguments parses command line arguments.
+void parseArguments(int argumentCount, char **argumentVector,
+	Parameters *parameters);
+
+// Function generateNormalizedTransitionMatrixFromFile reads through the entries
+// of the file specified in the arguments (parameters->graphFilename), using
+// them to populate the sparse array (transitionMatrix). The entries of the file
+// represent the edges of the web transition graph. The entries are then
+// modified to become the rows of the transition matrix.
+void generateNormalizedTransitionMatrixFromFile(CsrSparseMatrix *transitionMatrix,
+	Parameters *parameters);
+
+// 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,
+	int vectorSize, int iteration);
+
+// Function initialize allocates memory for the pagerank vector, reads the
+// dataset from the file and creates the transition probability distribution
+// matrix.
+void initialize(CsrSparseMatrix *transitionMatrix, double **pagerankVector,
+	Parameters *parameters);
+
+// Function vectorNorm calculates the first norm of a vector.
+double vectorNorm(double *vector, int vectorSize);
+
+// Function calculateNextPagerank calculates the next pagerank vector.
+void calculateNextPagerank(CsrSparseMatrix *transitionMatrix,
+	double *previousPagerankVector, double **pagerankVector,
+	double *linksFromConvergedPagesPagerankVector,
+	double *convergedPagerankVector, int vectorSize, double dampingFactor, pthread_t *threads, int threadNum);
+
+// 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,
+	bool *convergenceStatus, Parameters parameters);
+
+void csrSparseMatrixVectorMultiplication_threads(void* arg);
+void compPagerankVector_threads(void* arg);
+#endif	// SERIAL_GS_PAGERANK_FUNCTIONS_H