From 1c3b6ac65228597df37ce6f93b77e1d509194324 Mon Sep 17 00:00:00 2001
From: josh <josh@45c1a28c-8058-47b2-ae61-ca45b979098e>
Date: Sat, 27 Sep 2008 14:33:48 +0000
Subject: [PATCH] added test cases, skeleton logic for threaded

git-svn-id: svn://anubis/gvsu@176 45c1a28c-8058-47b2-ae61-ca45b979098e
---
 cs677/pa2/Makefile    | 7 +++++++
 cs677/pa2/e1.seq      | 1 +
 cs677/pa2/e1.unk      | 1 +
 cs677/pa2/e2.seq      | 1 +
 cs677/pa2/e2.unk      | 1 +
 cs677/pa2/threaded.cc | 9 +++++++--
 6 files changed, 18 insertions(+), 2 deletions(-)
 create mode 100644 cs677/pa2/e1.seq
 create mode 100644 cs677/pa2/e1.unk
 create mode 100644 cs677/pa2/e2.seq
 create mode 100644 cs677/pa2/e2.unk

diff --git a/cs677/pa2/Makefile b/cs677/pa2/Makefile
index b40f6cf..e792a6d 100644
--- a/cs677/pa2/Makefile
+++ b/cs677/pa2/Makefile
@@ -6,5 +6,12 @@ all: $(PROGS)
 %: %.cc
 	$(CXX) -o $@ -pthread -O3 $<
 
+.PHONY: test
+test: all
+	./sequential e1.*
+	./threaded e1.*
+	./sequential e2.*
+	./sequential e2.*
+
 clean:
 	-rm -f $(PROGS) *~ *.o
diff --git a/cs677/pa2/e1.seq b/cs677/pa2/e1.seq
new file mode 100644
index 0000000..031844a
--- /dev/null
+++ b/cs677/pa2/e1.seq
@@ -0,0 +1 @@
+GATATGCA
diff --git a/cs677/pa2/e1.unk b/cs677/pa2/e1.unk
new file mode 100644
index 0000000..73a6eb4
--- /dev/null
+++ b/cs677/pa2/e1.unk
@@ -0,0 +1 @@
+ATAGCT
diff --git a/cs677/pa2/e2.seq b/cs677/pa2/e2.seq
new file mode 100644
index 0000000..c944a8d
--- /dev/null
+++ b/cs677/pa2/e2.seq
@@ -0,0 +1 @@
+AATCGGATTC
diff --git a/cs677/pa2/e2.unk b/cs677/pa2/e2.unk
new file mode 100644
index 0000000..e307130
--- /dev/null
+++ b/cs677/pa2/e2.unk
@@ -0,0 +1 @@
+GACGGTTCGT
diff --git a/cs677/pa2/threaded.cc b/cs677/pa2/threaded.cc
index 0506721..3f47e51 100644
--- a/cs677/pa2/threaded.cc
+++ b/cs677/pa2/threaded.cc
@@ -142,6 +142,7 @@ void * calcSimMatrixThread(void * arg)
     int id = *realarg;
     int s_size = s->size();
     int t_size = t->size();
+    int last_step = s_size + t_size;
     int (*F)[s_size][t_size] = (int (*) [s_size][t_size]) matrix;
     int max_x = 0, max_y = 0, max_val = 0;
     int first_task_id, num_tasks;
@@ -152,10 +153,13 @@ void * calcSimMatrixThread(void * arg)
     for (int i = 0, idx = first_task_id; i < num_tasks; i++, idx++)
         (*F)[idx][0] = 0;               /* set first column to 0's */
     pthread_barrier_wait(&barrier);
-    for (int i = 1; i <= s_size; i++)
+    for (int step = 2; i <= last_step; i++)
     {
-        for (int j = 1; j <= t_size; j++)
+        /* TODO: figure out how many tasks there are in this step */
+        /* TODO: call taskAllocate() to get mine */
+        /* TODO: loop over tasks assigned by taskAllocate() */
         {
+            /* TODO: figure out i, j from step and task */
             /* Compute the value for the matrix */
             (*F)[i][j] =
                 max(
@@ -187,6 +191,7 @@ void * calcSimMatrixThread(void * arg)
                 }
             }
         }
+        pthread_barrier_wait(&barrier);
     }
 
     cout << "Maximum value is " << max_val << " at position ("