Somewhat evolved paralelism.

Samo Penic

2013-11-23 50f10f120936a429dc450f58a40951fa5d59458a

 src/timestep.c

@@ -13,42 +13,36 @@
#include "io.h"

ts_bool run_simulation(ts_vesicle *vesicle, ts_uint mcsweeps, ts_uint inititer, ts_uint iterations){
   ts_uint i, j;
   ts_uint i, j,k ;

   centermass(vesicle);
   cell_occupation(vesicle);
   ts_fprintf(stdout, "Starting simulation (first %d x %d MC sweeps will not be recorded on disk)\n", inititer, mcsweeps);
   pthread_t tid1,tid2, tid3, tid4;
   thdata data1, data2, data3, data4;
   pthread_mutex_t mutex;
   data1.thread_no=0;
   data2.thread_no=1;
   data1.vesicle=vesicle;
   data2.vesicle=vesicle;
          data3.thread_no=2;
   data4.thread_no=3;
   data3.vesicle=vesicle;
   data4.vesicle=vesicle;
   ts_fprintf(stdout, "Starting %d threads\n",vesicle->threads);

   data1.vtx_tainting_lock=&mutex;
   data2.vtx_tainting_lock=&mutex;
   data3.vtx_tainting_lock=&mutex;
   data4.vtx_tainting_lock=&mutex;
   pthread_t *tid=(pthread_t *)malloc(sizeof(pthread_t)*vesicle->threads);
   thdata *data=(thdata *)malloc(sizeof(thdata)*vesicle->threads);
   pthread_mutex_t mutex_taint, mutex_untaint;
   pthread_mutex_init(&mutex_taint,NULL);
   pthread_mutex_init(&mutex_untaint,NULL);

   pthread_mutex_init(&mutex,NULL);
   for(i=0;i<vesicle->threads;i++){
      data[i].thread_no=i;
      data[i].vesicle=vesicle;
      data[i].threads=vesicle->threads;
      data[i].vtx_tainting_lock=&mutex_taint;
      data[i].vtx_untainting_lock=&mutex_untaint;
   }

    for(i=0;i<inititer+iterations;i++){
      for(j=0;j<mcsweeps;j++){
         pthread_create(&tid1,NULL,single_timestep,(void *)&data1);
              pthread_create(&tid2,NULL,single_timestep,(void *)&data2);
              pthread_create(&tid3,NULL,single_timestep,(void *)&data3);
              pthread_create(&tid4,NULL,single_timestep,(void *)&data4);
              pthread_join(tid1,NULL);
              pthread_join(tid2,NULL);
              pthread_join(tid3,NULL);
              pthread_join(tid4,NULL);

//   single_timestep(vesicle);
         for(k=0;k<vesicle->threads;k++){
            pthread_create(&tid[k], NULL, single_timestep, (void *)&data[k]);
         }
         for(k=0;k<vesicle->threads;k++){
                 pthread_join(tid[k],NULL);
         }
      //   single_timestep(vesicle);
      }
      centermass(vesicle);
      cell_occupation(vesicle);
@@ -57,7 +51,8 @@
      }
   }

   pthread_mutex_destroy(&mutex);
   pthread_mutex_destroy(&mutex_taint);
   pthread_mutex_destroy(&mutex_untaint);
   pthread_exit(NULL);
   return TS_SUCCESS;
}
@@ -67,15 +62,16 @@
   data=(thdata *)thread_data;
   ts_vesicle *vesicle=data->vesicle;
   ts_uint thID=data->thread_no;
   ts_uint partition_size=(ts_uint)(vesicle->vlist->n/4);
   ts_uint partition_size=(ts_uint)(vesicle->vlist->n/data->threads);
   ts_uint end;
   if(thID==3){
   if(thID==data->threads-1){
      end=vesicle->vlist->n;
   } else {
      end=(thID+1)*partition_size;
   }
    ts_double rnvec[3];
    ts_uint i; //b;
    ts_uint i,j; //b;
//   ts_fprintf(stdout,"Thread thID=%d report for duty. My vtxes are in range from %d to %d.\n",thID,thID*partition_size, end-1);
    for(i=thID*partition_size;i<end;i++){
        rnvec[0]=drand48();
        rnvec[1]=drand48();
@@ -84,15 +80,25 @@
   /**** THREAD IS POTENTIALLY LOCKED ******/
   pthread_mutex_lock(data->vtx_tainting_lock); //taint if no other process is tainting or wait until you can taint
   //   ts_fprintf(stdout, "thID=%d:: Tainting vertex %d, level=%d. Waiting....\n",thID, i, vesicle->vlist->vtx[i]->locked);

   while(vertex_tainted(vesicle->vlist->vtx[i],1,1)){
      ts_fprintf(stdout, "thID=%d:: Vertex %d is tainted, so I cannot try vertexmove. Level=%d. WAITING!\n",thID, i, vesicle->vlist->vtx[i]->locked);
      ts_fprintf(stdout, "thID=%d:: Vertex %d is tainted, so I cannot try vertexmove. Level=%d. BU(H)TELJ!\n   neigh. vtxs: ",thID, i, vesicle->vlist->vtx[i]->locked);
      for(j=0; j<vesicle->vlist->vtx[i]->neigh_no; j++){
         ts_fprintf(stdout, "%d ", vesicle->vlist->vtx[i]->neigh[j]->idx);
      }
      ts_fprintf(stdout, ".\n");
   }
   vertex_taint(vesicle->vlist->vtx[i],1);
   pthread_mutex_lock(data->vtx_untainting_lock);
   vertex_taint(vesicle->vlist->vtx[i],2);
   pthread_mutex_unlock(data->vtx_untainting_lock);

   pthread_mutex_unlock(data->vtx_tainting_lock);
   /**** THREAD IS RELEASING MUTEX RESOURCES ******/

        single_verticle_timestep(vesicle,vesicle->vlist->vtx[i],rnvec);
   vertex_untaint(vesicle->vlist->vtx[i],1);
   pthread_mutex_lock(data->vtx_untainting_lock);
   vertex_untaint(vesicle->vlist->vtx[i],2);
   pthread_mutex_unlock(data->vtx_untainting_lock);
//      ts_fprintf(stdout, "Vertex %d should be untainted, level=%d.\n", i, vesicle->vlist->vtx[i]->locked);
    }