apostolof-ece-auth-gr
/
authParallelAndDistributedSystemsCourseExercise4
1
0
Fork 0
Code Releases Activity
Browse Source

Implement transition matrix pruning, Fix sparse matrices sizes, Fix output

master
Apostolos Fanakis 6 years ago
parent
457e7c4f55
commit
694f53cc0f
No known key found for this signature in database GPG Key ID: 56CE2DEDE9F1FB78
6 changed files with 98 additions and 75 deletions
Whitespace
Show all changes Ignore whitespace when comparing lines Ignore changes in amount of whitespace Ignore changes in whitespace at EOL
Unified View
Diff Options
Show Stats Download Patch File Download Diff File
  1. 4
      serial/coo_sparse_matrix.c
  2. 14
      serial/csr_sparse_matrix.c
  3. 4
      serial/csr_sparse_matrix.h
  4. 45
      serial/serial_gs_pagerank.c
  5. 98
      serial/serial_gs_pagerank_functions.c
  6. 4
      serial/serial_gs_pagerank_functions.h

4
serial/coo_sparse_matrix.c
View File

@ -49,7 +49,7 @@ void transposeSparseMatrix(CooSparseMatrix *sparseMatrix) {
void transformToCSR(CooSparseMatrix initialSparseMatrix, void transformToCSR(CooSparseMatrix initialSparseMatrix,
CsrSparseMatrix *transformedSparseMatrix) { CsrSparseMatrix *transformedSparseMatrix) {
// Checks if the sizes of the two matrices fit // 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"); printf("Transformed CSR matrix does not have enough space!\n");
exit(EXIT_FAILURE); exit(EXIT_FAILURE);
} }
@ -85,8 +85,6 @@ void transformToCSR(CooSparseMatrix initialSparseMatrix,
transformedSparseMatrix->rowCumulativeIndexes[i] = last; transformedSparseMatrix->rowCumulativeIndexes[i] = last;
last = temp; last = temp;
} }
transformedSparseMatrix->numberOfNonZeroElements = initialSparseMatrix.numberOfNonZeroElements;
} }
void cooSparseMatrixVectorMultiplication(CooSparseMatrix sparseMatrix, void cooSparseMatrixVectorMultiplication(CooSparseMatrix sparseMatrix,

14
serial/csr_sparse_matrix.c
View File

@ -3,7 +3,7 @@
CsrSparseMatrix initCsrSparseMatrix() { CsrSparseMatrix initCsrSparseMatrix() {
CsrSparseMatrix sparseMatrix; CsrSparseMatrix sparseMatrix;
sparseMatrix.size = 0; sparseMatrix.size = 0;
sparseMatrix.numberOfNonZeroElements = 0; sparseMatrix.numberOfElements = 0;
sparseMatrix.values = NULL; sparseMatrix.values = NULL;
sparseMatrix.columnIndexes = NULL; sparseMatrix.columnIndexes = NULL;
@ -11,17 +11,19 @@ CsrSparseMatrix initCsrSparseMatrix() {
return sparseMatrix; return sparseMatrix;
} }
void allocMemoryForCsr(CsrSparseMatrix *sparseMatrix, int numberOfElements) { void allocMemoryForCsr(CsrSparseMatrix *sparseMatrix, int size, int numberOfElements) {
sparseMatrix->values = (double *) malloc(numberOfElements * sizeof(double)); sparseMatrix->values = (double *) malloc(numberOfElements * sizeof(double));
sparseMatrix->columnIndexes = (int *) malloc( sparseMatrix->columnIndexes = (int *) malloc(
numberOfElements * sizeof(int)); numberOfElements * sizeof(int));
sparseMatrix->rowCumulativeIndexes = (int *) malloc( 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->rowCumulativeIndexes[i] = 0;
} }
sparseMatrix->size = numberOfElements;
sparseMatrix->size = size;
sparseMatrix->numberOfElements = numberOfElements;
} }
void zeroOutRow(CsrSparseMatrix *sparseMatrix, int row) { void zeroOutRow(CsrSparseMatrix *sparseMatrix, int row) {
@ -34,7 +36,7 @@ void zeroOutRow(CsrSparseMatrix *sparseMatrix, int row) {
} }
void zeroOutColumn(CsrSparseMatrix *sparseMatrix, int column) { 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){ if(sparseMatrix->columnIndexes[i] == column){
sparseMatrix->values[i] = 0; sparseMatrix->values[i] = 0;
} }

4
serial/csr_sparse_matrix.h
View File

@ -12,7 +12,7 @@
// A sparse matrix in compressed SparseRow format. // A sparse matrix in compressed SparseRow format.
typedef struct csrSparseMatrix { typedef struct csrSparseMatrix {
int size, numberOfNonZeroElements; int size, numberOfElements;
int *rowCumulativeIndexes, *columnIndexes; int *rowCumulativeIndexes, *columnIndexes;
double *values; double *values;
} CsrSparseMatrix; } CsrSparseMatrix;
@ -24,7 +24,7 @@ typedef struct csrSparseMatrix {
CsrSparseMatrix initCsrSparseMatrix(); CsrSparseMatrix initCsrSparseMatrix();
// allocMemoryForCsr allocates memory for the elements of the matrix. // allocMemoryForCsr allocates memory for the elements of the matrix.
void allocMemoryForCsr(CsrSparseMatrix *sparseMatrix, int numberOfElements); void allocMemoryForCsr(CsrSparseMatrix *sparseMatrix, int size, int numberOfElements);
// zeroOutRow assigns a zero value to all the elements of a row in the matrix. // zeroOutRow assigns a zero value to all the elements of a row in the matrix.
void zeroOutRow(CsrSparseMatrix *sparseMatrix, int row); void zeroOutRow(CsrSparseMatrix *sparseMatrix, int row);

45
serial/serial_gs_pagerank.c
View File

@ -15,22 +15,30 @@ int main(int argc, char **argv) {
initialize(&transitionMatrix, &pagerankVector, &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 // Starts wall-clock timer
gettimeofday (&startwtime, NULL); gettimeofday (&startwtime, NULL);
int* iterations = (int *)malloc(parameters.numberOfPages*sizeof(int)); int* iterations = (int *)malloc(parameters.numberOfPages*sizeof(int));
// Calculates pagerank
iterations = pagerank(&transitionMatrix, &pagerankVector, iterations = pagerank(&transitionMatrix, &pagerankVector,
&convergenceStatus, parameters, &maxIterationsForConvergence); &convergenceStatus, parameters, &maxIterationsForConvergence);
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, maxIterationsForConvergence);
} else {
printf(ANSI_COLOR_RED "Pagerank did not converge after max number of" \
" iterations (%d) was reached!\n" ANSI_COLOR_RESET, maxIterationsForConvergence);
}
}
// Stops wall-clock timer // Stops wall-clock timer
gettimeofday (&endwtime, NULL); gettimeofday (&endwtime, NULL);
@ -38,13 +46,20 @@ int main(int argc, char **argv) {
endwtime.tv_sec - startwtime.tv_sec); endwtime.tv_sec - startwtime.tv_sec);
printf("%s wall clock time = %f\n","Pagerank (Gauss-Seidel method), serial implementation", printf("%s wall clock time = %f\n","Pagerank (Gauss-Seidel method), serial implementation",
seq_time); seq_time);
if (!parameters.history) {
// Always outputs numberOfPages, max_iterations, last pagerank and iterations printf(ANSI_COLOR_YELLOW "\n----- RESULTS -----\n" ANSI_COLOR_RESET);
// for all pages if (convergenceStatus) {
savePagerankToFile(parameters.outputFilename, false, pagerankVector, printf(ANSI_COLOR_GREEN "Pagerank converged after %d iterations!\n" \
parameters.numberOfPages, iterations, maxIterationsForConvergence); 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); free(pagerankVector);
destroyCsrSparseMatrix(&transitionMatrix); destroyCsrSparseMatrix(&transitionMatrix);
} }

98
serial/serial_gs_pagerank_functions.c
View File

@ -24,15 +24,18 @@ int* pagerank(CsrSparseMatrix *transitionMatrix, double **pagerankVector,
bool *convergenceStatus, Parameters parameters, int* maxIterationsForConvergence) { bool *convergenceStatus, Parameters parameters, int* maxIterationsForConvergence) {
// Variables declaration // Variables declaration
int numberOfPages = parameters.numberOfPages; int numberOfPages = parameters.numberOfPages;
int *iterations;
double delta, *pagerankDifference, *previousPagerankVector, double delta, *pagerankDifference, *previousPagerankVector,
*convergedPagerankVector, *linksFromConvergedPagesPagerankVector; *convergedPagerankVector, *linksFromConvergedPagesPagerankVector;
CsrSparseMatrix originalTransitionMatrix = initCsrSparseMatrix();
CooSparseMatrix linksFromConvergedPages = initCooSparseMatrix(); CooSparseMatrix linksFromConvergedPages = initCooSparseMatrix();
bool *convergenceMatrix; bool *convergenceMatrix;
int* iterations = (int *)malloc(numberOfPages*sizeof(int));
// Space allocation // Space allocation
{ {
size_t sizeofDouble = sizeof(double); size_t sizeofDouble = sizeof(double);
// iterations until each page converged
iterations = (int *) malloc(numberOfPages * sizeof(int));
// pagerankDifference used to calculate delta // pagerankDifference used to calculate delta
pagerankDifference = (double *) malloc(numberOfPages * sizeofDouble); pagerankDifference = (double *) malloc(numberOfPages * sizeofDouble);
// previousPagerankVector holds last iteration's pagerank vector // previousPagerankVector holds last iteration's pagerank vector
@ -48,7 +51,16 @@ int* pagerank(CsrSparseMatrix *transitionMatrix, double **pagerankVector,
*convergenceStatus = false; *convergenceStatus = false;
// Initialization // Initialization
allocMemoryForCoo(&linksFromConvergedPages, transitionMatrix->numberOfNonZeroElements); // originalTransitionMatrix used to run pagerank in phases
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);
for (int i=0; i<numberOfPages; ++i) { for (int i=0; i<numberOfPages; ++i) {
convergedPagerankVector[i] = 0; convergedPagerankVector[i] = 0;
convergenceMatrix[i] = false; convergenceMatrix[i] = false;
@ -73,8 +85,8 @@ int* pagerank(CsrSparseMatrix *transitionMatrix, double **pagerankVector,
if (parameters.history) { if (parameters.history) {
// Outputs pagerank vector to file // Outputs pagerank vector to file
savePagerankToFile(parameters.outputFilename, true, savePagerankToFile(parameters.outputFilename, NULL, *pagerankVector,
*pagerankVector, numberOfPages, iterations, *maxIterationsForConvergence); numberOfPages, *maxIterationsForConvergence);
} }
// Periodically checks for convergence // Periodically checks for convergence
@ -92,6 +104,8 @@ int* pagerank(CsrSparseMatrix *transitionMatrix, double **pagerankVector,
} }
} }
++(*maxIterationsForConvergence);
// Periodically increases sparsity // Periodically increases sparsity
if ((*maxIterationsForConvergence) && !(*maxIterationsForConvergence % SPARSITY_INCREASE_ITERATION_PERIOD)) { if ((*maxIterationsForConvergence) && !(*maxIterationsForConvergence % SPARSITY_INCREASE_ITERATION_PERIOD)) {
bool *newlyConvergedPages = (bool *) malloc(numberOfPages * sizeof(bool)); bool *newlyConvergedPages = (bool *) malloc(numberOfPages * sizeof(bool));
@ -106,6 +120,7 @@ int* pagerank(CsrSparseMatrix *transitionMatrix, double **pagerankVector,
newlyConvergedPages[i] = true; newlyConvergedPages[i] = true;
convergenceMatrix[i] = true; convergenceMatrix[i] = true;
convergedPagerankVector[i] = (*pagerankVector)[i]; convergedPagerankVector[i] = (*pagerankVector)[i];
iterations[i] = *maxIterationsForConvergence;
} }
} }
@ -131,7 +146,7 @@ int* pagerank(CsrSparseMatrix *transitionMatrix, double **pagerankVector,
// Increases sparsity of the transition matrix by zeroing // Increases sparsity of the transition matrix by zeroing
// out elements that correspond to converged pages // out elements that correspond to converged pages
zeroOutRow(transitionMatrix, i); zeroOutRow(transitionMatrix, i);
zeroOutColumn(transitionMatrix, i); //zeroOutColumn(transitionMatrix, i);
// Builds the new linksFromConvergedPagesPagerankVector // Builds the new linksFromConvergedPagesPagerankVector
cooSparseMatrixVectorMultiplication(linksFromConvergedPages, cooSparseMatrixVectorMultiplication(linksFromConvergedPages,
@ -142,23 +157,29 @@ int* pagerank(CsrSparseMatrix *transitionMatrix, double **pagerankVector,
free(newlyConvergedPages); free(newlyConvergedPages);
} }
for(int i=0; i<numberOfPages; ++i){ // Prunes the transition matrix every 8 iterations
if(!convergenceMatrix[i]){ if (*maxIterationsForConvergence != 0 && (*maxIterationsForConvergence%8 == 0)) {
++iterations[i]; memcpy(transitionMatrix->values, originalTransitionMatrix.values,
transitionMatrix->numberOfElements * sizeof(double));
for (int i=0; i<numberOfPages; ++i) {
convergedPagerankVector[i] = 0;
convergenceMatrix[i] = false;
linksFromConvergedPagesPagerankVector[i] = 0;
} }
linksFromConvergedPages.numberOfNonZeroElements = 0;
} }
++(*maxIterationsForConvergence);
// Outputs information about this iteration // Outputs information about this iteration
if ((*maxIterationsForConvergence)%2) { if (parameters.verbose){
printf(ANSI_COLOR_BLUE "Iteration %d: delta = %f\n" ANSI_COLOR_RESET, *maxIterationsForConvergence, delta); if ((*maxIterationsForConvergence)%2) {
} else { printf(ANSI_COLOR_BLUE "Iteration %d: delta = %f\n" ANSI_COLOR_RESET, *maxIterationsForConvergence, delta);
printf(ANSI_COLOR_CYAN "Iteration %d: delta = %f\n" ANSI_COLOR_RESET, *maxIterationsForConvergence, delta); } else {
printf(ANSI_COLOR_CYAN "Iteration %d: delta = %f\n" ANSI_COLOR_RESET, *maxIterationsForConvergence, delta);
}
} }
} while (!*convergenceStatus && (parameters.maxIterations == 0 || } while (!*convergenceStatus && (parameters.maxIterations == 0 ||
*maxIterationsForConvergence < parameters.maxIterations)); *maxIterationsForConvergence < parameters.maxIterations));
// Frees memory // Frees memory
free(pagerankDifference); free(pagerankDifference);
free(previousPagerankVector); free(previousPagerankVector);
@ -231,7 +252,7 @@ void calculateNextPagerank(CsrSparseMatrix *transitionMatrix,
vectorNorm(*pagerankVector, vectorSize); vectorNorm(*pagerankVector, vectorSize);
for (int i=0; i<vectorSize; ++i) { for (int i=0; i<vectorSize; ++i) {
(*pagerankVector)[i] += dampingFactor* normDifference * webUniformProbability + (*pagerankVector)[i] += normDifference * webUniformProbability +
linksFromConvergedPagesPagerankVector[i] + convergedPagerankVector[i]; linksFromConvergedPagesPagerankVector[i] + convergedPagerankVector[i];
} }
} }
@ -255,13 +276,13 @@ double vectorNorm(double *vector, int vectorSize) {
* parseArguments parses the command line arguments given by the user. * parseArguments parses the command line arguments given by the user.
*/ */
void parseArguments(int argumentCount, char **argumentVector, Parameters *parameters) { void parseArguments(int argumentCount, char **argumentVector, Parameters *parameters) {
if (argumentCount < 2 || argumentCount > 10) { if (argumentCount < 2 || argumentCount > 12) {
validUsage(argumentVector[0]); validUsage(argumentVector[0]);
} }
(*parameters).numberOfPages = 0; (*parameters).numberOfPages = 0;
(*parameters).maxIterations = 0; (*parameters).maxIterations = 0;
(*parameters).convergenceCriterion = 1; (*parameters).convergenceCriterion = 0.001;
(*parameters).dampingFactor = 0.85; (*parameters).dampingFactor = 0.85;
(*parameters).verbose = false; (*parameters).verbose = false;
(*parameters).history = false; (*parameters).history = false;
@ -435,7 +456,7 @@ void generateNormalizedTransitionMatrixFromFile(CsrSparseMatrix *transitionMatri
// Transposes the temporary transition matrix (P^T). // Transposes the temporary transition matrix (P^T).
transposeSparseMatrix(&tempMatrix); transposeSparseMatrix(&tempMatrix);
allocMemoryForCsr(transitionMatrix, numberOfEdges); allocMemoryForCsr(transitionMatrix, (*parameters).numberOfPages, numberOfEdges);
// Transforms the temporary COO matrix to the desired CSR format // Transforms the temporary COO matrix to the desired CSR format
transformToCSR(tempMatrix, transitionMatrix); transformToCSR(tempMatrix, transitionMatrix);
destroyCooSparseMatrix(&tempMatrix); destroyCooSparseMatrix(&tempMatrix);
@ -474,47 +495,34 @@ int checkIncrement(int previousIndex, int maxIndex, char *programName) {
return ++previousIndex; return ++previousIndex;
} }
void savePagerankToFile(char *filename, bool append, double *pagerankVector, void savePagerankToFile(char *filename, int *iterationsUntilConvergence,
int vectorSize, int* iterations, int maxIterationsForConvergence) { double *pagerankVector, int vectorSize, int iteration) {
FILE *outputFile; FILE *outputFile;
if (append) { outputFile = fopen(filename, "a");
outputFile = fopen(filename, "a");
} else {
outputFile = fopen(filename, "w");
}
if (outputFile == NULL) { if (outputFile == NULL) {
printf("Error while opening the output file.\n"); printf("Error while opening the output file.\n");
return; return;
} }
fprintf(outputFile, "\n----- Iteration %d -----\n", iteration);
if(append){ // Saves the pagerank vector
double sum = 0; double sum = 0;
for (int i=0; i<vectorSize; ++i) { for (int i=0; i<vectorSize; ++i) {
sum += pagerankVector[i]; sum += pagerankVector[i];
}
for (int i=0; i<vectorSize; ++i) {
fprintf(outputFile, "%d = %.10g\n", i, pagerankVector[i]/sum);
}
} }
else{ if (iterationsUntilConvergence == NULL){
fprintf(outputFile, "numberOfPages = %d \t max_iterations_needed = %d \n", vectorSize, maxIterationsForConvergence);
double sum = 0;
for (int i=0; i<vectorSize; ++i) { for (int i=0; i<vectorSize; ++i) {
sum += pagerankVector[i]; fprintf(outputFile, "%d = %.10g\n", i, pagerankVector[i]/sum);
} }
} else {
for (int i=0; i<vectorSize; ++i) { for (int i=0; i<vectorSize; ++i) {
fprintf(outputFile, "%d \t %d \t %.10g\n", i, iterations[i], pagerankVector[i]/sum); fprintf(outputFile, "%d\t%d\t%.10g\n", i, iterationsUntilConvergence[i],
pagerankVector[i]/sum);
} }
} }
// Saves the pagerank vector
fclose(outputFile); fclose(outputFile);
} }

4
serial/serial_gs_pagerank_functions.h
View File

@ -71,8 +71,8 @@ void generateNormalizedTransitionMatrixFromFile(CsrSparseMatrix *transitionMatri
// Function savePagerankToFile appends or overwrites the pagerank vector // Function savePagerankToFile appends or overwrites the pagerank vector
// "pagerankVector" to the file with the filename supplied in the arguments. // "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* iterations, int maxIterationsForConvergence); double *pagerankVector, int vectorSize, int iteration);
// Function initialize allocates memory for the pagerank vector, reads the // Function initialize allocates memory for the pagerank vector, reads the
// dataset from the file and creates the transition probability distribution // dataset from the file and creates the transition probability distribution

Write Preview
Loading…
Cancel
Save