mirror of
https://github.com/Steffo99/unimore-hpc-assignments.git
synced 2024-11-23 08:34:23 +00:00
254 lines
10 KiB
C
254 lines
10 KiB
C
/*****************************************************************************/
|
|
/*IMPORTANT: READ BEFORE DOWNLOADING, COPYING, INSTALLING OR USING. */
|
|
/*By downloading, copying, installing or using the software you agree */
|
|
/*to this license. If you do not agree to this license, do not download, */
|
|
/*install, copy or use the software. */
|
|
/* */
|
|
/* */
|
|
/*Copyright (c) 2005 Northwestern University */
|
|
/*All rights reserved. */
|
|
|
|
/*Redistribution of the software in source and binary forms, */
|
|
/*with or without modification, is permitted provided that the */
|
|
/*following conditions are met: */
|
|
/* */
|
|
/*1 Redistributions of source code must retain the above copyright */
|
|
/* notice, this list of conditions and the following disclaimer. */
|
|
/* */
|
|
/*2 Redistributions in binary form must reproduce the above copyright */
|
|
/* notice, this list of conditions and the following disclaimer in the */
|
|
/* documentation and/or other materials provided with the distribution.*/
|
|
/* */
|
|
/*3 Neither the name of Northwestern University nor the names of its */
|
|
/* contributors may be used to endorse or promote products derived */
|
|
/* from this software without specific prior written permission. */
|
|
/* */
|
|
/*THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS */
|
|
/*IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED */
|
|
/*TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY, NON-INFRINGEMENT AND */
|
|
/*FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL */
|
|
/*NORTHWESTERN UNIVERSITY OR ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, */
|
|
/*INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES */
|
|
/*(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR */
|
|
/*SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) */
|
|
/*HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, */
|
|
/*STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN */
|
|
/*ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE */
|
|
/*POSSIBILITY OF SUCH DAMAGE. */
|
|
/******************************************************************************/
|
|
/*************************************************************************/
|
|
/** File: example.c **/
|
|
/** Description: Takes as input a file: **/
|
|
/** ascii file: containing 1 data point per line **/
|
|
/** binary file: first int is the number of objects **/
|
|
/** 2nd int is the no. of features of each **/
|
|
/** object **/
|
|
/** This example performs a fuzzy c-means clustering **/
|
|
/** on the data. Fuzzy clustering is performed using **/
|
|
/** min to max clusters and the clustering that gets **/
|
|
/** the best score according to a compactness and **/
|
|
/** separation criterion are returned. **/
|
|
/** Author: Wei-keng Liao **/
|
|
/** ECE Department Northwestern University **/
|
|
/** email: wkliao@ece.northwestern.edu **/
|
|
/** **/
|
|
/** Edited by: Jay Pisharath **/
|
|
/** Northwestern University. **/
|
|
/** **/
|
|
/** ================================================================ **/
|
|
/** **/
|
|
/** Edited by: Sang-Ha Lee **/
|
|
/** University of Virginia **/
|
|
/** **/
|
|
/** Description: No longer supports fuzzy c-means clustering; **/
|
|
/** only regular k-means clustering. **/
|
|
/** Simplified for main functionality: regular k-means **/
|
|
/** clustering. **/
|
|
/** **/
|
|
/*************************************************************************/
|
|
|
|
#include <stdio.h>
|
|
#include <stdlib.h>
|
|
#include <string.h>
|
|
#include <limits.h>
|
|
#include <math.h>
|
|
#include <sys/types.h>
|
|
#include <fcntl.h>
|
|
#include <omp.h>
|
|
#include "getopt.h"
|
|
|
|
#include "kmeans.h"
|
|
|
|
extern double wtime(void);
|
|
|
|
/*---< usage() >------------------------------------------------------------*/
|
|
void usage(char *argv0)
|
|
{
|
|
char *help =
|
|
"Usage: %s [switches] -i filename\n"
|
|
" -i filename : file containing data to be clustered\n"
|
|
" -b :input file is in binary format\n"
|
|
" -k : number of clusters (default is 8) \n"
|
|
" -t threshold : threshold value\n";
|
|
fprintf(stderr, help, argv0);
|
|
exit(-1);
|
|
}
|
|
|
|
/*---< main() >-------------------------------------------------------------*/
|
|
int main(int argc, char **argv)
|
|
{
|
|
int opt;
|
|
extern char *optarg;
|
|
extern int optind;
|
|
int nclusters = 5;
|
|
char *filename = 0;
|
|
float *buf;
|
|
float **attributes;
|
|
float **cluster_centres = NULL;
|
|
int i, j;
|
|
|
|
int numAttributes;
|
|
int numObjects;
|
|
char line[1024];
|
|
int isBinaryFile = 0;
|
|
int nloops;
|
|
float threshold = 0.001;
|
|
double timing;
|
|
|
|
while ((opt = getopt(argc, argv, "i:k:t:b")) != EOF)
|
|
{
|
|
switch (opt)
|
|
{
|
|
case 'i':
|
|
filename = optarg;
|
|
break;
|
|
case 'b':
|
|
isBinaryFile = 1;
|
|
break;
|
|
case 't':
|
|
threshold = atof(optarg);
|
|
break;
|
|
case 'k':
|
|
nclusters = atoi(optarg);
|
|
break;
|
|
case '?':
|
|
usage(argv[0]);
|
|
break;
|
|
default:
|
|
usage(argv[0]);
|
|
break;
|
|
}
|
|
}
|
|
|
|
if (filename == 0)
|
|
usage(argv[0]);
|
|
|
|
numAttributes = numObjects = 0;
|
|
|
|
/* from the input file, get the numAttributes and numObjects ------------*/
|
|
|
|
if (isBinaryFile)
|
|
{
|
|
int infile;
|
|
if ((infile = open(filename, O_RDONLY, "0600")) == -1)
|
|
{
|
|
fprintf(stderr, "Error: no such file (%s)\n", filename);
|
|
exit(1);
|
|
}
|
|
read(infile, &numObjects, sizeof(int));
|
|
read(infile, &numAttributes, sizeof(int));
|
|
|
|
/* allocate space for attributes[] and read attributes of all objects */
|
|
buf = (float *)malloc(numObjects * numAttributes * sizeof(float));
|
|
attributes = (float **)malloc(numObjects * sizeof(float *));
|
|
attributes[0] = (float *)malloc(numObjects * numAttributes * sizeof(float));
|
|
for (i = 1; i < numObjects; i++)
|
|
attributes[i] = attributes[i - 1] + numAttributes;
|
|
|
|
read(infile, buf, numObjects * numAttributes * sizeof(float));
|
|
|
|
close(infile);
|
|
}
|
|
else
|
|
{
|
|
FILE *infile;
|
|
if ((infile = fopen(filename, "r")) == NULL)
|
|
{
|
|
fprintf(stderr, "Error: no such file (%s)\n", filename);
|
|
exit(1);
|
|
}
|
|
while (fgets(line, 1024, infile) != NULL)
|
|
if (strtok(line, " \t\n") != 0)
|
|
numObjects++;
|
|
rewind(infile);
|
|
while (fgets(line, 1024, infile) != NULL)
|
|
{
|
|
if (strtok(line, " \t\n") != 0)
|
|
{
|
|
/* ignore the id (first attribute): numAttributes = 1; */
|
|
while (strtok(NULL, " ,\t\n") != NULL)
|
|
numAttributes++;
|
|
break;
|
|
}
|
|
}
|
|
|
|
/* allocate space for attributes[] and read attributes of all objects */
|
|
buf = (float *)malloc(numObjects * numAttributes * sizeof(float));
|
|
attributes = (float **)malloc(numObjects * sizeof(float *));
|
|
attributes[0] = (float *)malloc(numObjects * numAttributes * sizeof(float));
|
|
for (i = 1; i < numObjects; i++)
|
|
attributes[i] = attributes[i - 1] + numAttributes;
|
|
rewind(infile);
|
|
i = 0;
|
|
while (fgets(line, 1024, infile) != NULL)
|
|
{
|
|
if (strtok(line, " \t\n") == NULL)
|
|
continue;
|
|
for (j = 0; j < numAttributes; j++)
|
|
{
|
|
buf[i] = atof(strtok(NULL, " ,\t\n"));
|
|
i++;
|
|
}
|
|
}
|
|
fclose(infile);
|
|
}
|
|
|
|
nloops = 1;
|
|
printf("I/O completed\n");
|
|
|
|
memcpy(attributes[0], buf, numObjects * numAttributes * sizeof(float));
|
|
|
|
timing = omp_get_wtime();
|
|
for (i = 0; i < nloops; i++)
|
|
{
|
|
|
|
cluster_centres = NULL;
|
|
cluster(numObjects,
|
|
numAttributes,
|
|
attributes, /* [numObjects][numAttributes] */
|
|
nclusters,
|
|
threshold,
|
|
&cluster_centres);
|
|
}
|
|
timing = omp_get_wtime() - timing;
|
|
|
|
printf("number of Clusters %d\n", nclusters);
|
|
printf("number of Attributes %d\n\n", numAttributes);
|
|
/*printf("Cluster Centers Output\n");
|
|
printf("The first number is cluster number and the following data is arribute value\n");
|
|
printf("=============================================================================\n\n");
|
|
|
|
for (i=0; i<nclusters; i++) {
|
|
printf("%d: ", i);
|
|
for (j=0; j<numAttributes; j++)
|
|
printf("%f ", cluster_centres[i][j]);
|
|
printf("\n\n");
|
|
}*/
|
|
printf("Time for process: %f\n", timing);
|
|
|
|
free(attributes);
|
|
free(cluster_centres[0]);
|
|
free(cluster_centres);
|
|
free(buf);
|
|
return (0);
|
|
}
|