From 3ae437ac131018e57bce7a5f34cf476d18ac3e7f Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Wed, 25 Mar 2015 12:16:06 -0400
Subject: [PATCH] r1044: fixed an out-of-order bug in kthread

---
 kthread.c | 15 +++++++++------
 main.c    |  2 +-
 2 files changed, 10 insertions(+), 7 deletions(-)

diff --git a/kthread.c b/kthread.c
index 80f84cb..97359c0 100644
--- a/kthread.c
+++ b/kthread.c
@@ -67,13 +67,15 @@ struct ktp_t;
 
 typedef struct {
 	struct ktp_t *pl;
-	int step, running;
+	int64_t index;
+	int step;
 	void *data;
 } ktp_worker_t;
 
 typedef struct ktp_t {
 	void *shared;
 	void *(*func)(void*, int, void*);
+	int64_t index;
 	int n_workers, n_steps;
 	ktp_worker_t *workers;
 	pthread_mutex_t mutex;
@@ -92,13 +94,12 @@ static void *ktp_worker(void *data)
 			// test whether another worker is doing the same step
 			for (i = 0; i < p->n_workers; ++i) {
 				if (w == &p->workers[i]) continue; // ignore itself
-				if (p->workers[i].running && p->workers[i].step == w->step)
+				if (p->workers[i].step <= w->step && p->workers[i].index < w->index)
 					break;
 			}
-			if (i == p->n_workers) break; // no other workers doing w->step; then this worker will
+			if (i == p->n_workers) break; // no workers with smaller indices are doing w->step or the previous steps
 			pthread_cond_wait(&p->cv, &p->mutex);
 		}
-		w->running = 1;
 		pthread_mutex_unlock(&p->mutex);
 
 		// working on w->step
@@ -107,7 +108,7 @@ static void *ktp_worker(void *data)
 		// update step and let other workers know
 		pthread_mutex_lock(&p->mutex);
 		w->step = w->step == p->n_steps - 1 || w->data? (w->step + 1) % p->n_steps : p->n_steps;
-		w->running = 0;
+		if (w->step == 0) w->index = p->index++;
 		pthread_cond_broadcast(&p->cv);
 		pthread_mutex_unlock(&p->mutex);
 	}
@@ -125,13 +126,15 @@ void kt_pipeline(int n_threads, void *(*func)(void*, int, void*), void *shared_d
 	aux.n_steps = n_steps;
 	aux.func = func;
 	aux.shared = shared_data;
+	aux.index = 0;
 	pthread_mutex_init(&aux.mutex, 0);
 	pthread_cond_init(&aux.cv, 0);
 
 	aux.workers = alloca(n_threads * sizeof(ktp_worker_t));
 	for (i = 0; i < n_threads; ++i) {
 		ktp_worker_t *w = &aux.workers[i];
-		w->step = w->running = 0; w->pl = &aux; w->data = 0;
+		w->step = 0; w->pl = &aux; w->data = 0;
+		w->index = aux.index++;
 	}
 
 	tid = alloca(n_threads * sizeof(pthread_t));
diff --git a/main.c b/main.c
index 21e94c5..cdac445 100644
--- a/main.c
+++ b/main.c
@@ -4,7 +4,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.7.12-r1039"
+#define PACKAGE_VERSION "0.7.12-r1044"
 #endif
 
 int bwa_fa2pac(int argc, char *argv[]);