From 84af719f37b54185ddd7daf0627421143874905c Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Sun, 24 Nov 2013 12:05:41 +0000
Subject: [PATCH] ASK MIHAparaview ! Bug fixed, by removing cell change.
---
src/timestep.c | 77 ++++++++++++++++++++++++++------------
1 files changed, 53 insertions(+), 24 deletions(-)
diff --git a/src/timestep.c b/src/timestep.c
index c38b305..e2f89ef 100644
--- a/src/timestep.c
+++ b/src/timestep.c
@@ -2,6 +2,7 @@
#include<stdio.h>
#include<math.h>
#include<pthread.h>
+//#include<unistd.h> //usleep requires it
//#include "io.h"
#include "general.h"
#include "timestep.h"
@@ -12,25 +13,34 @@
#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;
- thdata data1, data2;
- data1.thread_no=0;
- data2.thread_no=1;
- data1.vesicle=vesicle;
- data2.vesicle=vesicle;
- 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_join(tid1,NULL);
- pthread_join(tid2,NULL);
+ ts_fprintf(stdout, "Starting %d threads\n",vesicle->threads);
-// single_timestep(vesicle);
+ pthread_t *tid=(pthread_t *)malloc(sizeof(pthread_t)*vesicle->threads);
+ thdata *data=(thdata *)malloc(sizeof(thdata)*vesicle->threads);
+ pthread_mutex_init(&(vesicle->mutex->vtx_taint),NULL);
+ pthread_mutex_init(&(vesicle->mutex->vtx_untaint),NULL);
+ pthread_mutex_init(&(vesicle->mutex->cell_modify),NULL);
+
+ for(i=0;i<vesicle->threads;i++){
+ data[i].thread_no=i;
+ data[i].vesicle=vesicle;
+ data[i].threads=vesicle->threads;
+ }
+
+ for(i=0;i<inititer+iterations;i++){
+ for(j=0;j<mcsweeps;j++){
+ 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);
@@ -38,6 +48,10 @@
write_vertex_xml_file(vesicle,i-inititer);
}
}
+
+ pthread_mutex_destroy(&(vesicle->mutex->vtx_taint));
+ pthread_mutex_destroy(&(vesicle->mutex->vtx_untaint));
+ pthread_exit(NULL);
return TS_SUCCESS;
}
@@ -46,29 +60,45 @@
data=(thdata *)thread_data;
ts_vesicle *vesicle=data->vesicle;
ts_uint thID=data->thread_no;
- ts_uint partition_size=(ts_uint)(vesicle->vlist->n/2);
+ ts_uint partition_size=(ts_uint)(vesicle->vlist->n/data->threads);
ts_uint end;
- if(thID==2){
+ 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();
rnvec[2]=drand48();
- vertex_taint(vesicle->vlist->vtx[i],1);
-// ts_fprintf(stdout, "Vertex %d should be tainted, level=%d.\n", i, vesicle->vlist->vtx[i]->locked);
+//TODO: you only need to taint (lock) vertices, that could be shared with another partition. You can leave out the rest. How can you test for that? Well, if any of vtx neighbours are in other partition, then you need to lock vertex and that neighbor. Otherwise not!
+
+ /**** THREAD IS POTENTIALLY LOCKED ******/
+ pthread_mutex_lock(&vesicle->mutex->vtx_taint); //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, "Vertex %d tainted, level=%d. Waiting....\n", i, vesicle->vlist->vtx[i]->locked);
- vertex_untaint(vesicle->vlist->vtx[i],1);
- //TODO: wait a random amount of time//
- vertex_taint(vesicle->vlist->vtx[i],1);
+ ts_fprintf(stdout, "thID=%d:: Vertex %d is tainted, so I cannot try vertexmove. Amount=%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(a=%d) ", vesicle->vlist->vtx[i]->neigh[j]->idx, vesicle->vlist->vtx[i]->neigh[j]->locked);
+ }
+ ts_fprintf(stdout, ".\n");
}
+
+ pthread_mutex_lock(&vesicle->mutex->vtx_untaint);
+ vertex_taint(vesicle->vlist->vtx[i],1);
+ pthread_mutex_unlock(&vesicle->mutex->vtx_untaint);
+
+ pthread_mutex_unlock(&vesicle->mutex->vtx_taint);
+ /**** THREAD IS RELEASING MUTEX RESOURCES ******/
+
single_verticle_timestep(vesicle,vesicle->vlist->vtx[i],rnvec);
+ pthread_mutex_lock(&vesicle->mutex->vtx_untaint);
vertex_untaint(vesicle->vlist->vtx[i],1);
+ pthread_mutex_unlock(&vesicle->mutex->vtx_untaint);
// ts_fprintf(stdout, "Vertex %d should be untainted, level=%d.\n", i, vesicle->vlist->vtx[i]->locked);
}
@@ -86,7 +116,6 @@
/* if(retval);
return TS_SUCCESS;
*/
-
pthread_exit(0); /* exit */
}
--
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