/*---< main() >-------------------------------------------------------------*/
int main(int argc, char **argv) {
int opt;
extern char *optarg;
extern int optind;
int i, j;
int isInFileBinary, isOutFileBinary, do_pnetcdf;
int is_output_timing, is_print_usage, verbose;
int numClusters, numCoords, numObjs, totalNumObjs;
int *membership; /* [numObjs] */
char *filename;
// TODO >> modified by VL: new variable representing the centers file name
char *centers_filename;
// TODO << end of the modification
char *var_name;
float **objects; /* [numObjs][numCoords] data objects */
float **clusters; /* [numClusters][numCoords] cluster center */
float threshold;
double timing, io_timing, clustering_timing;
int rank, nproc, mpi_namelen;
char mpi_name[MPI_MAX_PROCESSOR_NAME];
MPI_Init(&argc, &argv);
MPI_Comm_rank(MPI_COMM_WORLD, &rank);
MPI_Comm_size(MPI_COMM_WORLD, &nproc);
MPI_Get_processor_name(mpi_name,&mpi_namelen);
/* some default values */
_debug = 0;
verbose = 1;
threshold = 0.001;
numClusters = 0;
isInFileBinary = 0;
isOutFileBinary = 0;
is_output_timing = 0;
is_print_usage = 0;
filename = NULL;
// TODO >> modified by VL: initialization of the new variable
centers_filename = NULL;
// TODO << end of the modification
do_pnetcdf = 0;
var_name = NULL;
// TODO >> modified by VL: added the letter z
while ( (opt=getopt(argc,argv,"i:z:n:t:v:c:abdorhq"))!= EOF) {
// TODO << end of the modification
switch (opt) {
case 'i': filename=optarg;
break;
// TODO >> modified by VL: initialize centers filename
case 'z': centers_filename=optarg;
break;
// TODO << end of the modification
case 'b': isInFileBinary = 1;
break;
case 'r': isOutFileBinary = 1;
break;
case 't': threshold=atof(optarg);
break;
case 'n': numClusters = atoi(optarg);
break;
case 'o': is_output_timing = 1;
break;
case 'c': do_pnetcdf = 1;
var_name = optarg;
break;
case 'q': verbose = 0;
break;
case 'd': _debug = 1;
break;
case 'h':
default: is_print_usage = 1;
break;
}
}
if (filename == 0 || numClusters <= 1 || is_print_usage == 1 ||
(do_pnetcdf && var_name == NULL)) {
if (rank == 0) usage(argv[0], threshold);
MPI_Finalize();
exit(1);
}
if (_debug) printf("Proc %d of %d running on %s\n", rank, nproc, mpi_name);
#ifndef _PNETCDF_BUILT
if (do_pnetcdf) {
if (rank == 0) printf("Error: PnetCDF feature is not built\n");
MPI_Finalize();
exit(1);
}
#endif
MPI_Barrier(MPI_COMM_WORLD);
io_timing = MPI_Wtime();
/* read data points from file ------------------------------------------*/
#ifdef _PNETCDF_BUILT
if (do_pnetcdf)
objects = pnetcdf_read(filename, var_name, &numObjs, &numCoords,
MPI_COMM_WORLD);
else
#endif
objects = mpi_read(isInFileBinary, filename, &numObjs, &numCoords,
MPI_COMM_WORLD);
if (_debug) { /* print the first 4 objects' coordinates */
int num = (numObjs < 4) ? numObjs : 4;
for (i=0; i<num; i++) {
char strline[1024], strfloat[16];
sprintf(strline,"%d: objects[%d]= ",rank,i);
for (j=0; j<numCoords; j++) {
sprintf(strfloat,"%10f",objects[i][j]);
strcat(strline, strfloat);
}
strcat(strline, "\n");
printf("%s",strline);
}
}
timing = MPI_Wtime();
io_timing = timing - io_timing;
clustering_timing = timing;
/* allocate a 2D space for clusters[] (coordinates of cluster centers)
this array should be the same across all processes */
clusters = (float**) malloc(numClusters * sizeof(float*));
assert(clusters != NULL);
clusters[0] = (float*) malloc(numClusters * numCoords * sizeof(float));
assert(clusters[0] != NULL);
for (i=1; i<numClusters; i++)
clusters[i] = clusters[i-1] + numCoords;
MPI_Allreduce(&numObjs, &totalNumObjs, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
/* checking if numObjs < nproc is done in the I/O routine */
// TODO >> modified by VL: initialize variable "clusters"
// possibly load the centers from a file
if (centers_filename != NULL)
{ int num_centers, num_coords;
clusters = file_read(0, centers_filename, &num_centers, &num_coords);
// no control over the numbers of centers and coordinates
}
// otherwise, pick the first numClusters elements of objects[] as initial cluster centers
else
// TODO << end of the modification
/* pick first numClusters elements in feature[] as initial cluster centers*/
if (rank == 0) {
if (numObjs < numClusters) {
/* read the first numClusters data points from file */
read_n_objects(isInFileBinary, filename, numClusters, numCoords, clusters);
}
else {
/* copy the first numClusters elements in feature[] */
for (i=0; i<numClusters; i++)
for (j=0; j<numCoords; j++)
clusters[i][j] = objects[i][j];
}
}
MPI_Bcast(clusters[0], numClusters*numCoords, MPI_FLOAT, 0, MPI_COMM_WORLD);
/* membership: the cluster id for each data object */
membership = (int*) malloc(numObjs * sizeof(int));
assert(membership != NULL);
/* start the core computation -------------------------------------------*/
mpi_kmeans(objects, numCoords, numObjs, numClusters, threshold, membership,
clusters, MPI_COMM_WORLD);
free(objects[0]);
free(objects);
timing = MPI_Wtime();
clustering_timing = timing - clustering_timing;
/* output: the coordinates of the cluster centres ----------------------*/
#ifdef _PNETCDF_BUILT
if (do_pnetcdf)
pnetcdf_write(filename, 1, numClusters, numObjs, numCoords, clusters,
membership, totalNumObjs, MPI_COMM_WORLD, verbose);
else
#endif
mpi_write(isOutFileBinary, filename, numClusters, numObjs, numCoords,
clusters, membership, totalNumObjs, MPI_COMM_WORLD, verbose);
free(membership);
free(clusters[0]);
free(clusters);
/*---- output performance numbers ---------------------------------------*/
if (is_output_timing) {
double max_io_timing, max_clustering_timing;
io_timing += MPI_Wtime() - timing;
/* get the max timing measured among all processes */
MPI_Reduce(&io_timing, &max_io_timing, 1, MPI_DOUBLE,
MPI_MAX, 0, MPI_COMM_WORLD);
MPI_Reduce(&clustering_timing, &max_clustering_timing, 1, MPI_DOUBLE,
MPI_MAX, 0, MPI_COMM_WORLD);
if (rank == 0) {
printf("\nPerforming **** Simple Kmeans (MPI) ****\n");
printf("Num of processes = %d\n", nproc);
printf("Input file: %s\n", filename);
// TODO >> modified by VL: display centers filename
if(centers_filename!=NULL)
printf("Centers file: %s\n", centers_filename);
// TODO << end of the modifications
printf("numObjs = %d\n", totalNumObjs);
printf("numCoords = %d\n", numCoords);
printf("numClusters = %d\n", numClusters);
printf("threshold = %.4f\n", threshold);
printf("I/O time = %10.4f sec\n", max_io_timing);
printf("Computation timing = %10.4f sec\n", max_clustering_timing);
}
}
MPI_Finalize();
return(0);
}
int main(int argc, char **argv) {
int opt;
extern char *optarg;
extern int optind;
int i, j;
int isInFileBinary, isOutFileBinary;
int is_output_timing, is_print_usage;
int numClusters, numCoords, numObjs, totalNumObjs;
int *membership; /* [numObjs] */
char *filename;
float **objects; /* [numObjs][numCoords] data objects */
float **clusters; /* [numClusters][numCoords] cluster center */
float threshold;
double timing, io_timing, clustering_timing;
int rank, nproc, mpi_namelen;
char mpi_name[MPI_MAX_PROCESSOR_NAME];
MPI_Status status;
MPI_Init(&argc, &argv);
MPI_Comm_rank(MPI_COMM_WORLD, &rank);
MPI_Comm_size(MPI_COMM_WORLD, &nproc);
MPI_Get_processor_name(mpi_name,&mpi_namelen);
/* some default values */
_debug = 0;
threshold = 0.001;
numClusters = 0;
isInFileBinary = 0;
isOutFileBinary = 0;
is_output_timing = 0;
is_print_usage = 0;
filename = NULL;
while ( (opt=getopt(argc,argv,"p:i:n:t:abdorh"))!= EOF) {
switch (opt) {
case 'i': filename=optarg;
break;
case 'b': isInFileBinary = 1;
break;
case 'r': isOutFileBinary = 1;
break;
case 't': threshold=atof(optarg);
break;
case 'n': numClusters = atoi(optarg);
break;
case 'o': is_output_timing = 1;
break;
case 'd': _debug = 1;
break;
case 'h': is_print_usage = 1;
break;
default: is_print_usage = 1;
break;
}
}
if (filename == 0 || numClusters <= 1 || is_print_usage == 1) {
if (rank == 0) usage(argv[0], threshold);
MPI_Finalize();
exit(1);
}
if (_debug) printf("Proc %d of %d running on %s\n", rank, nproc, mpi_name);
MPI_Barrier(MPI_COMM_WORLD);
io_timing = MPI_Wtime();
/* read data points from file ------------------------------------------*/
objects = mpi_read(filename, &numObjs, &numCoords,
MPI_COMM_WORLD);
if (_debug) { /* print the first 4 objects' coordinates */
int num = (numObjs < 4) ? numObjs : 4;
for (i=0; i<num; i++) {
char strline[1024], strfloat[16];
sprintf(strline,"%d: objects[%d]= ",rank,i);
for (j=0; j<numCoords; j++) {
sprintf(strfloat,"%10f",objects[i][j]);
strcat(strline, strfloat);
}
strcat(strline, "\n");
printf("%s",strline);
}
}
timing = MPI_Wtime();
io_timing = timing - io_timing;
clustering_timing = timing;
/* allocate a 2D space for clusters[] (coordinates of cluster centers)
this array should be the same across all processes */
clusters = (float**) malloc(numClusters * sizeof(float*));
assert(clusters != NULL);
clusters[0] = (float*) malloc(numClusters * numCoords * sizeof(float));
assert(clusters[0] != NULL);
for (i=1; i<numClusters; i++)
clusters[i] = clusters[i-1] + numCoords;
MPI_Allreduce(&numObjs, &totalNumObjs, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
/* pick first numClusters elements in feature[] as initial cluster centers*/
if (rank == 0) {
for (i=0; i<numClusters; i++)
for (j=0; j<numCoords; j++)
clusters[i][j] = objects[i][j];
}
MPI_Bcast(clusters[0], numClusters*numCoords, MPI_FLOAT, 0, MPI_COMM_WORLD);
/* membership: the cluster id for each data object */
membership = (int*) malloc(numObjs * sizeof(int));
assert(membership != NULL);
/* start the core computation -------------------------------------------*/
mpi_kmeans(objects, numCoords, numObjs, numClusters, threshold, membership,
clusters, MPI_COMM_WORLD);
free(objects[0]);
free(objects);
timing = MPI_Wtime();
clustering_timing = timing - clustering_timing;
/* output: the coordinates of the cluster centres ----------------------*/
mpi_write(filename, numClusters, numObjs, numCoords,
clusters, membership, totalNumObjs, MPI_COMM_WORLD);
free(membership);
free(clusters[0]);
free(clusters);
/*---- output performance numbers ---------------------------------------*/
if (is_output_timing) {
double max_io_timing, max_clustering_timing;
io_timing += MPI_Wtime() - timing;
/* get the max timing measured among all processes */
MPI_Reduce(&io_timing, &max_io_timing, 1, MPI_DOUBLE,
MPI_MAX, 0, MPI_COMM_WORLD);
MPI_Reduce(&clustering_timing, &max_clustering_timing, 1, MPI_DOUBLE,
MPI_MAX, 0, MPI_COMM_WORLD);
if (rank == 0) {
printf("\nPerforming **** Simple Kmeans (MPI) ****\n");
printf("Num of processes = %d\n", nproc);
printf("Input file: %s\n", filename);
printf("numObjs = %d\n", totalNumObjs);
printf("numCoords = %d\n", numCoords);
printf("numClusters = %d\n", numClusters);
printf("threshold = %.4f\n", threshold);
printf("I/O time = %10.4f sec\n", max_io_timing);
printf("Computation timing = %10.4f sec\n", max_clustering_timing);
}
}
MPI_Finalize();
return(0);
}
