text: /***********************************************
  	streamcluster.cpp
  	: original source code of streamcluster with minor
  		modification regarding function calls
  	
  	- original code from PARSEC Benchmark Suite
  	- parallelization with CUDA API has been applied by
  	
  	Sang-Ha (a.k.a Shawn) Lee - sl4ge@virginia.edu
  	University of Virginia
  	Department of Electrical and Computer Engineering
  	Department of Computer Science
  	
  ***********************************************/
  
  #include "streamcluster_header.cu"
  
  #ifdef GEM5_FUSION
  #include <stdint.h>
  extern "C" {
  void m5_work_begin(uint64_t workid, uint64_t threadid);
  void m5_work_end(uint64_t workid, uint64_t threadid);
  }
  #endif
  
  using namespace std;
  
  #define MAXNAMESIZE 1024 			// max filename length
  #define SEED 1
  #define SP 1 						// number of repetitions of speedy must be >=1
  #define ITER 3 						// iterate ITER* k log k times; ITER >= 1
  //#define PRINTINFO 				// Enables printing output
  #define PROFILE 					// Enables timing info
  //#define ENABLE_THREADS			// Enables parallel execution
  //#define INSERT_WASTE				// Enables waste computation in dist function
  #define CACHE_LINE 512				// cache line in byte
  #ifdef GEM5_FUSION
  #define MAX_PGAIN 20
  #else
  #define MAX_PGAIN 10000000
  #endif
  
  // GLOBAL
  static bool *switch_membership;		//whether to switch membership in pgain
  static bool *is_center;				//whether a point is a center
  static int  *center_table;			//index table of centers
  static int nproc; 					//# of threads
  bool isCoordChanged;
  
  // GPU Timing Info
  unsigned pgain_count;
  double serial_t;
  double cpu_to_gpu_t;
  double gpu_to_cpu_t;
  double alloc_t;
  double kernel_t;
  double free_t;
  
  // instrumentation code
  #ifdef PROFILE
  double time_local_search;
  double time_speedy;
  double time_select_feasible;
  double time_gain;
  double time_shuffle;
  double time_gain_dist;
  double time_gain_init;
  #endif 
  
  void inttofile(int data, char *filename){
  	FILE *fp = fopen(filename, "w");
  	fprintf(fp, "%d ", data);
  	fclose(fp);	
  }
  
  double gettime() {
    struct timeval t;
    gettimeofday(&t,NULL);
    return t.tv_sec+t.tv_usec*1e-6;
  }
  
  int isIdentical(float *i, float *j, int D){
  // tells whether two points of D dimensions are identical
  
    int a = 0;
    int equal = 1;
  
    while (equal && a < D) {
      if (i[a] != j[a]) equal = 0;
      else a++;
    }
    if (equal) return 1;
    else return 0;
  
  }
  
  /* comparator for floating point numbers */
  static int floatcomp(const void *i, const void *j)
  {
    float a, b;
    a = *(float *)(i);
    b = *(float *)(j);
    if (a > b) return (1);
    if (a < b) return (-1);
    return(0);
  }
  
  /* shuffle points into random order */
  void shuffle(Points *points)
  {
  #ifdef PROFILE
    double t1 = gettime();
  #endif
    long i, j;
    Point temp;
    for (i=0;i<points->num-1;i++) {
      j=(lrand48()%(points->num - i)) + i;
      temp = points->p[i];
      points->p[i] = points->p[j];
      points->p[j] = temp;
    }
  #ifdef PROFILE
    double t2 = gettime();
    time_shuffle += t2-t1;
  #endif
  }
  
  /* shuffle an array of integers */
  void intshuffle(int *intarray, int length)
  {
  #ifdef PROFILE
    double t1 = gettime();
  #endif
    long i, j;
    int temp;
    for (i=0;i<length;i++) {
      j=(lrand48()%(length - i))+i;
      temp = intarray[i];
      intarray[i]=intarray[j];
      intarray[j]=temp;
    }
  #ifdef PROFILE
    double t2 = gettime();
    time_shuffle += t2-t1;
  #endif
  }
  
  #ifdef INSERT_WASTE
  float waste(float s )
  {
    for( int i =0 ; i< 4; i++ ) {
      s += pow(s,0.78);
    }
    return s;
  }
  #endif
  
  /* compute Euclidean distance squared between two points */
  float dist(Point p1, Point p2, int dim)
  {
    int i;
    float result=0.0;
    for (i=0;i<dim;i++)
      result += (p1.coord[i] - p2.coord[i])*(p1.coord[i] - p2.coord[i]);
  #ifdef INSERT_WASTE
    float s = waste(result);
    result += s;
    result -= s;
  #endif
    return(result);
  }
  
  /* run speedy on the points, return total cost of solution */
  float pspeedy(Points *points, float z, long *kcenter, int pid, pthread_barrier_t* barrier)
  {
  #ifdef PROFILE
    double t1 = gettime();
  #endif
  
  #ifdef ENABLE_THREADS
    pthread_barrier_wait(barrier);
  #endif
    //my block
    long bsize = points->num/nproc;
    long k1 = bsize * pid;
    long k2 = k1 + bsize;
    if( pid == nproc-1 ) k2 = points->num;
  
    static float totalcost;
    
    static bool open = false;
    static float* costs; //cost for each thread. 
    static int i;
  
  #ifdef ENABLE_THREADS
    static pthread_mutex_t mutex = PTHREAD_MUTEX_INITIALIZER;
    static pthread_cond_t cond = PTHREAD_COND_INITIALIZER;
  #endif
  
  #ifdef PRINTINFO
    if( pid == 0 ){
      fprintf(stderr, "Speedy: facility cost %lf\n", z);
    }
  #endif
  
    /* create center at first point, send it to itself */
    for( int k = k1; k < k2; k++ )    {
      float distance = dist(points->p[k],points->p[0],points->dim);
      points->p[k].cost = distance * points->p[k].weight;
      points->p[k].assign=0;
    }
  
    if( pid==0 )   {
      *kcenter = 1;
      costs = (float*)malloc(sizeof(float)*nproc);
    }
      
    if( pid != 0 ) { // we are not the master threads. we wait until a center is opened.
      while(1) {
  #ifdef ENABLE_THREADS
        pthread_mutex_lock(&mutex);
        while(!open) pthread_cond_wait(&cond,&mutex);
        pthread_mutex_unlock(&mutex);
  #endif
        if( i >= points->num ) break;
        for( int k = k1; k < k2; k++ )
  	{
  	  float distance = dist(points->p[i],points->p[k],points->dim);
  	  if( distance*points->p[k].weight < points->p[k].cost )
  	    {
  	      points->p[k].cost = distance * points->p[k].weight;
  	      points->p[k].assign=i;
  	    }
  	}
  #ifdef ENABLE_THREADS
        pthread_barrier_wait(barrier);
        pthread_barrier_wait(barrier);
  #endif
      } 
    }
    else  { // I am the master thread. I decide whether to open a center and notify others if so. 
      for(i = 1; i < points->num; i++ )  {
        bool to_open = ((float)lrand48()/(float)INT_MAX)<(points->p[i].cost/z);
        if( to_open )  {
  	(*kcenter)++;
  #ifdef ENABLE_THREADS
  	pthread_mutex_lock(&mutex);
  #endif
  	open = true;
  #ifdef ENABLE_THREADS
  	pthread_mutex_unlock(&mutex);
  	pthread_cond_broadcast(&cond);
  #endif
  	for( int k = k1; k < k2; k++ )  {
  	  float distance = dist(points->p[i],points->p[k],points->dim);
  	  if( distance*points->p[k].weight < points->p[k].cost )  {
  	    points->p[k].cost = distance * points->p[k].weight;
  	    points->p[k].assign=i;
  	  }
  	}
  #ifdef ENABLE_THREADS
  	pthread_barrier_wait(barrier);
  #endif
  	open = false;
  #ifdef ENABLE_THREADS
  	pthread_barrier_wait(barrier);
  #endif
        }
      }
  #ifdef ENABLE_THREADS
      pthread_mutex_lock(&mutex);
  #endif
      open = true;
  #ifdef ENABLE_THREADS
      pthread_mutex_unlock(&mutex);
      pthread_cond_broadcast(&cond);
  #endif
    }
  #ifdef ENABLE_THREADS
    pthread_barrier_wait(barrier);
  #endif
    open = false;
    float mytotal = 0;
    for( int k = k1; k < k2; k++ )  {
      mytotal += points->p[k].cost;
    }
    costs[pid] = mytotal;
  #ifdef ENABLE_THREADS
    pthread_barrier_wait(barrier);
  #endif
    // aggregate costs from each thread
    if( pid == 0 )
      {
        totalcost=z*(*kcenter);
        for( int i = 0; i < nproc; i++ )
  	{
  	  totalcost += costs[i];
  	} 
        free(costs);
      }
  #ifdef ENABLE_THREADS
    pthread_barrier_wait(barrier);
  #endif
  
  #ifdef PRINTINFO
    if( pid == 0 )
      {
        fprintf(stderr, "Speedy opened %d facilities for total cost %lf\n",
  	      *kcenter, totalcost);
        fprintf(stderr, "Distance Cost %lf\n", totalcost - z*(*kcenter));
      }
  #endif
  
  #ifdef PROFILE
    double t2 = gettime();
    if( pid== 0 ) {
      time_speedy += t2 -t1;
    }
  #endif
    return(totalcost);
  }
  
  
  /* facility location on the points using local search */
  /* z is the facility cost, returns the total cost and # of centers */
  /* assumes we are seeded with a reasonable solution */
  /* cost should represent this solution's cost */
  /* halt if there is < e improvement after iter calls to gain */
  /* feasible is an array of numfeasible points which may be centers */
  
  float pFL(Points *points, int *feasible, int numfeasible,
  	  float z, long *k, int kmax, float cost, long iter, float e, 
  	  int pid, pthread_barrier_t* barrier)
  {
  #ifdef ENABLE_THREADS
    pthread_barrier_wait(barrier);
  #endif
    long i;
    long x;
    float change;
    long numberOfPoints;
  
    change = cost;
    /* continue until we run iter iterations without improvement */
    /* stop instead if improvement is less than e */
    while (change/cost > 1.0*e) {
      change = 0.0;
      numberOfPoints = points->num;
      /* randomize order in which centers are considered */
  
      if( pid == 0 ) {
        intshuffle(feasible, numfeasible);
      }
  #ifdef ENABLE_THREADS
      pthread_barrier_wait(barrier);
  #endif
  
      for (i=0;i<iter && pgain_count < MAX_PGAIN;i++) {
  	    x = i%numfeasible;
  	    change += pgain(feasible[x], points, z, k, kmax, is_center, center_table, switch_membership, isCoordChanged,
  						&serial_t, &cpu_to_gpu_t, &gpu_to_cpu_t, &alloc_t, &kernel_t, &free_t, &pgain_count);
      }		
  
      cost -= change;
  #ifdef PRINTINFO
      if( pid == 0 ) {
        fprintf(stderr, "%d centers, cost %lf, total distance %lf\n",
  	      *k, cost, cost - z*(*k));
      }
  #endif
  #ifdef ENABLE_THREADS
      pthread_barrier_wait(barrier);
  #endif
      if (pgain_count >= MAX_PGAIN) return (cost);
    }
    return(cost);
  }
  
  int selectfeasible_fast(Points *points, int **feasible, int kmin, int pid, pthread_barrier_t* barrier)
  {
  #ifdef PROFILE
    double t1 = gettime();
  #endif
  
    int numfeasible = points->num;
    if (numfeasible > (ITER*kmin*log((float)kmin)))
      numfeasible = (int)(ITER*kmin*log((float)kmin));
    *feasible = (int *)malloc(numfeasible*sizeof(int));
    
    float* accumweight;
    float totalweight;
  
    /* 
       Calcuate my block. 
       For now this routine does not seem to be the bottleneck, so it is not parallelized. 
       When necessary, this can be parallelized by setting k1 and k2 to 
       proper values and calling this routine from all threads ( it is called only
       by thread 0 for now ). 
       Note that when parallelized, the randomization might not be the same and it might
       not be difficult to measure the parallel speed-up for the whole program. 
     */
    //  long bsize = numfeasible;
    long k1 = 0;
    long k2 = numfeasible;
  
    float w;
    int l,r,k;
  
    /* not many points, all will be feasible */
    if (numfeasible == points->num) {
      for (int i=k1;i<k2;i++)
        (*feasible)[i] = i;
      return numfeasible;
    }
  
    accumweight= (float*)malloc(sizeof(float)*points->num);
    accumweight[0] = points->p[0].weight;
    totalweight=0;
    for( int i = 1; i < points->num; i++ ) {
      accumweight[i] = accumweight[i-1] + points->p[i].weight;
    }
    totalweight=accumweight[points->num-1];
  
    for(int i=k1; i<k2; i++ ) {
      w = (lrand48()/(float)INT_MAX)*totalweight;
      //binary search
      l=0;
      r=points->num-1;
      if( accumweight[0] > w )  { 
        (*feasible)[i]=0; 
        continue;
      }
      while( l+1 < r ) {
        k = (l+r)/2;
        if( accumweight[k] > w ) {
  	r = k;
        } 
        else {
  	l=k;
        }
      }
      (*feasible)[i]=r;
    }
  
    free(accumweight); 
  
  #ifdef PROFILE
    double t2 = gettime();
    time_select_feasible += t2-t1;
  #endif
    return numfeasible;
  }
  
  /* compute approximate kmedian on the points */
  float pkmedian(Points *points, long kmin, long kmax, long* kfinal,
  	       int pid, pthread_barrier_t* barrier )
  {
    int i;
    float cost;
    float lastcost;
    float hiz, loz, z;
  
    static long k;
    static int *feasible;
    static int numfeasible;
    static float* hizs;
  
    if( pid==0 ) hizs = (float*)calloc(nproc,sizeof(float));
    hiz = loz = 0.0;
    long numberOfPoints = points->num;
    long ptDimension = points->dim;
  
    //my block
    long bsize = points->num/nproc;
    long k1 = bsize * pid;
    long k2 = k1 + bsize;
    if( pid == nproc-1 ) k2 = points->num;
  
  #ifdef PRINTINFO
    if( pid == 0 )
      {
        printf("Starting Kmedian procedure\n");
        printf("%i points in %i dimensions\n", numberOfPoints, ptDimension);
      }
  #endif
  
  #ifdef ENABLE_THREADS
    pthread_barrier_wait(barrier);
  #endif
  
    float myhiz = 0;
    for (long kk=k1;kk < k2; kk++ ) {
      myhiz += dist(points->p[kk], points->p[0],
  		      ptDimension)*points->p[kk].weight;
    }
    hizs[pid] = myhiz;
  
  #ifdef ENABLE_THREADS  
    pthread_barrier_wait(barrier);
  #endif
  
    for( int i = 0; i < nproc; i++ )   {
      hiz += hizs[i];
    }
  
    loz=0.0; z = (hiz+loz)/2.0;
    /* NEW: Check whether more centers than points! */
    if (points->num <= kmax) {
      /* just return all points as facilities */
      for (long kk=k1;kk<k2;kk++) {
        points->p[kk].assign = kk;
        points->p[kk].cost = 0;
      }
      cost = 0;
      if( pid== 0 ) {
        free(hizs); 
        *kfinal = k;
      }
      return cost;
    }
  
    if( pid == 0 ) shuffle(points);
    cost = pspeedy(points, z, &k, pid, barrier);
  
  #ifdef PRINTINFO
    if( pid == 0 )
      printf("thread %d: Finished first call to speedy, cost=%lf, k=%i\n",pid,cost,k);
  #endif
    i=0;
    /* give speedy SP chances to get at least kmin/2 facilities */
    while ((k < kmin)&&(i<SP)) {
      cost = pspeedy(points, z, &k, pid, barrier);
      i++;
    }
  
  #ifdef PRINTINFO
    if( pid==0)
      printf("thread %d: second call to speedy, cost=%lf, k=%d\n",pid,cost,k);
  #endif 
    /* if still not enough facilities, assume z is too high */
    while (k < kmin) {
  #ifdef PRINTINFO
      if( pid == 0 ) {
        printf("%lf %lf\n", loz, hiz);
        printf("Speedy indicates we should try lower z\n");
      }
  #endif
      if (i >= SP) {hiz=z; z=(hiz+loz)/2.0; i=0;}
      if( pid == 0 ) shuffle(points);
      cost = pspeedy(points, z, &k, pid, barrier);
      i++;
    }
  
    /* now we begin the binary search for real */
    /* must designate some points as feasible centers */
    /* this creates more consistancy between FL runs */
    /* helps to guarantee correct # of centers at the end */
    
    if( pid == 0 )
      {
        numfeasible = selectfeasible_fast(points,&feasible,kmin,pid,barrier);
        for( int i = 0; i< points->num; i++ ) {
  	is_center[points->p[i].assign]= true;
        }
      }
  
  #ifdef ENABLE_THREADS
    pthread_barrier_wait(barrier);
  #endif
  
    while(1) {
    
  #ifdef PRINTINFO
      if( pid==0 )
        {
  	printf("loz = %lf, hiz = %lf\n", loz, hiz);
  	printf("Running Local Search...\n");
        }
  #endif
      /* first get a rough estimate on the FL solution */
      //    pthread_barrier_wait(barrier);		
      lastcost = cost;
      cost = pFL(points, feasible, numfeasible,
  	       z, &k, kmax, cost, (long)(ITER*kmax*log((float)kmax)), 0.1, pid, barrier);
  
      /* if number of centers seems good, try a more accurate FL */
      if ((((k <= (1.1)*kmax)&&(k >= (0.9)*kmin))||
  	((k <= kmax+2)&&(k >= kmin-2))) && pgain_count < MAX_PGAIN) {
  
  #ifdef PRINTINFO
        if( pid== 0)
  	{
  	  printf("Trying a more accurate local search...\n");
  	}
  #endif
        /* may need to run a little longer here before halting without
  	 improvement */
  	 
        cost = pFL(points, feasible, numfeasible,
  		 z, &k, kmax, cost, (long)(ITER*kmax*log((float)kmax)), 0.001, pid, barrier);
      }
  
      if (k > kmax) {
        /* facilities too cheap */
        /* increase facility cost and up the cost accordingly */
        loz = z; z = (hiz+loz)/2.0;
        cost += (z-loz)*k;
      }
      if (k < kmin) {
        /* facilities too expensive */
        /* decrease facility cost and reduce the cost accordingly */
        hiz = z; z = (hiz+loz)/2.0;
        cost += (z-hiz)*k;
      }
  
      /* if k is good, return the result */
      /* if we're stuck, just give up and return what we have */
      if (((k <= kmax)&&(k >= kmin))||((loz >= (0.999)*hiz))  || pgain_count >= MAX_PGAIN)
        { 
  	break;
        }
  #ifdef ENABLE_THREADS
      pthread_barrier_wait(barrier);
  #endif
    }
  
    //clean up...
    if( pid==0 ) {
      free(feasible); 
      free(hizs);
      *kfinal = k;
    }
  
    return cost;
  }
  
  /* compute the means for the k clusters */
  int contcenters(Points *points)
  {
    long i, ii;
    float relweight;
  
    for (i=0;i<points->num;i++) {
      /* compute relative weight of this point to the cluster */
      if (points->p[i].assign != i) {
        relweight=points->p[points->p[i].assign].weight + points->p[i].weight;
        relweight = points->p[i].weight/relweight;
        for (ii=0;ii<points->dim;ii++) {
  				points->p[points->p[i].assign].coord[ii]*=1.0-relweight;
  				points->p[points->p[i].assign].coord[ii]+=
  				points->p[i].coord[ii]*relweight;
        }
        points->p[points->p[i].assign].weight += points->p[i].weight;
      }
    }
    
    return 0;
  }
  
  /* copy centers from points to centers */
  void copycenters(Points *points, Points* centers, long* centerIDs, long offset)
  {
    long i;
    long k;
  
    bool *is_a_median = (bool *) calloc(points->num, sizeof(bool));
  
    /* mark the centers */
    for ( i = 0; i < points->num; i++ ) {
      is_a_median[points->p[i].assign] = 1;
    }
  
    k=centers->num;
  
    /* count how many  */
    for ( i = 0; i < points->num; i++ ) {
      if ( is_a_median[i] ) {
        memcpy( centers->p[k].coord, points->p[i].coord, points->dim * sizeof(float));
        centers->p[k].weight = points->p[i].weight;
        centerIDs[k] = i + offset;
        k++;
      }
    }
  
    centers->num = k;
  
    free(is_a_median);
  }
  
  
  
  void* localSearchSub(void* arg_) {
    pkmedian_arg_t* arg= (pkmedian_arg_t*)arg_;
    pkmedian(arg->points,arg->kmin,arg->kmax,arg->kfinal,arg->pid,arg->barrier);
  
    return NULL;
  }
  
  void localSearch( Points* points, long kmin, long kmax, long* kfinal ) {
  #ifdef PROFILE
    double t1 = gettime();
  #endif
  
      pthread_barrier_t barrier;
  #ifdef ENABLE_THREADS
      pthread_barrier_init(&barrier,NULL,nproc);
  #endif
      pthread_t* threads = new pthread_t[nproc];
      pkmedian_arg_t* arg = new pkmedian_arg_t[nproc];
  
  
      for( int i = 0; i < nproc; i++ ) {
        arg[i].points = points;
        arg[i].kmin = kmin;
        arg[i].kmax = kmax;
        arg[i].pid = i;
        arg[i].kfinal = kfinal;
  
        arg[i].barrier = &barrier;
  #ifdef ENABLE_THREADS
        pthread_create(threads+i,NULL,localSearchSub,(void*)&arg[i]);
  #else
        localSearchSub(&arg[0]);
  #endif
      }
  
      for ( int i = 0; i < nproc; i++) {
  #ifdef ENABLE_THREADS
        pthread_join(threads[i],NULL);
  #endif
      }
  
      delete[] threads;
      delete[] arg;
  #ifdef ENABLE_THREADS
      pthread_barrier_destroy(&barrier);
  #endif
  
  #ifdef PROFILE
    double t2 = gettime();
    time_local_search += t2-t1;
  #endif
   
  }
  
  
  void outcenterIDs( Points* centers, long* centerIDs, char* outfile ) {
    FILE* fp = fopen(outfile, "w");
    if( fp==NULL ) {
      fprintf(stderr, "error opening %s\n",outfile);
      exit(1);
    }
    int* is_a_median = (int*)calloc( sizeof(int), centers->num );
    for( int i =0 ; i< centers->num; i++ ) {
      is_a_median[centers->p[i].assign] = 1;
    }
  
    for( int i = 0; i < centers->num; i++ ) {
      if( is_a_median[i] ) {
        fprintf(fp, "%u\n", centerIDs[i]);
        fprintf(fp, "%lf\n", centers->p[i].weight);
        for( int k = 0; k < centers->dim; k++ ) {
  	fprintf(fp, "%lf ", centers->p[i].coord[k]);
        }
        fprintf(fp,"\n\n");
      }
    }
    fclose(fp);
  }
  
  void streamCluster( PStream* stream, 
  		    long kmin, long kmax, int dim,
  		    long chunksize, long centersize, char* outfile )
  {
    float* block = (float*)malloc( chunksize*dim*sizeof(float) );
    float* centerBlock = (float*)malloc(centersize*dim*sizeof(float) );
    long* centerIDs = (long*)malloc(centersize*dim*sizeof(long));
  
    if( block == NULL ) { 
      fprintf(stderr,"not enough memory for a chunk!\n");
      exit(1);
    }
  
    Points points;
    points.dim = dim;
    points.num = chunksize;
    points.p = (Point *)malloc(chunksize*sizeof(Point));
    for( int i = 0; i < chunksize; i++ ) {
      points.p[i].coord = &block[i*dim];		
    }
  	
  
    Points centers;
    centers.dim = dim;
    centers.p = (Point *)malloc(centersize*sizeof(Point));
    centers.num = 0;
  
    for( int i = 0; i< centersize; i++ ) {
      centers.p[i].coord = &centerBlock[i*dim];
      centers.p[i].weight = 1.0;
    }
  
    long IDoffset = 0;
    long kfinal;
    while(1) {
  
      size_t numRead  = stream->read(block, dim, chunksize ); 
      fprintf(stderr,"read %d points\n",numRead);
  
      if( stream->ferror() || numRead < (unsigned int)chunksize && !stream->feof() ) {
        fprintf(stderr, "error reading data!\n");
        exit(1);
      }
  
      points.num = numRead;
      for( int i = 0; i < points.num; i++ ) {
        points.p[i].weight = 1.0;
      }
  
      switch_membership = (bool*)malloc(points.num*sizeof(bool));
      is_center = (bool*)calloc(points.num,sizeof(bool));
      center_table = (int*)malloc(points.num*sizeof(int));
  
      localSearch(&points,kmin, kmax,&kfinal);
  
      fprintf(stderr,"finish local search\n");
  
      contcenters(&points);
      isCoordChanged = true;
  
      if( kfinal + centers.num > centersize ) {
        //here we don't handle the situation where # of centers gets too large. 
        fprintf(stderr,"oops! no more space for centers\n");
        exit(1);
      }
  
  #ifdef PRINTINFO
      printf("finish cont center\n");
  #endif
  
      copycenters(&points, &centers, centerIDs, IDoffset);
      IDoffset += numRead;
  
  #ifdef PRINTINFO
      printf("finish copy centers\n"); 
  #endif
  
      free(is_center);
      free(switch_membership);
      free(center_table);
  
      if( stream->feof() ) {
        break;
      }
    }
  
    //finally cluster all temp centers
    switch_membership = (bool*)malloc(centers.num*sizeof(bool));
    is_center = (bool*)calloc(centers.num,sizeof(bool));
    center_table = (int*)malloc(centers.num*sizeof(int));
  
    localSearch( &centers, kmin, kmax ,&kfinal );
    contcenters(&centers);
    outcenterIDs( &centers, centerIDs, outfile);
  }
  
  int main(int argc, char **argv)
  {
    char *outfilename = new char[MAXNAMESIZE];
    char *infilename = new char[MAXNAMESIZE];
    long kmin, kmax, n, chunksize, clustersize;
    int dim;
  #ifdef PARSEC_VERSION
  #define __PARSEC_STRING(x) #x
  #define __PARSEC_XSTRING(x) __PARSEC_STRING(x)
          printf("PARSEC Benchmark Suite Version "__PARSEC_XSTRING(PARSEC_VERSION)"\n");
  	fflush(NULL);
  #else
          printf("PARSEC Benchmark Suite\n");
  	fflush(NULL);
  #endif //PARSEC_VERSION
  #ifdef ENABLE_PARSEC_HOOKS
    __parsec_bench_begin(__parsec_streamcluster);
  #endif
  
    if (argc<10) {
      fprintf(stderr,"usage: %s k1 k2 d n chunksize clustersize infile outfile nproc\n",
  	    argv[0]);
      fprintf(stderr,"  k1:          Min. number of centers allowed\n");
      fprintf(stderr,"  k2:          Max. number of centers allowed\n");
      fprintf(stderr,"  d:           Dimension of each data point\n");
      fprintf(stderr,"  n:           Number of data points\n");
      fprintf(stderr,"  chunksize:   Number of data points to handle per step\n");
      fprintf(stderr,"  clustersize: Maximum number of intermediate centers\n");
      fprintf(stderr,"  infile:      Input file (if n<=0)\n");
      fprintf(stderr,"  outfile:     Output file\n");
      fprintf(stderr,"  nproc:       Number of threads to use\n");
      fprintf(stderr,"\n");
      fprintf(stderr, "if n > 0, points will be randomly generated instead of reading from infile.\n");
      exit(1);
    }
    kmin = atoi(argv[1]);
    kmax = atoi(argv[2]);
    dim = atoi(argv[3]);
    n = atoi(argv[4]);
    chunksize = atoi(argv[5]);
    clustersize = atoi(argv[6]);
    strcpy(infilename, argv[7]);
    strcpy(outfilename, argv[8]);
    nproc = atoi(argv[9]);
  
    srand48(SEED);
    PStream* stream;
    if( n > 0 ) {
      stream = new SimStream(n);
    }
    else {
      stream = new FileStream(infilename);
    }
  
    double t1 = gettime();
  
  #ifdef ENABLE_PARSEC_HOOKS
    __parsec_roi_begin();
  #endif
  
    pgain_count = 0;
  	serial_t = 0.0;
  	cpu_to_gpu_t = 0.0;
  	gpu_to_cpu_t = 0.0;
  	alloc_t = 0.0;
  	free_t = 0.0;
  	kernel_t = 0.0;
  
  	isCoordChanged = false;
  	
  #ifdef GEM5_FUSION
      m5_work_begin(0, 0);
  #endif
  
    streamCluster(stream, kmin, kmax, dim, chunksize, clustersize, outfilename );
  
  #ifdef GEM5_FUSION
      m5_work_end(0, 0);
  #endif
  
  	freeDevMem();
  	freeHostMem();
  
  #ifdef ENABLE_PARSEC_HOOKS
    __parsec_roi_end();
  #endif
  
    double t2 = gettime();
  
    printf("time = %lfs\n",t2-t1);
  
    delete stream;
    
  #ifdef PROFILE
    printf("time pgain = %lfs\n", time_gain);
    printf("time pgain_dist = %lfs\n", time_gain_dist);
    printf("time pgain_init = %lfs\n", time_gain_init);
    printf("time pselect = %lfs\n", time_select_feasible);
    printf("time pspeedy = %lfs\n", time_speedy);
    printf("time pshuffle = %lfs\n", time_shuffle);
    printf("time localSearch = %lfs\n", time_local_search);
    printf("\n\n");
    printf("====CUDA Timing info (pgain)====\n");
    printf("time serial = %lfs\n", serial_t/1000);
    printf("time CPU to GPU memory copy = %lfs\n", cpu_to_gpu_t/1000);
    printf("time GPU to CPU memory copy back = %lfs\n", gpu_to_cpu_t/1000);
    printf("time GPU malloc = %lfs\n", alloc_t/1000);
    printf("time GPU free = %lfs\n", free_t/1000);
    printf("time kernel = %lfs\n", kernel_t/1000);
   #endif
    
  #ifdef ENABLE_PARSEC_HOOKS
    __parsec_bench_end();
  #endif
    
    return 0;
  }
  