From 94ddbad8d315e02d81e20a62560f2e67b4bae115 Mon Sep 17 00:00:00 2001
From: hackbard <hackbard@sage.physik.uni-augsburg.de>
Date: Thu, 25 Sep 2008 14:45:15 +0200
Subject: [PATCH] added pthreads (for io only by now) + refresh screen for i
 count + longer save file names

---
 Makefile |  1 +
 moldyn.c | 91 +++++++++++++++++++++++++++++++++++++++++++++++++++++---
 2 files changed, 88 insertions(+), 4 deletions(-)

diff --git a/Makefile b/Makefile
index 462a9b7..2a74cb0 100644
--- a/Makefile
+++ b/Makefile
@@ -7,6 +7,7 @@ CFLAGS += -g
 #CFLAGS += -ffloat-store
 
 #CFLAGS+= -DPARALLEL -fopenmp
+CFLAGS+= -DPTHREADS -lpthread
 
 CFLAGS += -DALBE
 CFLAGS += -DALBE_FAST
diff --git a/moldyn.c b/moldyn.c
index 3ac0a2d..4788a81 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -23,6 +23,10 @@
 #include <omp.h>
 #endif
 
+#ifdef PTHREADS
+#include <pthread.h>
+#endif
+
 #include "moldyn.h"
 #include "report/report.h"
 
@@ -1604,6 +1608,33 @@ int moldyn_set_schedule_hook(t_moldyn *moldyn,set_hook hook,void *hook_params) {
  *
  */
 
+/* helper / special functions */
+
+#ifdef PTHREADS
+void *write_save_file(void *ptr) {
+
+	int fd;
+	char dir[128];
+	t_moldyn *moldyn;
+
+	moldyn=ptr;
+
+	snprintf(dir,128,"%s/s-%08.f.save",moldyn->vlsdir,moldyn->time);
+	fd=open(dir,O_WRONLY|O_TRUNC|O_CREAT,S_IRUSR|S_IWUSR);
+	if(fd<0) perror("[moldyn] save fd open");
+	else {
+		write(fd,moldyn,sizeof(t_moldyn));
+		write(fd,moldyn->atom,moldyn->count*sizeof(t_atom));
+	}
+
+	close(fd);
+
+	pthread_exit(NULL);
+
+	return 0;
+}
+#endif
+
 /* start the integration */
 
 int moldyn_integrate(t_moldyn *moldyn) {
@@ -1613,13 +1644,26 @@ int moldyn_integrate(t_moldyn *moldyn) {
 	t_3dvec momentum;
 	t_moldyn_schedule *sched;
 	t_atom *atom;
+#ifndef PTHREADS
 	int fd;
 	char dir[128];
+#endif
 	double ds;
 	double energy_scale;
 	struct timeval t1,t2;
 	//double tp;
 
+#ifdef PTHREADS
+	u8 first,change;
+	pthread_t io_thread;
+	int ret;
+	t_moldyn md_copy;
+	t_atom *atom_copy;
+
+	first=1;
+	change=0;
+#endif
+
 	sched=&(moldyn->schedule);
 	atom=moldyn->atom;
 
@@ -1668,6 +1712,16 @@ int moldyn_integrate(t_moldyn *moldyn) {
 	/* debugging, ignore */
 	moldyn->debug=0;
 
+	/* zero & init moldyn copy */
+#ifdef PTHREADS
+	memset(&md_copy,0,sizeof(t_moldyn));
+	atom_copy=malloc(moldyn->count*sizeof(t_atom));
+	if(atom_copy==NULL) {
+		perror("[moldyn] malloc atom copy (init)");
+		return -1;
+	}
+#endif
+
 	/* tell the world */
 	printf("[moldyn] integration start, go get a coffee ...\n");
 
@@ -1752,7 +1806,35 @@ int moldyn_integrate(t_moldyn *moldyn) {
 		}
 		if(s) {
 			if(!(moldyn->total_steps%s)) {
-				snprintf(dir,128,"%s/s-%07.f.save",
+#ifdef PTHREADS
+	/* check whether thread has not terminated yet */
+	if(!first) {
+		ret=pthread_join(io_thread,NULL);
+	}
+	first=0;
+	/* prepare and start thread */
+	if(moldyn->count!=md_copy.count) {
+		free(atom_copy);
+		change=1;
+	}
+	memcpy(&md_copy,moldyn,sizeof(t_moldyn));
+	if(change) {
+		atom_copy=malloc(moldyn->count*sizeof(t_atom));
+		if(atom_copy==NULL) {
+			perror("[moldyn] malloc atom copy (change)");
+			return -1;
+		}
+	}
+	md_copy.atom=atom_copy;
+	memcpy(atom_copy,moldyn->atom,moldyn->count*sizeof(t_atom));
+	change=0;
+	ret=pthread_create(&io_thread,NULL,write_save_file,&md_copy);
+	if(ret) {
+		perror("[moldyn] create save file thread\n");
+		return -1;
+	}
+#else
+				snprintf(dir,128,"%s/s-%08.f.save",
 				         moldyn->vlsdir,moldyn->time);
 				fd=open(dir,O_WRONLY|O_TRUNC|O_CREAT,
 				        S_IRUSR|S_IWUSR);
@@ -1763,6 +1845,7 @@ int moldyn_integrate(t_moldyn *moldyn) {
 					      moldyn->count*sizeof(t_atom));
 				}
 				close(fd);
+#endif
 			}	
 		}
 		if(a) {
@@ -1772,7 +1855,7 @@ int moldyn_integrate(t_moldyn *moldyn) {
 		}
 
 		/* display progress */
-		if(!(moldyn->total_steps%10)) {
+		if(!(i%10)) {
 			/* get current time */
 			gettimeofday(&t2,NULL);
 
@@ -2937,7 +3020,7 @@ int visual_atoms(t_moldyn *moldyn) {
 
 	help=(dim.x+dim.y);
 
-	sprintf(file,"%s/atomic_conf_%07.f.xyz",v->fb,moldyn->time);
+	sprintf(file,"%s/atomic_conf_%08.f.xyz",v->fb,moldyn->time);
 	vb.fd=open(file,O_WRONLY|O_CREAT|O_TRUNC,S_IRUSR|S_IWUSR);
 	if(vb.fd<0) {
 		perror("open visual save file fd");
@@ -2947,7 +3030,7 @@ int visual_atoms(t_moldyn *moldyn) {
 	/* write the actual data file */
 
 	// povray header
-	dprintf(vb.fd,"# [P] %d %07.f <%f,%f,%f>\n",
+	dprintf(vb.fd,"# [P] %d %08.f <%f,%f,%f>\n",
 	        moldyn->count,moldyn->time,help/40.0,help/40.0,-0.8*help);
 
 	// atomic configuration
-- 
2.20.1