From 50f10f120936a429dc450f58a40951fa5d59458a Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Sat, 23 Nov 2013 21:11:15 +0000
Subject: [PATCH] Somewhat evolved paralelism.
---
src/timestep.c | 74 ++++++++++++++++++++-----------------
src/io.c | 13 ++++--
src/taint_test.c | 4 +-
src/tape | 2
src/timestep.h | 4 +
src/general.h | 1
src/vertexmove.c | 1
7 files changed, 57 insertions(+), 42 deletions(-)
diff --git a/src/general.h b/src/general.h
index 1dfb3a7..b4ce974 100644
--- a/src/general.h
+++ b/src/general.h
@@ -239,6 +239,7 @@
ts_double cm[3];
ts_double volume;
ts_spharm *sphHarmonics;
+ ts_uint threads;
} ts_vesicle;
diff --git a/src/io.c b/src/io.c
index 9e278ec..4a36f88 100644
--- a/src/io.c
+++ b/src/io.c
@@ -297,7 +297,8 @@
ts_vesicle *parsetape(ts_uint *mcsweeps, ts_uint *inititer, ts_uint *iterations){
long int nshell=17,ncxmax=60, ncymax=60, nczmax=60; // THIS IS DUE TO CONFUSE BUG!
char *buf=malloc(255*sizeof(char));
- long int brezveze0=1;
+ buf[0]=0;
+ long int smps=1;
long int brezveze1=1;
long int brezveze2=1;
ts_double xk0=25.0, dmax=1.67,stepsize=0.15;
@@ -314,8 +315,8 @@
CFG_SIMPLE_INT("mcsweeps",&mcsw),
CFG_SIMPLE_INT("inititer", &init),
CFG_SIMPLE_BOOL("quiet",&quiet),
- CFG_SIMPLE_STR("multiprocessing",buf),
- CFG_SIMPLE_INT("smp_cores",&brezveze0),
+ CFG_SIMPLE_STR("multiprocessing",&buf),
+ CFG_SIMPLE_INT("smp_cores",&smps),
CFG_SIMPLE_INT("cluster_nodes",&brezveze1),
CFG_SIMPLE_INT("distributed_processes",&brezveze2),
CFG_END()
@@ -343,7 +344,11 @@
vesicle->clist->ncmax[1]=ncymax;
vesicle->clist->ncmax[2]=nczmax;
vesicle->clist->max_occupancy=8;
-
+ if(strcmp(buf,"smp")==0){
+ vesicle->threads=smps;
+ } else {
+ vesicle->threads=1;
+ }
cfg_free(cfg);
free(buf);
// fprintf(stderr,"NSHELL=%u\n",vesicle->nshell);
diff --git a/src/taint_test.c b/src/taint_test.c
index 9898fba..07b53c1 100644
--- a/src/taint_test.c
+++ b/src/taint_test.c
@@ -25,7 +25,7 @@
for(i=0;i<vesicle->vlist->n;i++){
vertex_taint(vesicle->vlist->vtx[i],1);
vertex_untaint(vesicle->vlist->vtx[i],1);
- printf("%d taint level %d\n",i,vesicle->vlist->vtx[i]->locked);
+ printf("%d taint amount %d\n",i,vesicle->vlist->vtx[i]->locked);
if(vertex_tainted(vesicle->vlist->vtx[i], 0, 1)) printf("Ooops, Main %d is tainted!\n",i);
for(j=0;j<vesicle->vlist->vtx[i]->neigh_no;j++){
if(vertex_tainted(vesicle->vlist->vtx[i]->neigh[j], 0, 1)){
@@ -37,7 +37,7 @@
}
-printf("At the end you should see no Ooopses and all taint levels should be 0!\n");
+printf("At the end you should see no Ooopses and all taint amounts should be 0!\n");
vesicle_free(vesicle);
return 0;
}
diff --git a/src/tape b/src/tape
index d6e814d..2d86c6e 100644
--- a/src/tape
+++ b/src/tape
@@ -29,7 +29,7 @@
#what type of multiprocessing? (*none, smp, cluster, distributed, cuda, auto)
#currently only none makes sense.
-multiprocessing=none
+multiprocessing=smp
#how many cores are allowed to process in SMP?
smp_cores=2
#how many nodes in cluster?
diff --git a/src/timestep.c b/src/timestep.c
index 3290184..30d6406 100644
--- a/src/timestep.c
+++ b/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);
}
diff --git a/src/timestep.h b/src/timestep.h
index 15ad6d1..8cc79e8 100644
--- a/src/timestep.h
+++ b/src/timestep.h
@@ -4,9 +4,11 @@
typedef struct str_thdata
{
- int thread_no;
+ ts_uint thread_no;
+ ts_uint threads;
ts_vesicle *vesicle;
pthread_mutex_t *vtx_tainting_lock;
+ pthread_mutex_t *vtx_untainting_lock;
} thdata;
diff --git a/src/vertexmove.c b/src/vertexmove.c
index a79b2f0..2cb6550 100644
--- a/src/vertexmove.c
+++ b/src/vertexmove.c
@@ -108,6 +108,7 @@
}
//update the normals of triangles that share bead i.
+ //TODO: check if we could backup that too?
for(i=0;i<vtx->tristar_no;i++) triangle_normal_vector(vtx->tristar[i]);
return TS_FAIL;
--
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